├── .gitignore ├── .whitesource ├── LICENSE ├── README.md ├── doc └── pb_manual.pdf ├── pypi_files_internal ├── MANIFEST.in ├── PKG-INFO ├── README.md ├── README.rst ├── pbalancing │ ├── SBtab.py │ ├── __init__.py │ ├── balancer.py │ ├── files │ │ ├── default_files │ │ │ ├── definitions.tsv │ │ │ ├── pb_options.tsv │ │ │ └── pb_prior.tsv │ │ ├── example_files │ │ │ ├── ecoli │ │ │ │ ├── ecoli_carlsson_modified_data.tsv │ │ │ │ ├── ecoli_carlsson_modified_model.xml │ │ │ │ ├── ecoli_carlsson_modified_prior.tsv │ │ │ │ ├── ecoli_noor_2016.tsv │ │ │ │ ├── ecoli_noor_2016.xml │ │ │ │ ├── ecoli_noor_2016_data.tsv │ │ │ │ ├── ecoli_noor_result.tsv │ │ │ │ ├── ecoli_wortel_2018.xml │ │ │ │ ├── ecoli_wortel_2018_data.tsv │ │ │ │ └── ecoli_wortel_result.tsv │ │ │ ├── hynne │ │ │ │ ├── BIOMD0000000061_modeldata.tsv │ │ │ │ ├── hynne.xml │ │ │ │ ├── hynne_data.tsv │ │ │ │ ├── hynne_inh.xml │ │ │ │ └── hynne_result.tsv │ │ │ ├── jiang │ │ │ │ ├── jiang.xml │ │ │ │ ├── jiang_data.tsv │ │ │ │ └── jiang_modeldata.tsv │ │ │ ├── jol │ │ │ │ ├── jol.tsv │ │ │ │ └── jol.xml │ │ │ ├── pfk │ │ │ │ ├── pfk.xml │ │ │ │ ├── pfk_data.tsv │ │ │ │ ├── pfk_modeldata.tsv │ │ │ │ └── pfk_result.tsv │ │ │ └── teusink │ │ │ │ ├── teusink.xml │ │ │ │ ├── teusink_data.tsv │ │ │ │ ├── teusink_modeldata.tsv │ │ │ │ └── teusink_result.tsv │ │ ├── kegg_reactions_CC_ph7.0.tsv │ │ └── pb_manual.pdf │ ├── kineticizer.py │ ├── misc.py │ ├── parameter_balancing_core.py │ ├── tablibIO.py │ └── validatorSBtab.py ├── setup.cfg └── setup.py ├── requirements.txt ├── standalone_version ├── README.md ├── SBtab.py ├── __init__.py ├── balancer.py ├── files │ ├── default_files │ │ ├── definitions.tsv │ │ ├── pb_options.tsv │ │ └── pb_prior.tsv │ ├── example_files │ │ ├── ecoli │ │ │ ├── ecoli_carlsson_modified_data.tsv │ │ │ ├── ecoli_carlsson_modified_model.xml │ │ │ ├── ecoli_carlsson_modified_prior.tsv │ │ │ ├── ecoli_noor_2016.tsv │ │ │ ├── ecoli_noor_2016.xml │ │ │ ├── ecoli_noor_2016_data.tsv │ │ │ ├── ecoli_noor_result.tsv │ │ │ ├── ecoli_wortel_2018.xml │ │ │ ├── ecoli_wortel_2018_data.tsv │ │ │ └── ecoli_wortel_result.tsv │ │ ├── hynne │ │ │ ├── BIOMD0000000061_modeldata.tsv │ │ │ ├── hynne.xml │ │ │ ├── hynne_data.tsv │ │ │ ├── hynne_inh.xml │ │ │ └── hynne_result.tsv │ │ ├── jiang │ │ │ ├── jiang.xml │ │ │ ├── jiang_data.tsv │ │ │ └── jiang_modeldata.tsv │ │ ├── jol │ │ │ ├── jol.tsv │ │ │ └── jol.xml │ │ ├── pfk │ │ │ ├── pfk.xml │ │ │ ├── pfk_data.tsv │ │ │ ├── pfk_modeldata.tsv │ │ │ └── pfk_result.tsv │ │ └── teusink │ │ │ ├── teusink.xml │ │ │ ├── teusink_data.tsv │ │ │ ├── teusink_modeldata.tsv │ │ │ └── teusink_result.tsv │ ├── kegg_reactions_CC_ph7.0.tsv │ └── pb_manual.pdf ├── kineticizer.py ├── misc.py ├── parameter_balancing.py ├── parameter_balancing_core.py ├── tablibIO.py └── validatorSBtab.py └── web_version ├── ABOUT ├── LICENSE ├── README.md ├── controllers ├── appadmin.py └── default.py ├── cron ├── crontab └── crontab.example ├── databases ├── c8b669d15150d7109e5f7ab36744a5b7_auth_cas.table ├── c8b669d15150d7109e5f7ab36744a5b7_auth_event.table ├── c8b669d15150d7109e5f7ab36744a5b7_auth_group.table ├── c8b669d15150d7109e5f7ab36744a5b7_auth_membership.table ├── c8b669d15150d7109e5f7ab36744a5b7_auth_permission.table ├── c8b669d15150d7109e5f7ab36744a5b7_auth_user.table └── storage.sqlite ├── languages ├── cs.py ├── default.py ├── es.py ├── fr-ca.py ├── fr.py ├── hi.py ├── hu.py ├── id.py ├── it.py ├── my.py ├── nl.py ├── pl.py ├── plural-cs.py ├── plural-en.py ├── plural-es.py ├── plural-ru.py ├── plural-uk.py ├── pt-br.py ├── pt.py ├── ro.py ├── ru.py ├── sk.py ├── tr.py ├── uk.py ├── zh-cn.py ├── zh-tw.py └── zh.py ├── models ├── db.py └── menu.py ├── modules ├── SBtab.py ├── __init__.py ├── balancer.py ├── kineticizer.py ├── misc.py ├── sbml2sbtab.py ├── sbtab2sbml.py ├── tablibIO.py └── validatorSBtab.py ├── routes.example.py ├── static ├── 403.html ├── 404.html ├── 500.html ├── README.md ├── contact.html ├── css │ ├── bootstrap.min.css │ ├── calendar.css │ ├── css_template │ │ ├── contact.html │ │ ├── css │ │ │ ├── bootstrap-theme.css │ │ │ ├── bootstrap-theme.css.map │ │ │ ├── bootstrap-theme.min.css │ │ │ ├── bootstrap-theme.min.css.map │ │ │ ├── bootstrap.css │ │ │ ├── bootstrap.css.map │ │ │ ├── bootstrap.min.css │ │ │ ├── bootstrap.min.css.map │ │ │ ├── custom.css │ │ │ └── custom.css~ │ │ ├── documentation.html │ │ ├── download.html │ │ ├── fonts │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ └── glyphicons-halflings-regular.woff2 │ │ ├── gettingstarted.html │ │ ├── img │ │ │ ├── example_sbml.png │ │ │ ├── example_sbtab_config.png │ │ │ ├── example_sbtab_prior.png │ │ │ ├── example_sbtab_quantity.png │ │ │ ├── facebook.png │ │ │ ├── favicon.ico │ │ │ ├── favicon.png │ │ │ ├── glyphicons-halflings-white.png │ │ │ ├── glyphicons-halflings.png │ │ │ ├── gplus-32.png │ │ │ ├── online_balancing_01.png │ │ │ ├── online_balancing_02.png │ │ │ ├── online_balancing_02_blank.png │ │ │ ├── online_balancing_03.png │ │ │ ├── online_balancing_04.png │ │ │ ├── pb-logo.png │ │ │ ├── pb-logo.svg │ │ │ ├── pb-logo_old.png │ │ │ ├── pfk_data_example.tsv │ │ │ ├── pfk_model_example.tsv │ │ │ ├── pfk_options_example.tsv │ │ │ ├── sbtab_config_example.png │ │ │ ├── sbtab_data_example.png │ │ │ ├── sbtab_model_example.png │ │ │ └── twitter.png │ │ ├── js │ │ │ ├── bootstrap.js │ │ │ ├── bootstrap.min.js │ │ │ └── npm.js │ │ └── main.html │ ├── pb.css~ │ ├── web2py-bootstrap4.css │ └── web2py.css ├── documentation.html ├── examples.html ├── faq.html ├── file_format.html ├── files │ ├── default_files │ │ ├── definitions.tsv │ │ ├── pb_options.tsv │ │ └── pb_prior.tsv │ ├── example_files │ │ ├── ecoli │ │ │ ├── ecoli_carlsson_modified_data.tsv │ │ │ ├── ecoli_carlsson_modified_model.xml │ │ │ ├── ecoli_carlsson_modified_prior.tsv │ │ │ ├── ecoli_noor_2016.tsv │ │ │ ├── ecoli_noor_2016.xml │ │ │ ├── ecoli_noor_2016_data.tsv │ │ │ ├── ecoli_noor_result.tsv │ │ │ ├── ecoli_wortel_2018.xml │ │ │ ├── ecoli_wortel_2018_data.tsv │ │ │ └── ecoli_wortel_result.tsv │ │ ├── hynne │ │ │ ├── BIOMD0000000061_modeldata.tsv │ │ │ ├── hynne.xml │ │ │ ├── hynne_data.tsv │ │ │ ├── hynne_inh.xml │ │ │ └── hynne_result.tsv │ │ ├── jiang │ │ │ ├── jiang.xml │ │ │ ├── jiang_data.tsv │ │ │ └── jiang_modeldata.tsv │ │ ├── jol │ │ │ ├── jol.tsv │ │ │ └── jol.xml │ │ ├── pfk │ │ │ ├── pfk.xml │ │ │ ├── pfk_data.tsv │ │ │ ├── pfk_modeldata.tsv │ │ │ └── pfk_result.tsv │ │ └── teusink │ │ │ ├── teusink.xml │ │ │ ├── teusink_data.tsv │ │ │ ├── teusink_modeldata.tsv │ │ │ └── teusink_result.tsv │ ├── kegg_reactions_CC_ph7.0.tsv │ ├── manual.pdf │ ├── sitemap.xml │ └── sitemap_no_www.xml ├── fonts │ ├── glyphicons-halflings-regular.eot │ ├── glyphicons-halflings-regular.svg │ ├── glyphicons-halflings-regular.ttf │ ├── glyphicons-halflings-regular.woff │ └── glyphicons-halflings-regular.woff2 ├── images │ ├── example_sbml.png │ ├── example_sbtab_config.png │ ├── example_sbtab_prior.png │ ├── example_sbtab_quantity.png │ ├── facebook.png │ ├── favicon.ico │ ├── favicon.png │ ├── glyphicons-halflings-white.png │ ├── glyphicons-halflings.png │ ├── gplus-32.png │ ├── pb_screenshot.png │ └── twitter.png ├── img │ ├── favicon.ico │ ├── germany.ico │ ├── glyphicons-halflings-regular.eot │ ├── glyphicons-halflings-regular.svg │ ├── glyphicons-halflings-regular.ttf │ ├── glyphicons-halflings-regular.woff │ ├── glyphicons-halflings-regular.woff2 │ ├── logo.svg │ ├── logo_small.png │ ├── logo_small.svg │ ├── p_read.jpg │ ├── s_dev.jpg │ ├── uk.ico │ ├── w_dev.png │ └── young_fella.jpg ├── introduction.html ├── js │ ├── analytics.min.js │ ├── bootstrap.js │ ├── bootstrap.min.js │ ├── calendar.js │ ├── dd_belatedpng.js │ ├── jquery.js │ ├── modernizr.custom.js │ ├── npm.js │ ├── share.js │ ├── web2py.js │ └── web2py_bootstrap.js ├── main.html ├── quantities.html ├── software.html └── workflow.html └── views ├── __init__.py ├── appadmin.html ├── default ├── balanced.html ├── balancing.html ├── config.html ├── index.html ├── prior_table.html ├── upload_sbtab.html └── user.html ├── generic.html ├── generic.ics ├── generic.json ├── generic.jsonp ├── generic.load ├── generic.map ├── generic.pdf ├── generic.rss ├── generic.xml ├── layout.html └── web2py_ajax.html /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | env/ 12 | build/ 13 | develop-eggs/ 14 | dist/ 15 | downloads/ 16 | eggs/ 17 | .eggs/ 18 | lib/ 19 | lib64/ 20 | parts/ 21 | sdist/ 22 | var/ 23 | wheels/ 24 | *.egg-info/ 25 | .installed.cfg 26 | *.egg 27 | 28 | web_version/errors 29 | 30 | # PyInstaller 31 | # Usually these files are written by a python script from a template 32 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 33 | *.manifest 34 | *.spec 35 | 36 | # Installer logs 37 | pip-log.txt 38 | pip-delete-this-directory.txt 39 | 40 | # Unit test / coverage reports 41 | htmlcov/ 42 | .tox/ 43 | .coverage 44 | .coverage.* 45 | .cache 46 | nosetests.xml 47 | coverage.xml 48 | *.cover 49 | .hypothesis/ 50 | 51 | # Translations 52 | *.mo 53 | *.pot 54 | 55 | # Django stuff: 56 | *.log 57 | local_settings.py 58 | 59 | # Flask stuff: 60 | instance/ 61 | .webassets-cache 62 | 63 | # Scrapy stuff: 64 | .scrapy 65 | 66 | # Sphinx documentation 67 | docs/_build/ 68 | 69 | # PyBuilder 70 | target/ 71 | 72 | # Jupyter Notebook 73 | .ipynb_checkpoints 74 | 75 | # pyenv 76 | .python-version 77 | 78 | # celery beat schedule file 79 | celerybeat-schedule 80 | 81 | # SageMath parsed files 82 | *.sage.py 83 | 84 | # dotenv 85 | .env 86 | 87 | # virtualenv 88 | .venv 89 | venv/ 90 | ENV/ 91 | 92 | # Spyder project settings 93 | .spyderproject 94 | .spyproject 95 | 96 | # Rope project settings 97 | .ropeproject 98 | 99 | # mkdocs documentation 100 | /site 101 | 102 | # mypy 103 | .mypy_cache/ 104 | 105 | DMPy.pdf 106 | pb_manual.tgz 107 | pb_manual/ 108 | applications_note/ 109 | standalone_version/tests/ 110 | web_version/sessions/ 111 | web_version/static/css/old/ 112 | web_version/static/files/default_files/pb_options.tsv~ 113 | web_version/static/files/example_files/pfk/pfk_balanced.tsv 114 | web_version/static/files/example_files/pfk/pfk_balanced.xml 115 | web_version/static/files/example_files/teusink/teusink_data_minmax.tsv 116 | web_version/modules/olde/ -------------------------------------------------------------------------------- /.whitesource: -------------------------------------------------------------------------------- 1 | { 2 | "generalSettings": { 3 | "shouldScanRepo": true 4 | }, 5 | "checkRunSettings": { 6 | "vulnerableCheckRunConclusionLevel": "failure" 7 | } 8 | } -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2018 tlubitz 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Parameter Balancing, v2.1 2 | 3 | Parameter balancing is a tool for metabolic modelling in systems biology. It is implemented in Python3 and its code underlies the PEP8 guidelines. There are 5 major ways of employing parameter balancing for your project: 4 | 5 | 1. Online version 6 | 7 | The tool can be employed via www.parameterbalancing.net. All required knowledge can be found on the webpage. 8 | 9 | 2. Python PyPi installer 10 | 11 | To install parameter balancing as a Python3 package, first of all you need Python3. Next, you will need the pip3 installer. You can find information 12 | on how to do this here: https://pip.pypa.io/en/stable/installing/ 13 | Afterwards, install parameter balancing by typing in your command line: 14 | 15 | ```python 16 | sudo pip3 install pbalancing 17 | ``` 18 | 19 | This will also install libsbml and tablib on your computer if these libraries are missing. You can now employ 20 | parameter balancing as a Python3 package by, e.g., writing a script such as 21 | 22 | ```python 23 | from pbalancing import parameter_balancing_core 24 | parameter_balancing_core.parameter_balancing_wrapper('model.xml') 25 | ``` 26 | 27 | In this example case, 'model.xml' is the file name of an SBML model. Further optional arguments are an SBtab parameter 28 | file, an SBtab prior distribution file, and an SBtab configuration file. You will find examples for all these 29 | file types in parameter_balancing/standalone_version/files/. 30 | 31 | 3. Standalone commandline version 32 | 33 | To run parameter balancing as a commandline tool, the package needs to be installed as explained in (2). Then, 34 | it can be executed in the commandline as follows: 35 | 36 | ```python 37 | python3 -m pbalancing.parameter_balancing_core model.xml 38 | ``` 39 | 40 | where model.xml corresponds to the path of your SBML model. It is also possible to provide further input files, such as 41 | an SBtab parameter files (.tsv), an SBtab prior information file (.tsv), and an SBtab options file (.tsv) for the 42 | configuration of parameter balancing. Providing complete file information would look like this: 43 | 44 | ```python 45 | python3 -m pbalancing.parameter_balancing_core model.xml --sbtab_data data_file.tsv --sbtab_prior prior_file.tsv --sbtab_options options_file.tsv 46 | ``` 47 | 48 | You can create a log file by setting the flag -l, you can use pseudo values to account for a lack of data by setting the flag -p, you can 49 | watch program outputs on your commandline by setting the flag -v. Information on the SBtab format can be found on www.sbtab.net, more information 50 | on the mentioned file types can be found in the parameter balancing manual in parameter_balancing/standalone_version/files/manual.pdf, 51 | and example files can be found in parameter_balancing/standalone_version/files/example_files/. 52 | 53 | If you do not want to install the pip package, you can still use the commandline modules in the subdirectory parameter_balancing/standalone_version. 54 | The usage works as a standard call of a Python module: 55 | 56 | ```python 57 | python3 parameter_balancing.py model.xml 58 | ``` 59 | 60 | Here, as well, you can use the optional file provision like explained above. You will be required to install several Python packages, though. A list of these packages can be found in parameter_balancing/requirements.txt. 61 | 62 | 4. Standalone server version 63 | 64 | The online tool, which is hosted on www.parameterbalancing.net, is open source and can also be hosted as an offline server. Thus, you can tailor it to your specific needs and use it via your browser of choice. You will need to download a version of the web framework [web2py](http://www.web2py.com/). Then, you can directly download the parameter balancing application into the applications folder of your web2py server (web2py/applications/). You will find the parameter balancing application in this repository (parameter_balancing/web_version). For manipulating the code and user interface, you will require basic knowledge about the web2py web framework. 65 | 66 | 5. Matlab 67 | 68 | There is a Matlab version of parameter balancing which is part of the Metabolic Network Toolbox. It can be found in the [repository](https://github.com/liebermeister/mnt/) 69 | 70 | If you use parameter balancing, please cite http://pubs.acs.org/doi/abs/10.1021/jp108764b for details. 71 | 72 | For questions and feedback,please consult the repository admin. 73 | -------------------------------------------------------------------------------- /doc/pb_manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tlubitz/parameter_balancing/cb57d51548741a926fcc9ab1e7dfc80225f5de77/doc/pb_manual.pdf -------------------------------------------------------------------------------- /pypi_files_internal/MANIFEST.in: -------------------------------------------------------------------------------- 1 | # Include the data files 2 | recursive-include data * 3 | recursive-include pbalancing/files * 4 | -------------------------------------------------------------------------------- /pypi_files_internal/PKG-INFO: -------------------------------------------------------------------------------- 1 | Metadata-Version: 1.1 2 | Name: pbalancing 3 | Version: 2.0.16 4 | Summary: Parameter Balancing for Kinetic Metabolic Models 5 | Home-page: https://www.parameterbalancing.net 6 | Author: Timo Lubitz 7 | Author-email: timo.lubitz@gmail.com 8 | License: MIT 9 | Description: Parameter Balancing - A Systems Biology tool to determine thermodynamically consistent parameter sets for kinetic models of cell metabolism 10 | Keywords: modelling systems biology kinetic parameter estimation thermodynamics 11 | Platform: UNKNOWN 12 | Classifier: Development Status :: 4 - Beta 13 | Classifier: Intended Audience :: Developers 14 | Classifier: Topic :: Software Development 15 | Classifier: Programming Language :: Python :: 3.0 16 | -------------------------------------------------------------------------------- /pypi_files_internal/README.md: -------------------------------------------------------------------------------- 1 | # Parameter Balancing: PyPi version 2 | 3 | This directory holds the files required for the build up of the pip installer. Its content is not required by parameter balancing users. If you want to use parameter balancing, please go back to the main directory of the repository and check out the available options. 4 | -------------------------------------------------------------------------------- /pypi_files_internal/README.rst: -------------------------------------------------------------------------------- 1 | ### Python modules for parameter balancing ### 2 | 3 | This is a standalone library to use parameter balancing in kinetic models. 4 | 5 | To perform parameter balancing in the command line, call parameter_balancing.py by typing 6 | 7 | > python parameter_balancing.py argument1 argument2 argument3 argument4 8 | 9 | where argument1 = path to SBML model (obligatory). The other three arguments are optional: argument2 = SBtab data file; 10 | argument3 = path to a file with prior distributions; argument4 = path to a file with configuration options. 11 | 12 | Examples for these file types are found in the static directory. 13 | 14 | If the provided SBML model is valid, the script is started automatically. After successful balancing of the model it 15 | will ask the user for a name for the output files. This is optional; if no name is provided, the file will be named 16 | after the input SBML file. 17 | 18 | The SBML model can be validated beforehand on http://sbml.org/Facilities/Validator/ 19 | The SBtab files can be validated using the validation tool on www.sbtab.net. 20 | 21 | More information on parameter balancing and the input files can be found on www.parameterbalancing.net. 22 | -------------------------------------------------------------------------------- /pypi_files_internal/pbalancing/__init__.py: -------------------------------------------------------------------------------- 1 | from . import balancer 2 | from . import kineticizer 3 | from . import misc 4 | from . import parameter_balancing_core 5 | from . import SBtab 6 | from . import tablibIO 7 | from . import validatorSBtab 8 | -------------------------------------------------------------------------------- /pypi_files_internal/pbalancing/files/default_files/pb_options.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableName="Parameter balancing configuration file" TableType="Config" Date="2018-03-16" TableID="ConfigurePB" 2 | !ID !Value 3 | use_pseudo_values True 4 | ph 7 5 | temperature 298.15 6 | overwrite_kinetics True 7 | cell_volume 43 8 | parametrisation hal 9 | enzyme_prefactor True 10 | default_inhibition complete 11 | default_activation complete 12 | model_name outputname 13 | boundary_values ignore 14 | size_limit 300 15 | -------------------------------------------------------------------------------- /pypi_files_internal/pbalancing/files/default_files/pb_prior.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableName="Parameter prior" TableType="QuantityInfo" Date="2018-04-06" TableID="PriorTable" 2 | !QuantityType !Unit !BiologicalElement !MathematicalType !PriorMedian !PriorStd !PriorGeometricStd !LowerBound !UpperBound !DataStd !DataGeometricStd !Symbol !PhysicalType !Dependence !UseAsPriorInformation !SBMLElement !Abbreviation !MatrixInfo 3 | standard chemical potential kJ/mol Species Additive 0 500 -500 500 10 mu0 Thermodynamic Basic 1 Global parameter scp [I_species, 0, 0, 0, 0, 0, 0, 0] 4 | catalytic rate constant geometric mean 1/s Reaction Multiplicative 10 100 0.0000001 10000 10 1.2 KV Kinetic Basic 1 Local parameter kcrg [0, I_reaction, 0, 0, 0, 0, 0, 0] 5 | Michaelis constant mM Reaction/Species Multiplicative 0.1 10 0.000001 1000 1 1.2 KM Kinetic Basic 1 Local parameter kmc [0, 0, I_KM, 0, 0, 0, 0, 0] 6 | activation constant mM Reaction/Species Multiplicative 0.1 10 0.0001 100 1 1.2 KA Kinetic Basic 1 Local parameter kac [0, 0, 0, I_KA, 0, 0, 0, 0] 7 | inhibitory constant mM Reaction/Species Multiplicative 0.1 10 0.0001 100 1 1.2 KI Kinetic Basic 1 Local parameter kic [0, 0, 0, 0, I_KI, 0, 0, 0] 8 | concentration mM Species Multiplicative 0.1 10 0.000001 1000 1 1.2 c Dynamic Basic 1 Species (conc.) c [0, 0, 0, 0, 0, I_species, 0, 0] 9 | concentration of enzyme mM Reaction Multiplicative 0.001 100 0.000001 0.5 0.05 1.2 u Dynamic Basic 1 Local parameter eco [0, 0, 0, 0, 0, 0, I_reaction, 0] 10 | pH dimensionless None Additive 7 1 0 14 1 pH Dynamic Basic 1 Global parameter ph [0, 0, 0, 0, 0, 0, 0, 1] 11 | standard Gibbs energy of reaction kJ/mol Reaction Additive 0 500 -1000 1000 10 dmu0 Thermodynamic Derived 0 Global parameter dscp [Nt, 0, 0, 0, 0, 0, 0, 0] 12 | equilibrium constant dimensionless Reaction Multiplicative 1 100 0.0000000001 100000000 10 1.2 Keq Thermodynamic Derived 1 Local parameter keq [[-1/RT * Nt], 0, 0, 0, 0, 0, 0, 0] 13 | substrate catalytic rate constant 1/s Reaction Multiplicative 10 100 0.01 10000000 10 1.2 Kcatf Kinetic Derived 1 Local parameter kcrf [[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, 0, 0] 14 | product catalytic rate constant 1/s Reaction Multiplicative 10 100 0.000000001 10000000 10 1.2 Kcatr Kinetic Derived 1 Local parameter kcrr [[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, 0, 0] 15 | chemical potential kJ/mol Species Additive 0 500 -500 500 10 mu Dynamic Derived 0 cp [I_species, 0, 0, 0, 0, [RT * I_species], 0, 0] 16 | reaction affinity kJ/mol Reaction Additive 0 500 -100 100 10 A Dynamic Derived 0 raf [[-1 * Nt], 0, 0, 0, 0, [-RT * Nt], 0, 0] 17 | forward maximal velocity mM/s Reaction Multiplicative 0.01 100 0.00000001 1000000 0.1 2 Vmaxf Dynamic Derived 0 Local parameter vmaf [[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, I_reaction, 0] 18 | reverse maximal velocity mM/s Reaction Multiplicative 0.01 100 0.00000001 1000000 0.1 2 Vmaxr Dynamic Derived 0 Local parameter vmar [[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, I_reaction, 0] 19 | forward mass action term 1/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 2 thetaf Dynamic Derived 0 thtf [[-1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nft, 0, 0] 20 | reverse mass action term 1/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 2 thetar Dynamic Derived 0 thtr [[ 1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nrt, 0, 0] 21 | forward enzyme mass action term mM/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 2 tauf Dynamic Derived 0 tauf [[-1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nft, I_reaction, 0] 22 | reverse enzyme mass action term mM/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 2 taur Dynamic Derived 0 taur [[ 1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nrt, I_reaction, 0] 23 | Michaelis constant product mM Reaction Multiplicative 1 1000 0.001 1000 1 2 KMprod Kinetic Derived 0 Local parameter kmprod [0, 0, Nkm, 0, 0, 0, 0, 0] 24 | catalytic constant ratio dimensionless Reaction Multiplicative 1 10 0.0000000001 10000000000 1 2 Kcatratio Kinetic Derived 0 Local parameter kcrat [-1/RT * Nt], I_reaction, [-1 * Nkm], 0, 0, 0, 0, 0] -------------------------------------------------------------------------------- /pypi_files_internal/pbalancing/files/example_files/ecoli/ecoli_carlsson_modified_prior.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableName='Quantity info' TableType='QuantityInfo' TableID='QuantityInfo' 2 | !QuantityType !Symbol !Unit !Constant !RelatedElement !Scaling !Dependence !PriorMode !PriorStd !LowerBound !UpperBound !ErrorStd !SBMLElement !Abbreviation !MatrixInfo 3 | standard chemical potential mu0 kJ/mol Thermodynamic Species Original Basic -880 1500 -3000 2000 10 Global parameter scp [I_species, 0, 0, 0, 0, 0, 0] 4 | standard Gibbs energy of reaction dmu0 kJ/mol Thermodynamic Reaction Original Derived 0 1500 -1000 1000 10 Global parameter dscp [Nt, 0, 0, 0, 0, 0, 0] 5 | catalytic rate constant geometric mean KV 1/s Kinetic Reaction Logarithmic Basic 10 1 0.0000001 10000 0.5 Local parameter kcrg [0, I_reaction, 0, 0, 0, 0, 0] 6 | Michaelis constant KM mM Kinetic Reaction/Species Logarithmic Basic 0.1 1 0.000001 1000 0.5 Local parameter kmc [0, 0, I_KM, 0, 0, 0, 0] 7 | activation constant KA mM Kinetic Reaction/Species Logarithmic Basic 0.1 1 0.0001 100 0.5 Local parameter kac [0, 0, 0, I_KA, 0, 0, 0] 8 | inhibitory constant KI mM Kinetic Reaction/Species Logarithmic Basic 0.1 1 0.0001 100 0.5 Local parameter kic [0, 0, 0, 0, I_KI, 0, 0] 9 | equilibrium constant Keq dimensionless Thermodynamic Reaction Logarithmic Derived 1 1.5 0.0000000001 100000000 0.5 Local parameter keq [[-1/RT * Nt], 0, 0, 0, 0, 0, 0] 10 | substrate catalytic rate constant Kcatf 1/s Kinetic Reaction Logarithmic Derived 10 1.5 0.01 10000000 0.5 Local parameter kcrf [[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, 0] 11 | product catalytic rate constant Kcatr 1/s Kinetic Reaction Logarithmic Derived 10 3 0.000000001 10000000 0.5 Local parameter kcrr [[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, 0] 12 | concentration c mM Dynamic Species Logarithmic Basic 0.1 1.5 0.000001 1000 0.5 Species (conc.) c [0, 0, 0, 0, 0, I_species, 0] 13 | concentration of enzyme u mM Dynamic Reaction Logarithmic Basic 0.00001 1.5 0.000001 2 0.5 Local parameter eco [0, 0, 0, 0, 0, 0, I_reaction] 14 | forward maximal velocity Vmaxf mM/s Dynamic Reaction Logarithmic Derived 1 2 0.00000001 1000000 0.5 Local parameter vmaf [[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, I_reaction] 15 | reverse maximal velocity Vmaxr mM/s Dynamic Reaction Logarithmic Derived 1 2 0.00000001 1000000 0.5 Local parameter vmar [[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, I_reaction] 16 | chemical potential mu kJ/mol Dynamic Species Original Derived -880 1500 -3000 2000 20 cp [I_species, 0, 0, 0, 0, [RT * I_species], 0] 17 | reaction affinity A kJ/mol Dynamic Reaction Original Derived 0 10 -60 60 10 raf [[-1 * Nt], 0, 0, 0, 0, [-RT * Nt], 0] 18 | forward enzyme mass action term tauf mM/s Dynamic Reaction Logarithmic Derived 1 1.5 0.0000001 10000000 1 tauf [[-1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nft, I_reaction] 19 | reverse enzyme mass action term taur mM/s Dynamic Reaction Logarithmic Derived 1 1.5 0.0000001 10000000 1 taur [[ 1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nrt, I_reaction] 20 | pH pH 1 Dynamic None Original Basic 7 1 0 14 1 Global parameter ph [0, 0, 0, 0, 0, 0, 0] 21 | Michaelis constant product KMprod mM Kinetic Reaction Logarithmic Derived 0.1 1 0.000001 1000 0.5 Local parameter kmprod [0, 0, Nkm, 0, 0, 0, 0] -------------------------------------------------------------------------------- /pypi_files_internal/pbalancing/files/example_files/pfk/pfk_data.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableID='ParameterData' TableType='Quantity' Version='0.1' Level='1.0' 2 | !QuantityType !Reaction:SBML:reaction:id !Compound:SBML:species:id !Mean !Std !Unit !Organism !Reaction:Identifiers:kegg.reaction !Compound:Identifiers:kegg.compound !Reference 3 | concentration of enzyme R04779 nan 0.089 nan mM Saccharomyces cerevisiae R04779 nan yeastGFP 4 | concentration of enzyme R04779 nan 0.090 nan mM Saccharomyces cerevisiae R04779 nan yeastGFP 5 | inhibitory constant R04779 ATP_c 2.5 nan mM Oryctolagus cuniculus R04779 C00002 Brenda 6 | inhibitory constant R04779 ATP_c 0.8 nan mM Ascaris suum R04779 C00002 Brenda 7 | inhibitory constant R04779 ATP_c 0.5 nan mM Fasciola hepatica R04779 C00002 Brenda 8 | inhibitory constant R04779 ATP_c 1.4 nan mM Fasciola hepatica R04779 C00002 Brenda 9 | inhibitory constant R04779 ATP_c 0.3 nan mM Sus scrofa R04779 C00002 Brenda 10 | inhibitory constant R04779 ADP_c 1.8 nan mM nan R04779 C00008 Brenda 11 | standard chemical potential nan beta_D_fructofuranose_1_6_bisphosphate_c -2206.1 nan kJ/mol nan nan C05378 Alberty 12 | concentration nan ATP_c 1.5 0.4 mM Saccharomyces cerevisiae nan C00002 nan 13 | standard chemical potential nan ATP_c -2292.3 nan kJ/mol nan nan C00002 Alberty 14 | standard chemical potential nan beta_D_fructofuranose_6_phosphate_c -1316.6 nan kJ/mol nan nan C05345 Alberty 15 | concentration nan ADP_c 0.8 0.5 mM Saccharomyces cerevisiae nan C00008 nan 16 | standard chemical potential nan ADP_c -1425.2 nan kJ/mol nan nan C00008 Alberty 17 | Michaelis constant R04779 beta_D_fructofuranose_6_phosphate_c 0.7 nan mM nan nan C05345 Brenda 18 | Michaelis constant R04779 beta_D_fructofuranose_1_6_bisphosphate_c 12.5 nan mM nan nan C05378 Brenda 19 | Michaelis constant R04779 ATP_c 0.1 nan mM nan nan C00002 Brenda 20 | Michaelis constant R04779 ADP_c 0.9 nan mM nan nan C00008 Brenda 21 | equilibrium constant R04779 nan 0.1 nan dimensionless nan R04779 nan Nissler et. al 22 | -------------------------------------------------------------------------------- /pypi_files_internal/pbalancing/files/example_files/pfk/pfk_result.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableID="ParameterBalanced" TableType="QuantityData" Version="0.1" Level="1.0" TableName="PFK Result" 2 | !QuantityType !SBML:reaction:id !SBML:species:id !Mode !Value !Std !Unit !Provenance !Type 3 | standard chemical potential None enzyme_R04779_c -877.128823387 -877.128823387 480.842256677 kJ/mol Balanced parameter value Basic 4 | standard chemical potential None beta_D_fructofuranose_1_6_bisphosphate_c -2191.91903371 -2191.91903371 30.2323043166 kJ/mol Balanced parameter value Basic 5 | standard chemical potential None ATP_c -2292.06896057 -2292.06896057 30.2323039147 kJ/mol Balanced parameter value Basic 6 | standard chemical potential None beta_D_fructofuranose_6_phosphate_c -1321.47362395 -1321.47362395 30.2323043167 kJ/mol Balanced parameter value Basic 7 | standard chemical potential None ADP_c -1415.06387901 -1415.06387901 30.2323039989 kJ/mol Balanced parameter value Basic 8 | chemical potential None ATP_c -2291.18020579 -2291.18020579 30.239302839 kJ/mol Balanced parameter value Derived 9 | chemical potential None beta_D_fructofuranose_6_phosphate_c -1323.59730166 -1323.59730166 30.3543342094 kJ/mol Balanced parameter value Derived 10 | chemical potential None ADP_c -1416.09917968 -1416.09917968 30.2634322181 kJ/mol Balanced parameter value Derived 11 | chemical potential None beta_D_fructofuranose_1_6_bisphosphate_c -2192.47216276 -2192.47216276 30.3542965659 kJ/mol Balanced parameter value Derived 12 | chemical potential None enzyme_R04779_c -882.871176613 -882.871176613 480.842256677 kJ/mol Balanced parameter value Derived 13 | concentration None enzyme_R04779_c 0.1 0.1 38.8842320107 mM Balanced parameter value Basic 14 | concentration None ATP_c 1.4281 1.4281 0.3928816712 mM Balanced parameter value Basic 15 | concentration None beta_D_fructofuranose_1_6_bisphosphate_c 0.8011 0.8011 2.2040121515 mM Balanced parameter value Basic 16 | concentration None beta_D_fructofuranose_6_phosphate_c 0.4268 0.4268 1.1747415541 mM Balanced parameter value Basic 17 | concentration None ADP_c 0.6603 0.6603 0.4580606275 mM Balanced parameter value Basic 18 | Michaelis constant R04779 beta_D_fructofuranose_6_phosphate_c 0.5669 0.5669 0.3056352867 mM Balanced parameter value Basic 19 | Michaelis constant R04779 beta_D_fructofuranose_1_6_bisphosphate_c 8.9574 8.9574 4.8294292186 mM Balanced parameter value Basic 20 | Michaelis constant R04779 ATP_c 0.0927 0.0927 0.0499760756 mM Balanced parameter value Basic 21 | Michaelis constant R04779 ADP_c 0.7516 0.7516 0.4052432267 mM Balanced parameter value Basic 22 | equilibrium constant R04779 None 0.0721 0.0721 0.0395839013 dimensionless Balanced parameter value Derived 23 | concentration of enzyme R04779 None 0.0032 0.0032 0.0011771037 mM Balanced parameter value Basic 24 | substrate catalytic rate constant R04779 None 18.253 18.253 102.939814093 1/s Balanced parameter value Derived 25 | product catalytic rate constant R04779 None 1.9764 1.9764 11.1459995047 1/s Balanced parameter value Derived 26 | catalytic rate constant geometric mean R04779 None 6.0062 6.0062 25.6018361108 1/s Balanced parameter value Derived 27 | reaction affinity R04779 None 0.0027840724 0.0027840724 0.0047114567 kJ/mol Balanced parameter value Derived 28 | forward maximal velocity R04779 None 0.0063 0.0063 0.0386754561 mM/s Balanced parameter value Derived 29 | reverse maximal velocity R04779 None 0.0579 0.0579 0.3571904216 mM/s Balanced parameter value Derived 30 | inhibitory constant R04779 ATP_c 0.3763 0.3763 0.102763523 mM Balanced parameter value Basic 31 | -------------------------------------------------------------------------------- /pypi_files_internal/pbalancing/files/pb_manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tlubitz/parameter_balancing/cb57d51548741a926fcc9ab1e7dfc80225f5de77/pypi_files_internal/pbalancing/files/pb_manual.pdf -------------------------------------------------------------------------------- /pypi_files_internal/setup.cfg: -------------------------------------------------------------------------------- 1 | [bdist_wheel] 2 | universal = 1 3 | 4 | [egg_info] 5 | tag_build = 6 | tag_date = 0 7 | tag_svn_revision = 0 8 | 9 | -------------------------------------------------------------------------------- /pypi_files_internal/setup.py: -------------------------------------------------------------------------------- 1 | """ 2 | Setup file for parameter balancing standalone version. 3 | The standalone version can be integrated into existing workflows of Systems Biology. 4 | See: https://bitbucket.org/tlubitz/pb 5 | 6 | """ 7 | 8 | from setuptools import setup,find_packages 9 | 10 | setup(name='pbalancing',version='2.1.5',description='Parameter Balancing for Kinetic Metabolic Models',long_description='Parameter Balancing - A Systems Biology tool to determine thermodynamically consistent parameter sets for kinetic models of cell metabolism',url='http://www.parameterbalancing.net',author='Timo Lubitz',author_email='timo.lubitz@gmail.com',license='MIT',classifiers=['Development Status :: 4 - Beta','Intended Audience :: Developers', 'Topic :: Software Development', 'Programming Language :: Python :: 3.0'],keywords='modelling systems biology kinetic parameter estimation thermodynamics',packages=find_packages(),install_requires=['python-libsbml','tablib'],python_requires='>=3.0',include_package_data=True) 11 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | python3 2 | numpy 3 | scipy 4 | libsbml 5 | tablib 6 | -------------------------------------------------------------------------------- /standalone_version/README.md: -------------------------------------------------------------------------------- 1 | # Parameter Balancing: Standalone Version 2 | 3 | Parameter balancing is a tool for metabolic modelling in systems biology. It is implemented in Python3 and its code underlies the PEP8 guidelines. This subdirectory of the project holds the files for the standalone Python3 version. It can either be downloaded and used from commandline as is or embedded in your own Python3 projects. In both cases, you will be required to install Python packages to make the scripts work. A list of these packages can be found in parameter_balancing/requirements.txt. 4 | 5 |

Parameter balancing on the commandline

6 | 7 | Parameter balancing can be employed on the commandline by 8 | 9 | > python3 parameter_balancing.py model.xml 10 | 11 | where model.xml corresponds to the path of your SBML model. It is also possible to provide further input files, such as 12 | an SBtab parameter files (.tsv), an SBtab prior information file (.tsv), and an SBtab options file (.tsv) for the 13 | configuration of parameter balancing. Providing complete file information would look like this: 14 | 15 | > python3 parameter_balancing.py model.xml --sbtab_data data_file.tsv --sbtab_prior prior_file.tsv --sbtab_options options_file.tsv 16 | 17 | You can create a log file by setting the flag -l, you can use pseudo values to account for a lack of data by setting the flag -p, you can watch program outputs on your commandline by setting the flag -v. Information on the SBtab format can be found on www.sbtab.net, more information on the mentioned file types can be found in the parameter balancing manual in this repository's parameter_balancing/standalone_version/files/manual.pdf, and example files can be found in parameter_balancing/standalone_version/files/example_files/. 18 | 19 |

Embedding parameter balancing in your Python3 package

20 | 21 | You can embed the modules of parameter balancing in your own Python3 workflow. 22 | 23 | ```python 24 | import parameter_balancing_core 25 | 26 | (balanced_sbml, balanced_sbtab) = parameter_balancing_core.parameter_balancing_wrapper(sbml, sbtab_data, sbtab_prior, sbtab_options, verbose, no_pseudo_values, output_name, pb_log) 27 | ``` 28 | Input arguments 29 | 39 | 40 | Output parameters 41 | 45 | 46 | 47 |

Citation and Contact

48 | 49 | If you use parameter balancing, please cite http://pubs.acs.org/doi/abs/10.1021/jp108764b for details. 50 | 51 | If you are encountering trouble with any of the above, please file a bug report in Github. You can also feel free to file feature requests in the same manner. 52 | -------------------------------------------------------------------------------- /standalone_version/__init__.py: -------------------------------------------------------------------------------- 1 | from . import balancer 2 | from . import kineticizer 3 | from . import misc 4 | from . import parameter_balancing_core 5 | from . import SBtab 6 | from . import tablibIO 7 | from . import validatorSBtab 8 | -------------------------------------------------------------------------------- /standalone_version/files/default_files/pb_options.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableName="Parameter balancing configuration file" TableType="Config" Date="2018-03-16" TableID="ConfigurePB" 2 | !ID !Value 3 | use_pseudo_values True 4 | ph 7 5 | temperature 298.15 6 | overwrite_kinetics True 7 | cell_volume 43 8 | parametrisation hal 9 | enzyme_prefactor True 10 | default_inhibition complete 11 | default_activation complete 12 | model_name outputname 13 | boundary_values ignore 14 | size_limit 300 15 | -------------------------------------------------------------------------------- /standalone_version/files/default_files/pb_prior.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableName="Parameter prior" TableType="QuantityInfo" Date="2018-04-06" TableID="PriorTable" 2 | !QuantityType !Unit !BiologicalElement !MathematicalType !PriorMedian !PriorStd !PriorGeometricStd !LowerBound !UpperBound !DataStd !DataGeometricStd !Symbol !PhysicalType !Dependence !UseAsPriorInformation !SBMLElement !Abbreviation !MatrixInfo 3 | standard chemical potential kJ/mol Species Additive 0 500 -500 500 10 mu0 Thermodynamic Basic 1 Global parameter scp [I_species, 0, 0, 0, 0, 0, 0, 0] 4 | catalytic rate constant geometric mean 1/s Reaction Multiplicative 10 100 0.0000001 10000 10 1.2 KV Kinetic Basic 1 Local parameter kcrg [0, I_reaction, 0, 0, 0, 0, 0, 0] 5 | Michaelis constant mM Reaction/Species Multiplicative 0.1 10 0.000001 1000 1 1.2 KM Kinetic Basic 1 Local parameter kmc [0, 0, I_KM, 0, 0, 0, 0, 0] 6 | activation constant mM Reaction/Species Multiplicative 0.1 10 0.0001 100 1 1.2 KA Kinetic Basic 1 Local parameter kac [0, 0, 0, I_KA, 0, 0, 0, 0] 7 | inhibitory constant mM Reaction/Species Multiplicative 0.1 10 0.0001 100 1 1.2 KI Kinetic Basic 1 Local parameter kic [0, 0, 0, 0, I_KI, 0, 0, 0] 8 | concentration mM Species Multiplicative 0.1 10 0.000001 1000 1 1.2 c Dynamic Basic 1 Species (conc.) c [0, 0, 0, 0, 0, I_species, 0, 0] 9 | concentration of enzyme mM Reaction Multiplicative 0.001 100 0.000001 0.5 0.05 1.2 u Dynamic Basic 1 Local parameter eco [0, 0, 0, 0, 0, 0, I_reaction, 0] 10 | pH dimensionless None Additive 7 1 0 14 1 pH Dynamic Basic 1 Global parameter ph [0, 0, 0, 0, 0, 0, 0, 1] 11 | standard Gibbs energy of reaction kJ/mol Reaction Additive 0 500 -1000 1000 10 dmu0 Thermodynamic Derived 0 Global parameter dscp [Nt, 0, 0, 0, 0, 0, 0, 0] 12 | equilibrium constant dimensionless Reaction Multiplicative 1 100 0.0000000001 100000000 10 1.2 Keq Thermodynamic Derived 1 Local parameter keq [[-1/RT * Nt], 0, 0, 0, 0, 0, 0, 0] 13 | substrate catalytic rate constant 1/s Reaction Multiplicative 10 100 0.01 10000000 10 1.2 Kcatf Kinetic Derived 1 Local parameter kcrf [[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, 0, 0] 14 | product catalytic rate constant 1/s Reaction Multiplicative 10 100 0.000000001 10000000 10 1.2 Kcatr Kinetic Derived 1 Local parameter kcrr [[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, 0, 0] 15 | chemical potential kJ/mol Species Additive 0 500 -500 500 10 mu Dynamic Derived 0 cp [I_species, 0, 0, 0, 0, [RT * I_species], 0, 0] 16 | reaction affinity kJ/mol Reaction Additive 0 500 -100 100 10 A Dynamic Derived 0 raf [[-1 * Nt], 0, 0, 0, 0, [-RT * Nt], 0, 0] 17 | forward maximal velocity mM/s Reaction Multiplicative 0.01 100 0.00000001 1000000 0.1 2 Vmaxf Dynamic Derived 0 Local parameter vmaf [[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, I_reaction, 0] 18 | reverse maximal velocity mM/s Reaction Multiplicative 0.01 100 0.00000001 1000000 0.1 2 Vmaxr Dynamic Derived 0 Local parameter vmar [[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, I_reaction, 0] 19 | forward mass action term 1/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 2 thetaf Dynamic Derived 0 thtf [[-1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nft, 0, 0] 20 | reverse mass action term 1/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 2 thetar Dynamic Derived 0 thtr [[ 1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nrt, 0, 0] 21 | forward enzyme mass action term mM/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 2 tauf Dynamic Derived 0 tauf [[-1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nft, I_reaction, 0] 22 | reverse enzyme mass action term mM/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 2 taur Dynamic Derived 0 taur [[ 1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nrt, I_reaction, 0] 23 | Michaelis constant product mM Reaction Multiplicative 1 1000 0.001 1000 1 2 KMprod Kinetic Derived 0 Local parameter kmprod [0, 0, Nkm, 0, 0, 0, 0, 0] 24 | catalytic constant ratio dimensionless Reaction Multiplicative 1 10 0.0000000001 10000000000 1 2 Kcatratio Kinetic Derived 0 Local parameter kcrat [-1/RT * Nt], I_reaction, [-1 * Nkm], 0, 0, 0, 0, 0] -------------------------------------------------------------------------------- /standalone_version/files/example_files/ecoli/ecoli_carlsson_modified_prior.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableName='Quantity info' TableType='QuantityInfo' TableID='QuantityInfo' 2 | !QuantityType !Symbol !Unit !Constant !RelatedElement !Scaling !Dependence !PriorMode !PriorStd !LowerBound !UpperBound !ErrorStd !SBMLElement !Abbreviation !MatrixInfo 3 | standard chemical potential mu0 kJ/mol Thermodynamic Species Original Basic -880 1500 -3000 2000 10 Global parameter scp [I_species, 0, 0, 0, 0, 0, 0] 4 | standard Gibbs energy of reaction dmu0 kJ/mol Thermodynamic Reaction Original Derived 0 1500 -1000 1000 10 Global parameter dscp [Nt, 0, 0, 0, 0, 0, 0] 5 | catalytic rate constant geometric mean KV 1/s Kinetic Reaction Logarithmic Basic 10 1 0.0000001 10000 0.5 Local parameter kcrg [0, I_reaction, 0, 0, 0, 0, 0] 6 | Michaelis constant KM mM Kinetic Reaction/Species Logarithmic Basic 0.1 1 0.000001 1000 0.5 Local parameter kmc [0, 0, I_KM, 0, 0, 0, 0] 7 | activation constant KA mM Kinetic Reaction/Species Logarithmic Basic 0.1 1 0.0001 100 0.5 Local parameter kac [0, 0, 0, I_KA, 0, 0, 0] 8 | inhibitory constant KI mM Kinetic Reaction/Species Logarithmic Basic 0.1 1 0.0001 100 0.5 Local parameter kic [0, 0, 0, 0, I_KI, 0, 0] 9 | equilibrium constant Keq dimensionless Thermodynamic Reaction Logarithmic Derived 1 1.5 0.0000000001 100000000 0.5 Local parameter keq [[-1/RT * Nt], 0, 0, 0, 0, 0, 0] 10 | substrate catalytic rate constant Kcatf 1/s Kinetic Reaction Logarithmic Derived 10 1.5 0.01 10000000 0.5 Local parameter kcrf [[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, 0] 11 | product catalytic rate constant Kcatr 1/s Kinetic Reaction Logarithmic Derived 10 3 0.000000001 10000000 0.5 Local parameter kcrr [[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, 0] 12 | concentration c mM Dynamic Species Logarithmic Basic 0.1 1.5 0.000001 1000 0.5 Species (conc.) c [0, 0, 0, 0, 0, I_species, 0] 13 | concentration of enzyme u mM Dynamic Reaction Logarithmic Basic 0.00001 1.5 0.000001 2 0.5 Local parameter eco [0, 0, 0, 0, 0, 0, I_reaction] 14 | forward maximal velocity Vmaxf mM/s Dynamic Reaction Logarithmic Derived 1 2 0.00000001 1000000 0.5 Local parameter vmaf [[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, I_reaction] 15 | reverse maximal velocity Vmaxr mM/s Dynamic Reaction Logarithmic Derived 1 2 0.00000001 1000000 0.5 Local parameter vmar [[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, I_reaction] 16 | chemical potential mu kJ/mol Dynamic Species Original Derived -880 1500 -3000 2000 20 cp [I_species, 0, 0, 0, 0, [RT * I_species], 0] 17 | reaction affinity A kJ/mol Dynamic Reaction Original Derived 0 10 -60 60 10 raf [[-1 * Nt], 0, 0, 0, 0, [-RT * Nt], 0] 18 | forward enzyme mass action term tauf mM/s Dynamic Reaction Logarithmic Derived 1 1.5 0.0000001 10000000 1 tauf [[-1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nft, I_reaction] 19 | reverse enzyme mass action term taur mM/s Dynamic Reaction Logarithmic Derived 1 1.5 0.0000001 10000000 1 taur [[ 1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nrt, I_reaction] 20 | pH pH 1 Dynamic None Original Basic 7 1 0 14 1 Global parameter ph [0, 0, 0, 0, 0, 0, 0] 21 | Michaelis constant product KMprod mM Kinetic Reaction Logarithmic Derived 0.1 1 0.000001 1000 0.5 Local parameter kmprod [0, 0, Nkm, 0, 0, 0, 0] -------------------------------------------------------------------------------- /standalone_version/files/example_files/pfk/pfk_data.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableID='ParameterData' TableType='Quantity' Version='0.1' Level='1.0' 2 | !QuantityType !Reaction:SBML:reaction:id !Compound:SBML:species:id !Mean !Std !Unit !Organism !Reaction:Identifiers:kegg.reaction !Compound:Identifiers:kegg.compound !Reference 3 | concentration of enzyme R04779 nan 0.089 nan mM Saccharomyces cerevisiae R04779 nan yeastGFP 4 | concentration of enzyme R04779 nan 0.090 nan mM Saccharomyces cerevisiae R04779 nan yeastGFP 5 | inhibitory constant R04779 ATP_c 2.5 nan mM Oryctolagus cuniculus R04779 C00002 Brenda 6 | inhibitory constant R04779 ATP_c 0.8 nan mM Ascaris suum R04779 C00002 Brenda 7 | inhibitory constant R04779 ATP_c 0.5 nan mM Fasciola hepatica R04779 C00002 Brenda 8 | inhibitory constant R04779 ATP_c 1.4 nan mM Fasciola hepatica R04779 C00002 Brenda 9 | inhibitory constant R04779 ATP_c 0.3 nan mM Sus scrofa R04779 C00002 Brenda 10 | inhibitory constant R04779 ADP_c 1.8 nan mM nan R04779 C00008 Brenda 11 | standard chemical potential nan beta_D_fructofuranose_1_6_bisphosphate_c -2206.1 nan kJ/mol nan nan C05378 Alberty 12 | concentration nan ATP_c 1.5 0.4 mM Saccharomyces cerevisiae nan C00002 nan 13 | standard chemical potential nan ATP_c -2292.3 nan kJ/mol nan nan C00002 Alberty 14 | standard chemical potential nan beta_D_fructofuranose_6_phosphate_c -1316.6 nan kJ/mol nan nan C05345 Alberty 15 | concentration nan ADP_c 0.8 0.5 mM Saccharomyces cerevisiae nan C00008 nan 16 | standard chemical potential nan ADP_c -1425.2 nan kJ/mol nan nan C00008 Alberty 17 | Michaelis constant R04779 beta_D_fructofuranose_6_phosphate_c 0.7 nan mM nan nan C05345 Brenda 18 | Michaelis constant R04779 beta_D_fructofuranose_1_6_bisphosphate_c 12.5 nan mM nan nan C05378 Brenda 19 | Michaelis constant R04779 ATP_c 0.1 nan mM nan nan C00002 Brenda 20 | Michaelis constant R04779 ADP_c 0.9 nan mM nan nan C00008 Brenda 21 | equilibrium constant R04779 nan 0.1 nan dimensionless nan R04779 nan Nissler et. al 22 | -------------------------------------------------------------------------------- /standalone_version/files/example_files/pfk/pfk_result.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableID="ParameterBalanced" TableType="QuantityData" Version="0.1" Level="1.0" TableName="PFK Result" 2 | !QuantityType !SBML:reaction:id !SBML:species:id !Mode !Value !Std !Unit !Provenance !Type 3 | standard chemical potential None enzyme_R04779_c -877.128823387 -877.128823387 480.842256677 kJ/mol Balanced parameter value Basic 4 | standard chemical potential None beta_D_fructofuranose_1_6_bisphosphate_c -2191.91903371 -2191.91903371 30.2323043166 kJ/mol Balanced parameter value Basic 5 | standard chemical potential None ATP_c -2292.06896057 -2292.06896057 30.2323039147 kJ/mol Balanced parameter value Basic 6 | standard chemical potential None beta_D_fructofuranose_6_phosphate_c -1321.47362395 -1321.47362395 30.2323043167 kJ/mol Balanced parameter value Basic 7 | standard chemical potential None ADP_c -1415.06387901 -1415.06387901 30.2323039989 kJ/mol Balanced parameter value Basic 8 | chemical potential None ATP_c -2291.18020579 -2291.18020579 30.239302839 kJ/mol Balanced parameter value Derived 9 | chemical potential None beta_D_fructofuranose_6_phosphate_c -1323.59730166 -1323.59730166 30.3543342094 kJ/mol Balanced parameter value Derived 10 | chemical potential None ADP_c -1416.09917968 -1416.09917968 30.2634322181 kJ/mol Balanced parameter value Derived 11 | chemical potential None beta_D_fructofuranose_1_6_bisphosphate_c -2192.47216276 -2192.47216276 30.3542965659 kJ/mol Balanced parameter value Derived 12 | chemical potential None enzyme_R04779_c -882.871176613 -882.871176613 480.842256677 kJ/mol Balanced parameter value Derived 13 | concentration None enzyme_R04779_c 0.1 0.1 38.8842320107 mM Balanced parameter value Basic 14 | concentration None ATP_c 1.4281 1.4281 0.3928816712 mM Balanced parameter value Basic 15 | concentration None beta_D_fructofuranose_1_6_bisphosphate_c 0.8011 0.8011 2.2040121515 mM Balanced parameter value Basic 16 | concentration None beta_D_fructofuranose_6_phosphate_c 0.4268 0.4268 1.1747415541 mM Balanced parameter value Basic 17 | concentration None ADP_c 0.6603 0.6603 0.4580606275 mM Balanced parameter value Basic 18 | Michaelis constant R04779 beta_D_fructofuranose_6_phosphate_c 0.5669 0.5669 0.3056352867 mM Balanced parameter value Basic 19 | Michaelis constant R04779 beta_D_fructofuranose_1_6_bisphosphate_c 8.9574 8.9574 4.8294292186 mM Balanced parameter value Basic 20 | Michaelis constant R04779 ATP_c 0.0927 0.0927 0.0499760756 mM Balanced parameter value Basic 21 | Michaelis constant R04779 ADP_c 0.7516 0.7516 0.4052432267 mM Balanced parameter value Basic 22 | equilibrium constant R04779 None 0.0721 0.0721 0.0395839013 dimensionless Balanced parameter value Derived 23 | concentration of enzyme R04779 None 0.0032 0.0032 0.0011771037 mM Balanced parameter value Basic 24 | substrate catalytic rate constant R04779 None 18.253 18.253 102.939814093 1/s Balanced parameter value Derived 25 | product catalytic rate constant R04779 None 1.9764 1.9764 11.1459995047 1/s Balanced parameter value Derived 26 | catalytic rate constant geometric mean R04779 None 6.0062 6.0062 25.6018361108 1/s Balanced parameter value Derived 27 | reaction affinity R04779 None 0.0027840724 0.0027840724 0.0047114567 kJ/mol Balanced parameter value Derived 28 | forward maximal velocity R04779 None 0.0063 0.0063 0.0386754561 mM/s Balanced parameter value Derived 29 | reverse maximal velocity R04779 None 0.0579 0.0579 0.3571904216 mM/s Balanced parameter value Derived 30 | inhibitory constant R04779 ATP_c 0.3763 0.3763 0.102763523 mM Balanced parameter value Basic 31 | -------------------------------------------------------------------------------- /standalone_version/files/pb_manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tlubitz/parameter_balancing/cb57d51548741a926fcc9ab1e7dfc80225f5de77/standalone_version/files/pb_manual.pdf -------------------------------------------------------------------------------- /standalone_version/parameter_balancing.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | import argparse 3 | 4 | try: from . import parameter_balancing_core 5 | except: import parameter_balancing_core 6 | 7 | if __name__ == '__main__': 8 | 9 | parser = argparse.ArgumentParser() 10 | 11 | parser.add_argument('sbml', help='Path to an SBML file.') 12 | parser.add_argument('--sbtab_data', help='Path to an SBtab data file.') 13 | parser.add_argument('--sbtab_prior', help='Path to an SBtab prior file.') 14 | parser.add_argument('--sbtab_options', help='Path to an SBtab options file.') 15 | parser.add_argument('--output_name', help='Choose a name for the output files.') 16 | parser.add_argument('-l', '--pb_log', help='Flag to print a log file.', action='store_true') 17 | parser.add_argument('-c', '--concat', help='Flag to print a file with concatenated input/output file.', action='store_true') 18 | parser.add_argument('-p', '--no_pseudo_values', help='Flag for disabling the usage of pseudo values.', action='store_true') 19 | parser.add_argument('-v', '--verbose', help='Flag to display script messages.', action='store_true') 20 | 21 | args = parser.parse_args() 22 | parameter_balancing_core.parameter_balancing_wrapper(args.sbml, 23 | args.sbtab_data, 24 | args.sbtab_prior, 25 | args.sbtab_options, 26 | args.verbose, 27 | args.no_pseudo_values, 28 | args.output_name, 29 | args.pb_log, 30 | args.concat) 31 | 32 | -------------------------------------------------------------------------------- /web_version/ABOUT: -------------------------------------------------------------------------------- 1 | Write something about this app. 2 | Developed with web2py. 3 | -------------------------------------------------------------------------------- /web_version/LICENSE: -------------------------------------------------------------------------------- 1 | The web2py welcome app is licensed under public domain 2 | (except for the css and js files that it includes, which have their own third party licenses). 3 | 4 | You can modify this license when you add your own code. 5 | -------------------------------------------------------------------------------- /web_version/README.md: -------------------------------------------------------------------------------- 1 | # Parameter Balancing: Web2py version 2 | 3 | Parameter balancing is a tool for metabolic modelling in systems biology. It is implemented in Python3 and its code underlies the PEP8 guidelines. This subdirectory holds the files for the web2py application tool, which is also hosted online on www.parameterbalancing.net. If you want to run it on an own offline server, you will need to download a version of the web framework [web2py](http://www.web2py.com/). Then, you can directly download the parameter balancing application into the applications folder of your web2py server (web2py/applications/). For manipulating the code and user interface, you will require basic knowledge about the web2py web framework. 4 | 5 | If you use parameter balancing, please cite http://pubs.acs.org/doi/abs/10.1021/jp108764b for details. 6 | 7 | For questions and feedback,please consult the repository admin. -------------------------------------------------------------------------------- /web_version/cron/crontab: -------------------------------------------------------------------------------- 1 | #crontab -------------------------------------------------------------------------------- /web_version/cron/crontab.example: -------------------------------------------------------------------------------- 1 | #crontab -------------------------------------------------------------------------------- /web_version/databases/c8b669d15150d7109e5f7ab36744a5b7_auth_cas.table: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tlubitz/parameter_balancing/cb57d51548741a926fcc9ab1e7dfc80225f5de77/web_version/databases/c8b669d15150d7109e5f7ab36744a5b7_auth_cas.table -------------------------------------------------------------------------------- /web_version/databases/c8b669d15150d7109e5f7ab36744a5b7_auth_event.table: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tlubitz/parameter_balancing/cb57d51548741a926fcc9ab1e7dfc80225f5de77/web_version/databases/c8b669d15150d7109e5f7ab36744a5b7_auth_event.table -------------------------------------------------------------------------------- /web_version/databases/c8b669d15150d7109e5f7ab36744a5b7_auth_group.table: -------------------------------------------------------------------------------- 1 | (dp1 2 | S'role' 3 | p2 4 | (dp3 5 | S'length' 6 | p4 7 | I512 8 | sS'unique' 9 | p5 10 | I00 11 | sS'sortable' 12 | p6 13 | I2 14 | sS'sql' 15 | p7 16 | S'CHAR(512)' 17 | p8 18 | sS'notnull' 19 | p9 20 | I00 21 | sS'type' 22 | p10 23 | S'string' 24 | p11 25 | ssS'id' 26 | p12 27 | (dp13 28 | g4 29 | I512 30 | sg5 31 | I00 32 | sg6 33 | I1 34 | sg7 35 | S'INTEGER PRIMARY KEY AUTOINCREMENT' 36 | p14 37 | sg9 38 | I00 39 | sg10 40 | g12 41 | ssS'description' 42 | p15 43 | (dp16 44 | g4 45 | I32768 46 | sg5 47 | I00 48 | sg6 49 | I3 50 | sg7 51 | S'TEXT' 52 | p17 53 | sg9 54 | I00 55 | sg10 56 | S'text' 57 | p18 58 | ss. -------------------------------------------------------------------------------- /web_version/databases/c8b669d15150d7109e5f7ab36744a5b7_auth_membership.table: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tlubitz/parameter_balancing/cb57d51548741a926fcc9ab1e7dfc80225f5de77/web_version/databases/c8b669d15150d7109e5f7ab36744a5b7_auth_membership.table -------------------------------------------------------------------------------- /web_version/databases/c8b669d15150d7109e5f7ab36744a5b7_auth_permission.table: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tlubitz/parameter_balancing/cb57d51548741a926fcc9ab1e7dfc80225f5de77/web_version/databases/c8b669d15150d7109e5f7ab36744a5b7_auth_permission.table -------------------------------------------------------------------------------- /web_version/databases/c8b669d15150d7109e5f7ab36744a5b7_auth_user.table: -------------------------------------------------------------------------------- 1 | (dp1 2 | S'first_name' 3 | p2 4 | (dp3 5 | S'length' 6 | p4 7 | I128 8 | sS'unique' 9 | p5 10 | I00 11 | sS'sortable' 12 | p6 13 | I2 14 | sS'sql' 15 | p7 16 | S'CHAR(128)' 17 | p8 18 | sS'notnull' 19 | p9 20 | I00 21 | sS'type' 22 | p10 23 | S'string' 24 | p11 25 | ssS'last_name' 26 | p12 27 | (dp13 28 | g4 29 | I128 30 | sg5 31 | I00 32 | sg6 33 | I3 34 | sg7 35 | S'CHAR(128)' 36 | p14 37 | sg9 38 | I00 39 | sg10 40 | g11 41 | ssS'registration_id' 42 | p15 43 | (dp16 44 | g4 45 | I512 46 | sg5 47 | I00 48 | sg6 49 | I8 50 | sg7 51 | S'CHAR(512)' 52 | p17 53 | sg9 54 | I00 55 | sg10 56 | g11 57 | ssS'email' 58 | p18 59 | (dp19 60 | g4 61 | I512 62 | sg5 63 | I00 64 | sg6 65 | I4 66 | sg7 67 | S'CHAR(512)' 68 | p20 69 | sg9 70 | I00 71 | sg10 72 | g11 73 | ssS'reset_password_key' 74 | p21 75 | (dp22 76 | g4 77 | I512 78 | sg5 79 | I00 80 | sg6 81 | I7 82 | sg7 83 | S'CHAR(512)' 84 | p23 85 | sg9 86 | I00 87 | sg10 88 | g11 89 | ssS'password' 90 | p24 91 | (dp25 92 | g4 93 | I512 94 | sg5 95 | I00 96 | sg6 97 | I5 98 | sg7 99 | S'CHAR(512)' 100 | p26 101 | sg9 102 | I00 103 | sg10 104 | g24 105 | ssS'registration_key' 106 | p27 107 | (dp28 108 | g4 109 | I512 110 | sg5 111 | I00 112 | sg6 113 | I6 114 | sg7 115 | S'CHAR(512)' 116 | p29 117 | sg9 118 | I00 119 | sg10 120 | g11 121 | ssS'id' 122 | p30 123 | (dp31 124 | g4 125 | I512 126 | sg5 127 | I00 128 | sg6 129 | I1 130 | sg7 131 | S'INTEGER PRIMARY KEY AUTOINCREMENT' 132 | p32 133 | sg9 134 | I00 135 | sg10 136 | g30 137 | ss. -------------------------------------------------------------------------------- /web_version/databases/storage.sqlite: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tlubitz/parameter_balancing/cb57d51548741a926fcc9ab1e7dfc80225f5de77/web_version/databases/storage.sqlite -------------------------------------------------------------------------------- /web_version/languages/default.py: -------------------------------------------------------------------------------- 1 | # coding: utf8 2 | { 3 | '!langcode!': 'en-us', 4 | '!langname!': 'English (US)', 5 | '%s %%(shop)': '%s %%(shop)', 6 | '%s %%(shop[0])': '%s %%(shop[0])', 7 | '%s %%{quark[0]}': '%s %%{quark[0]}', 8 | '%s %%{shop[0]}': '%s %%{shop[0]}', 9 | '%s %%{shop}': '%s %%{shop}', 10 | '%Y-%m-%d': '%Y-%m-%d', 11 | '%Y-%m-%d %H:%M:%S': '%Y-%m-%d %H:%M:%S', 12 | '@markmin\x01**Hello World**': '**Hello World**', 13 | 'About': 'About', 14 | 'Access Control': 'Access Control', 15 | 'Administrative Interface': 'Administrative Interface', 16 | 'Ajax Recipes': 'Ajax Recipes', 17 | 'Are you sure you want to delete this object?': 'Are you sure you want to delete this object?', 18 | 'Buy this book': 'Buy this book', 19 | 'Cannot be empty': 'Cannot be empty', 20 | 'Check to delete': 'Check to delete', 21 | 'Client IP': 'Client IP', 22 | 'Community': 'Community', 23 | 'Components and Plugins': 'Components and Plugins', 24 | 'Controller': 'Controller', 25 | 'Copyright': 'Copyright', 26 | 'Created By': 'Created By', 27 | 'Created On': 'Created On', 28 | 'customize me!': 'customize me!', 29 | 'Database': 'Database', 30 | 'DB Model': 'DB Model', 31 | 'Demo': 'Demo', 32 | 'Deployment Recipes': 'Deployment Recipes', 33 | 'Description': 'Description', 34 | 'Documentation': 'Documentation', 35 | "Don't know what to do?": "Don't know what to do?", 36 | 'Download': 'Download', 37 | 'E-mail': 'E-mail', 38 | 'Email and SMS': 'Email and SMS', 39 | 'enter an integer between %(min)g and %(max)g': 'enter an integer between %(min)g and %(max)g', 40 | 'enter date and time as %(format)s': 'enter date and time as %(format)s', 41 | 'Errors': 'Errors', 42 | 'FAQ': 'FAQ', 43 | 'First name': 'First name', 44 | 'Forms and Validators': 'Forms and Validators', 45 | 'Free Applications': 'Free Applications', 46 | 'Group %(group_id)s created': 'Group %(group_id)s created', 47 | 'Group ID': 'Group ID', 48 | 'Group uniquely assigned to user %(id)s': 'Group uniquely assigned to user %(id)s', 49 | 'Groups': 'Groups', 50 | 'Hello World': 'Hello World', 51 | 'Hello World ## comment': 'Hello World ', 52 | 'Hello World## comment': 'Hello World', 53 | 'Home': 'Home', 54 | 'How did you get here?': 'How did you get here?', 55 | 'Introduction': 'Introduction', 56 | 'Invalid email': 'Invalid email', 57 | 'Is Active': 'Is Active', 58 | 'Last name': 'Last name', 59 | 'Layout': 'Layout', 60 | 'Layout Plugins': 'Layout Plugins', 61 | 'Layouts': 'Layouts', 62 | 'Live Chat': 'Live Chat', 63 | 'Logged in': 'Logged in', 64 | 'Logged out': 'Logged out', 65 | 'Login': 'Login', 66 | 'Logout': 'Logout', 67 | 'Lost Password': 'Lost Password', 68 | 'Lost password?': 'Lost password?', 69 | 'Menu Model': 'Menu Model', 70 | 'Modified By': 'Modified By', 71 | 'Modified On': 'Modified On', 72 | 'My Sites': 'My Sites', 73 | 'Name': 'Name', 74 | 'Object or table name': 'Object or table name', 75 | 'Online examples': 'Online examples', 76 | 'Origin': 'Origin', 77 | 'Other Plugins': 'Other Plugins', 78 | 'Other Recipes': 'Other Recipes', 79 | 'Overview': 'Overview', 80 | 'Password': 'Password', 81 | "Password fields don't match": "Password fields don't match", 82 | 'please input your password again': 'please input your password again', 83 | 'Plugins': 'Plugins', 84 | 'Powered by': 'Powered by', 85 | 'Preface': 'Preface', 86 | 'Profile': 'Profile', 87 | 'Python': 'Python', 88 | 'Quick Examples': 'Quick Examples', 89 | 'Recipes': 'Recipes', 90 | 'Record ID': 'Record ID', 91 | 'Register': 'Register', 92 | 'Registration identifier': 'Registration identifier', 93 | 'Registration key': 'Registration key', 94 | 'Registration successful': 'Registration successful', 95 | 'Remember me (for 30 days)': 'Remember me (for 30 days)', 96 | 'Reset Password key': 'Reset Password key', 97 | 'Role': 'Role', 98 | 'Semantic': 'Semantic', 99 | 'Services': 'Services', 100 | 'Stylesheet': 'Stylesheet', 101 | 'Support': 'Support', 102 | 'The Core': 'The Core', 103 | 'The output of the file is a dictionary that was rendered by the view %s': 'The output of the file is a dictionary that was rendered by the view %s', 104 | 'The Views': 'The Views', 105 | 'This App': 'This App', 106 | 'Timestamp': 'Timestamp', 107 | 'Twitter': 'Twitter', 108 | 'User %(id)s Logged-in': 'User %(id)s Logged-in', 109 | 'User %(id)s Logged-out': 'User %(id)s Logged-out', 110 | 'User %(id)s Registered': 'User %(id)s Registered', 111 | 'User ID': 'User ID', 112 | 'value already in database or empty': 'value already in database or empty', 113 | 'Verify Password': 'Verify Password', 114 | 'Videos': 'Videos', 115 | 'View': 'View', 116 | 'Welcome': 'Welcome', 117 | 'Welcome to web2py!': 'Welcome to web2py!', 118 | 'Which called the function %s located in the file %s': 'Which called the function %s located in the file %s', 119 | 'You are successfully running web2py': 'You are successfully running web2py', 120 | 'You can modify this application and adapt it to your needs': 'You can modify this application and adapt it to your needs', 121 | 'You visited the url %s': 'You visited the url %s', 122 | } 123 | -------------------------------------------------------------------------------- /web_version/languages/hi.py: -------------------------------------------------------------------------------- 1 | # coding: utf8 2 | { 3 | '!langcode!': 'hi-in', 4 | '!langname!': 'हिन्दी', 5 | '"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN', 6 | '%s %%{row} deleted': '%s पंक्तियाँ मिटाएँ', 7 | '%s %%{row} updated': '%s पंक्तियाँ अद्यतन', 8 | '%s selected': '%s चुना हुआ', 9 | '%Y-%m-%d': '%Y-%m-%d', 10 | '%Y-%m-%d %H:%M:%S': '%Y-%m-%d %H:%M:%S', 11 | 'About': 'About', 12 | 'Access Control': 'Access Control', 13 | 'Administrative Interface': 'Administrative Interface', 14 | 'Administrative interface': 'प्रशासनिक इंटरफेस के लिए यहाँ क्लिक करें', 15 | 'Ajax Recipes': 'Ajax Recipes', 16 | 'appadmin is disabled because insecure channel': 'अप आडमिन (appadmin) अक्षम है क्योंकि असुरक्षित चैनल', 17 | 'Are you sure you want to delete this object?': 'Are you sure you want to delete this object?', 18 | 'Available Databases and Tables': 'उपलब्ध डेटाबेस और तालिका', 19 | 'Buy this book': 'Buy this book', 20 | 'cache': 'cache', 21 | 'Cache': 'Cache', 22 | 'Cache Keys': 'Cache Keys', 23 | 'Cannot be empty': 'खाली नहीं हो सकता', 24 | 'Change Password': 'पासवर्ड बदलें', 25 | 'change password': 'change password', 26 | 'Check to delete': 'हटाने के लिए चुनें', 27 | 'Clear CACHE?': 'Clear CACHE?', 28 | 'Clear DISK': 'Clear DISK', 29 | 'Clear RAM': 'Clear RAM', 30 | 'Community': 'Community', 31 | 'Components and Plugins': 'Components and Plugins', 32 | 'Controller': 'Controller', 33 | 'Copyright': 'Copyright', 34 | 'Current request': 'वर्तमान अनुरोध', 35 | 'Current response': 'वर्तमान प्रतिक्रिया', 36 | 'Current session': 'वर्तमान सेशन', 37 | 'customize me!': 'मुझे अनुकूलित (कस्टमाइज़) करें!', 38 | 'data uploaded': 'डाटा अपलोड सम्पन्न ', 39 | 'Database': 'डेटाबेस', 40 | 'Database %s select': 'डेटाबेस %s चुनी हुई', 41 | 'db': 'db', 42 | 'DB Model': 'DB Model', 43 | 'Delete:': 'मिटाना:', 44 | 'Demo': 'Demo', 45 | 'Deployment Recipes': 'Deployment Recipes', 46 | 'design': 'रचना करें', 47 | 'DISK': 'DISK', 48 | 'Disk Cache Keys': 'Disk Cache Keys', 49 | 'Disk Cleared': 'Disk Cleared', 50 | 'Documentation': 'Documentation', 51 | "Don't know what to do?": "Don't know what to do?", 52 | 'done!': 'हो गया!', 53 | 'Download': 'Download', 54 | 'Edit': 'Edit', 55 | 'Edit current record': 'वर्तमान रेकॉर्ड संपादित करें ', 56 | 'edit profile': 'edit profile', 57 | 'Edit Profile': 'प्रोफ़ाइल संपादित करें', 58 | 'Edit This App': 'Edit This App', 59 | 'Email and SMS': 'Email and SMS', 60 | 'Errors': 'Errors', 61 | 'export as csv file': 'csv फ़ाइल के रूप में निर्यात', 62 | 'FAQ': 'FAQ', 63 | 'Forms and Validators': 'Forms and Validators', 64 | 'Free Applications': 'Free Applications', 65 | 'Groups': 'Groups', 66 | 'Hello from MyApp': 'Hello from MyApp', 67 | 'Hello World': 'Hello World', 68 | 'Home': 'Home', 69 | 'How did you get here?': 'How did you get here?', 70 | 'import': 'import', 71 | 'Import/Export': 'आयात / निर्यात', 72 | 'Index': 'Index', 73 | 'insert new': 'नया डालें', 74 | 'insert new %s': 'नया %s डालें', 75 | 'Internal State': 'आंतरिक स्थिति', 76 | 'Introduction': 'Introduction', 77 | 'Invalid Query': 'अमान्य प्रश्न', 78 | 'invalid request': 'अवैध अनुरोध', 79 | 'Key': 'Key', 80 | 'Layout': 'Layout', 81 | 'Layout Plugins': 'Layout Plugins', 82 | 'Layouts': 'Layouts', 83 | 'Live Chat': 'Live Chat', 84 | 'login': 'login', 85 | 'Login': 'लॉग इन', 86 | 'logout': 'logout', 87 | 'Logout': 'लॉग आउट', 88 | 'Lost Password': 'पासवर्ड खो गया', 89 | 'Main Menu': 'Main Menu', 90 | 'Manage Cache': 'Manage Cache', 91 | 'Menu Model': 'Menu Model', 92 | 'My Sites': 'My Sites', 93 | 'New Record': 'नया रेकॉर्ड', 94 | 'new record inserted': 'नया रेकॉर्ड डाला', 95 | 'next 100 rows': 'अगले 100 पंक्तियाँ', 96 | 'No databases in this application': 'इस अनुप्रयोग में कोई डेटाबेस नहीं हैं', 97 | 'Online examples': 'ऑनलाइन उदाहरण के लिए यहाँ क्लिक करें', 98 | 'or import from csv file': 'या csv फ़ाइल से आयात', 99 | 'Other Plugins': 'Other Plugins', 100 | 'Other Recipes': 'Other Recipes', 101 | 'Overview': 'Overview', 102 | 'Plugins': 'Plugins', 103 | 'Powered by': 'Powered by', 104 | 'Preface': 'Preface', 105 | 'previous 100 rows': 'पिछले 100 पंक्तियाँ', 106 | 'Python': 'Python', 107 | 'Query:': 'प्रश्न:', 108 | 'Quick Examples': 'Quick Examples', 109 | 'RAM': 'RAM', 110 | 'RAM Cache Keys': 'RAM Cache Keys', 111 | 'Ram Cleared': 'Ram Cleared', 112 | 'Recipes': 'Recipes', 113 | 'Record': 'Record', 114 | 'record does not exist': 'रिकॉर्ड मौजूद नहीं है', 115 | 'Record id': 'रिकॉर्ड पहचानकर्ता (आईडी)', 116 | 'Register': 'पंजीकृत (रजिस्टर) करना ', 117 | 'register': 'register', 118 | 'Rows in Table': 'तालिका में पंक्तियाँ ', 119 | 'Rows selected': 'चयनित (चुने गये) पंक्तियाँ ', 120 | 'Semantic': 'Semantic', 121 | 'Services': 'Services', 122 | 'Size of cache:': 'Size of cache:', 123 | 'state': 'स्थिति', 124 | 'Statistics': 'Statistics', 125 | 'Stylesheet': 'Stylesheet', 126 | 'submit': 'submit', 127 | 'Support': 'Support', 128 | 'Sure you want to delete this object?': 'सुनिश्चित हैं कि आप इस वस्तु को हटाना चाहते हैं?', 129 | 'Table': 'तालिका', 130 | 'The "query" is a condition like "db.table1.field1==\'value\'". Something like "db.table1.field1==db.table2.field2" results in a SQL JOIN.': 'The "query" is a condition like "db.table1.field1==\'value\'". Something like "db.table1.field1==db.table2.field2" results in a SQL JOIN.', 131 | 'The Core': 'The Core', 132 | 'The output of the file is a dictionary that was rendered by the view %s': 'The output of the file is a dictionary that was rendered by the view %s', 133 | 'The Views': 'The Views', 134 | 'This App': 'This App', 135 | 'Time in Cache (h:m:s)': 'Time in Cache (h:m:s)', 136 | 'Twitter': 'Twitter', 137 | 'unable to parse csv file': 'csv फ़ाइल पार्स करने में असमर्थ', 138 | 'Update:': 'अद्यतन करना:', 139 | 'Use (...)&(...) for AND, (...)|(...) for OR, and ~(...) for NOT to build more complex queries.': 'Use (...)&(...) for AND, (...)|(...) for OR, and ~(...) for NOT to build more complex queries.', 140 | 'Videos': 'Videos', 141 | 'View': 'View', 142 | 'Welcome %s': 'Welcome %s', 143 | 'Welcome to web2py': 'वेब२पाइ (web2py) में आपका स्वागत है', 144 | 'Welcome to web2py!': 'Welcome to web2py!', 145 | 'Which called the function %s located in the file %s': 'Which called the function %s located in the file %s', 146 | 'You are successfully running web2py': 'You are successfully running web2py', 147 | 'You can modify this application and adapt it to your needs': 'You can modify this application and adapt it to your needs', 148 | 'You visited the url %s': 'You visited the url %s', 149 | } 150 | -------------------------------------------------------------------------------- /web_version/languages/hu.py: -------------------------------------------------------------------------------- 1 | # coding: utf8 2 | { 3 | '!langcode!': 'hu', 4 | '!langname!': 'Magyar', 5 | '"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN', 6 | '%s %%{row} deleted': '%s sorok törlődtek', 7 | '%s %%{row} updated': '%s sorok frissítődtek', 8 | '%s selected': '%s kiválasztott', 9 | '%Y-%m-%d': '%Y.%m.%d.', 10 | '%Y-%m-%d %H:%M:%S': '%Y.%m.%d. %H:%M:%S', 11 | 'About': 'About', 12 | 'Access Control': 'Access Control', 13 | 'Administrative Interface': 'Administrative Interface', 14 | 'Administrative interface': 'az adminisztrációs felületért kattints ide', 15 | 'Ajax Recipes': 'Ajax Recipes', 16 | 'appadmin is disabled because insecure channel': 'az appadmin a biztonságtalan csatorna miatt letiltva', 17 | 'Are you sure you want to delete this object?': 'Are you sure you want to delete this object?', 18 | 'Available Databases and Tables': 'Elérhető adatbázisok és táblák', 19 | 'Buy this book': 'Buy this book', 20 | 'cache': 'gyorsítótár', 21 | 'Cache': 'Cache', 22 | 'Cache Keys': 'Cache Keys', 23 | 'Cannot be empty': 'Nem lehet üres', 24 | 'change password': 'jelszó megváltoztatása', 25 | 'Check to delete': 'Törléshez válaszd ki', 26 | 'Clear CACHE?': 'Clear CACHE?', 27 | 'Clear DISK': 'Clear DISK', 28 | 'Clear RAM': 'Clear RAM', 29 | 'Client IP': 'Client IP', 30 | 'Community': 'Community', 31 | 'Components and Plugins': 'Components and Plugins', 32 | 'Controller': 'Controller', 33 | 'Copyright': 'Copyright', 34 | 'Current request': 'Jelenlegi lekérdezés', 35 | 'Current response': 'Jelenlegi válasz', 36 | 'Current session': 'Jelenlegi folyamat', 37 | 'customize me!': 'változtass meg!', 38 | 'data uploaded': 'adat feltöltve', 39 | 'Database': 'adatbázis', 40 | 'Database %s select': 'adatbázis %s kiválasztás', 41 | 'db': 'db', 42 | 'DB Model': 'DB Model', 43 | 'Delete:': 'Töröl:', 44 | 'Demo': 'Demo', 45 | 'Deployment Recipes': 'Deployment Recipes', 46 | 'Description': 'Description', 47 | 'design': 'design', 48 | 'DISK': 'DISK', 49 | 'Disk Cache Keys': 'Disk Cache Keys', 50 | 'Disk Cleared': 'Disk Cleared', 51 | 'Documentation': 'Documentation', 52 | "Don't know what to do?": "Don't know what to do?", 53 | 'done!': 'kész!', 54 | 'Download': 'Download', 55 | 'E-mail': 'E-mail', 56 | 'Edit': 'Szerkeszt', 57 | 'Edit current record': 'Aktuális bejegyzés szerkesztése', 58 | 'edit profile': 'profil szerkesztése', 59 | 'Edit This App': 'Alkalmazást szerkeszt', 60 | 'Email and SMS': 'Email and SMS', 61 | 'Errors': 'Errors', 62 | 'export as csv file': 'exportál csv fájlba', 63 | 'FAQ': 'FAQ', 64 | 'First name': 'First name', 65 | 'Forms and Validators': 'Forms and Validators', 66 | 'Free Applications': 'Free Applications', 67 | 'Group ID': 'Group ID', 68 | 'Groups': 'Groups', 69 | 'Hello World': 'Hello Világ', 70 | 'Home': 'Home', 71 | 'How did you get here?': 'How did you get here?', 72 | 'import': 'import', 73 | 'Import/Export': 'Import/Export', 74 | 'Index': 'Index', 75 | 'insert new': 'új beillesztése', 76 | 'insert new %s': 'új beillesztése %s', 77 | 'Internal State': 'Internal State', 78 | 'Introduction': 'Introduction', 79 | 'Invalid email': 'Invalid email', 80 | 'Invalid Query': 'Hibás lekérdezés', 81 | 'invalid request': 'hibás kérés', 82 | 'Key': 'Key', 83 | 'Last name': 'Last name', 84 | 'Layout': 'Szerkezet', 85 | 'Layout Plugins': 'Layout Plugins', 86 | 'Layouts': 'Layouts', 87 | 'Live Chat': 'Live Chat', 88 | 'login': 'belép', 89 | 'logout': 'kilép', 90 | 'lost password': 'elveszett jelszó', 91 | 'Lost Password': 'Lost Password', 92 | 'Main Menu': 'Főmenü', 93 | 'Manage Cache': 'Manage Cache', 94 | 'Menu Model': 'Menü model', 95 | 'My Sites': 'My Sites', 96 | 'Name': 'Name', 97 | 'New Record': 'Új bejegyzés', 98 | 'new record inserted': 'új bejegyzés felvéve', 99 | 'next 100 rows': 'következő 100 sor', 100 | 'No databases in this application': 'Nincs adatbázis ebben az alkalmazásban', 101 | 'Online examples': 'online példákért kattints ide', 102 | 'or import from csv file': 'vagy betöltés csv fájlból', 103 | 'Origin': 'Origin', 104 | 'Other Plugins': 'Other Plugins', 105 | 'Other Recipes': 'Other Recipes', 106 | 'Overview': 'Overview', 107 | 'Password': 'Password', 108 | 'Plugins': 'Plugins', 109 | 'Powered by': 'Powered by', 110 | 'Preface': 'Preface', 111 | 'previous 100 rows': 'előző 100 sor', 112 | 'Python': 'Python', 113 | 'Query:': 'Lekérdezés:', 114 | 'Quick Examples': 'Quick Examples', 115 | 'RAM': 'RAM', 116 | 'RAM Cache Keys': 'RAM Cache Keys', 117 | 'Ram Cleared': 'Ram Cleared', 118 | 'Recipes': 'Recipes', 119 | 'Record': 'bejegyzés', 120 | 'record does not exist': 'bejegyzés nem létezik', 121 | 'Record ID': 'Record ID', 122 | 'Record id': 'bejegyzés id', 123 | 'Register': 'Register', 124 | 'register': 'regisztráció', 125 | 'Registration key': 'Registration key', 126 | 'Reset Password key': 'Reset Password key', 127 | 'Role': 'Role', 128 | 'Rows in Table': 'Sorok a táblában', 129 | 'Rows selected': 'Kiválasztott sorok', 130 | 'Semantic': 'Semantic', 131 | 'Services': 'Services', 132 | 'Size of cache:': 'Size of cache:', 133 | 'state': 'állapot', 134 | 'Statistics': 'Statistics', 135 | 'Stylesheet': 'Stylesheet', 136 | 'submit': 'submit', 137 | 'Support': 'Support', 138 | 'Sure you want to delete this object?': 'Biztos törli ezt az objektumot?', 139 | 'Table': 'tábla', 140 | 'Table name': 'Table name', 141 | 'The "query" is a condition like "db.table1.field1==\'value\'". Something like "db.table1.field1==db.table2.field2" results in a SQL JOIN.': 'The "query" is a condition like "db.table1.field1==\'value\'". Something like "db.table1.field1==db.table2.field2" results in a SQL JOIN.', 142 | 'The Core': 'The Core', 143 | 'The output of the file is a dictionary that was rendered by the view %s': 'The output of the file is a dictionary that was rendered by the view %s', 144 | 'The Views': 'The Views', 145 | 'This App': 'This App', 146 | 'Time in Cache (h:m:s)': 'Time in Cache (h:m:s)', 147 | 'Timestamp': 'Timestamp', 148 | 'Twitter': 'Twitter', 149 | 'unable to parse csv file': 'nem lehet a csv fájlt beolvasni', 150 | 'Update:': 'Frissít:', 151 | 'Use (...)&(...) for AND, (...)|(...) for OR, and ~(...) for NOT to build more complex queries.': 'Use (...)&(...) for AND, (...)|(...) for OR, and ~(...) for NOT to build more complex queries.', 152 | 'User ID': 'User ID', 153 | 'Videos': 'Videos', 154 | 'View': 'Nézet', 155 | 'Welcome %s': 'Welcome %s', 156 | 'Welcome to web2py': 'Isten hozott a web2py-ban', 157 | 'Welcome to web2py!': 'Welcome to web2py!', 158 | 'Which called the function %s located in the file %s': 'Which called the function %s located in the file %s', 159 | 'You are successfully running web2py': 'You are successfully running web2py', 160 | 'You can modify this application and adapt it to your needs': 'You can modify this application and adapt it to your needs', 161 | 'You visited the url %s': 'You visited the url %s', 162 | } 163 | -------------------------------------------------------------------------------- /web_version/languages/pl.py: -------------------------------------------------------------------------------- 1 | # coding: utf8 2 | { 3 | '!langcode!': 'pl', 4 | '!langname!': 'Polska', 5 | '"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"Uaktualnij" jest dodatkowym wyrażeniem postaci "pole1=\'nowawartość\'". Nie możesz uaktualnić lub usunąć wyników z JOIN:', 6 | '%s %%{row} deleted': 'Wierszy usuniętych: %s', 7 | '%s %%{row} updated': 'Wierszy uaktualnionych: %s', 8 | '%s selected': '%s wybranych', 9 | '%Y-%m-%d': '%Y-%m-%d', 10 | '%Y-%m-%d %H:%M:%S': '%Y-%m-%d %H:%M:%S', 11 | 'About': 'About', 12 | 'Access Control': 'Access Control', 13 | 'Administrative Interface': 'Administrative Interface', 14 | 'Administrative interface': 'Kliknij aby przejść do panelu administracyjnego', 15 | 'Ajax Recipes': 'Ajax Recipes', 16 | 'appadmin is disabled because insecure channel': 'administracja aplikacji wyłączona z powodu braku bezpiecznego połączenia', 17 | 'Are you sure you want to delete this object?': 'Are you sure you want to delete this object?', 18 | 'Authentication': 'Uwierzytelnienie', 19 | 'Available Databases and Tables': 'Dostępne bazy danych i tabele', 20 | 'Buy this book': 'Buy this book', 21 | 'cache': 'cache', 22 | 'Cache': 'Cache', 23 | 'Cache Keys': 'Cache Keys', 24 | 'Cannot be empty': 'Nie może być puste', 25 | 'Change Password': 'Zmień hasło', 26 | 'change password': 'change password', 27 | 'Check to delete': 'Zaznacz aby usunąć', 28 | 'Check to delete:': 'Zaznacz aby usunąć:', 29 | 'Clear CACHE?': 'Clear CACHE?', 30 | 'Clear DISK': 'Clear DISK', 31 | 'Clear RAM': 'Clear RAM', 32 | 'Client IP': 'IP klienta', 33 | 'Community': 'Community', 34 | 'Components and Plugins': 'Components and Plugins', 35 | 'Controller': 'Kontroler', 36 | 'Copyright': 'Copyright', 37 | 'Current request': 'Aktualne żądanie', 38 | 'Current response': 'Aktualna odpowiedź', 39 | 'Current session': 'Aktualna sesja', 40 | 'customize me!': 'dostosuj mnie!', 41 | 'data uploaded': 'dane wysłane', 42 | 'Database': 'baza danych', 43 | 'Database %s select': 'wybór z bazy danych %s', 44 | 'db': 'baza danych', 45 | 'DB Model': 'Model bazy danych', 46 | 'Delete:': 'Usuń:', 47 | 'Demo': 'Demo', 48 | 'Deployment Recipes': 'Deployment Recipes', 49 | 'Description': 'Opis', 50 | 'design': 'projektuj', 51 | 'DISK': 'DISK', 52 | 'Disk Cache Keys': 'Disk Cache Keys', 53 | 'Disk Cleared': 'Disk Cleared', 54 | 'Documentation': 'Documentation', 55 | "Don't know what to do?": "Don't know what to do?", 56 | 'done!': 'zrobione!', 57 | 'Download': 'Download', 58 | 'E-mail': 'Adres e-mail', 59 | 'Edit': 'Edycja', 60 | 'Edit current record': 'Edytuj obecny rekord', 61 | 'edit profile': 'edit profile', 62 | 'Edit Profile': 'Edytuj profil', 63 | 'Edit This App': 'Edytuj tę aplikację', 64 | 'Email and SMS': 'Email and SMS', 65 | 'Errors': 'Errors', 66 | 'export as csv file': 'eksportuj jako plik csv', 67 | 'FAQ': 'FAQ', 68 | 'First name': 'Imię', 69 | 'Forms and Validators': 'Forms and Validators', 70 | 'Free Applications': 'Free Applications', 71 | 'Function disabled': 'Funkcja wyłączona', 72 | 'Group ID': 'ID grupy', 73 | 'Groups': 'Groups', 74 | 'Hello World': 'Witaj Świecie', 75 | 'Home': 'Home', 76 | 'How did you get here?': 'How did you get here?', 77 | 'import': 'import', 78 | 'Import/Export': 'Importuj/eksportuj', 79 | 'Index': 'Indeks', 80 | 'insert new': 'wstaw nowy rekord tabeli', 81 | 'insert new %s': 'wstaw nowy rekord do tabeli %s', 82 | 'Internal State': 'Stan wewnętrzny', 83 | 'Introduction': 'Introduction', 84 | 'Invalid email': 'Błędny adres email', 85 | 'Invalid Query': 'Błędne zapytanie', 86 | 'invalid request': 'Błędne żądanie', 87 | 'Key': 'Key', 88 | 'Last name': 'Nazwisko', 89 | 'Layout': 'Układ', 90 | 'Layout Plugins': 'Layout Plugins', 91 | 'Layouts': 'Layouts', 92 | 'Live Chat': 'Live Chat', 93 | 'login': 'login', 94 | 'Login': 'Zaloguj', 95 | 'logout': 'logout', 96 | 'Logout': 'Wyloguj', 97 | 'Lost Password': 'Przypomnij hasło', 98 | 'Main Menu': 'Menu główne', 99 | 'Manage Cache': 'Manage Cache', 100 | 'Menu Model': 'Model menu', 101 | 'My Sites': 'My Sites', 102 | 'Name': 'Nazwa', 103 | 'New Record': 'Nowy rekord', 104 | 'new record inserted': 'nowy rekord został wstawiony', 105 | 'next 100 rows': 'następne 100 wierszy', 106 | 'No databases in this application': 'Brak baz danych w tej aplikacji', 107 | 'Online examples': 'Kliknij aby przejść do interaktywnych przykładów', 108 | 'or import from csv file': 'lub zaimportuj z pliku csv', 109 | 'Origin': 'Źródło', 110 | 'Other Plugins': 'Other Plugins', 111 | 'Other Recipes': 'Other Recipes', 112 | 'Overview': 'Overview', 113 | 'Password': 'Hasło', 114 | "Password fields don't match": 'Pola hasła nie są zgodne ze sobą', 115 | 'Plugins': 'Plugins', 116 | 'Powered by': 'Zasilane przez', 117 | 'Preface': 'Preface', 118 | 'previous 100 rows': 'poprzednie 100 wierszy', 119 | 'Python': 'Python', 120 | 'Query:': 'Zapytanie:', 121 | 'Quick Examples': 'Quick Examples', 122 | 'RAM': 'RAM', 123 | 'RAM Cache Keys': 'RAM Cache Keys', 124 | 'Ram Cleared': 'Ram Cleared', 125 | 'Recipes': 'Recipes', 126 | 'Record': 'rekord', 127 | 'record does not exist': 'rekord nie istnieje', 128 | 'Record ID': 'ID rekordu', 129 | 'Record id': 'id rekordu', 130 | 'Register': 'Zarejestruj', 131 | 'register': 'register', 132 | 'Registration key': 'Klucz rejestracji', 133 | 'Role': 'Rola', 134 | 'Rows in Table': 'Wiersze w tabeli', 135 | 'Rows selected': 'Wybrane wiersze', 136 | 'Semantic': 'Semantic', 137 | 'Services': 'Services', 138 | 'Size of cache:': 'Size of cache:', 139 | 'state': 'stan', 140 | 'Statistics': 'Statistics', 141 | 'Stylesheet': 'Arkusz stylów', 142 | 'submit': 'submit', 143 | 'Submit': 'Wyślij', 144 | 'Support': 'Support', 145 | 'Sure you want to delete this object?': 'Czy na pewno chcesz usunąć ten obiekt?', 146 | 'Table': 'tabela', 147 | 'Table name': 'Nazwa tabeli', 148 | 'The "query" is a condition like "db.table1.field1==\'value\'". Something like "db.table1.field1==db.table2.field2" results in a SQL JOIN.': '"Zapytanie" jest warunkiem postaci "db.tabela1.pole1==\'wartość\'". Takie coś jak "db.tabela1.pole1==db.tabela2.pole2" oznacza SQL JOIN.', 149 | 'The Core': 'The Core', 150 | 'The output of the file is a dictionary that was rendered by the view %s': 'The output of the file is a dictionary that was rendered by the view %s', 151 | 'The Views': 'The Views', 152 | 'This App': 'This App', 153 | 'Time in Cache (h:m:s)': 'Time in Cache (h:m:s)', 154 | 'Timestamp': 'Znacznik czasu', 155 | 'Twitter': 'Twitter', 156 | 'unable to parse csv file': 'nie można sparsować pliku csv', 157 | 'Update:': 'Uaktualnij:', 158 | 'Use (...)&(...) for AND, (...)|(...) for OR, and ~(...) for NOT to build more complex queries.': 'Użyj (...)&(...) jako AND, (...)|(...) jako OR oraz ~(...) jako NOT do tworzenia bardziej skomplikowanych zapytań.', 159 | 'User %(id)s Registered': 'Użytkownik %(id)s został zarejestrowany', 160 | 'User ID': 'ID użytkownika', 161 | 'Verify Password': 'Potwierdź hasło', 162 | 'Videos': 'Videos', 163 | 'View': 'Widok', 164 | 'Welcome %s': 'Welcome %s', 165 | 'Welcome to web2py': 'Witaj w web2py', 166 | 'Welcome to web2py!': 'Welcome to web2py!', 167 | 'Which called the function %s located in the file %s': 'Which called the function %s located in the file %s', 168 | 'You are successfully running web2py': 'You are successfully running web2py', 169 | 'You can modify this application and adapt it to your needs': 'You can modify this application and adapt it to your needs', 170 | 'You visited the url %s': 'You visited the url %s', 171 | } 172 | -------------------------------------------------------------------------------- /web_version/languages/plural-cs.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | { 3 | # "singular form (0)": ["first plural form (1)", "second plural form (2)", ...], 4 | 'vteřina': ['vteřiny', 'vteřin'], 5 | 'vteřinou': ['vteřinami', 'vteřinami'], 6 | 'minuta': ['minuty', 'minut'], 7 | 'minutou': ['minutami', 'minutami'], 8 | 'hodina': ['hodiny','hodin'], 9 | 'hodinou': ['hodinami','hodinami'], 10 | 'den': ['dny','dnů'], 11 | 'dnem': ['dny','dny'], 12 | 'týden': ['týdny','týdnů'], 13 | 'týdnem': ['týdny','týdny'], 14 | 'měsíc': ['měsíce','měsíců'], 15 | 'měsícem': ['měsíci','měsíci'], 16 | 'rok': ['roky','let'], 17 | 'rokem': ['roky','lety'], 18 | 'záznam': ['záznamy', 'záznamů'], 19 | 'soubor': ['soubory', 'souborů'] 20 | } 21 | -------------------------------------------------------------------------------- /web_version/languages/plural-en.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | { 3 | # "singular form (0)": ["first plural form (1)", "second plural form (2)", ...], 4 | 'account': ['accounts'], 5 | 'book': ['books'], 6 | 'is': ['are'], 7 | 'man': ['men'], 8 | 'miss': ['misses'], 9 | 'person': ['people'], 10 | 'quark': ['quarks'], 11 | 'shop': ['shops'], 12 | 'this': ['these'], 13 | 'was': ['were'], 14 | 'woman': ['women'], 15 | } 16 | -------------------------------------------------------------------------------- /web_version/languages/plural-es.py: -------------------------------------------------------------------------------- 1 | # coding: utf-8 2 | { 3 | # "singular form (0)": ["first plural form (1)", "second plural form (2)", ...], 4 | 'fila': ['filas'], 5 | 'eliminada': ['eliminadas'], 6 | 'actualizada': ['actualizadas'], 7 | 'seleccionado': ['seleccionados'], 8 | } 9 | -------------------------------------------------------------------------------- /web_version/languages/plural-ru.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | { 3 | # "singular form (0)": ["first plural form (1)", "second plural form (2)", ...], 4 | 'выбрана': ['выбраны','выбрано'], 5 | 'запись': ['записи','записей'], 6 | 'изменена': ['изменены','изменено'], 7 | 'строка': ['строки','строк'], 8 | 'удалена': ['удалены','удалено'], 9 | 'день': ['дня', 'дней'], 10 | 'месяц': ['месяца','месяцев'], 11 | 'неделю': ['недели','недель'], 12 | 'год': ['года','лет'], 13 | 'час': ['часа','часов'], 14 | 'минуту': ['минуты','минут'], 15 | 'секунду': ['секунды','секунд'], 16 | } 17 | -------------------------------------------------------------------------------- /web_version/languages/plural-uk.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | { 3 | # "singular form (0)": ["first plural form (1)", "second plural form (2)", ...], 4 | 'байт': ['байти','байтів'], 5 | 'годину': ['години','годин'], 6 | 'день': ['дні','днів'], 7 | 'елемент': ['елементи','елементів'], 8 | 'запис': ['записи','записів'], 9 | 'місяць': ['місяці','місяців'], 10 | 'поцілювання': ['поцілювання','поцілювань'], 11 | 'рядок': ['рядки','рядків'], 12 | 'рік': ['роки','років'], 13 | 'секунду': ['секунди','секунд'], 14 | 'схибнення': ['схибнення','схибнень'], 15 | 'тиждень': ['тижні','тижнів'], 16 | 'хвилину': ['хвилини','хвилин'], 17 | } 18 | -------------------------------------------------------------------------------- /web_version/languages/tr.py: -------------------------------------------------------------------------------- 1 | # coding: utf8 2 | { 3 | '!langcode!': 'tr', 4 | '!langname!': 'Türkçe', 5 | '%s %%(shop)': '%s %%(shop)', 6 | '%s %%(shop[0])': '%s %%(shop[0])', 7 | '%s %%{quark[0]}': '%s %%{quark[0]}', 8 | '%s %%{shop[0]}': '%s %%{shop[0]}', 9 | '%s %%{shop}': '%s %%{shop}', 10 | '%Y-%m-%d': '%Y-%m-%d', 11 | '%Y-%m-%d %H:%M:%S': '%Y-%m-%d %H:%M:%S', 12 | '@markmin\x01**Hello World**': '**Merhaba Dünya**', 13 | 'About': 'Hakkında', 14 | 'Access Control': 'Erişim Denetimi', 15 | 'Administrative Interface': 'Yönetim Arayüzü', 16 | 'Ajax Recipes': 'Ajax Tarifleri', 17 | 'An error occured, please %s the page': 'Bir hata meydana geldi, lütfen sayfayı %s', 18 | 'Are you sure you want to delete this object?': 'Bu nesneyi silmek istediğinden emin misin?', 19 | 'Buy this book': 'Bu kitabı satın alın', 20 | 'Cannot be empty': 'Boş bırakılamaz', 21 | 'Check to delete': 'Silmek için denetle', 22 | 'Client IP': ' IP', 23 | 'Community': 'Topluluk', 24 | 'Components and Plugins': 'Bileşenler ve Eklentiler', 25 | 'Controller': 'Denetçi', 26 | 'Copyright': 'Telif', 27 | 'Created By': 'Tasarlayan', 28 | 'Created On': 'Oluşturma tarihi', 29 | 'customize me!': 'burayı değiştir!', 30 | 'Database': 'Veritabanı', 31 | 'DB Model': 'DB Model', 32 | 'Demo': 'Demo', 33 | 'Deployment Recipes': 'Yayınlama tarifleri', 34 | 'Description': 'Açıklama', 35 | 'Documentation': 'Kitap', 36 | "Don't know what to do?": 'Neleri nasıl yapacağını bilmiyor musun?', 37 | 'Download': 'İndir', 38 | 'E-mail': 'E-posta', 39 | 'Email and SMS': 'E-posta ve kısa mesaj (SMS)', 40 | 'enter an integer between %(min)g and %(max)g': '%(min)g ve %(max)g arasında bir sayı girin', 41 | 'enter date and time as %(format)s': 'tarih ve saati %(format)s biçiminde girin', 42 | 'Errors': 'Hatalar', 43 | 'FAQ': 'SSS', 44 | 'First name': 'Ad', 45 | 'Forgot username?': 'Kullanıcı adını mı unuttun?', 46 | 'Forms and Validators': 'Biçimler ve Doğrulayıcılar', 47 | 'Free Applications': 'Ücretsiz uygulamalar', 48 | 'Giriş': 'Giriş', 49 | 'Group %(group_id)s created': '%(group_id)s takımı oluşturuldu', 50 | 'Group ID': 'Takım ID', 51 | 'Group uniquely assigned to user %(id)s': 'Group uniquely assigned to user %(id)s', 52 | 'Groups': 'Topluluklar', 53 | 'Hello World': 'Merhaba Dünyalı', 54 | 'Hello World ## comment': 'Merhaba Dünyalı ', 55 | 'Hello World## comment': 'Merhaba Dünyalı', 56 | 'Home': 'Anasayfa', 57 | 'How did you get here?': 'Bu sayfayı görüntüleme uğruna neler mi oldu?', 58 | 'Introduction': 'Giriş', 59 | 'Invalid email': 'Yanlış eposta', 60 | 'Is Active': 'Etkin', 61 | 'Kayıt ol': 'Kayıt ol', 62 | 'Last name': 'Soyad', 63 | 'Layout': 'Şablon', 64 | 'Layout Plugins': 'Şablon Eklentileri', 65 | 'Layouts': 'Şablonlar', 66 | 'Live Chat': 'Canlı Sohbet', 67 | 'Logged in': 'Giriş yapıldı', 68 | 'Logged out': 'Çıkış yapıldı', 69 | 'Login': 'Giriş', 70 | 'Logout': 'Terket', 71 | 'Lost Password': 'Şifremi unuttum', 72 | 'Lost password?': 'Şifrenizimi unuttunuz?', 73 | 'Menu Model': 'Menu Model', 74 | 'Modified By': 'Değiştiren', 75 | 'Modified On': 'Değiştirilme tarihi', 76 | 'My Sites': 'Sitelerim', 77 | 'Name': 'İsim', 78 | 'Object or table name': 'Nesne ya da tablo adı', 79 | 'Online examples': 'Canlı örnekler', 80 | 'Origin': 'Origin', 81 | 'Other Plugins': 'Diğer eklentiler', 82 | 'Other Recipes': 'Diğer Tarifler', 83 | 'Overview': 'Göz gezdir', 84 | 'Password': 'Şifre', 85 | "Password fields don't match": 'Şifreler uyuşmuyor', 86 | 'please input your password again': 'lütfen şifrenizi tekrar girin', 87 | 'Plugins': 'Eklentiler', 88 | 'Powered by': 'Yazılım Temeli', 89 | 'Preface': 'Preface', 90 | 'Profile': 'Hakkımda', 91 | 'Python': 'Python', 92 | 'Quick Examples': 'Hızlı Örnekler', 93 | 'Recipes': 'Recipes', 94 | 'Record ID': 'Kayıt ID', 95 | 'Register': 'Kayıt ol', 96 | 'Registration identifier': 'Registration identifier', 97 | 'Registration key': 'Kayıt anahtarı', 98 | 'Registration successful': 'Kayıt başarılı', 99 | 'reload': 'reload', 100 | 'Remember me (for 30 days)': 'Beni hatırla (30 gün)', 101 | 'Request reset password': 'Şifre sıfırla', 102 | 'Reset Password key': 'Şifre anahtarını sıfırla', 103 | 'Role': 'Role', 104 | 'Semantic': 'Semantik', 105 | 'Services': 'Hizmetler', 106 | 'Stylesheet': 'Stil Şablonu', 107 | 'Support': 'Destek', 108 | 'The Core': 'Çekirdek', 109 | 'The output of the file is a dictionary that was rendered by the view %s': 'Son olarak fonksiyonların vs. işlenip %s dosyasıyla tasarıma yedirilmesiyle sayfayı görüntüledin', 110 | 'The Views': 'The Views', 111 | 'This App': 'Bu Uygulama', 112 | 'Timestamp': 'Zaman damgası', 113 | 'Twitter': 'Twitter', 114 | 'User %(id)s Logged-in': '%(id)s Giriş yaptı', 115 | 'User %(id)s Logged-out': '%(id)s çıkış yaptı', 116 | 'User %(id)s Password reset': 'User %(id)s Password reset', 117 | 'User %(id)s Registered': '%(id)s Kayıt oldu', 118 | 'User ID': 'Kullanıcı ID', 119 | 'value already in database or empty': 'değer boş ya da veritabanında zaten mevcut', 120 | 'Verify Password': 'Şifreni Onayla', 121 | 'Videos': 'Videolar', 122 | 'View': 'View', 123 | 'Welcome': 'Hoşgeldin', 124 | 'Welcome to web2py!': 'Welcome to web2py!', 125 | 'Which called the function %s located in the file %s': 'Bu ziyaretle %s fonksiyonunu %s dosyasından çağırmış oldun ', 126 | 'You are successfully running web2py': 'web2py çatısını çalıştırmayı başardın', 127 | 'You can modify this application and adapt it to your needs': 'Artık uygulamayı kafana göre düzenleyebilirsin!', 128 | 'You visited the url %s': '%s adresini ziyaret ettin', 129 | } 130 | -------------------------------------------------------------------------------- /web_version/models/db.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | 3 | ######################################################################### 4 | ## This scaffolding model makes your app work on Google App Engine too 5 | ## File is released under public domain and you can use without limitations 6 | ######################################################################### 7 | 8 | ## if SSL/HTTPS is properly configured and you want all HTTP requests to 9 | ## be redirected to HTTPS, uncomment the line below: 10 | # request.requires_https() 11 | 12 | if not request.env.web2py_runtime_gae: 13 | ## if NOT running on Google App Engine use SQLite or other DB 14 | db = DAL('sqlite://storage.sqlite',pool_size=1,check_reserved=['all']) 15 | else: 16 | ## connect to Google BigTable (optional 'google:datastore://namespace') 17 | db = DAL('google:datastore') 18 | ## store sessions and tickets there 19 | session.connect(request, response, db=db) 20 | ## or store session in Memcache, Redis, etc. 21 | ## from gluon.contrib.memdb import MEMDB 22 | ## from google.appengine.api.memcache import Client 23 | ## session.connect(request, response, db = MEMDB(Client())) 24 | 25 | ## by default give a view/generic.extension to all actions from localhost 26 | ## none otherwise. a pattern can be 'controller/function.extension' 27 | response.generic_patterns = ['*'] if request.is_local else [] 28 | ## (optional) optimize handling of static files 29 | # response.optimize_css = 'concat,minify,inline' 30 | # response.optimize_js = 'concat,minify,inline' 31 | ## (optional) static assets folder versioning 32 | # response.static_version = '0.0.0' 33 | ######################################################################### 34 | ## Here is sample code if you need for 35 | ## - email capabilities 36 | ## - authentication (registration, login, logout, ... ) 37 | ## - authorization (role based authorization) 38 | ## - services (xml, csv, json, xmlrpc, jsonrpc, amf, rss) 39 | ## - old style crud actions 40 | ## (more options discussed in gluon/tools.py) 41 | ######################################################################### 42 | 43 | from gluon.tools import Auth, Crud, Service, PluginManager, prettydate 44 | auth = Auth(db) 45 | crud, service, plugins = Crud(db), Service(), PluginManager() 46 | 47 | ## create all tables needed by auth if not custom tables 48 | auth.define_tables(username=False, signature=False) 49 | 50 | ## configure email 51 | mail = auth.settings.mailer 52 | mail.settings.server = 'logging' or 'smtp.gmail.com:587' 53 | mail.settings.sender = 'you@gmail.com' 54 | mail.settings.login = 'username:password' 55 | 56 | ## configure auth policy 57 | auth.settings.registration_requires_verification = False 58 | auth.settings.registration_requires_approval = False 59 | auth.settings.reset_password_requires_verification = True 60 | 61 | ## if you need to use OpenID, Facebook, MySpace, Twitter, Linkedin, etc. 62 | ## register with janrain.com, write your domain:api_key in private/janrain.key 63 | from gluon.contrib.login_methods.rpx_account import use_janrain 64 | use_janrain(auth, filename='private/janrain.key') 65 | 66 | ######################################################################### 67 | ## Define your tables below (or better in another model file) for example 68 | ## 69 | ## >>> db.define_table('mytable',Field('myfield','string')) 70 | ## 71 | ## Fields can be 'string','text','password','integer','double','boolean' 72 | ## 'date','time','datetime','blob','upload', 'reference TABLENAME' 73 | ## There is an implicit 'id integer autoincrement' field 74 | ## Consult manual for more options, validators, etc. 75 | ## 76 | ## More API examples for controllers: 77 | ## 78 | ## >>> db.mytable.insert(myfield='value') 79 | ## >>> rows=db(db.mytable.myfield=='value').select(db.mytable.ALL) 80 | ## >>> for row in rows: print row.id, row.myfield 81 | ######################################################################### 82 | 83 | ## after defining tables, uncomment below to enable auditing 84 | # auth.enable_record_versioning(db) 85 | -------------------------------------------------------------------------------- /web_version/models/menu.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # this file is released under public domain and you can use without limitations 3 | 4 | ######################################################################### 5 | ## Customize your APP title, subtitle and menus here 6 | ######################################################################### 7 | 8 | response.logo = A(B('web',SPAN(2),'py'),XML('™ '), 9 | _class="brand",_href="http://www.web2py.com/") 10 | response.title = request.application.replace('_',' ').title() 11 | response.subtitle = '' 12 | 13 | ## read more at http://dev.w3.org/html5/markup/meta.name.html 14 | response.meta.author = 'Your Name ' 15 | response.meta.description = 'a cool new app' 16 | response.meta.keywords = 'web2py, python, framework' 17 | response.meta.generator = 'Web2py Web Framework' 18 | 19 | ## your http://google.com/analytics id 20 | response.google_analytics_id = None 21 | 22 | ######################################################################### 23 | ## this is the main application menu add/remove items as required 24 | ######################################################################### 25 | 26 | response.menu = [ 27 | (T('Home'), False, URL('default', 'index'), []) 28 | ] 29 | 30 | DEVELOPMENT_MENU = True 31 | 32 | ######################################################################### 33 | ## provide shortcuts for development. remove in production 34 | ######################################################################### 35 | 36 | def _(): 37 | # shortcuts 38 | app = request.application 39 | ctr = request.controller 40 | # useful links to internal and external resources 41 | response.menu += [ 42 | (SPAN('web2py', _class='highlighted'), False, 'http://web2py.com', [ 43 | (T('My Sites'), False, URL('admin', 'default', 'site')), 44 | (T('This App'), False, URL('admin', 'default', 'design/%s' % app), [ 45 | (T('Controller'), False, 46 | URL( 47 | 'admin', 'default', 'edit/%s/controllers/%s.py' % (app, ctr))), 48 | (T('View'), False, 49 | URL( 50 | 'admin', 'default', 'edit/%s/views/%s' % (app, response.view))), 51 | (T('Layout'), False, 52 | URL( 53 | 'admin', 'default', 'edit/%s/views/layout.html' % app)), 54 | (T('Stylesheet'), False, 55 | URL( 56 | 'admin', 'default', 'edit/%s/static/css/web2py.css' % app)), 57 | (T('DB Model'), False, 58 | URL( 59 | 'admin', 'default', 'edit/%s/models/db.py' % app)), 60 | (T('Menu Model'), False, 61 | URL( 62 | 'admin', 'default', 'edit/%s/models/menu.py' % app)), 63 | (T('Database'), False, URL(app, 'appadmin', 'index')), 64 | (T('Errors'), False, URL( 65 | 'admin', 'default', 'errors/' + app)), 66 | (T('About'), False, URL( 67 | 'admin', 'default', 'about/' + app)), 68 | ]), 69 | ('web2py.com', False, 'http://www.web2py.com', [ 70 | (T('Download'), False, 71 | 'http://www.web2py.com/examples/default/download'), 72 | (T('Support'), False, 73 | 'http://www.web2py.com/examples/default/support'), 74 | (T('Demo'), False, 'http://web2py.com/demo_admin'), 75 | (T('Quick Examples'), False, 76 | 'http://web2py.com/examples/default/examples'), 77 | (T('FAQ'), False, 'http://web2py.com/AlterEgo'), 78 | (T('Videos'), False, 79 | 'http://www.web2py.com/examples/default/videos/'), 80 | (T('Free Applications'), 81 | False, 'http://web2py.com/appliances'), 82 | (T('Plugins'), False, 'http://web2py.com/plugins'), 83 | (T('Layouts'), False, 'http://web2py.com/layouts'), 84 | (T('Recipes'), False, 'http://web2pyslices.com/'), 85 | (T('Semantic'), False, 'http://web2py.com/semantic'), 86 | ]), 87 | (T('Documentation'), False, 'http://www.web2py.com/book', [ 88 | (T('Preface'), False, 89 | 'http://www.web2py.com/book/default/chapter/00'), 90 | (T('Introduction'), False, 91 | 'http://www.web2py.com/book/default/chapter/01'), 92 | (T('Python'), False, 93 | 'http://www.web2py.com/book/default/chapter/02'), 94 | (T('Overview'), False, 95 | 'http://www.web2py.com/book/default/chapter/03'), 96 | (T('The Core'), False, 97 | 'http://www.web2py.com/book/default/chapter/04'), 98 | (T('The Views'), False, 99 | 'http://www.web2py.com/book/default/chapter/05'), 100 | (T('Database'), False, 101 | 'http://www.web2py.com/book/default/chapter/06'), 102 | (T('Forms and Validators'), False, 103 | 'http://www.web2py.com/book/default/chapter/07'), 104 | (T('Email and SMS'), False, 105 | 'http://www.web2py.com/book/default/chapter/08'), 106 | (T('Access Control'), False, 107 | 'http://www.web2py.com/book/default/chapter/09'), 108 | (T('Services'), False, 109 | 'http://www.web2py.com/book/default/chapter/10'), 110 | (T('Ajax Recipes'), False, 111 | 'http://www.web2py.com/book/default/chapter/11'), 112 | (T('Components and Plugins'), False, 113 | 'http://www.web2py.com/book/default/chapter/12'), 114 | (T('Deployment Recipes'), False, 115 | 'http://www.web2py.com/book/default/chapter/13'), 116 | (T('Other Recipes'), False, 117 | 'http://www.web2py.com/book/default/chapter/14'), 118 | (T('Buy this book'), False, 119 | 'http://stores.lulu.com/web2py'), 120 | ]), 121 | (T('Community'), False, None, [ 122 | (T('Groups'), False, 123 | 'http://www.web2py.com/examples/default/usergroups'), 124 | (T('Twitter'), False, 'http://twitter.com/web2py'), 125 | (T('Live Chat'), False, 126 | 'http://webchat.freenode.net/?channels=web2py'), 127 | ]), 128 | (T('Plugins'), False, None, [ 129 | ('plugin_wiki', False, 130 | 'http://web2py.com/examples/default/download'), 131 | (T('Other Plugins'), False, 132 | 'http://web2py.com/plugins'), 133 | (T('Layout Plugins'), 134 | False, 'http://web2py.com/layouts'), 135 | ]) 136 | ] 137 | )] 138 | if DEVELOPMENT_MENU: _() 139 | 140 | if "auth" in locals(): auth.wikimenu() 141 | -------------------------------------------------------------------------------- /web_version/modules/__init__.py: -------------------------------------------------------------------------------- 1 | from . import balancer 2 | from . import kineticizer 3 | from . import misc 4 | from . import SBtab 5 | from . import validatorSBtab 6 | from . import sbtab2sbml 7 | from . import sbml2sbtab 8 | -------------------------------------------------------------------------------- /web_version/routes.example.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | 3 | # This is an app-specific example router 4 | # 5 | # This simple router is used for setting languages from app/languages directory 6 | # as a part of the application path: app//controller/function 7 | # Language from default.py or 'en' (if the file is not found) is used as 8 | # a default_language 9 | # 10 | # See /router.example.py for parameter's detail 11 | #------------------------------------------------------------------------------------- 12 | # To enable this route file you must do the steps: 13 | # 14 | # 1. rename /router.example.py to routes.py 15 | # 2. rename this APP/routes.example.py to APP/routes.py 16 | # (where APP - is your application directory) 17 | # 3. restart web2py (or reload routes in web2py admin interfase) 18 | # 19 | # YOU CAN COPY THIS FILE TO ANY APPLICATION'S ROOT DIRECTORY WITHOUT CHANGES! 20 | 21 | from fileutils import abspath 22 | from languages import read_possible_languages 23 | 24 | possible_languages = read_possible_languages(abspath('applications', app)) 25 | #NOTE! app - is an application based router's parameter with name of an 26 | # application. E.g.'welcome' 27 | 28 | routers = { 29 | app: dict( 30 | default_language = possible_languages['default'][0], 31 | languages = [lang for lang in possible_languages 32 | if lang != 'default'] 33 | ) 34 | } 35 | 36 | #NOTE! To change language in your application using these rules add this line 37 | #in one of your models files: 38 | # if request.uri_language: T.force(request.uri_language) 39 | -------------------------------------------------------------------------------- /web_version/static/403.html: -------------------------------------------------------------------------------- 1 | 403 2 | -------------------------------------------------------------------------------- /web_version/static/404.html: -------------------------------------------------------------------------------- 1 | 404 2 | -------------------------------------------------------------------------------- /web_version/static/500.html: -------------------------------------------------------------------------------- 1 | 500 2 | -------------------------------------------------------------------------------- /web_version/static/README.md: -------------------------------------------------------------------------------- 1 | ### Static files of the Parameter Balancing Repository ### 2 | 3 | The static files comprise static HTML files for the website (*.html), images for the website visualisation (/static/images/*), and a variety of default and exemplary data files (/static/files/*). 4 | 5 | The exemplary data files include SBtab kinetic parameter files, SBML model files (*.xml), and the following SBtab default files, which are crucial to the parameter balancing workflow: 6 | 7 | - pb_options.tsv (customary configuration options of the parameter balancing; numerous settings of the tool can be changed via this file) 8 | - definitions.tsv (definitions of the SBtab table types and allowed columns; this is required for the validation of SBtab files and can be extended according to individual needs. Please see www.sbtab.org for more details) 9 | - pb_prior.tsv (file that holds information on the prior distributions of the different kinetic parameter types; these are required for the Bayesian estimation within the parameter balancing) -------------------------------------------------------------------------------- /web_version/static/contact.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Parameter Balancing for Kinetic Models of Cell Metabolism 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 36 |
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Parameter balancing
for kinetic metabolic models

19 | 20 |

21 | 22 |

23 | Main | 24 | Online Balancing | 25 | Documentation | 26 | Download | 27 | Contact 28 |

29 | 30 |

Contact

31 |

32 | For feedback, questions, or suggestions for parameter balancing please contact

33 | Wolfram Liebermeister and Timo Lubitz. 34 |

35 |
37 | 38 | 39 | -------------------------------------------------------------------------------- /web_version/static/css/calendar.css: -------------------------------------------------------------------------------- 1 | .calendar{z-index:2000;position:relative;display:none;background:#fff;border:2px solid #000;font-size:11px;color:#000;cursor:default;font-family:Arial,Helvetica,sans-serif; 2 | border-radius: 10px; 3 | -moz-border-radius: 10px; 4 | -webkit-border-radius: 10px; 5 | }.calendar table{margin:0px;font-size:11px;color:#000;cursor:default;font-family:tahoma,verdana,sans-serif;}.calendar .button{text-align:center;padding:1px;color:#fff;background:#000;}.calendar .nav{background:#000;color:#fff}.calendar thead .title{font-weight:bold;padding:1px;background:#000;color:#fff;text-align:center;}.calendar thead .name{padding:2px;text-align:center;background:#bbb;}.calendar thead .weekend{color:#f00;}.calendar thead .hilite {background-color:#666;}.calendar thead .active{padding:2px 0 0 2px;background-color:#c4c0b8;}.calendar tbody .day{width:2em;text-align:right;padding:2px 4px 2px 2px;}.calendar tbody .day.othermonth{color:#aaa;}.calendar tbody .day.othermonth.oweekend{color:#faa;}.calendar table .wn{padding:2px 3px 2px 2px;background:#bbb;}.calendar tbody .rowhilite td{background:#ddd;}.calendar tbody td.hilite{background:#bbb;}.calendar tbody td.active{background:#bbb;}.calendar tbody td.selected{font-weight:bold;background:#ddd;}.calendar tbody td.weekend{color:#f00;}.calendar tbody td.today{font-weight:bold;color:#00f;}.calendar tbody .disabled{color:#999;}.calendar tbody .emptycell{visibility:hidden;}.calendar tbody .emptyrow{display:none;}.calendar tfoot .ttip{background:#bbb;padding:1px;background:#000;color:#fff;text-align:center;}.calendar tfoot .hilite{background:#ddd;}.calendar tfoot .active{}.calendar .combo{position:absolute;display:none;width:4em;top:0;left:0;cursor:default;background:#e4e0d8;padding:1px;z-index:2001;}.calendar .combo .label,.calendar .combo .label-IEfix{text-align:center;padding:1px;}.calendar .combo .label-IEfix{width:4em;}.calendar .combo .active{background:#c4c0b8;}.calendar .combo .hilite{background:#048;color:#fea;}.calendar td.time{padding:1px 0;text-align:center;background-color:#bbb;}.calendar td.time .hour,.calendar td.time .minute,.calendar td.time .ampm{padding:0 3px 0 4px;font-weight:bold;}.calendar td.time .ampm{text-align:center;}.calendar td.time .colon{padding:0 2px 0 3px;font-weight:bold;}.calendar td.time span.hilite{}.calendar td.time span.active{border-color:#f00;background-color:#000;color:#0f0;}.hour,.minute{font-size:2em;} 6 | 7 | #CP_hourcont{z-index:2000;padding:0;position:absolute;border:1px dashed #666;background-color:#eee;display:none;}#CP_minutecont{z-index:2000;background-color:#ddd;padding:1px;position:absolute;width:45px;display:none;}.floatleft{float:left;}.CP_hour{z-index:2000;padding:1px;font-family:Arial,Helvetica,sans-serif;font-size:9px;white-space:nowrap;cursor:pointer;width:35px;}.CP_minute{z-index:2000;padding:1px;font-family:Arial,Helvetica,sans-serif;font-size:9px;white-space:nowrap;cursor:pointer;width:auto;}.CP_over{background-color:#fff;z-index:2000} 8 | -------------------------------------------------------------------------------- /web_version/static/css/css_template/contact.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | Parameter Balancing - Contact Page 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 49 | 50 |
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Contact

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62 | Parameter balancing has been developed at Humboldt Universität Berlin, Charité - Universitätsmedizin Berlin,
and at INRA (Institut National de la Recherche Agronomique) Jouy-en-Josas.

63 | For feedback, questions, or suggestions for parameter balancing please contact

64 | Wolfram Liebermeister and Timo Lubitz. 65 |

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0.3 nan mM R04779 Brenda 10 | inhibitory constant R04779 ADP_c 1.8 nan mM R04779 Brenda 11 | standard chemical potential nan beta_D_16_PP -2206.1 nan kJ/mol nan Alberty 12 | concentration nan ATP_c 1.5 0.4 mM nan nan 13 | standard chemical potential nan ATP_c -2292.3 nan kJ/mol nan Alberty 14 | standard chemical potential nan beta_D_6_P -1316.6 nan kJ/mol nan Alberty 15 | concentration nan ADP_c 0.8 0.5 mM nan nan 16 | standard chemical potential nan ADP_c -1425.2 nan kJ/mol nan Alberty 17 | Michaelis constant R04779 beta_D_6_P 0.7 nan mM nan Brenda 18 | Michaelis constant R04779 beta_D_16_PP 12.5 nan mM nan Brenda 19 | Michaelis constant R04779 ATP_c 0.1 nan mM nan Brenda 20 | Michaelis constant R04779 ADP_c 0.9 nan mM nan Brenda 21 | equilibrium constant R04779 nan 0.1 nan dimensionless R04779 Nissler et. al 22 | -------------------------------------------------------------------------------- /web_version/static/css/css_template/img/pfk_model_example.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab SBtabVersion='1.0' Document='pfk_reaction' TableType='Compartment' TableName='Compartment' 2 | !ID !Name !Size 3 | c cytosol 1 4 | 5 | !!SBtab SBtabVersion='1.0' Document='pfk_reaction' TableType='Compound' TableName='Compound' 6 | !ID !Name !Location !Charge !IsConstant 7 | ATP_c ATP c 0 False 8 | beta_D_6_P beta-D-fructofuranose 6-phosphate c 0 False 9 | ADP_c ADP c 0 False 10 | beta_D_16_PP beta-D-fructofuranose 1_6-bisphosphate c 0 False 11 | enzyme_R04779_c enzyme_R04779 c 0 False 12 | 13 | !!SBtab SBtabVersion='1.0' Document='pfk_reaction' TableType='Reaction' TableName='Reaction' 14 | !ID !Name !ReactionFormula !Regulator !IsReversible 15 | R04779 _6_phosphofructokinase_activity ATP_c + beta_D_6_P <=> ADP_c + beta_D_16_PP ATP_c True 16 | -------------------------------------------------------------------------------- /web_version/static/css/css_template/img/pfk_options_example.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableName="Parameter balancing configuration file" TableType="Config" Date="2018-03-16" TableID="ConfigurePB" 2 | !ID !Value 3 | use_pseudo_values True 4 | ph 7 5 | temperature 298.15 6 | overwrite_kinetics True 7 | cell_volume 43 8 | parametrisation hal 9 | enzyme_prefactor True 10 | default_inhibition complete 11 | default_activation complete 12 | model_name outputname 13 | boundary_values ignore 14 | -------------------------------------------------------------------------------- /web_version/static/css/css_template/img/sbtab_config_example.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tlubitz/parameter_balancing/cb57d51548741a926fcc9ab1e7dfc80225f5de77/web_version/static/css/css_template/img/sbtab_config_example.png -------------------------------------------------------------------------------- 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You can require() this file in a CommonJS environment. 2 | require('../../js/transition.js') 3 | require('../../js/alert.js') 4 | require('../../js/button.js') 5 | require('../../js/carousel.js') 6 | require('../../js/collapse.js') 7 | require('../../js/dropdown.js') 8 | require('../../js/modal.js') 9 | require('../../js/tooltip.js') 10 | require('../../js/popover.js') 11 | require('../../js/scrollspy.js') 12 | require('../../js/tab.js') 13 | require('../../js/affix.js') -------------------------------------------------------------------------------- /web_version/static/css/css_template/main.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | Parameter Balancing for Kinetic Models of Cell Metabolism 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 50 | 51 |
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55 | Parameter Balancing Logo 56 |

57 |

Parameter balancing for kinetic metabolic models

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Parameter balancing is a computational 69 | method for obtaining consistent parameter sets for kinetic 70 | metabolic models. Experimentally measured values, when inserted 71 | into models directly, would be likely to yield incomplete and 72 | inconsistent parameter sets. Balanced parameter sets, computed from measured kinetic 73 | constants and other experimental data, respect constraints 74 | between biochemical quantities and assumptions about typical 75 | ranges, represented by prior values and bounds.

76 | 77 |

On this website, users can apply parameter 78 | balancing to their own metabolic models. Aside from the metabolic 79 | model itself (in SBML 80 | or SBtab format), users can upload 81 | additional SBtab files describing measured kinetic and other data, 82 | prior distributions for different types of kinetic parameters, and 83 | configuration options for the balancing process. The balanced parameter 84 | set, and the model with rate laws and model parameters inserted, 85 | can be downloaded in SBtab and SBML format. 86 |

87 | 88 |

To get acquainted with parameter balancing, please 89 | read the documentation page 90 | and the manual. 91 |

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101 | 107 | 108 | 109 | 110 | 111 | 112 | -------------------------------------------------------------------------------- /web_version/static/css/pb.css~: -------------------------------------------------------------------------------- 1 | /* css stylesheet for proteomap web pages */ 2 | 3 | body {background-color:#FFFFFF; color: #404040; font-size: 14px} 4 | 5 | h1,h2,h3,h4,p,ul,ol,li,div,td,th,address,blockquote,nobr,b,i { font-family:Arial,sans-serif; } 6 | 7 | h1 { font-size:30px; margin-bottom:26px; } 8 | 9 | h2 { font-size:21px; margin-bottom:18px; } 10 | 11 | h3 { font-size:18px; } 12 | 13 | h4 { font-size:14px; } 14 | 15 | p {color: #202040; font-size:14px; "Arial,Helvetica"; text-align:justify; margin-left:0px;} 16 | 17 | ul,ol,li,div,td,th,address,blockquote { color: #404040; font-size:14px; "Arial,Helvetica"; } 18 | 19 | table {color: #404040; font-face: "Arial,Helvetica"; font-size: 14px} 20 | 21 | td {color: #000000; font-face: "Arial,Helvetica"; font-size: 14px} 22 | 23 | li { margin-top:3px; width:700px;} 24 | 25 | pre { font-family:Courier New,Courier; font-size:14px; color:#000000; } 26 | 27 | code,kbd,tt { font-family:Courier New,Courier; color:#000000; } 28 | 29 | var { font-style:normal; color:#000000; } 30 | 31 | blockquote,cite { font-style:italic; } 32 | 33 | a {text-decoration:none; } 34 | 35 | a:link { color:#ff4400; } 36 | 37 | a:visited { color:#ff4400; } 38 | 39 | a:active { color:#ff4400; } 40 | 41 | ins { color:#009900; font-weight:bold; text-decoration:none; } 42 | 43 | del { color:#990000; font-weight:bold; text-decoration:line-through; } 44 | -------------------------------------------------------------------------------- /web_version/static/examples.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Parameter Balancing for Kinetic Models of Cell Metabolism 5 | 6 | 7 | 8 | 9 | 10 |

Parameter Balancing for Kinetic Models of Cell Metabolism

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Models and data sets

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Phosphofructokinase Reaction (PFK)

16 | 17 |

Our SBML model of the Phosphofructokinase reaction was constructed 18 | from the KEGG 19 | Reaction R04779 20 | with semanticSBML-fill.

21 | 22 | 27 | 28 | 29 |

Glycolysis (Teusink et al, 2000)

30 | 31 |

Teusink's glycolysis model 32 | (Teusink et al, (2000)) 33 | has been assembled from enzymatic rate laws determined in vitro.

34 | 35 | 40 | 41 |

Glycolysis model (Hynne et al., 2001)

42 | 43 |

Hynne's glycolysis model ((Hynne et al., 2001)) was created to describe glycolysis in yeast at 44 | the onset of metabolic oscillations. In the encoded version from 45 | BioModels Database, SBO terms for allosteric inhibitors are 46 | missing. We provide a second version in which these SBO terms have 47 | been added.

48 | 49 | 55 | 56 |

Pancreatic Beta Cell Model (Jiang et al.,2007)

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Jiang's model of the glucose-stimulated secretion system in 58 | pancreatic beta cells 59 | ((Jiang 60 | et al.,2007)) is one of the largest kinetic models in BioModels 61 | Database.

62 | 67 | 68 |

E coli central metabolism (unpublished)

69 | 70 | 71 |

Additional data files concerning E. coli central metabolism can be found here. 72 | 73 |

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Data provenance

76 | 77 |

Data for the examples were collected from the following public data 78 | sources:

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  1. Brenda: Brenda Enzyme Database

    2. 81 |

  2. NIST: Thermodynamics of Enzyme-Catalyzed Reactions, see R.N. Goldberg, Y.B. Tewari and T.N. Bhat (2004), 82 | Thermodynamics of enzyme-catalyzed reactions - a database for 83 | quantitative biochemistry, Bioinformatics 20 (16), 2874-2877 84 |

    3. 85 |

  3. yeastGFP: Yeast GFP Fusion Localization Database

    4. 86 |

  4. Alberty: Alberty, R.A. (1998), Calculation 87 | of standard transformed Gibbs energies and standard transformed 88 | enthalpies of biochemical reactants, Archives of Biochemistry and 89 | Biophysics, 353 (1), 116-130

    5. 90 |
91 | 92 |
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94 | Main | 95 | Introduction | 96 | Workflow | 97 | Online Balancing | 98 | Configure Online Balancing | 99 | File format | 100 | FAQ | 101 | Quantities | 102 | Examples | 103 | Software | 104 | Contact | 105 |

106 | 107 | 108 | -------------------------------------------------------------------------------- /web_version/static/file_format.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Parameter Balancing for Kinetic Models of Cell Metabolism 5 | 6 | 7 | 8 | 9 | 10 |

Parameter Balancing for Kinetic Models of Cell Metabolism

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File format

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Input files for parameter balancing must be prepared in the SBtab format. 15 | Some example files can be found here. 16 |

    17 |
  1. Data tables must be provided as tab-seperated text in a specific file format. The columns 18 | QuantityType, SBMLReactionID, SBMLSpeciesID, and Mean (data value, arithmetic mean) are obligatory, 19 | while the columns Std (data value, standard error), Unit, and other columns are optional. 20 | Example files can be found here.
    2. 21 |
  2. Entries in the data table have to refer to species and reactions in the SBML file via the SBML 22 | element identifiers ("id") given in the columns SBMLSpeciesID and SBMLReactionID.
    3. 23 |
  3. Please make sure that the modifiers (inhibitors or stimulators) in your model are identified 24 | clearly by the corresponding SBO terms (inhibitor:20, stimulator:459). Otherwise, the software 25 | will not recognize them, and the allosteric regulations will be ignored.
    4. 26 |
  4. The model reactions are assumed to refer to biochemical reactants (e.g. ATP) and not to individual 27 | protonation states (like ATP4-). This means that the equilibrium constants or chemical potentials 28 | considered in the model are in fact transformed thermodynamic quantities, which refer to the biochemical 29 | reactants and will depend on the pH. This implies that protons (H+) may not appear in the reaction 30 | formulas in the model and that the data used must also refer to transformed quantities. For more 31 | information on this topic, see the review 32 | Biochemical thermodynamics 33 | by R. Alberty.
    5. 34 |
  5. Some quantities depend on the specific definition of the reaction sum formula (nominal direction, 35 | appearance of small molecules like water); in particular for equilibrium constants, catalytic rate 36 | constants, and maximal velocities, make sure that the definitions match between model and data set.
    6. 37 |
  6. Gibbs free energies can be used as proxies for the standard chemical potentials. However, make sure 38 | not to mix values from different data sets. It is possible that they will follow different conventions 39 | (setting the GFE for some large molecules to zero values for convenience) and will therefore be 40 | incompatible.
    7. 41 |
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43 | 44 |
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46 | Main | 47 | Introduction | 48 | Workflow | 49 | Online Balancing | 50 | Configure Online Balancing | 51 | File format | 52 | FAQ | 53 | Quantities | 54 | Examples | 55 | Software | 56 | Contact | 57 |

58 | 59 | 60 | -------------------------------------------------------------------------------- /web_version/static/files/default_files/pb_options.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableName="Parameter balancing configuration file" TableType="Config" Date="2018-03-16" TableID="ConfigurePB" 2 | !ID !Value 3 | use_pseudo_values True 4 | ph 7 5 | temperature 298.15 6 | overwrite_kinetics True 7 | cell_volume 43 8 | parametrisation hal 9 | enzyme_prefactor True 10 | default_inhibition complete 11 | default_activation complete 12 | model_name outputname 13 | boundary_values ignore 14 | size_limit 300 15 | -------------------------------------------------------------------------------- /web_version/static/files/default_files/pb_prior.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableName="Parameter prior" TableType="QuantityInfo" Date="2018-04-06" TableID="PriorTable" 2 | !QuantityType !Unit !BiologicalElement !MathematicalType !PriorMedian !PriorStd !PriorGeometricStd !LowerBound !UpperBound !DataStd !DataGeometricStd !Symbol !PhysicalType !Dependence !UseAsPriorInformation !SBMLElement !Abbreviation !MatrixInfo 3 | standard chemical potential kJ/mol Species Additive 0 500 -500 500 10 mu0 Thermodynamic Basic 1 Global parameter scp [I_species, 0, 0, 0, 0, 0, 0, 0] 4 | catalytic rate constant geometric mean 1/s Reaction Multiplicative 10 100 0.0000001 10000 10 1.2 KV Kinetic Basic 1 Local parameter kcrg [0, I_reaction, 0, 0, 0, 0, 0, 0] 5 | Michaelis constant mM Reaction/Species Multiplicative 0.1 10 0.000001 1000 1 1.2 KM Kinetic Basic 1 Local parameter kmc [0, 0, I_KM, 0, 0, 0, 0, 0] 6 | activation constant mM Reaction/Species Multiplicative 0.1 10 0.0001 100 1 1.2 KA Kinetic Basic 1 Local parameter kac [0, 0, 0, I_KA, 0, 0, 0, 0] 7 | inhibitory constant mM Reaction/Species Multiplicative 0.1 10 0.0001 100 1 1.2 KI Kinetic Basic 1 Local parameter kic [0, 0, 0, 0, I_KI, 0, 0, 0] 8 | concentration mM Species Multiplicative 0.1 10 0.000001 1000 1 1.2 c Dynamic Basic 1 Species (conc.) c [0, 0, 0, 0, 0, I_species, 0, 0] 9 | concentration of enzyme mM Reaction Multiplicative 0.001 100 0.000001 0.5 0.05 1.2 u Dynamic Basic 1 Local parameter eco [0, 0, 0, 0, 0, 0, I_reaction, 0] 10 | pH dimensionless None Additive 7 1 0 14 1 pH Dynamic Basic 1 Global parameter ph [0, 0, 0, 0, 0, 0, 0, 1] 11 | standard Gibbs energy of reaction kJ/mol Reaction Additive 0 500 -1000 1000 10 dmu0 Thermodynamic Derived 0 Global parameter dscp [Nt, 0, 0, 0, 0, 0, 0, 0] 12 | equilibrium constant dimensionless Reaction Multiplicative 1 100 0.0000000001 100000000 10 1.2 Keq Thermodynamic Derived 1 Local parameter keq [[-1/RT * Nt], 0, 0, 0, 0, 0, 0, 0] 13 | substrate catalytic rate constant 1/s Reaction Multiplicative 10 100 0.01 10000000 10 1.2 Kcatf Kinetic Derived 1 Local parameter kcrf [[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, 0, 0] 14 | product catalytic rate constant 1/s Reaction Multiplicative 10 100 0.000000001 10000000 10 1.2 Kcatr Kinetic Derived 1 Local parameter kcrr [[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, 0, 0] 15 | chemical potential kJ/mol Species Additive 0 500 -500 500 10 mu Dynamic Derived 0 cp [I_species, 0, 0, 0, 0, [RT * I_species], 0, 0] 16 | reaction affinity kJ/mol Reaction Additive 0 500 -100 100 10 A Dynamic Derived 0 raf [[-1 * Nt], 0, 0, 0, 0, [-RT * Nt], 0, 0] 17 | forward maximal velocity mM/s Reaction Multiplicative 0.01 100 0.00000001 1000000 0.1 2 Vmaxf Dynamic Derived 0 Local parameter vmaf [[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, I_reaction, 0] 18 | reverse maximal velocity mM/s Reaction Multiplicative 0.01 100 0.00000001 1000000 0.1 2 Vmaxr Dynamic Derived 0 Local parameter vmar [[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, I_reaction, 0] 19 | forward mass action term 1/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 2 thetaf Dynamic Derived 0 thtf [[-1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nft, 0, 0] 20 | reverse mass action term 1/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 2 thetar Dynamic Derived 0 thtr [[ 1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nrt, 0, 0] 21 | forward enzyme mass action term mM/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 2 tauf Dynamic Derived 0 tauf [[-1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nft, I_reaction, 0] 22 | reverse enzyme mass action term mM/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 2 taur Dynamic Derived 0 taur [[ 1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nrt, I_reaction, 0] 23 | Michaelis constant product mM Reaction Multiplicative 1 1000 0.001 1000 1 2 KMprod Kinetic Derived 0 Local parameter kmprod [0, 0, Nkm, 0, 0, 0, 0, 0] 24 | catalytic constant ratio dimensionless Reaction Multiplicative 1 10 0.0000000001 10000000000 1 2 Kcatratio Kinetic Derived 0 Local parameter kcrat [-1/RT * Nt], I_reaction, [-1 * Nkm], 0, 0, 0, 0, 0] -------------------------------------------------------------------------------- /web_version/static/files/example_files/ecoli/ecoli_carlsson_modified_prior.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableName='Quantity info' TableType='QuantityInfo' TableID='QuantityInfo' 2 | !QuantityType !Symbol !Unit !Constant !RelatedElement !Scaling !Dependence !PriorMode !PriorStd !LowerBound !UpperBound !ErrorStd !SBMLElement !Abbreviation !MatrixInfo 3 | standard chemical potential mu0 kJ/mol Thermodynamic Species Original Basic -880 1500 -3000 2000 10 Global parameter scp [I_species, 0, 0, 0, 0, 0, 0] 4 | standard Gibbs energy of reaction dmu0 kJ/mol Thermodynamic Reaction Original Derived 0 1500 -1000 1000 10 Global parameter dscp [Nt, 0, 0, 0, 0, 0, 0] 5 | catalytic rate constant geometric mean KV 1/s Kinetic Reaction Logarithmic Basic 10 1 0.0000001 10000 0.5 Local parameter kcrg [0, I_reaction, 0, 0, 0, 0, 0] 6 | Michaelis constant KM mM Kinetic Reaction/Species Logarithmic Basic 0.1 1 0.000001 1000 0.5 Local parameter kmc [0, 0, I_KM, 0, 0, 0, 0] 7 | activation constant KA mM Kinetic Reaction/Species Logarithmic Basic 0.1 1 0.0001 100 0.5 Local parameter kac [0, 0, 0, I_KA, 0, 0, 0] 8 | inhibitory constant KI mM Kinetic Reaction/Species Logarithmic Basic 0.1 1 0.0001 100 0.5 Local parameter kic [0, 0, 0, 0, I_KI, 0, 0] 9 | equilibrium constant Keq dimensionless Thermodynamic Reaction Logarithmic Derived 1 1.5 0.0000000001 100000000 0.5 Local parameter keq [[-1/RT * Nt], 0, 0, 0, 0, 0, 0] 10 | substrate catalytic rate constant Kcatf 1/s Kinetic Reaction Logarithmic Derived 10 1.5 0.01 10000000 0.5 Local parameter kcrf [[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, 0] 11 | product catalytic rate constant Kcatr 1/s Kinetic Reaction Logarithmic Derived 10 3 0.000000001 10000000 0.5 Local parameter kcrr [[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, 0] 12 | concentration c mM Dynamic Species Logarithmic Basic 0.1 1.5 0.000001 1000 0.5 Species (conc.) c [0, 0, 0, 0, 0, I_species, 0] 13 | concentration of enzyme u mM Dynamic Reaction Logarithmic Basic 0.00001 1.5 0.000001 2 0.5 Local parameter eco [0, 0, 0, 0, 0, 0, I_reaction] 14 | forward maximal velocity Vmaxf mM/s Dynamic Reaction Logarithmic Derived 1 2 0.00000001 1000000 0.5 Local parameter vmaf [[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, I_reaction] 15 | reverse maximal velocity Vmaxr mM/s Dynamic Reaction Logarithmic Derived 1 2 0.00000001 1000000 0.5 Local parameter vmar [[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, I_reaction] 16 | chemical potential mu kJ/mol Dynamic Species Original Derived -880 1500 -3000 2000 20 cp [I_species, 0, 0, 0, 0, [RT * I_species], 0] 17 | reaction affinity A kJ/mol Dynamic Reaction Original Derived 0 10 -60 60 10 raf [[-1 * Nt], 0, 0, 0, 0, [-RT * Nt], 0] 18 | forward enzyme mass action term tauf mM/s Dynamic Reaction Logarithmic Derived 1 1.5 0.0000001 10000000 1 tauf [[-1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nft, I_reaction] 19 | reverse enzyme mass action term taur mM/s Dynamic Reaction Logarithmic Derived 1 1.5 0.0000001 10000000 1 taur [[ 1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nrt, I_reaction] 20 | pH pH 1 Dynamic None Original Basic 7 1 0 14 1 Global parameter ph [0, 0, 0, 0, 0, 0, 0] 21 | Michaelis constant product KMprod mM Kinetic Reaction Logarithmic Derived 0.1 1 0.000001 1000 0.5 Local parameter kmprod [0, 0, Nkm, 0, 0, 0, 0] -------------------------------------------------------------------------------- /web_version/static/files/example_files/pfk/pfk_data.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableID='ParameterData' TableType='Quantity' Version='0.1' Level='1.0' 2 | !QuantityType !Reaction:SBML:reaction:id !Compound:SBML:species:id !Mean !Std !Unit !Organism !Reaction:Identifiers:kegg.reaction !Compound:Identifiers:kegg.compound !Reference 3 | concentration of enzyme R04779 nan 0.089 nan mM Saccharomyces cerevisiae R04779 nan yeastGFP 4 | concentration of enzyme R04779 nan 0.090 nan mM Saccharomyces cerevisiae R04779 nan yeastGFP 5 | inhibitory constant R04779 ATP_c 2.5 nan mM Oryctolagus cuniculus R04779 C00002 Brenda 6 | inhibitory constant R04779 ATP_c 0.8 nan mM Ascaris suum R04779 C00002 Brenda 7 | inhibitory constant R04779 ATP_c 0.5 nan mM Fasciola hepatica R04779 C00002 Brenda 8 | inhibitory constant R04779 ATP_c 1.4 nan mM Fasciola hepatica R04779 C00002 Brenda 9 | inhibitory constant R04779 ATP_c 0.3 nan mM Sus scrofa R04779 C00002 Brenda 10 | inhibitory constant R04779 ADP_c 1.8 nan mM nan R04779 C00008 Brenda 11 | standard chemical potential nan beta_D_fructofuranose_1_6_bisphosphate_c -2206.1 nan kJ/mol nan nan C05378 Alberty 12 | concentration nan ATP_c 1.5 0.4 mM Saccharomyces cerevisiae nan C00002 nan 13 | standard chemical potential nan ATP_c -2292.3 nan kJ/mol nan nan C00002 Alberty 14 | standard chemical potential nan beta_D_fructofuranose_6_phosphate_c -1316.6 nan kJ/mol nan nan C05345 Alberty 15 | concentration nan ADP_c 0.8 0.5 mM Saccharomyces cerevisiae nan C00008 nan 16 | standard chemical potential nan ADP_c -1425.2 nan kJ/mol nan nan C00008 Alberty 17 | Michaelis constant R04779 beta_D_fructofuranose_6_phosphate_c 0.7 nan mM nan nan C05345 Brenda 18 | Michaelis constant R04779 beta_D_fructofuranose_1_6_bisphosphate_c 12.5 nan mM nan nan C05378 Brenda 19 | Michaelis constant R04779 ATP_c 0.1 nan mM nan nan C00002 Brenda 20 | Michaelis constant R04779 ADP_c 0.9 nan mM nan nan C00008 Brenda 21 | equilibrium constant R04779 nan 0.1 nan dimensionless nan R04779 nan Nissler et. al 22 | -------------------------------------------------------------------------------- /web_version/static/files/example_files/pfk/pfk_result.tsv: -------------------------------------------------------------------------------- 1 | !!SBtab TableID="ParameterBalanced" TableType="QuantityData" Version="0.1" Level="1.0" TableName="PFK Result" 2 | !QuantityType !SBML:reaction:id !SBML:species:id !Mode !Value !Std !Unit !Provenance !Type 3 | standard chemical potential None enzyme_R04779_c -877.128823387 -877.128823387 480.842256677 kJ/mol Balanced parameter value Basic 4 | standard chemical potential None beta_D_fructofuranose_1_6_bisphosphate_c -2191.91903371 -2191.91903371 30.2323043166 kJ/mol Balanced parameter value Basic 5 | standard chemical potential None ATP_c -2292.06896057 -2292.06896057 30.2323039147 kJ/mol Balanced parameter value Basic 6 | standard chemical potential None beta_D_fructofuranose_6_phosphate_c -1321.47362395 -1321.47362395 30.2323043167 kJ/mol Balanced parameter value Basic 7 | standard chemical potential None ADP_c -1415.06387901 -1415.06387901 30.2323039989 kJ/mol Balanced parameter value Basic 8 | chemical potential None ATP_c -2291.18020579 -2291.18020579 30.239302839 kJ/mol Balanced parameter value Derived 9 | chemical potential None beta_D_fructofuranose_6_phosphate_c -1323.59730166 -1323.59730166 30.3543342094 kJ/mol Balanced parameter value Derived 10 | chemical potential None ADP_c -1416.09917968 -1416.09917968 30.2634322181 kJ/mol Balanced parameter value Derived 11 | chemical potential None beta_D_fructofuranose_1_6_bisphosphate_c -2192.47216276 -2192.47216276 30.3542965659 kJ/mol Balanced parameter value Derived 12 | chemical potential None enzyme_R04779_c -882.871176613 -882.871176613 480.842256677 kJ/mol Balanced parameter value Derived 13 | concentration None enzyme_R04779_c 0.1 0.1 38.8842320107 mM Balanced parameter value Basic 14 | concentration None ATP_c 1.4281 1.4281 0.3928816712 mM Balanced parameter value Basic 15 | concentration None beta_D_fructofuranose_1_6_bisphosphate_c 0.8011 0.8011 2.2040121515 mM Balanced parameter value Basic 16 | concentration None beta_D_fructofuranose_6_phosphate_c 0.4268 0.4268 1.1747415541 mM Balanced parameter value Basic 17 | concentration None ADP_c 0.6603 0.6603 0.4580606275 mM Balanced parameter value Basic 18 | Michaelis constant R04779 beta_D_fructofuranose_6_phosphate_c 0.5669 0.5669 0.3056352867 mM Balanced parameter value Basic 19 | Michaelis constant R04779 beta_D_fructofuranose_1_6_bisphosphate_c 8.9574 8.9574 4.8294292186 mM Balanced parameter value Basic 20 | Michaelis constant R04779 ATP_c 0.0927 0.0927 0.0499760756 mM Balanced parameter value Basic 21 | Michaelis constant R04779 ADP_c 0.7516 0.7516 0.4052432267 mM Balanced parameter value Basic 22 | equilibrium constant R04779 None 0.0721 0.0721 0.0395839013 dimensionless Balanced parameter value Derived 23 | concentration of enzyme R04779 None 0.0032 0.0032 0.0011771037 mM Balanced parameter value Basic 24 | substrate catalytic rate constant R04779 None 18.253 18.253 102.939814093 1/s Balanced parameter value Derived 25 | product catalytic rate constant R04779 None 1.9764 1.9764 11.1459995047 1/s Balanced parameter value Derived 26 | catalytic rate constant geometric mean R04779 None 6.0062 6.0062 25.6018361108 1/s Balanced parameter value Derived 27 | reaction affinity R04779 None 0.0027840724 0.0027840724 0.0047114567 kJ/mol Balanced parameter value Derived 28 | forward maximal velocity R04779 None 0.0063 0.0063 0.0386754561 mM/s Balanced parameter value Derived 29 | reverse maximal velocity R04779 None 0.0579 0.0579 0.3571904216 mM/s Balanced parameter value Derived 30 | inhibitory constant R04779 ATP_c 0.3763 0.3763 0.102763523 mM Balanced parameter value Basic 31 | -------------------------------------------------------------------------------- /web_version/static/files/manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tlubitz/parameter_balancing/cb57d51548741a926fcc9ab1e7dfc80225f5de77/web_version/static/files/manual.pdf -------------------------------------------------------------------------------- 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   68 | 69 | 70 | 71 | 76 | 77 | 81 | 82 | 83 |
72 | 73 | 74 | 75 | 78 |
79 |

Parameter balancing
for kinetic metabolic models

80 |
84 | 85 |

86 | 87 |

88 | Main | 89 | Online Balancing | 90 | Documentation | 91 | Download | 92 | Contact 93 |

94 |
95 | 96 |

Parameter balancing is a computational 97 | method for obtaining consistent parameter sets for kinetic 98 | metabolic models. Experimentally measured values, when inserted 99 | into models directly, would be likely to yield incomplete and 100 | inconsistent parameter sets. Balanced parameter sets, computed from measured kinetic 101 | constants and other experimental data, are complete and consistent: they respect constraints 102 | between biochemical quantities and assumptions about typical 103 | ranges, represented by prior values and bounds.

104 | 105 |

On this website, users can apply parameter 106 | balancing to their own metabolic models. Aside from the metabolic 107 | model itself (in SBML 108 | or SBtab format), users can upload 109 | additional SBtab files describing (i) measured kinetic and other data, (ii) 110 | prior distributions for different types of kinetic parameters, and 111 | (iii) configuration options for the balancing process. 112 |

113 | 114 |

To get acquainted with parameter balancing, please 115 | read the documentation page 116 | and the manual. 117 |

118 |
122 | 123 | 124 | 125 | -------------------------------------------------------------------------------- /web_version/static/software.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Parameter Balancing for Kinetic Models of Cell Metabolism 5 | 6 | 7 | 8 | 9 | 10 |

Parameter Balancing for Kinetic Models of Cell Metabolism

11 | 12 |

Software

13 | 14 |

15 | Python code for parameter balancing 16 |

17 | Python code for parameter balancing can be freely downloaded from 18 | bitbucket. Please see 19 | the instructions that come with the code. 20 |

21 | Matlab code for parameter balancing 22 |

23 | MATLAB code for parameter balancing is included in the Metabolic Networks 24 | Toolbox. The toolbox can be freely downloaded from 25 | github. 26 |

27 |

28 | 29 |
30 |

31 | Main | 32 | Introduction | 33 | Workflow | 34 | Online Balancing | 35 | Configure Online Balancing | 36 | File format | 37 | FAQ | 38 | Quantities | 39 | Examples | 40 | Software | 41 | Contact | 42 |

43 | 44 | 45 | -------------------------------------------------------------------------------- /web_version/static/workflow.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Parameter Balancing for Kinetic Models of Cell Metabolism 5 | 6 | 7 | 8 | 9 | 10 |

Parameter Balancing for Kinetic Models of Cell Metabolism

11 | 12 |

The parameter balancing workflow

13 | 14 |

Parameter balancing helps you find a consistent parameter set 15 | for a kinetic model, based on (i) kinetic constants and other data collected from 16 | experiments or the literature; (ii) constraints between biochemical quantities due 17 | to their definition or the laws of thermodynamics; (iii) assumptions about typical 18 | ranges, represented by prior distributions and pseudo values. As our standard rate 19 | laws, we use 20 | modular 21 | rate laws. 22 |

    23 |
  1. (1/4) Upload your SBML model. Please make sure that your SBML model is 24 | valid. You can use the official SBML online validator for this.
    2. 25 |
  2. (2/4) Upload your SBtab file. Here again, make sure that the SBtab file is 26 | valid. You can use the official SBtab online validator 27 | for this. Please also keep in mind that the SBML species and reaction IDs need to comply with 28 | the IDs that are used in the SBtab file.
    3. 29 |
  3. (3/4) Choose your prior file. This file holds information on the prior distributions on the 30 | parameter types. Initially, you can use the default prior table which is already loaded. If you want 31 | to use an alternative prior table, you can choose one from the list or 32 | create your own prior table (keep in mind to adhere to the syntax of the prior tables).
    4. 33 |
  4. (4/4) Download the balancing results. If the balancing process was successful, 34 | you can download the SBML file with the balanced parameters and convenience kinetics from the SBML list. 35 | Analogously, you can download the SBtab parameter file with the balanced parameters from the SBtab list.
    5. 36 |
37 |

38 | 39 |

Alternately, you can also use the Fast Lane Balancing option: 40 | All required information are provided in one single SBtab document file, which consists 41 | of several SBtab tables. Mandatory for this option is an SBtab Reaction table, which can 42 | be translated to an SBMl model. Optional are 43 | SBtab Compartment, Parameter, and Compound tables, which are employed as additional model 44 | building information (see more information on the SBtab <-> SBML conversion on www.sbtab.net). 45 | Furthermore, the user can also provide an SBtab Quantity table, 46 | which holds the kinetic parameters for the balancing. Also, an SBtab QuantityInfo table 47 | can be part of this one SBtab document file, and it holds the information on the prior 48 | distributions for the balancing (see Quantities for more 49 | information). Finally, an SBtab Config table can help you set configuration 50 | options for the balancing process (see Configure Online Balancing 51 | for more information). 52 |

53 | 54 |
55 |

56 | Main | 57 | Introduction | 58 | Workflow | 59 | Online Balancing | 60 | Configure Online Balancing | 61 | File format | 62 | FAQ | 63 | Quantities | 64 | Examples | 65 | Software | 66 | Contact | 67 |

68 | 69 | 70 | -------------------------------------------------------------------------------- /web_version/views/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /web_version/views/default/balanced.html: -------------------------------------------------------------------------------- 1 | {{extend 'layout.html'}} 2 | 3 |
4 |
5 |

Parameter Balancing Online: Results

6 |
7 |
8 | 9 |
10 |
11 |
12 |
13 |
14 | {{if RESULT_SBML_NAME:}} 15 |
16 |
17 |

Download area SBML

18 |
19 | 20 |
21 |

22 | {{=RESULT_SBML_NAME[0]}} 23 |

24 |
25 |
26 | 27 | 28 |
29 |
30 |
31 |
32 | {{pass}} 33 | 34 | {{if RESULT_SBTAB_NAME:}} 35 |
36 |
37 |

Download area SBtab

38 |
39 |
40 | {{for pos,f in enumerate(RESULT_SBTAB_NAME):}} 41 |

42 | {{=f}} 43 |

44 |
45 |
46 | 47 | 48 |
49 |
50 | {{pass}} 51 |
52 | {{pass}} 53 | 54 | 55 | 56 | {{if (WARNINGS and RESULT_SBML_NAME) or (WARNINGS and RESULT_SBTAB_NAME) :}} 57 | {{for pos,f in enumerate(WARNINGS):}} 58 | {{=f}} 59 | {{pass}} 60 | 61 | {{elif RESULT_SBML_NAME or RESULT_SBTAB_NAME:}} 62 | No file warnings detected. Please see log file for parameter balancing warnings. 63 | {{else:}} 64 | There are no more files to show here. Please return to the homepage. 65 | {{pass}} 66 |
67 | 77 |
78 |
79 |
80 |
81 |
82 |
83 | 89 | 90 | 91 | 92 | 93 | -------------------------------------------------------------------------------- /web_version/views/default/config.html: -------------------------------------------------------------------------------- 1 | {{extend 'layout.html'}} 2 |

3 | 4 |

5 | Main | 6 | Documentation | 7 | Online Balancing | 8 | Configure Online Balancing | 9 | Download | 10 | Contact 11 |

12 | 13 |

14 | 15 | 16 |

Update the configuration file for online Parameter Balancing

17 | 18 | An SBtab configuration file can be employed to choose several options for the online Parameter Balancing.
19 |
20 | 21 | {{=CONFIG_FORM}} 22 | 23 | {{if CONFIG_NAME:}} 24 | 25 |
26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 |
Currently loaded config file for your session:
{{=CONFIG_NAME}}
35 | 36 | {{if WARNINGS:}} 37 | 38 | 39 | 43 | 44 | 45 |
40 | 41 | {{=WARNINGS[0]}} 42 |
46 | {{else:}} 47 | 48 | 49 |
No warnings detected.
50 | {{pass}} 51 | 52 | 53 | {{pass}} 54 | 55 | 56 | {{if not CONFIG_NAME:}} 57 | 58 | 68 |
59 | 60 | 63 | 66 |
61 | Example Config
SBtab file (.tsv): 62 | 		64 | 65 |
67 |
69 | {{pass}} 70 | 71 | 72 | 99 |
73 | Parameter balancing can be configured via several options. The options are 74 |
    75 |
  • use_pseudos (True or False): Since independent priors can capture only some types 76 | of kinetic constants (the mutually independent ones), pseudo values can be used, in addition, 77 | to represent prior knowledge on other, dependent kinetic constants (default: True).
    • 78 |
  • pH (float): pH value that is assumed as modelling condition (default: 7).
    • 79 |
  • temperature (float; in Kelvin): temperature value that is assumed 80 | as modelling condition (default: 300).
    • 81 |
  • overwrite_kinetics (True or False): The kinetic laws of the SBML model can either 82 | be kept or overwritten with convenience kinetics and inserted balanced parameters (default: True).
    • 83 |
  • cell_volume (float; in µM): Volume of the cell the model is part of (default: 43 (yeast)).
    • 84 |
  • parametrisation (string): For the convenience kinetics that are inserted in the model, three 85 | different parametrisations can be chosen ('hal': Haldane parametrisation; 'weg': Wegscheider parametrisation; 86 | 'cat': ;). Please see http://bioinformatics.oxfordjournals.org/content/26/12/1528.full for more details on 87 | the parametrisation (default: 'hal'.
    • 88 |
  • enzyme_prefac (True or False): Usage of a prefactor for enzyme concentrations (default: True).
    • 89 |
  • default_inhibition ('complete_inh','comp', or 'non-comp'): Default type of reaction inhibition, 90 | which can be either complete, competetitive or non-competetive (default: 'complete_inh').
    • 91 |
  • default_activation ('complete_act','essential', or 'non-essential'): Default type of reaction activation, 92 | which can be either complete, essential, or non-essential (default: 'complete_act').
    • 93 |
  • model_name (string): A name for the output model and SBtab file (default: inputfilename+'_balanced').
    • 94 |
  • samples (int): How many sample models shall be drawn from the posterior distribution?
    • 95 |
  • boundary_values ('enforce', 'ignore', or 'warning'): Usage of numerical boundaries: the balanced parameters can either be forced 96 | to be within the given boundaries, or they only produce a warning in the log file if they are outside the boundaries.
    • 97 |
98 |
100 | 101 |

102 | 103 |

104 | Main | 105 | Documentation | 106 | Online Balancing | 107 | Configure Online Balancing | 108 | Download | 109 | Contact 110 |

111 | 112 |

113 | -------------------------------------------------------------------------------- /web_version/views/default/index.html: -------------------------------------------------------------------------------- 1 | {{left_sidebar_enabled,right_sidebar_enabled=False,('message' in globals())}} 2 | {{extend 'layout.html'}} 3 | 4 | {{if 'message' in globals():}} 5 |

{{=message}}

6 | 7 |

{{=T('How did you get here?')}}

8 |
    9 |
  1. {{=T('You are successfully running web2py')}}
    2. 10 |
  2. {{=XML(T('You visited the url %s', A(request.env.path_info,_href=request.env.path_info)))}}
    3. 11 |
  3. {{=XML(T('Which called the function %s located in the file %s', 12 | (A(request.function+'()',_href='#'), 13 | A('web2py/applications/%(application)s/controllers/%(controller)s.py'%request, 14 | _href=URL('admin','default','peek', args=(request.application,'controllers',request.controller+'.py'))))))}}
    4. 15 |
  4. {{=XML(T('The output of the file is a dictionary that was rendered by the view %s', 16 | A('web2py/applications/%(application)s/views/%(controller)s/index.html'%request, 17 | _href=URL('admin','default','peek',args=(request.application,'views',request.controller,'index.html')))))}}
    5. 18 |
  5. {{=T('You can modify this application and adapt it to your needs')}}
    6. 19 |
20 | {{elif 'content' in globals():}} 21 | {{=content}} 22 | {{else:}} 23 | {{=BEAUTIFY(response._vars)}} 24 | {{pass}} 25 | 26 | {{block right_sidebar}} 27 | {{=A(T("Administrative Interface"), _href=URL('admin','default','index'), _class='btn', 28 | _style='margin-top: 1em;')}} 29 |
{{=T("Don't know what to do?")}}
30 | 35 | {{end}} 36 | -------------------------------------------------------------------------------- /web_version/views/default/prior_table.html: -------------------------------------------------------------------------------- 1 | {{extend 'layout.html'}} 2 |

3 | 4 |

5 | Main | 6 | Documentation | 7 | Online Balancing | 8 | Download | 9 | Contact 10 |

11 | 12 | 13 | 14 |

Parameter Balancing Online (3/4): Choose the prior distribution values

15 | 16 |
Please choose a prior table for balancing the chosen model file {{=SBML_NAME}} and the corresponding parameter file {{=SBTAB_NAME}}. 17 | A default prior table can be found in the list.
18 | 19 | {{=PRIOR_FORM}} 20 | 21 | {{if PRIOR_NAMES:}} 22 | 23 | 24 | 74 | {{pass}} 75 |
25 | 26 | 28 | 29 | 30 | {{for pos,f in enumerate(PRIOR_NAMES):}} 31 | 32 | 36 | 37 | 40 | 41 | {{if f != 'default_prior.tsv':}} 42 | 43 | 46 | 47 | {{else:}} 48 | 49 | 51 | 52 | 53 | {{pass}} 54 | {{pass}} 55 | 56 |
27 |
33 | • 34 | {{=f}} 35 |
38 | 39 |
44 | 45 |
50 |
57 | 58 | 59 | {{if WARNINGS:}} 60 | 61 | 62 | 64 | 65 | 66 |
63 | {{=WARNINGS[0]}}
67 | {{else:}} 68 | 69 | 70 |
No warnings detected.
71 | {{pass}} 72 | 73 |
76 | 77 | {{if len(PRIOR_NAMES)==1:}} 78 | 79 | 89 |
80 | 81 | 84 | 87 |
82 | Example PriorInfo
SBtab file (.tsv): 83 | 		85 | 86 |
88 |
90 | {{pass}} 91 | 92 |

93 | Information on the use of online balancing can be found on the documentation page.
94 | Alternative prior tables can be found on the quantities page.

95 |

96 | -------------------------------------------------------------------------------- /web_version/views/default/upload_sbtab.html: -------------------------------------------------------------------------------- 1 | {{extend 'layout.html'}} 2 |

3 | 4 |

5 | Main | 6 | Documentation | 7 | Online Balancing | 8 | Download | 9 | Contact 10 |

11 | 12 | 13 | 14 |

Parameter Balancing Online (2/4): Upload your SBtab parameter file

15 | 16 | 17 | 18 | Please choose a parameter SBtab file for your chosen model file {{=SBML_NAME}}

19 | 20 | 21 | 24 |
22 |
If you want to proceed without providing an SBtab parameter file, please click .
23 |
25 | 26 |
27 | 28 | {{=SBTAB_FORM}} 29 | 30 | {{if SBTAB_NAMES:}} 31 | 32 | 33 | 82 | {{pass}} 83 | {{pass}} 84 | 85 | 86 | 87 | 88 | {{if not SBTAB_NAMES:}} 89 |
34 | 35 | 39 | 40 | {{else:}} 41 | 42 | 43 | {{pass}} 44 | 45 | {{for pos,f in enumerate(SBTAB_NAMES):}} 46 | 47 | 51 | 52 | 55 | 56 | 57 | 60 | 61 | 62 | {{pass}} 63 | 64 |
36 | 37 | {{if len(SBTAB_NAMES)>1:}} 38 |
48 | • 49 | {{=f}} 50 |
53 | 54 |
58 | 59 |
65 | 66 | {{if WARNINGS:}} 67 | 68 | {{for f in WARNINGS:}} 69 | 70 | 72 | 73 | 74 | {{pass}} 75 |
71 | {{=f}}
76 | {{else:}} 77 | 78 | 79 |
No warnings detected.
80 | {{pass}} 81 |
90 | 91 | 102 |
92 | 93 | 97 | 100 |
94 | Example Quantity
95 | SBtab file (.tsv): 96 | 		98 | 99 |
101 |
103 | {{pass}} 104 |

105 | Information on the use of online balancing can be found on the documentation page.
106 |

107 | 108 | 109 | -------------------------------------------------------------------------------- /web_version/views/default/user.html: -------------------------------------------------------------------------------- 1 | {{extend 'layout.html'}} 2 | 3 |

{{=T( request.args(0).replace('_',' ').capitalize() )}}

4 |
5 | {{ 6 | if request.args(0)=='login': 7 | if not 'register' in auth.settings.actions_disabled: 8 | form.add_button(T('Register'),URL(args='register', vars={'_next': request.vars._next} if request.vars._next else None),_class='btn') 9 | pass 10 | if not 'request_reset_password' in auth.settings.actions_disabled: 11 | form.add_button(T('Lost Password'),URL(args='request_reset_password'),_class='btn') 12 | pass 13 | pass 14 | =form 15 | }} 16 |
17 | 25 | 26 | -------------------------------------------------------------------------------- /web_version/views/generic.html: -------------------------------------------------------------------------------- 1 | {{extend 'layout.html'}} 2 | {{""" 3 | 4 | You should not modify this file. 5 | It is used as default when a view is not provided for your controllers 6 | 7 | """}} 8 |

{{=' '.join(x.capitalize() for x in request.function.split('_'))}}

9 | {{if len(response._vars)==1:}} 10 | {{=BEAUTIFY(response._vars.values()[0])}} 11 | {{elif len(response._vars)>1:}} 12 | {{=BEAUTIFY(response._vars)}} 13 | {{pass}} 14 | {{if request.is_local:}} 15 | {{=response.toolbar()}} 16 | {{pass}} 17 | -------------------------------------------------------------------------------- /web_version/views/generic.ics: -------------------------------------------------------------------------------- 1 | {{ 2 | ### 3 | # response._vars contains the dictionary returned by the controller action 4 | # Assuming something like: 5 | # 6 | # db.define_table('event', 7 | # Field('title'), 8 | # Field('start_datetime','datetime'), 9 | # Field('stop_datetime','datetime')) 10 | # events = db(db.event).select() 11 | # 12 | # Aor this to work the action must return something like 13 | # 14 | # dict(events=events, title='title',link=URL('action'),timeshift=0) 15 | # 16 | ### 17 | from gluon.serializers import ics}}{{=XML(ics(**response._vars))}} 18 | -------------------------------------------------------------------------------- /web_version/views/generic.json: -------------------------------------------------------------------------------- 1 | {{from gluon.serializers import json}}{{=XML(json(response._vars))}} 2 | -------------------------------------------------------------------------------- /web_version/views/generic.jsonp: -------------------------------------------------------------------------------- 1 | {{ 2 | ### 3 | # response._vars contains the dictionary returned by the controller action 4 | ### 5 | 6 | # security check! This file is an example for a jsonp view. 7 | # it is not safe to use as a generic.jsonp because of security implications. 8 | 9 | if response.view == 'generic.jsonp': 10 | raise HTTP(501,'generic.jsonp diasbled for security reasons') 11 | 12 | try: 13 | from gluon.serializers import json 14 | result = "%s(%s)" % (request.vars['callback'], json(response._vars)) 15 | response.write(result, escape=False) 16 | response.headers['Content-Type'] = 'application/jsonp' 17 | except (TypeError, ValueError): 18 | raise HTTP(405, 'JSON serialization error') 19 | except ImportError: 20 | raise HTTP(405, 'JSON not available') 21 | except: 22 | raise HTTP(405, 'JSON error') 23 | }} -------------------------------------------------------------------------------- /web_version/views/generic.load: -------------------------------------------------------------------------------- 1 | {{''' 2 | # License: Public Domain 3 | # Author: Iceberg at 21cn dot com 4 | 5 | With this generic.load file, you can use same function to serve two purposes. 6 | 7 | = regular action 8 | - ajax callback (when called with .load) 9 | 10 | Example modified from http://www.web2py.com/AlterEgo/default/show/252: 11 | 12 | def index(): 13 | return dict( 14 | part1='hello world', 15 | part2=LOAD(url=URL(r=request,f='auxiliary.load'),ajax=True)) 16 | 17 | def auxiliary(): 18 | form=SQLFORM.factory(Field('name')) 19 | if form.accepts(request.vars): 20 | response.flash = 'ok' 21 | return dict(message="Hello %s" % form.vars.name) 22 | return dict(form=form) 23 | 24 | Notice: 25 | 26 | - no need to set response.headers['web2py-response-flash'] 27 | - no need to return a string 28 | even if the function is called via ajax. 29 | 30 | '''}}{{if len(response._vars)==1:}}{{=response._vars.values()[0]}}{{else:}}{{=BEAUTIFY(response._vars)}}{{pass}} -------------------------------------------------------------------------------- /web_version/views/generic.map: -------------------------------------------------------------------------------- 1 | {{""" 2 | this is an example of usage of google map 3 | the web2py action should be something like: 4 | 5 | def map(): 6 | return dict( 7 | googlemap_key='...', 8 | center_latitude = 41.878, 9 | center_longitude = -87.629, 10 | scale = 7, 11 | maker = lambda point: A(row.id,_href='...') 12 | points = db(db.point).select() where a points have latitute and longitude 13 | ) 14 | 15 | the corresponding views/defaut/map.html should be something like: 16 | 17 | \{\{extend 'layout.html'\}\} 18 |
\{\{include 'generic.map'\}\}
19 | 20 | """}} 21 | 22 | 68 |
69 | 70 | -------------------------------------------------------------------------------- /web_version/views/generic.pdf: -------------------------------------------------------------------------------- 1 | {{ 2 | import os 3 | from gluon.contrib.generics import pdf_from_html 4 | filename = '%s/%s.html' % (request.controller,request.function) 5 | if os.path.exists(os.path.join(request.folder,'views',filename)): 6 | html=response.render(filename) 7 | else: 8 | html=BODY(BEAUTIFY(response._vars)).xml() 9 | pass 10 | =pdf_from_html(html) 11 | }} 12 | -------------------------------------------------------------------------------- /web_version/views/generic.rss: -------------------------------------------------------------------------------- 1 | {{ 2 | ### 3 | # response._vars contains the dictionary returned by the controller action 4 | # for this to work the action must return something like 5 | # 6 | # dict(title=...,link=...,description=...,created_on='...',items=...) 7 | # 8 | # items is a list of dictionaries each with title, link, description, pub_date. 9 | ### 10 | from gluon.serializers import rss}}{{=XML(rss(response._vars))}} 11 | -------------------------------------------------------------------------------- /web_version/views/generic.xml: -------------------------------------------------------------------------------- 1 | {{from gluon.serializers import xml}}{{=XML(xml(response._vars,quote=False))}} 2 | -------------------------------------------------------------------------------- /web_version/views/layout.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | {{block title}} 11 | Parameter Balancing for Kinetic Models of Cell Metabolism 12 | {{end}} 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 49 | 50 | 51 | {{block center}} 52 | {{include}} 53 | {{end}} 54 | 55 | 56 | 58 | 59 | 60 | 61 | {{if response.google_analytics_id:}} 62 | 63 | 67 | {{pass}} 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | -------------------------------------------------------------------------------- /web_version/views/web2py_ajax.html: -------------------------------------------------------------------------------- 1 | 9 | {{ 10 | response.files.insert(0,URL('static','js/jquery.js')) 11 | response.files.insert(1,URL('static','css/calendar.css')) 12 | response.files.insert(2,URL('static','js/calendar.js')) 13 | response.files.insert(3,URL('static','js/web2py.js')) 14 | response.include_meta() 15 | response.include_files() 16 | }} 17 | --------------------------------------------------------------------------------