├── twitter.gif ├── covid-19-bh20.png ├── covid19biohackathon.png ├── images └── overview_pubSeqRes.png ├── .github └── ISSUE_TEMPLATE │ └── feature_request.md ├── archive └── slack-channels │ └── README.md ├── README.md ├── compute_resources.md ├── datasets_and_tools.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md └── LICENSE /twitter.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/virtual-biohackathons/covid-19-bh20/HEAD/twitter.gif -------------------------------------------------------------------------------- /covid-19-bh20.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/virtual-biohackathons/covid-19-bh20/HEAD/covid-19-bh20.png -------------------------------------------------------------------------------- /covid19biohackathon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/virtual-biohackathons/covid-19-bh20/HEAD/covid19biohackathon.png -------------------------------------------------------------------------------- /images/overview_pubSeqRes.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/virtual-biohackathons/covid-19-bh20/HEAD/images/overview_pubSeqRes.png -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Feature request 3 | about: Suggest an idea for this project 4 | title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | **Is your feature request related to a problem? Please describe.** 11 | A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] 12 | 13 | **Describe the solution you'd like** 14 | A clear and concise description of what you want to happen. 15 | 16 | **Describe alternatives you've considered** 17 | A clear and concise description of any alternative solutions or features you've considered. 18 | 19 | **Additional context** 20 | Add any other context or screenshots about the feature request here. 21 | -------------------------------------------------------------------------------- /archive/slack-channels/README.md: -------------------------------------------------------------------------------- 1 | Add JSON dumps of your Slack channel here. 2 | 3 | Andrea Guarracino wrote: 4 | 5 | Hi @channel, the Slack system will be up to 22 June. I think you all 6 | agree that it is better to preserve all the amount of information that 7 | we have exchanged during these 2 months. For this reason, I write a 8 | brief procedure to save the history for a channel 9 | 10 | 1. Install 11 | https://dashhackathon.slack.com/apps/A19P6G35Y-export 12 | 2. Excute the command '/export' in a Slack channel 13 | 3. Click on 'Click here to begin the export process' that will appear 14 | as a message 15 | 4. Choose the format (JSON seems to work fine) and click 'Export' 16 | 5. Wait and download the channel history in the chosen format. 17 | 18 | If everyone backups its channel, we could preserve a lot of 19 | information. We would be also interested to analyze the activity in the 20 | different channels and do some statistics on them. 21 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ![Biohackathon](./covid19biohackathon.png "covid-19-bh20") 2 | 3 | # covid-19-bh20 4 | 5 | Over the internet we are organizing the *COVID-19 Biohackathon April 6 | 5-11 2020*! 7 | 8 | # Goals 9 | 10 | The goal of COVID-19-BH20 is to create a cohesive effort and work on 11 | tooling for COVID-19 analysis. The biohackathon will lead to more 12 | readily accessible data, protocols, detection kits, protein 13 | predictions etc. 14 | 15 | We will also push for policy change where it comes to non-public or 16 | hard to access data because we are facing such challenges! 17 | 18 | 19 | # Free software, free data 20 | 21 | The biohackathon is about applying free and open source software on 22 | open data for scientific endeavour and biomedical progress. 23 | 24 | # When? 25 | 26 | The biohackathon wil run from April 5th-11th 2020. Before that time 27 | working groups will start preparations. After the biohackathon 28 | collaborations often continue. 29 | 30 | # How? 31 | 32 | Over the internet we are forming groups with 33 | [topics](https://github.com/virtual-biohackathons/covid-19-bh20/wiki) 34 | to work on. There will be working groups for FAIR data, workflows and 35 | pipelines, pangenomes and variation graphs, machine learning, text 36 | mining and visualisations. You can create your own group and get 37 | people interested in your area of work. We will use video 38 | conferencing, E-mail, IRC, messaging, wiki's and source code 39 | repositories to make it all happen. 40 | 41 | # Examples 42 | 43 | A concrete outcome is that if someone sequences a new patient they 44 | should be able to immediately compare it with all other known strains 45 | in a variation graph/pangenome. Standardized FAIR (metadata) and 46 | public repositories of (raw) data - that people can contribute to - as 47 | well as workflows that can be run by anyone (in the cloud) are 48 | all concrete outcomes. 49 | 50 | The following wiki page lists known [resources](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Resources). 51 | 52 | # Who? 53 | 54 | Anyone can join and contribute. Thanks to the annual biohackathons in 55 | Japan and Europe we already have an experienced community. One benefit 56 | of this virtual biohackathon is that we can expand and be as inclusive 57 | as possible. Even if you are a student and not so experienced you can 58 | sign-up and contribute! All hands are welcome! 59 | 60 | To participate become a member of 61 | the [mailing list](https://groups.google.com/forum/#!forum/virtual-biohackathon), join a topic/group and add to the [wiki](https://github.com/virtual-biohackathons/covid-19-bh20/wiki)! 62 | 63 | We will organize goals and mini-publications for each group. Contributors will get credit for work. 64 | 65 | # Code of conduct 66 | 67 | Anyone participating agrees to abide by the code of conduct as given 68 | by [Code of Conduct](./CODE_OF_CONDUCT.md). Please bring any concerns to the immediate attention of our 69 | coordinating team: 70 | 71 | # Coordinating team 72 | 73 | 1. Pjotr Prins, USA (pjotr.public708 at thebird.nl) 74 | 2. [Tazro Ohta](https://github.com/inutano), Japan (t.ohta at dbcls.rois.ac.jp) 75 | 3. Leyla Garcia, Germany (ljgarciaco at gmail.com) 76 | 77 | # Contribute 78 | 79 | Contribute by adding and/or signing up to ideas on the Biohackathon 80 | [Wiki](https://github.com/virtual-biohackathons/covid-19-bh20/wiki). You can also edit these pages and send a pull request. 81 | 82 | # Contact 83 | 84 | Sign up with the [mailing list](https://groups.google.com/forum/#!forum/virtual-biohackathon) and ask! 85 | 86 | [![Twitter covid_19_bh20](./twitter.gif "covid_19_bh20") #covid_19_bh20](https://twitter.com/search?q=%23covid_19_bh20) 87 | 88 | ![BH logo](./covid-19-bh20.png "covid-19-bh20") 89 | 90 | # Acknowledgements 91 | 92 | * [ELIXIR Europe](https://elixir-europe.org/) and [Galaxy](https://galaxyproject.org/) have kindly agreed to provide computing resources 93 | * [Slack](https://slack.com/) has kindly provided the full Slack version free of charge for up to 90 days. 94 | * [Curii Corporation](https://www.curii.com/) has provided engineering time to setup the [biohackathon.curii.com](https://biohackathon.curii.com) instance of the [Arvados](https://www.arvados.org) workflow platform. 95 | * [Amazon AWS](aws.amazon.com) for cloud credits to power [biohackathon.curii.com](https://biohackathon.curii.com) 96 | -------------------------------------------------------------------------------- /compute_resources.md: -------------------------------------------------------------------------------- 1 | # Compute resources 2 | 3 | [ELIXIR Europe](https://elixir-europe.org/) and [Galaxy](https://galaxyproject.org/) have kindly agreed to contribute with computing resources. If you can do so as well, please add your resources and your information here. 4 | 5 | ## European Galaxy server (https://usegalaxy.eu) 6 | 7 | The European Galaxy server is offering all its compute resource for all researchers. You have access to more than 2400 tools from different scientific domains (genomics, proteomics, metabolomics, cheminformatics ...), more than 3,000 CPU cores, 50TB of memory and GPUs. The majority of resources are contributed by the de.NBI cloud. If more resources are needed we can shortly access the [pulsar-network](https://pulsar-network.readthedocs.io) and distribute jobs across Europe. 8 | 9 | Galaxy can be accessed and controlled via a rich API. For example via Python using a library called [bioblend](https://bioblend.readthedocs.io/en/latest/). 10 | 11 | With https://live.usegalaxy.eu the Galaxy project is also offering Juypter Notebooks or RStudio instances for everyone that needs external compute resources. Those environments can access the storage resources from Galaxy and therefor permanent storage that can easily linked to Notebooks. 12 | 13 | If you have any questions or problems, please contact `galaxy@informatik.uni-freiburg.de`. 14 | 15 | ## Arvados instance (https://biohackathon.curii.com) 16 | 17 | Arvados is an open source platform for managing biomedical data and 18 | running Common Workflow Language (CWL) workflows on that data. It has 19 | both web-based and command line user interfaces available. Curii has 20 | set up an instance of the Arvados platform to support the virtual 21 | Biohackathon. 22 | 23 | https://biohackathon.curii.com 24 | 25 | Requires Google account to log in. After you have created an account, 26 | ask @Peter Amstutz or @Michael Crusoe on the biohackathon Slack 27 | (#tech-helpdesk or #workflows) to activate your account. 28 | 29 | ## ELIXIR Compute Platform Resources 30 | 31 | ELIXIR Nodes run [computing services](https://elixir-europe.org/services/tag/compute) that can be accessed by research projects. Many additional computing resources have been made available to support COVID-19 research projects including: 32 | * Access to Docker Orchestrators including Mesos and OpenStack access, Kubernetes/OKD and potentially GPUs where needed. For access request & other queries please join `#elixir-resources`slack [channel](https://join.slack.com/share/I0113JB2P9Q/tHQPzqdxPXJjPpAcRrNJxwt5/enQtMTAzNzYyMzA5MTMzMC1jYmI1MTkzNGQ2ZTZiMTExZjhmYTQzNGMyNDllOWYwOTAyZDllNmEyNTkwNGM1NTE5NTllNDVkMzljMmY4ZWM1) 33 | * [de.NBI cloud, ELIXIR-Germany](https://www.denbi.de/news/866-de-nbi-cloud-resources-available-to-fight-covid-19) provides priority access for projects relating to COVID-19 34 | * CSC (ELIXIR-Finland) has [prioritised access](https://www.csc.fi/-/resursseja-covid-19-pandemian-vastaiseen-tutkimukseen) to its [cloud services](https://research.csc.fi/computing) for COVID-19 research 35 | * [e-INFRA CZ](https://e-infra.cz) (ELIXIR-Czech) offer relaxed access conditions to supercomputer resources, storage services and distributed compute resources 36 | * A specific Galaxy COVID-19 instance for genomic analysis is available through [Laniakea](https://laniakea-elixir-it.github.io/2020/03/27/covid19-docker-flavor.html), ELIXIR Italy’s on-demand platform 37 | * EMBL-EBI located in the UK is contributing [EMBASSY Cloud resources](https://www.embassycloud.org) as detailed on the European Open Science Cloud, [EOSC Marketplace](https://marketplace.eosc-portal.eu/services/embassy-cloud) 38 | * SIB (ELIXIR-Swiss) is providing a ready-to-use slurm workload manager with a scientific software stack via the [ExPASy SIB Portal](https://www.expasy.org/) 39 | * ELIXIR-Swiss and ELIXIR-Finland have provided a common Virtual Machine (VM) that contains key resources in a single directory for the Gene Expression hackathon group but should be extensible to e.g. collaborative teams and wider hackathon type events. This helps lower technical barriers and get more people involved more quickly. 40 | * [IFB (ELIXIR France)](https://www.france-bioinformatique.fr/en/action-covid-19) is providing a [federated set of high performance compute and cloud resources](https://www.france-bioinformatique.fr/en/infrastructure-0) including national and regional servers 41 | 42 | 43 | ### What can you do with it? 44 | 45 | * Manage data 46 | * Upload/download files from browser, command line, or SDK 47 | * Identify collections of files by name, uuid, or content address (hash) 48 | * Set and query structured metadata on collections of files 49 | * Share projects with other users and groups 50 | * Run CWL workflows 51 | * Scale-out across compute nodes, run workflows from multiple users 52 | * A foundation to build other applications 53 | * Use the APIs for data storage and access, permissions, running workflows, etc 54 | * We may be able to spin up servers for teams building web apps, just ask! 55 | 56 | ### Learn more 57 | 58 | During the biohackathon 59 | 60 | * We will do an Arvados training (TBD) 61 | * We will share the slides used for the training 62 | * We will be on the biohackathon Slack at #tech-helpdesk and Gitter at 63 | https://gitter.im/arvados/community to answer questions 64 | -------------------------------------------------------------------------------- /datasets_and_tools.md: -------------------------------------------------------------------------------- 1 | # Available resources 2 | 3 | We are using this page to compile a list of available datasets and tools. If you are intersted in compute resources, please visit the [Compute Resources page](https://github.com/virtual-biohackathons/covid-19-bh20/blob/master/compute_resources.md). Please bear in mind that this list comes from the community and given the pace things are moving, it could become out-of-date quite easy. If you know of any dataset or tool not listed here, please add it. And always remember to double check the usage policies and licenses before using someone else's data or tool. Topics/groups might include a subset of the lists included here as some will be more relevant than others depending the topic/group. 4 | 5 | ## Tutorials 6 | - [Peterjc's Biopython Introductory workshop](https://github.com/peterjc/biopython_workshop) 7 | 8 | ## Datasets 9 | - [Johns Hopkins repo](https://github.com/CSSEGISandData/COVID-19/tree/master/who_covid_19_situation_reports) 10 | - [European Centre for Disease Prevention and Control](https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide) 11 | - [Automated Data Collection: COVID-19/SARS-COV-2 Cases in EU by Country, State/Province/Local Authorities, and Date](https://github.com/covid19-eu-zh/covid19-eu-data) 12 | - [EBI Data](https://www.ebi.ac.uk/ena/pathogens/covid-19) 13 | - [SARS-CoV-2 sequences GenBank](https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/) 14 | - [nCoV sequences GISAID](https://www.gisaid.org/epiflu-applications/next-hcov-19-app/) 15 | - Please be aware of the licenses 16 | - [Kaggle (all COVID-19 Related challenges)](https://www.kaggle.com/covid19) 17 | - [Kaggle COVID-19 Open Research Dataset Challenge (CORD-19)](https://www.kaggle.com/allen-institute-for-ai/CORD-19-research-challenge#019ede0c6f1c02b64dea8e05e3bc8c7cb5811fae.json) 18 | - [COVID Epidemiology](https://covid19.fyi/#/) 19 | - [NY Times data](https://github.com/nytimes/covid-19-data) 20 | - [NHS Covid19 symptom tracker](https://covid.joinzoe.com/) 21 | - [Ministerio de Sanidad sobre coronavirus España](https://covid19.isciii.es/) (link to up-to-date data in bottom left) 22 | 23 | 24 | ## Tools 25 | - [Coronavirus Tracker API](https://github.com/ExpDev07/coronavirus-tracker-api) 26 | - [R package for the data colated by Johns Hopkins](https://github.com/rOpenStats/COVID19) 27 | - [Penn Medicine - COVID19 Hospital Impact Model for Epidemics](https://penn-chime.phl.io/) 28 | - [Epidemic Calculator by Gabriel Goh](https://gabgoh.github.io/COVID/) 29 | - [Error estimates in SIR model predictions, ETH Zurich](https://cse-lab.ethz.ch/coronavirus/) 30 | - [COVID-19 Scenario simulator, University of Basel](https://neherlab.org/covid19/) 31 | - [GitHub repo](https://github.com/neherlab/covid19_scenarios) 32 | - [Pandemic Preparedness Planning for COVID-19](http://covidsim.de/), by Markus Schwehm and Martin Eichner together with the Landesgesundheitsamt Baden-Württemberg/Germany 33 | - [Worldometers COVID19 real-time stats](https://www.worldometers.info/coronavirus/) 34 | - [Bioinformatics resources for SARS-CoV-2 from Clinical Bioinformatics Area from FPS (Junta de Andalucía, Spain)](http://www.clinbioinfosspa.es/CovidResources) 35 | - [Cheminformatics from quarantine: some interactive COVID-19 resources](https://cheminf20.org/2020/03/28/cheminformatics-from-quarantine-some-interactive-covid-19-resources/) 36 | - [ZEQ Szenario Calculator/ZEQ Szenarienrechner](https://www.zeq.de/fileadmin/Medien/Bilder/Grafiken/COVID/ZEQ-COVID19-Szenariorechner_Version_2.2_30.03.2020.xlsx) from Munich Hospital Collaboration; more information [here](https://www.zeq.de/unternehmen/aktuelles/newsdetails/article/zeq-covid19-szenariorechner-zum-betten-und-personalbedarf-verfuegbar.html) and [here](https://www.zeq.de/covid-19/corona-virus-covid-19/covid-19-szenariorechner.html) 37 | - [epydemic, a Python library for modeling epidemic processes on networks](https://github.com/simoninireland/epydemic) 38 | - [SEIRS+, a Python library for modeling epidemic processes on networks](https://github.com/ryansmcgee/seirsplus) 39 | - [NDlib, a Python library for modeling stochastic processes on networks](https://github.com/GiulioRossetti/ndlib) 40 | - [nlopt, a general-purpose library for optimization, includes a Python interface](https://nlopt.readthedocs.io/) 41 | 42 | ## Workflows 43 | - [Galaxy workflows. A lot is here already! Check for overlap.](https://covid19.galaxyproject.org/genomics/) 44 | - [Nexstrain workflows. Here too: look for gaps, no reinventing wheels](https://github.com/nextstrain/ncov/blob/master/DEV_DOCS.md) 45 | - [Nexstrain narrative](https://nextstrain.org/ncov) 46 | 47 | 48 | ## Models / Methods 49 | 50 | - [Models repo by Pedro Mendes of University of Connecticut](https://github.com/pmendes/COVID19) 51 | - [Potential Long-Term Intervention Strategies for COVID-19](https://covid-measures.github.io/) 52 | - [Projecting the Spread of COVID19 for German (medrxiv)](https://www.medrxiv.org/content/10.1101/2020.03.26.20044214v1) 53 | - [Contagiousness of COVID-19 Part I: Improvements of Mathematical Fitting](https://www.r-bloggers.com/contagiousness-of-covid-19-part-i-improvements-of-mathematical-fitting-guest-post/) 54 | 55 | 56 | ## R packages 57 | - [covid19us (R wrapper around the COVID Tracking Project API)](https://github.com/aedobbyn/covid19us) 58 | -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- 1 | # Code of Condct for the Covid-19-BH20 Event 2 | 3 | As a community we welcome everyone, and encourage a friendly and positive environment. 4 | 5 | This code of conduct outlines our expectations for participants within the 6 | community, as well as steps to reporting unacceptable behavior. We are committed 7 | to providing a welcoming and inspiring community for all and expect our code of 8 | conduct to be honored. Anyone who violates this code of conduct may be banned 9 | from the community. 10 | 11 | Our open source community strives to: 12 | 13 | - **Be friendly and patient.** 14 | 15 | - **Be welcoming**: We strive to be a community that welcomes and supports 16 | people of all backgrounds and identities. This includes, but is not limited to 17 | members of any race, ethnicity, culture, national origin, colour, immigration 18 | status, social and economic class, educational level, sex, sexual orientation, 19 | gender identity and expression, age, size, family status, political belief, 20 | religion, and mental and physical ability. 21 | 22 | - **Be considerate**: Your work will be used by other people, and you in turn 23 | will depend on the work of others. Any decision you take will affect users and 24 | colleagues, and you should take those consequences into account when making 25 | decisions. Remember that we're a world-wide community, so you might not be 26 | communicating in someone else's primary language. 27 | 28 | - **Be respectful**: Not all of us will agree all the time, but disagreement is 29 | no excuse for poor behavior and poor manners. We might all experience some 30 | frustration now and then, but we cannot allow that frustration to turn into a 31 | personal attack. It’s important to remember that a community where people feel 32 | uncomfortable or threatened is not a productive one. 33 | 34 | - **Be careful in the words that we choose**: We are a community of 35 | professionals, and we conduct ourselves professionally. Be kind to others. Do 36 | not insult or put down other participants. Harassment and other exclusionary 37 | behavior aren't acceptable. This includes, but is not limited to: Violent 38 | threats or language directed against another person, Discriminatory jokes and 39 | language, Posting sexually explicit or violent material, Posting (or 40 | threatening to post) other people’s personally identifying information 41 | (“doxing”), Personal insults, especially those using racist or sexist terms, 42 | Unwelcome sexual attention, Advocating for, or encouraging, any of the above 43 | behavior, Repeated harassment of others. In general, if someone asks you to 44 | stop, then stop. 45 | 46 | - **Try to understand why we disagree**: Disagreements, both social and 47 | technical, happen all the time. It is important that we resolve disagreements 48 | and differing views constructively. Remember that we’re different. Diversity 49 | contributes to the strength of our community, which is composed of people from 50 | a wide range of backgrounds. Different people have different perspectives on 51 | issues. Being unable to understand why someone holds a viewpoint doesn’t mean 52 | that they’re wrong. Don’t forget that it is human to err and blaming each 53 | other doesn’t get us anywhere. Instead, focus on helping to resolve issues and 54 | learning from mistakes. 55 | 56 | ### Diversity Statement 57 | 58 | We encourage everyone to participate and are committed to building a community 59 | for all. Although we will fail at times, we seek to treat everyone both as 60 | fairly and equally as possible. Whenever a participant has made a mistake, we 61 | expect them to take responsibility for it. If someone has been harmed or 62 | offended, it is our responsibility to listen carefully and respectfully, and do 63 | our best to right the wrong. 64 | 65 | Although this list cannot be exhaustive, we explicitly honor diversity in age, 66 | gender, gender identity or expression, culture, ethnicity, language, national 67 | origin, political beliefs, profession, race, religion, sexual orientation, 68 | socioeconomic status, and technical ability. We will not tolerate discrimination 69 | based on any of the protected characteristics above, including participants with 70 | disabilities. 71 | 72 | ### Reporting Issues 73 | 74 | If you experience or witness unacceptable behavior, or have any other concerns, 75 | please report it by contacting the CoC committee: 76 | Jennifer Harrow (email: jen.harrow@elixir-europe.org), Katharina Lauer (email: katharina.lauer@elixir-europe.org), Fotis Psomopoulos (email: fpsom@certh.gr) and Mateusz Kuzak (email: m.kuzak@esciencecenter.nl). 77 | 78 | To report an issue involving one of the members, please email other members individually. 79 | 80 | All reports will be handled with discretion. In your report please include: 81 | 82 | - Your contact information. 83 | 84 | - Names (real, nicknames, or pseudonyms) of any individuals involved. If there 85 | are additional witnesses, please include them as well. Your account of what 86 | occurred, and if you believe the incident is ongoing. If there is a publicly 87 | available record (e.g. a mailing list archive or a public IRC logger), please 88 | include a link. 89 | 90 | - Any additional information that may be helpful. 91 | 92 | After filing a report, a representative will contact you personally, review the 93 | incident, follow up with any additional questions, and make a decision as to how 94 | to respond. If the person who is harassing you is part of the response team, 95 | they will recuse themselves from handling your incident. If the complaint 96 | originates from a member of the response team, it will be handled by a different 97 | member of the response team. We will respect confidentiality requests for the 98 | purpose of protecting victims of abuse. 99 | 100 | ### Attribution & Acknowledgements 101 | 102 | This code of conduct is based on the Open Code of Conduct from the [TODO Group](https://github.com/todogroup/opencodeofconduct/). 103 | -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | # How to contribute? 2 | 3 | First of all, thanks for taking the time to contribute! :tada::+1: 4 | 5 | Your contributions are important to make this project and event successful. 6 | You can report mistakes and errors, propose a project, offer dataset and resources or create more content. 7 | 8 | Whatever is your background, there is a way to contribute on this [GitHub repository](https://github.com/virtual-biohackathons/covid-19-bh20), 9 | on our [mailing list](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!forum/virtual-biohackathon), other [related projects listed on our wiki page](https://github.com/virtual-biohackathons/covid-19-bh20/wiki) or via [slack conversations](https://virtualbiohac-xt62674.slack.com/join/shared_invite/zt-cuur40oj-wdrVz50NocwVrH7vgKTdPg). 10 | 11 | You can raise any issue relevant to this project/event publicly in the mailing list (google group), we will address and/or assess your change proposal as promptly as we can to make your participation easier. 12 | 13 | We have a [Code of Conduct](https://github.com/virtual-biohackathons/covid-19-bh20/blob/master/CODE_OF_CONDUCT.md) that applies to all the activities and projects involved in this event. 14 | 15 | For any organisation related queries or concern, you can directly reach out to the organisers Leyla Garcia (email: ljgarciaco@gmail.com), Pjotr Prins (email: pjotr.public708@thebird.nl) 16 | and Tazro Ohta (email: t.ohta@dbcls.rois.ac.jp). 17 | 18 | - With such a large group of participants, we are encouraging a bottom-up approach, where groups are formed around projects/topics and work (kind of) independently from others. 19 | - If you need any information from another group/topic, you can always reach people via email or slack (please note that as the hacking starts, Slack might become more interactive, you can also directly ping people there, be patient please and re-ping if needed or look for an alternative contact). 20 | - Every group/topic will have leader/coordinator/facilitator, please check the wiki to get more information (as we get close to the hacking week, we expect the wiki to change quickly and people to add more group/topic details there). 21 | - We also expect group/topic leaders/coordinators/facilitators to provide a quick (daily if possible) summary via the wiki so everybody can get an idea on it. 22 | 23 | ## How can I participate at this event? 24 | 25 | Join the [Google group mailing list](https://groups.google.com/forum/#!forum/virtual-biohackathon) and the [virtualbiohackathoncovid19 slack](https://join.slack.com/t/virtualbiohac-xt62674/shared_invite/zt-cuur40oj-wdrVz50NocwVrH7vgKTdPg) and join the conversation! No approval needed. 26 | 27 | ## How can I join the hackathon? 28 | - Please have a look at the [GitHub wiki](https://github.com/virtual-biohackathons/covid-19-bh20/wiki) to see the existing projects. 29 | - When you’ve found a project you’d like to contribute to, 30 | do a quick scan to make sure that the project is suitable for accepting contributions. 31 | - Commonly, channels are created on our Slack workspace, so please have a look there to see if the group/topic you are interested in is already there. 32 | - If there is no channel, go to "general" slack channel or [COVID-19 Google group mailing list](https://groups.google.com/forum/#!forum/virtual-biohackathon) and raise a question on how to join that group/topic/project. Members working on that project would help you participate. 33 | 34 | ## How can I fix something on the repository? 35 | 36 | - Raise mistakes, error or missing information on this repository by opening a Pull Request 37 | - Submit trivial fixes (for example, a typo, a broken link or an obvious error) 38 | - Start work on a contribution that was already asked for, or that you’ve already discussed, in a mailing list 39 | - A pull request doesn’t have to represent finished work. It’s usually better to open a pull request early on, so others can watch or give feedback on your progress. Just mark it as a “WIP” (Work in Progress) in the subject line. You can always add more commits later. 40 | - [Read details for open a Pull request](https://opensource.guide/how-to-contribute/#opening-a-pull-request) 41 | 42 | ## How can I join the mailing list and participate in an ongoing conversation? 43 | 44 | The mailing list works via a Google group, so by [joining the group](https://groups.google.com/forum/#!forum/virtual-biohackathon) you will get new messages and will be allowed to post. 45 | 46 | We also have a [slack]((https://virtualbiohac-xt62674.slack.com/join/shared_invite/zt-cuur40oj-wdrVz50NocwVrH7vgKTdPg)) where channels (commonly corresponding to groups/topics/projects) are created and people can join and contribute to the discussion. 47 | 48 | ## How can I offer dataset and other compute resources? What are the data protection policies? 49 | 50 | People are pointing to data or offering compute resources via email. A dedicated wiki entry will include more details on the known/available data and compute resources. 51 | 52 | ## How can I use dataset and other compute resources? 53 | 54 | We have community-based list of available [datasets and tools](./datasets_and_tools.md) as well as a list of [computing resources](./compute_resources.md). Please visit those pages for more information. 55 | 56 | ## What data protection policies and licenses are applied? 57 | 58 | - As different datasets, tools and resources will be used, we, therefore, encourage you to double-check for any limitations the data and tools you are using. Wherever possible please document those limitations and how you are troubleshooting those issues within your team. 59 | - A lot of freely available and open access initiatives have been put in place as a way to contribute to solutions around COVID-19. If the dataset/tool you want to use has any restrictions, please contact the responsible team/owner. If the owners can not relax their regular policies/licenses for the use in this hackathon, please find an alternative data/tool to use. Make sure that you document these restrictions to be shared with your team members and anyone who would like to join your team during the hackathon or use your work afterwards. 60 | 61 | ## Are there more ways to participate? 62 | 63 | Other than joining the conversation and contributing to any of the topics, you can also offer additional compute support, or data or tools. For instance, [ELIXIR Europe](https://elixir-europe.org/) and [Galaxy](https://galaxyproject.org/) have kindly agreed to contribute with cloud resources, servers and others. See the section above related to datasets and compute resources. 64 | 65 | Do you have other ideas for contributions? Contact the organisers Leyla Garcia (email: ljgarciaco@gmail.com), Pjotr Prins (email: pjotr.public708@thebird.nl) and 66 | Tazro Ohta (email: t.ohta@dbcls.rois.ac.jp) 67 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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If the Program does not specify a version number of the 576 | GNU General Public License, you may choose any version ever published 577 | by the Free Software Foundation. 578 | 579 | If the Program specifies that a proxy can decide which future 580 | versions of the GNU General Public License can be used, that proxy's 581 | public statement of acceptance of a version permanently authorizes you 582 | to choose that version for the Program. 583 | 584 | Later license versions may give you additional or different 585 | permissions. However, no additional obligations are imposed on any 586 | author or copyright holder as a result of your choosing to follow a 587 | later version. 588 | 589 | 15. Disclaimer of Warranty. 590 | 591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 592 | APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT 593 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY 594 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, 595 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 596 | PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM 597 | IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF 598 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 599 | 600 | 16. Limitation of Liability. 601 | 602 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS 604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY 605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE 606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF 607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD 608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), 609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF 610 | SUCH DAMAGES. 611 | 612 | 17. Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | --------------------------------------------------------------------------------