├── .gitignore ├── .gitmodules ├── .landscape.yaml ├── .travis.yml ├── CITATION.cff ├── CONTRIBUTING.md ├── Dockerfile ├── INSTALL.rst ├── LICENSE ├── NOTICE ├── README.rst ├── docs ├── bootstrap │ └── css │ │ ├── bootstrap-responsive.css │ │ ├── bootstrap-responsive.min.css │ │ ├── bootstrap.css │ │ └── bootstrap.min.css ├── index.html ├── logos │ ├── nlesc.jpg │ ├── nmc.png │ └── wur.gif ├── poster_Ridder_April2014.pdf ├── potential_green_tea_derived_metabolites.ridder2014.zip └── robots.txt ├── emetabolomics_site ├── bootstrap │ └── css │ │ ├── bootstrap-responsive.css │ │ ├── bootstrap-responsive.min.css │ │ ├── bootstrap.css │ │ └── bootstrap.min.css ├── green_tea_hmdb.html ├── index.html ├── logos │ ├── nlesc.jpg │ ├── nmc.png │ └── wur.gif ├── poster_Ridder_April2014.pdf ├── potential_green_tea_derived_metabolites.ridder2014.zip ├── results.html ├── results_CASMI2013.html ├── results_CASMI2014.html ├── results_tea_urine.html └── robots.txt ├── job ├── .gitignore ├── MANIFEST.in ├── README.rst ├── magma │ ├── __init__.py │ ├── data │ │ ├── glycosidase.smirks │ │ ├── gut.smirks │ │ ├── phase1.smirks │ │ ├── phase1_selected.smirks │ │ ├── phase2.smirks │ │ └── phase2_selected.smirks │ ├── errors.py │ ├── fragmentation_cy.pyx │ ├── fragmentation_py.py │ ├── models.py │ ├── pars.py │ ├── script │ │ └── __init__.py │ ├── tests │ │ ├── HMDB_MAGMa_test.db │ │ ├── __init__.py │ │ ├── ramped_collision_data.mzXML │ │ ├── test_fragmentengine.py │ │ ├── test_script.py │ │ ├── theogallin.mzXML │ │ └── theogallin.sdf │ └── types.py ├── setup.cfg └── setup.py ├── pubchem ├── .gitignore ├── README.rst ├── magma_db_service.py ├── process_hmdb.py └── process_pubchem.py └── web ├── .gitignore ├── CHANGES.txt ├── MANIFEST.in ├── README.rst ├── alembic.ini ├── alembic ├── README ├── env.py ├── script.py.mako └── versions │ ├── 14322145f9b5_fill_reactionsequence.py │ ├── 185259a481ee_remove_metabolite_options_from_run.py │ ├── 28182dc2d089_added_reactions.py │ ├── 4509bacbb81e_237_standardized_names.py │ └── 4e953e8c6a7e_added_natoms.py ├── docs ├── Makefile ├── api.rst ├── conf.py ├── index.rst ├── install.rst ├── launcher.rst ├── user.rst └── ws_consumer.rst ├── karma.conf.js ├── magmaweb ├── __init__.py ├── config.py ├── job.py ├── jobquery.py ├── magmaweb.results-4.2.1.jsb3 ├── models.py ├── rpc.py ├── script.py ├── static │ ├── ChemDoodleWeb │ │ ├── ChemDoodleWeb-libs.js │ │ ├── ChemDoodleWeb.css │ │ ├── ChemDoodleWeb.js │ │ └── sketcher │ │ │ ├── ChemDoodleWeb-sketcher.js │ │ │ ├── images │ │ │ ├── ui-bg_flat_0_aaaaaa_40x100.png │ │ │ ├── ui-bg_flat_0_eeeeee_40x100.png │ │ │ ├── ui-bg_flat_55_c0402a_40x100.png │ │ │ ├── ui-bg_flat_55_eeeeee_40x100.png │ │ │ ├── ui-bg_glass_100_f8f8f8_1x400.png │ │ │ ├── ui-bg_glass_35_dddddd_1x400.png │ │ │ ├── ui-bg_glass_60_eeeeee_1x400.png │ │ │ ├── ui-bg_inset-hard_75_999999_1x100.png │ │ │ ├── ui-bg_inset-soft_50_c9c9c9_1x100.png │ │ │ ├── ui-icons_3383bb_256x240.png │ │ │ ├── ui-icons_454545_256x240.png │ │ │ ├── ui-icons_70b2e1_256x240.png │ │ │ ├── ui-icons_999999_256x240.png │ │ │ └── ui-icons_fbc856_256x240.png │ │ │ ├── jquery-ui-1.9.2.custom.css │ │ │ └── jquery-ui-1.9.2.custom.min.js │ ├── app │ │ ├── controller │ │ │ ├── Fragments.js │ │ │ ├── MSpectras.js │ │ │ ├── Molecules.js │ │ │ └── Scans.js │ │ ├── model │ │ │ ├── Fragment.js │ │ │ └── Molecule.js │ │ ├── resultsApp.js │ │ ├── store │ │ │ ├── Fragments.js │ │ │ ├── Molecules.js │ │ │ ├── Scenarios.js │ │ │ └── proxy │ │ │ │ └── AjaxSingle.js │ │ └── view │ │ │ ├── Viewport.js │ │ │ ├── fragment │ │ │ ├── AnnotateFieldSet.js │ │ │ ├── AnnotateForm.js │ │ │ └── Tree.js │ │ │ ├── molecule │ │ │ ├── AddFieldSet.js │ │ │ ├── AddForm.js │ │ │ ├── List.js │ │ │ ├── MetabolizeFieldSet.js │ │ │ ├── MetabolizeForm.js │ │ │ ├── MetabolizeOneForm.js │ │ │ ├── Panel.js │ │ │ ├── ReactionColumn.js │ │ │ ├── ReactionFilter.js │ │ │ └── ScenarioField.js │ │ │ └── scan │ │ │ ├── Panel.js │ │ │ ├── UploadFieldSet.js │ │ │ └── UploadForm.js │ ├── d3 │ │ ├── LICENSE │ │ ├── d3.js │ │ └── d3.min.js │ ├── esc │ │ ├── chemdoodle │ │ │ └── Column.js │ │ ├── d3 │ │ │ ├── Abstract.js │ │ │ ├── Chromatogram.js │ │ │ └── MSpectra.js │ │ └── form │ │ │ └── field │ │ │ └── TextareaTab.js │ ├── img │ │ ├── logos │ │ │ ├── ESCIENCE_logo_C_nl_small_cyanblack.png │ │ │ ├── nmc.png │ │ │ └── wur.gif │ │ └── metabolites.png │ └── style.css ├── templates │ ├── error.mak │ ├── help.mak │ ├── home.mak │ ├── login.mak │ ├── logos.mak │ ├── results.mak │ ├── runinfo.mak │ ├── status.mak │ ├── uploaddb.mak │ └── workspace.mak ├── tests │ ├── __init__.py │ ├── js │ │ ├── app │ │ │ ├── app-test.js │ │ │ ├── data │ │ │ │ ├── chromatogram.json │ │ │ │ ├── extractedionchromatogram.352.json │ │ │ │ ├── fragments.s1133.m352.json │ │ │ │ ├── molecules.csv │ │ │ │ ├── molecules.json │ │ │ │ ├── mspectra.1133.json │ │ │ │ ├── mspectra.1134.json │ │ │ │ ├── runinfo.json │ │ │ │ └── stderr.txt │ │ │ ├── loader.js │ 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