From 87db20ff7db2be43769bd577f51f5aa5fc73cd89 Mon Sep 17 00:00:00 2001 From: johan-gson <32481323+johan-gson@users.noreply.github.com> Date: Tue, 24 Nov 2020 11:31:36 +0100 Subject: [PATCH] Initial commit --- .github/CODE_OF_CONDUCT.md | 41 ++++ .github/CONTRIBUTING.md | 0 .github/ISSUE_TEMPLATE.md | 25 +++ .github/PULL_REQUEST_TEMPLATE.md | 9 + .gitignore | 314 +++++++++++++++++++++++++++++++ .standard-GEM.md | 109 +++++++++++ LICENSE.md | 159 ++++++++++++++++ README.md | 69 +++++++ code/README.md | 0 data/README.md | 0 model/.keep | 0 version.txt | 1 + 12 files changed, 727 insertions(+) create mode 100644 .github/CODE_OF_CONDUCT.md create mode 100644 .github/CONTRIBUTING.md create mode 100644 .github/ISSUE_TEMPLATE.md create mode 100644 .github/PULL_REQUEST_TEMPLATE.md create mode 100644 .gitignore create mode 100644 .standard-GEM.md create mode 100644 LICENSE.md create mode 100644 README.md create mode 100644 code/README.md create mode 100644 data/README.md create mode 100644 model/.keep create mode 100644 version.txt diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..e756550 --- /dev/null +++ b/.github/CODE_OF_CONDUCT.md @@ -0,0 +1,41 @@ +## Our Pledge + +In the interest of fostering an open and welcoming environment, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities. We are committed to making participation in our projects and our community a harassment-free experience for everyone, regardless of level of experience, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project teams are obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct may be removed from the project team. + +## Attribution + +This Code of Conduct is adapted from the Contributor Covenant, version 1.4, available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md new file mode 100644 index 0000000..e69de29 diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md new file mode 100644 index 0000000..60e55f4 --- /dev/null +++ b/.github/ISSUE_TEMPLATE.md @@ -0,0 +1,25 @@ +### Description of the issue: +*Try to be as clear as possible: Is it something wrong/missing in the model? Is it a simulation issue? PLEASE DELETE THIS LINE.* + + +#### Expected feature/value/output: +*How the reaction/metabolite/gene/simulation result should look (cite literature if needed). PLEASE DELETE THIS LINE.* + + +#### Current feature/value/output: +*How the reaction/metabolite/gene/simulation actually looks in the `master` branch. PLEASE DELETE THIS LINE.* + + +#### Reproducing these results: +*Please attach any code used below (if it's python code replace the keyword "matlab" with "python". PLEASE DELETE THIS LINE.* +```matlab + +``` + +**I hereby confirm that I have:** +- [ ] Tested my code with [all requirements](https://github.com/SysBioChalmers/yeast-GEM#required-software---user) for running the model +- [ ] Done this analysis in the `master` branch of the repository +- [ ] Checked that a similar issue does not exist already +- [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM) about the issue + +*Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE* diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000..5c2d4ab --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,9 @@ +### Main improvements in this PR: +*Try to be as clear as possible: Is it fixing/adding something in the model? Is it an additional test/function/dataset? PLEASE DELETE THIS LINE.* + +**I hereby confirm that I have:** + +- [ ] Tested my code on my own computer for running the model +- [ ] Selected `devel` as a target branch + +*Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE* diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..9c92715 --- /dev/null +++ b/.gitignore @@ -0,0 +1,314 @@ +### Source https://github.com/github/gitignore/ + + +## R.gitignore +# History files +.Rhistory +.Rapp.history + +# Session Data files +.RData + +# User-specific files +.Ruserdata + +# Example code in package build process +*-Ex.R + +# Output files from R CMD build +/*.tar.gz + +# Output files from R CMD check +/*.Rcheck/ + +# RStudio files +.Rproj.user/ + +# produced vignettes +vignettes/*.html +vignettes/*.pdf + +# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 +.httr-oauth + +# knitr and R markdown default cache directories +*_cache/ +/cache/ + +# Temporary files created by R markdown +*.utf8.md +*.knit.md + +# R Environment Variables +.Renviron + + +## Julia.gitignore +# Files generated by invoking Julia with --code-coverage +*.jl.cov +*.jl.*.cov + +# Files generated by invoking Julia with --track-allocation +*.jl.mem + +# System-specific files and directories generated by the BinaryProvider and BinDeps packages +# They contain absolute paths specific to the host computer, and so should not be committed +deps/deps.jl +deps/build.log +deps/downloads/ +deps/usr/ +deps/src/ + +# Build artifacts for creating documentation generated by the Documenter package +docs/build/ +docs/site/ + +# File generated by Pkg, the package manager, based on a corresponding Project.toml +# It records a fixed state of all packages used by the project. As such, it should not be +# committed for packages, but should be committed for applications that require a static +# environment. +Manifest.toml + + +## Python.gitignore +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + + +## Java.gitignore + +# Compiled class file +*.class + +# Log file +*.log + +# BlueJ files +*.ctxt + +# Mobile Tools for Java (J2ME) +.mtj.tmp/ + +# Package Files # +*.jar +*.war +*.nar +*.ear +*.zip +*.tar.gz +*.rar + +# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml +hs_err_pid* + + +### Source https://github.com/jupyter/notebook/blob/master/.gitignore +MANIFEST +build +dist +_build +docs/man/*.gz +docs/source/api/generated +docs/source/config.rst +docs/gh-pages +notebook/i18n/*/LC_MESSAGES/*.mo +notebook/i18n/*/LC_MESSAGES/nbjs.json +notebook/static/components +notebook/static/style/*.min.css* +notebook/static/*/js/built/ +notebook/static/*/built/ +notebook/static/built/ +notebook/static/*/js/main.min.js* +notebook/static/lab/*bundle.js +node_modules +*.py[co] +__pycache__ +*.egg-info +*~ +*.bak +.ipynb_checkpoints +.tox +.DS_Store +\#*# +.#* +.coverage +.pytest_cache +src + +*.swp +*.map +.idea/ +Read the Docs +config.rst +*.iml +/.project +/.pydevproject + +package-lock.json +geckodriver.log +*.iml + + +### Source https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore +# Windows default autosave extension +*.asv + +# OSX / *nix default autosave extension +*.m~ + +# Compiled MEX binaries (all platforms) +*.mex* + +# Packaged app and toolbox files +*.mlappinstall +*.mltbx + +# Generated helpsearch folders +helpsearch*/ + +# Simulink code generation folders +slprj/ +sccprj/ + +# Matlab code generation folders +codegen/ + +# Simulink autosave extension +*.autosave + +# Simulink cache files +*.slxc + +# Octave session info +octave-workspace + + +### Misc +.DS_Store diff --git a/.standard-GEM.md b/.standard-GEM.md new file mode 100644 index 0000000..154a857 --- /dev/null +++ b/.standard-GEM.md @@ -0,0 +1,109 @@ +standard-GEM 0.5 +================= + +For details about the [aims](https://github.com/MetabolicAtlas/standard-GEM/wiki/Aims,-scope-and-terminology#aims), [scope](https://github.com/MetabolicAtlas/standard-GEM/wiki/Aims,-scope-and-terminology#scope), and [use case](https://github.com/MetabolicAtlas/standard-GEM/wiki/Use-case) of this standard see the [wiki pages of the `standard-GEM` repository](https://github.com/MetabolicAtlas/standard-GEM/wiki). + +### Terminology +To facilitate understanding, the definitions used throughout this guide are copied below [from the wiki](https://github.com/MetabolicAtlas/standard-GEM/wiki/Aims,-scope-and-terminology#terminology). For easier differentiation, we have associated colors to each of them. +``` +Based on the ISO guidelines, tweaked for easy understanding. +🟥 Requirements: must, must not +🟧 Recommendations: should, should not +🟨 Possibility and capability: can +``` + +### Instructions +This document serves as a checklist for creating an open source genome-scale metabolic model (GEM) on GitHub. + +- [ ] 🟥 All GEMs that follow the `standard-GEM` must contain this file. +This serves as a traceable adherence to the standard, manually confirmed by the original authors. This file must be edited only with [checkmarks](https://help.github.com/en/github/managing-your-work-on-github/about-task-lists), in order to support automatic parsing and validation of this file. Some of the checkmarks are pre-applied based on the contents of the `standard-GEM` template repository. GEM authors have the responsibility of checking that their model repository does follow the guidelines entirely. +With further updates to `standard-GEM`, one should paste over the new version of this file, and see that the changes in the new guidelines are met. + +Repository creation +------------------- +- [ ] 🟨 Navigate to [standard-GEM](https://github.com/MetabolicAtlas/standard-GEM/) and click on the button `Use this template` +The `standard-GEM` template can be used to initiate a repository. This will copy the contents of the _master_ branch into the new repository, which can be either private or public. + +- [ ] 🟥 Pick a repository name +The name must be either a common name, KEGG organism, or taxonomy-derived short name, followed by the extension `-GEM` or `-GSMM`. The `-GEM` extension is preferred to ease pronunciation. The name can be prefixed by an abbreviation, eg `ec` (enzyme constrained), `sec` (with secretory pathways), `mito` (with mitochondrion pathways), `pro` (with protein structures). +Example: `ecYeast-GEM` + +- [ ] 🟥 Pick a repository description +The description must include the taxonomic classification in full. +Example: `The consensus GEM for Saccharomyces cerevisiae` + +- [ ] 🟥 Add repository topic +The topic `standard-GEM` must be added. Other topics like `genome-scale-models`, `systems-biology` can be added. Having this topic on your repository enables automatic finding using the GitHub API, and automatic validation of the standard. +Topics are not copied from `standard-GEM`, so they need to be added manually. + +- [ ] 🟨 Add a repository URL +The URL can be the link to the publication/pre-print/website where the model is introduced, for example via an identifier system (doi/EuropePMC/PubMed). + + +Repository workflow +------------------- +- [ ] 🟥 Git branches +The GEM repository must have at least two branches: _master_ and _develop_. + +- [ ] 🟥 Releases +Releases must use the tag format `X.X.X` where X are numbers, according to [semantic versioning principles](https://semver.org/). The last field, also called “patch”, can also be used to indicate changes to the repository that do not actually change the GEM itself. The use of a `v` before the version number (`v1.0`) [is discouraged](https://semver.org/#is-v123-a-semantic-version). For more information about releases see the [documentation at GitHub](https://docs.github.com/en/github/administering-a-repository/managing-releases-in-a-repository). + +- [ ] 🟨 Commits +Commit messages can follow the style of semantic commits. + + +File tree +--------- +`/` signifies the root of the repository. +`.keep` files are used to indicate that the empty folder should not be ignored by _git_ - without it _git_ would simply not want to version empty directories. Once folders are not empty, it is okay to remove these files. + +- [x] 🟥 `/.gitignore` +The repository must contain a `/.gitignore` file. This generic [.gitignore](https://git-scm.com/docs/gitignore) was prepared for multiple programming languages. While it does not require modification, it can be further adapted to the needs of the repository. + +- [x] 🟥 `/.github` +The repository must contain a `/.github` folder, in which the contributing guidelines, code of conduct, issue templates and pull request templates must be placed. Defaults are provided and they do not require any modification. + +- [ ] 🟥 `/.github/CONTRIBUTING.md` +This file is provided by the template, but it is empty. It must be filled in with the adequate contributing guideline instructions; a good example is https://github.com/SysBioChalmers/yeast-GEM/blob/master/.github/CONTRIBUTING.md. + +- [ ] 🟥 `/code/README.md` +The repository must contain a `/code` folder. This folder must contain all the code used in generating the model. It must also include a `README.md` file that describes how the folder is organized. + +- [ ] 🟥 `/data/README.md` +The repository must contain a `/data` folder. This folder contains the data used in generating the model. It must also include a `README.md` file that describes how the folder is organized. + +- [ ] 🟥 `/model` +The repository must contain `/model` folder. +This folder must contain the model files, in multiple formats, according to the table below. As a general guideline, binary formats (`.mat`, `.xlsx`) must not exist on any other branches than _master_. The main reason for this is that binary files cannot be diff'ed, which means changes cannot be compared to previous versions, thus increasing the chance of errors. Moreover, with time, the size of the repository can create difficulties, and we cannot yet recommend storing these files with Git LFS, as it introducs complexity. +For more information on the `sbtab` file format, see [sbtab.net](https://sbtab.net). +All model files must be named the same as the repository, and with the appropriate extension. +Example: `yeast-GEM.mat` + +| Model file format | _master_ branch | _develop_ and other branches | +| ----------------- | --------------- | ---------------------------- | +| JSON `.json` | can || +| Matlab `.mat` | should | must not | +| sbtab `.tsv` | can || +| Text file `.txt` | must || +| Excel `.xlsx` | must | must not | +| SBML `.xml` | must || +| YAML `.yml` | must || + + +- [x] 🟥 `/LICENSE.md` +The repository must contain a license file. The default license is [CC-BY 4.0 International](https://creativecommons.org/licenses/by/4.0/). Unless a different license is desired, the file does not require modification. + +- [ ] 🟥 `/README.md` +The repository must contain a `README.md` file. A default file is provided, and the adequate contents must be filled in. +The `/README.md` file must include a version badge. A default is provided in the file. +Additionally, the `/README.md` file should contain the [Zenodo](https://zenodo.org) badge. As soon as the first public release is in made, the repository [should be archived via Zenodo](https://github.com/MetabolicAtlas/standard-GEM/wiki/FAQ#zenodo), and the corresponding badge be updated. A default is provided in the file. +The `/README.md` can contain a contact badge, for example [Gitter](https://gitter.io). When setting up the Gitter chat room, the GitHub activity should be synced with Gitter in order to see the latest updates of the repository in the chat room. A default for this badge is provided in the file. + +- [x] 🟥 `/version.txt` +The repository must contain this file, which is required for the version badge in the `/README.md`. The value refers to the version of the GEM, not of the `standard-GEM`. The value must be updated with each release. + +- [ ] 🟨 Files for continuous integration testing +The repository can be set up for continuous integration testing using memote with eg. Travis CI (`.travis.yml`), Jenkins (`Jenkinsfile`), GitHub Actions (under `.github/workflows`). + +- [ ] 🟨 _MEMOTE_ report +The repository could contain a [MEMOTE](https://www.nature.com/articles/s41587-020-0446-y) report on the _master_ branch, in `.html` format. diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..a7ba38e --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,159 @@ +## Creative Commons + +# Attribution 4.0 International + +Creative Commons Corporation (“Creative Commons”) is not a law firm and does not provide legal services or legal advice. Distribution of Creative Commons public licenses does not create a lawyer-client or other relationship. Creative Commons makes its licenses and related information available on an “as-is” basis. Creative Commons gives no warranties regarding its licenses, any material licensed under their terms and conditions, or any related information. Creative Commons disclaims all liability for damages resulting from their use to the fullest extent possible. + +### Using Creative Commons Public Licenses + +Creative Commons public licenses provide a standard set of terms and conditions that creators and other rights holders may use to share original works of authorship and other material subject to copyright and certain other rights specified in the public license below. The following considerations are for informational purposes only, are not exhaustive, and do not form part of our licenses. + +* __Considerations for licensors:__ Our public licenses are intended for use by those authorized to give the public permission to use material in ways otherwise restricted by copyright and certain other rights. Our licenses are irrevocable. Licensors should read and understand the terms and conditions of the license they choose before applying it. Licensors should also secure all rights necessary before applying our licenses so that the public can reuse the material as expected. Licensors should clearly mark any material not subject to the license. This includes other CC-licensed material, or material used under an exception or limitation to copyright. [More considerations for licensors](http://wiki.creativecommons.org/Considerations_for_licensors_and_licensees#Considerations_for_licensors). + +* __Considerations for the public:__ By using one of our public licenses, a licensor grants the public permission to use the licensed material under specified terms and conditions. If the licensor’s permission is not necessary for any reason–for example, because of any applicable exception or limitation to copyright–then that use is not regulated by the license. Our licenses grant only permissions under copyright and certain other rights that a licensor has authority to grant. Use of the licensed material may still be restricted for other reasons, including because others have copyright or other rights in the material. A licensor may make special requests, such as asking that all changes be marked or described. Although not required by our licenses, you are encouraged to respect those requests where reasonable. [More considerations for the public](http://wiki.creativecommons.org/Considerations_for_licensors_and_licensees#Considerations_for_licensees). + +## Creative Commons Attribution 4.0 International Public License + +By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution 4.0 International Public License ("Public License"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions. + +### Section 1 – Definitions. + +a. __Adapted Material__ means material subject to Copyright and Similar Rights that is derived from or based upon the Licensed Material and in which the Licensed Material is translated, altered, arranged, transformed, or otherwise modified in a manner requiring permission under the Copyright and Similar Rights held by the Licensor. For purposes of this Public License, where the Licensed Material is a musical work, performance, or sound recording, Adapted Material is always produced where the Licensed Material is synched in timed relation with a moving image. + +b. __Adapter's License__ means the license You apply to Your Copyright and Similar Rights in Your contributions to Adapted Material in accordance with the terms and conditions of this Public License. + +c. __Copyright and Similar Rights__ means copyright and/or similar rights closely related to copyright including, without limitation, performance, broadcast, sound recording, and Sui Generis Database Rights, without regard to how the rights are labeled or categorized. For purposes of this Public License, the rights specified in Section 2(b)(1)-(2) are not Copyright and Similar Rights. + +d. __Effective Technological Measures__ means those measures that, in the absence of proper authority, may not be circumvented under laws fulfilling obligations under Article 11 of the WIPO Copyright Treaty adopted on December 20, 1996, and/or similar international agreements. + +e. __Exceptions and Limitations__ means fair use, fair dealing, and/or any other exception or limitation to Copyright and Similar Rights that applies to Your use of the Licensed Material. + +f. __Licensed Material__ means the artistic or literary work, database, or other material to which the Licensor applied this Public License. + +g. __Licensed Rights__ means the rights granted to You subject to the terms and conditions of this Public License, which are limited to all Copyright and Similar Rights that apply to Your use of the Licensed Material and that the Licensor has authority to license. + +h. __Licensor__ means the individual(s) or entity(ies) granting rights under this Public License. + +i. __Share__ means to provide material to the public by any means or process that requires permission under the Licensed Rights, such as reproduction, public display, public performance, distribution, dissemination, communication, or importation, and to make material available to the public including in ways that members of the public may access the material from a place and at a time individually chosen by them. + +j. __Sui Generis Database Rights__ means rights other than copyright resulting from Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, as amended and/or succeeded, as well as other essentially equivalent rights anywhere in the world. + +k. __You__ means the individual or entity exercising the Licensed Rights under this Public License. Your has a corresponding meaning. + +### Section 2 – Scope. + +a. ___License grant.___ + + 1. Subject to the terms and conditions of this Public License, the Licensor hereby grants You a worldwide, royalty-free, non-sublicensable, non-exclusive, irrevocable license to exercise the Licensed Rights in the Licensed Material to: + + A. reproduce and Share the Licensed Material, in whole or in part; and + + B. produce, reproduce, and Share Adapted Material. + + 2. __Exceptions and Limitations.__ For the avoidance of doubt, where Exceptions and Limitations apply to Your use, this Public License does not apply, and You do not need to comply with its terms and conditions. + + 3. __Term.__ The term of this Public License is specified in Section 6(a). + + 4. __Media and formats; technical modifications allowed.__ The Licensor authorizes You to exercise the Licensed Rights in all media and formats whether now known or hereafter created, and to make technical modifications necessary to do so. The Licensor waives and/or agrees not to assert any right or authority to forbid You from making technical modifications necessary to exercise the Licensed Rights, including technical modifications necessary to circumvent Effective Technological Measures. For purposes of this Public License, simply making modifications authorized by this Section 2(a)(4) never produces Adapted Material. + + 5. __Downstream recipients.__ + + A. __Offer from the Licensor – Licensed Material.__ Every recipient of the Licensed Material automatically receives an offer from the Licensor to exercise the Licensed Rights under the terms and conditions of this Public License. + + B. __No downstream restrictions.__ You may not offer or impose any additional or different terms or conditions on, or apply any Effective Technological Measures to, the Licensed Material if doing so restricts exercise of the Licensed Rights by any recipient of the Licensed Material. + + 6. __No endorsement.__ Nothing in this Public License constitutes or may be construed as permission to assert or imply that You are, or that Your use of the Licensed Material is, connected with, or sponsored, endorsed, or granted official status by, the Licensor or others designated to receive attribution as provided in Section 3(a)(1)(A)(i). + +b. ___Other rights.___ + + 1. Moral rights, such as the right of integrity, are not licensed under this Public License, nor are publicity, privacy, and/or other similar personality rights; however, to the extent possible, the Licensor waives and/or agrees not to assert any such rights held by the Licensor to the limited extent necessary to allow You to exercise the Licensed Rights, but not otherwise. + + 2. Patent and trademark rights are not licensed under this Public License. + + 3. To the extent possible, the Licensor waives any right to collect royalties from You for the exercise of the Licensed Rights, whether directly or through a collecting society under any voluntary or waivable statutory or compulsory licensing scheme. In all other cases the Licensor expressly reserves any right to collect such royalties. + +### Section 3 – License Conditions. + +Your exercise of the Licensed Rights is expressly made subject to the following conditions. + +a. ___Attribution.___ + + 1. If You Share the Licensed Material (including in modified form), You must: + + A. retain the following if it is supplied by the Licensor with the Licensed Material: + + i. identification of the creator(s) of the Licensed Material and any others designated to receive attribution, in any reasonable manner requested by the Licensor (including by pseudonym if designated); + + ii. a copyright notice; + + iii. a notice that refers to this Public License; + + iv. a notice that refers to the disclaimer of warranties; + + v. a URI or hyperlink to the Licensed Material to the extent reasonably practicable; + + B. indicate if You modified the Licensed Material and retain an indication of any previous modifications; and + + C. indicate the Licensed Material is licensed under this Public License, and include the text of, or the URI or hyperlink to, this Public License. + + 2. You may satisfy the conditions in Section 3(a)(1) in any reasonable manner based on the medium, means, and context in which You Share the Licensed Material. For example, it may be reasonable to satisfy the conditions by providing a URI or hyperlink to a resource that includes the required information. + + 3. If requested by the Licensor, You must remove any of the information required by Section 3(a)(1)(A) to the extent reasonably practicable. + + 4. If You Share Adapted Material You produce, the Adapter's License You apply must not prevent recipients of the Adapted Material from complying with this Public License. + +### Section 4 – Sui Generis Database Rights. + +Where the Licensed Rights include Sui Generis Database Rights that apply to Your use of the Licensed Material: + +a. for the avoidance of doubt, Section 2(a)(1) grants You the right to extract, reuse, reproduce, and Share all or a substantial portion of the contents of the database; + +b. if You include all or a substantial portion of the database contents in a database in which You have Sui Generis Database Rights, then the database in which You have Sui Generis Database Rights (but not its individual contents) is Adapted Material; and + +c. You must comply with the conditions in Section 3(a) if You Share all or a substantial portion of the contents of the database. + +For the avoidance of doubt, this Section 4 supplements and does not replace Your obligations under this Public License where the Licensed Rights include other Copyright and Similar Rights. + +### Section 5 – Disclaimer of Warranties and Limitation of Liability. + +a. __Unless otherwise separately undertaken by the Licensor, to the extent possible, the Licensor offers the Licensed Material as-is and as-available, and makes no representations or warranties of any kind concerning the Licensed Material, whether express, implied, statutory, or other. This includes, without limitation, warranties of title, merchantability, fitness for a particular purpose, non-infringement, absence of latent or other defects, accuracy, or the presence or absence of errors, whether or not known or discoverable. Where disclaimers of warranties are not allowed in full or in part, this disclaimer may not apply to You.__ + +b. __To the extent possible, in no event will the Licensor be liable to You on any legal theory (including, without limitation, negligence) or otherwise for any direct, special, indirect, incidental, consequential, punitive, exemplary, or other losses, costs, expenses, or damages arising out of this Public License or use of the Licensed Material, even if the Licensor has been advised of the possibility of such losses, costs, expenses, or damages. Where a limitation of liability is not allowed in full or in part, this limitation may not apply to You.__ + +c. The disclaimer of warranties and limitation of liability provided above shall be interpreted in a manner that, to the extent possible, most closely approximates an absolute disclaimer and waiver of all liability. + +### Section 6 – Term and Termination. + +a. This Public License applies for the term of the Copyright and Similar Rights licensed here. However, if You fail to comply with this Public License, then Your rights under this Public License terminate automatically. + +b. Where Your right to use the Licensed Material has terminated under Section 6(a), it reinstates: + + 1. automatically as of the date the violation is cured, provided it is cured within 30 days of Your discovery of the violation; or + + 2. upon express reinstatement by the Licensor. + + For the avoidance of doubt, this Section 6(b) does not affect any right the Licensor may have to seek remedies for Your violations of this Public License. + +c. For the avoidance of doubt, the Licensor may also offer the Licensed Material under separate terms or conditions or stop distributing the Licensed Material at any time; however, doing so will not terminate this Public License. + +d. Sections 1, 5, 6, 7, and 8 survive termination of this Public License. + +### Section 7 – Other Terms and Conditions. + +a. The Licensor shall not be bound by any additional or different terms or conditions communicated by You unless expressly agreed. + +b. Any arrangements, understandings, or agreements regarding the Licensed Material not stated herein are separate from and independent of the terms and conditions of this Public License. + +### Section 8 – Interpretation. + +a. For the avoidance of doubt, this Public License does not, and shall not be interpreted to, reduce, limit, restrict, or impose conditions on any use of the Licensed Material that could lawfully be made without permission under this Public License. + +b. To the extent possible, if any provision of this Public License is deemed unenforceable, it shall be automatically reformed to the minimum extent necessary to make it enforceable. If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions. + +c. No term or condition of this Public License will be waived and no failure to comply consented to unless expressly agreed to by the Licensor. + +d. Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority. + +> Creative Commons is not a party to its public licenses. Notwithstanding, Creative Commons may elect to apply one of its public licenses to material it publishes and in those instances will be considered the “Licensor.” Except for the limited purpose of indicating that material is shared under a Creative Commons public license or as otherwise permitted by the Creative Commons policies published at [creativecommons.org/policies](http://creativecommons.org/policies), Creative Commons does not authorize the use of the trademark “Creative Commons” or any other trademark or logo of Creative Commons without its prior written consent including, without limitation, in connection with any unauthorized modifications to any of its public licenses or any other arrangements, understandings, or agreements concerning use of licensed material. For the avoidance of doubt, this paragraph does not form part of the public licenses. +> +> Creative Commons may be contacted at creativecommons.org diff --git a/README.md b/README.md new file mode 100644 index 0000000..41866cd --- /dev/null +++ b/README.md @@ -0,0 +1,69 @@ +> Introduction (please delete after reading): +[standard-GEM](https://github.com/MetabolicAtlas/standard-GEM) is a template repository that aims to standardize the format of genome-scale metabolic models (GEMs) versioned with git. In addition to encouraging the open-sourcing of GEMs, it facilitates the import of GEMs into databases and online websites. Moreover, it provides the community with a familiar structure that is easy to adopt through this repository itself. The template comes with a set of requirements and recommendations, packaged as to-do items in a hidden Markdown file in this repository `.standard-GEM.md`. After downloading this repository, or using it as a template, those to-do items provide guidance to how adherence to the standard can be obtained. + +> Instructions for this `README` (please delete after reading): +This is the `README.md` template provided by [standard-GEM](https://github.com/MetabolicAtlas/standard-GEM) and was crafted to cover most use-cases. +Feel free to edit this template `README`. Blanks are indicated by `{{ test }}`. One may use a search function to find these `{{`. Here are some examples of blanks used throughout this file: `{{organization or username}}` is the organization name or username for this GitHub repository, eg. `SysBioChalmers`; `{{repository name}}` is the name of this GitHub repository, eg. `yeast-GEM`. +If you find this template does not fit your needs, we would appreciate if you could report this by creating a new issue on [standard-GEM](https://github.com/MetabolicAtlas/standard-GEM/issues). + + +## {{repository name}}: {{repository description}} + +[![Version](https://badge.fury.io/gh/{{organization or username}}%2F{{repository name}}.svg)](https://badge.fury.io/gh/sysbiochalmers/yeast-gem) +[![Zenodo](https://zenodo.org/badge/{{Zenodo ID}}.svg)](https://zenodo.org/badge/latestdoi/{{Zenodo ID}}) +[![Gitter chat](https://badges.gitter.im/{{organization or username}}/{{repository name}}.svg)](https://gitter.im/{{organization or username}}/{{repository name}}) + + +#### Description + +{{ fill in a short description or the paper abstract }} + + +#### Citation + +{{ provide the citation once available, for example: + > Lu, H., Li, F., Sánchez, B.J. et al (2019). A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nat Commun 10, 3586 [doi:10.1038/s41467-019-11581-3](https://doi.org/10.1038/s41467-019-11581-3) + +}} + + +#### Keywords + +> Keywords are be separated by semicolons. +> The `Model source` field contains the source(s) of the current model, eg existing GEMs. If possible, use the Markdown format to add the URL with the DOI. The (NCBI) taxonomy ID should be provided in the [format from identifiers.org](https://registry.identifiers.org/registry/taxonomy). For the genome identifier, please provide the ENA/GenBank/RefSeq identifier via *identifiers.org*, or from other sources such as PATRIC or KBase. + +**Utilisation:** {{ experimental data reconstruction; multi-omics integrative analysis;, _in silico_ strain design; model template }} +**Field:** {{ metabolic-network reconstruction }} +**Type of model:** {{ reconstruction; curated }} +**Model source:** {{ [YeastMetabolicNetwork](http://doi.org/10.1038/nbt1492) }} +**Omic source:** {{ genomics; metabolomics }} +**Taxonomic name:** {{ _Saccharomyces cerevisiae_ }} +**Taxonomy ID:** {{ [taxonomy:559292](https://identifiers.org/taxonomy:559292) }} +**Genome ID:** {{ [insdc.gca:GCA_000146045.2](https://identifiers.org/insdc.gca:GCA_000146045.2) }} +**Metabolic system:** {{ general metabolism }} +**Tissue:** +**Bioreactor:** +**Cell type:** +**Cell line:** +**Strain:** {{ S288C }} +**Condition:** {{ aerobic; glucose-limited; defined media }} + + +### Installation + +{{ Be mindful of users who do not have a typical background - provide a clear overview of the required software. Also, there might be different requirements for users and collaborators. }} + + +### Usage + +{{ Describe how to load and save the model. }} + + +### Contributing + +Contributions are always welcome! Please read the [contributing guideline](.github/CONTRIBUTING.md) to get started. + + +### Contributors + +Code contributors are reported automatically by GitHub under [Contributors](https://github.com/{{organization or username}}/{{repository name}}/graphs/contributors), while other contributions come in as [Issues](https://github.com/{{organization or username}}/{{repository name}}/issues). \ No newline at end of file diff --git a/code/README.md b/code/README.md new file mode 100644 index 0000000..e69de29 diff --git a/data/README.md b/data/README.md new file mode 100644 index 0000000..e69de29 diff --git a/model/.keep b/model/.keep new file mode 100644 index 0000000..e69de29 diff --git a/version.txt b/version.txt new file mode 100644 index 0000000..77d6f4c --- /dev/null +++ b/version.txt @@ -0,0 +1 @@ +0.0.0