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# Contributing to the Collaborative Distributed Science Guide
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# Contributing to the ABC Guide
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Thank you for your interest in contributing to the Collaborative Distributed Science Guide! This document outlines the standards and guidelines for contributing to this template repository.
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Thank you for your interest in contributing to the ABC Guide!
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## Overview
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This document outlines the standards and guidelines for contributing to the ABC Guide. Before you begin, please review the information provided here.
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First, is your contribution specific to the AI & Biodiversity Change (ABC) Global Center, or would it be more broadly applicable? If more general, please consider instead directing the update or suggestion to the [Collaborative Distributed Science Guide](https://github.com/Imageomics/Collaborative-distributed-science-guide); updates to the template repository will be incorporated both here and in other other guides developed from it. If it _is_ ABC Center-specific, please continue to review this document—we look forward to your input!
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The Collaborative Distributed Science Guide is built with [MkDocs Material](https://squidfunk.github.io/mkdocs-material/) and deployed via GitHub Pages. All documentation is written in Markdown and follows specific formatting standards to ensure consistent rendering and maintainability.
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## Overview
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This is a template repository designed to be forked and customized by different organizations for their collaborative science documentation needs.
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The ABC Guide is built with [MkDocs Material](https://squidfunk.github.io/mkdocs-material/) and deployed via GitHub Pages. All documentation is written in Markdown and follows specific formatting standards to ensure consistent rendering and maintainability.
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## Getting Started
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mkdocs serve
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```
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5. View the site at <http://127.0.0.1:8000/Collaborative-distributed-science-guide/>
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5. View the site at <http://127.0.0.1:8000/ABC-guide/>
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### Testing Changes
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## Getting Help
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- Open an [issue](https://github.com/Imageomics/Collaborative-distributed-science-guide/issues) for questions or problems
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- Open an [issue](https://github.com/ABC-Center/ABC-guide/issues) for questions or problems
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- Reference existing guides and templates for examples
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- Check the [MkDocs Material documentation](https://squidfunk.github.io/mkdocs-material/) for advanced features
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---
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Thank you for helping improve the Collaborative Distributed Science Guide! Your contributions help make collaborative scientific computing more accessible and effective.
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Thank you for helping improve the ABC Guide! Your contributions help make collaborative scientific computing more accessible and effective.
# AI & Biodiversity Change (ABC) Global Center Guide
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Welcome to the Collaborative Distributed Science Guide!
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Welcome to the ABC Guide!
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Just joining or starting a new project?
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Check out the [Collaborative Distributed Science Guide](https://imageomics.github.io/Collaborative-distributed-science-guide/) for guidance on conventions and best practices.
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Check out the [ABC Guide](https://ABC-Center.github.io/ABC-guide/) for guidance on conventions and best practices.
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## About the Guide
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This guide started as an Imageomics Institute-internal wiki, focused on providing guidance and best practices for collaborative and interdisciplinary (computer science + biology) work. Recognizing that the topics and suggestions are broadly applicable to anyone working in similar or adjacent fields, we moved the vast majority to this [guide](https://imageomics.github.io/Collaborative-distributed-science-guide/). To increase accessibility for those less familiar with GitHub, we generated the website from our Markdown documents (which used to be wiki pages) with [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/).
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This guide provides guidance and best practices for collaborative and interdisciplinary (computer science + biology/ecology) work at the ABC Global Center. It is focused on ABC member needs while remaining broadly applicable to anyone working in similar or adjacent fields. The website is generated from Markdown documents with [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/) to increase accessibility for those less familiar with GitHub.
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Please feel free to open an [issue](https://github.com/Imageomics/Collaborative-distributed-science-guide/issues) with any questions regarding the content of this guide.
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Please feel free to open an [issue](https://github.com/ABC-Center/ABC-guide/issues) with any questions regarding the content of this guide.
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### How to Use the Guide
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This Guide is set up as a template repository such that there are two primary means of interacting with it:
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1. Building a personalized version of the Guide: select "Use this Template" at the top of the repo to generate your own version. This will create a new repository (generated from the template repo) that does _not_ share the commit history of the template. Updates could still be added from the template upstream through [`git cherry-pick`](https://git-scm.com/docs/git-cherry-pick). More details are provided below, in [Personalizing the Guide](#personalizing-the-guide).
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2. Contributing to the Guide: fork this repo, make changes, and submit a pull request (PR) for review. Some guidance is provided in the [Pull Request Guide](https://imageomics.github.io/Collaborative-distributed-science-guide/wiki-guide/The-GitHub-Pull-Request-Guide/); please provide a detailed description of your changes and review the contributing guidelines (coming soon).
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### Personalizing the Guide
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Welcome to your new guide repo! The first step in updating your new guide is to give it a name; ideally this should match the name you give to the repo when using the template. You will need to update the name and hardcoded repo links across various files.
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Primary pages to personalize are:
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### History
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-[`mkdocs.yaml`](mkdocs.yaml) has comments indicating locations to personalize (e.g., updating name, logos, socials). All pages use relative links within the repository, so those connections only need to be updated if adding or removing pages.
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-[`index.md`](docs/index.md): this is the homepage for the site and should reflect your organization or group's priorities.
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-[`CITATION.cff`](CITATION.cff): please set the Collaborative Distributed Science Guide citation as a reference in your citation file after making your own modifications (see [template](https://imageomics.github.io/Collaborative-distributed-science-guide/wiki-guide/GitHub-Repo-Guide/#citation) for guidance on formatting).
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-[`Digital-products-release-licensing-policy.md`](docs/wiki-guide/Digital-products-release-licensing-policy.md): at a minimum, links should be redirected to your GitHub and Hugging Face organization pages.
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- Other locations in pages such as the [`GitHub-Repo-Guide`](docs/wiki-guide/GitHub-Repo-Guide.md) and [`Hugging-Face-Repo-Guide.md`](docs/wiki-guide/Hugging-Face-Repo-Guide.md) also have links to our organization pages. A search and replace for "Imageomics" can be done to update these.
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-[`Technical-Infrastructure.md`](docs/wiki-guide/Technical-Infrastructure.md): this page is Imageomics-specific and includes internal-only links.
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-[Glossary for Imageomics](docs/wiki-guide/Glossary-for-Imageomics.md): this page should be updated to a topic relevant to your field or focus.
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- Templates should be updated for your organization (mainly the `Acknowledgements` sections, pre-filled URL suggestions, domain-specific suggestions and guidance).
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This guide houses the information needed to get started with and use center resources readily available to all ABC members. It was developed based on the more general [Collaborative Distributed Science Guide](https://imageomics.github.io/Collaborative-distributed-science-guide/), which was a joint effort between ABC and Imageomics to generalize the [Imageomics Guide](https://imageomics.github.io/Imageomics-guide/) for a broader audience (please see the [template repository](https://github.com/Imageomics/Collaborative-distributed-science-guide) for more information). The template guide solution was born out of the desire to host an analogous site for the [AI and Biodiversity Change (ABC) Global Center](http://abcresearchcenter.org) while limiting duplicative updates between guides (ABC and Imageomics share some team members on this project).
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## Contributing
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mkdocs serve
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```
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Then the site will run at <http://127.0.0.1:8000/Collaborative-distributed-science-guide/>.
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### History
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This guide was developed alongside the [Imageomics Guide](https://imageomics.github.io/Imageomics-guide/), which houses the information needed to get started with and use institute resources readily available to all members. However, most of its content is applicable to anyone working more broadly in the field of [_imageomics_](https://imageomics.github.io/Collaborative-distributed-science-guide/wiki-guide/Glossary-for-Imageomics.md/#imageomics) or adjacent fields of computer and data science, and it is tailored to help domain scientists bridging that gap. _This guide_ is intended to serve as a template for others wishing to develop a similar organization-specific guide, and this solution was born out of the desire to do so for the [AI and Biodiversity Change (ABC) Global Center](http://abcresearchcenter.org) while limiting duplicative updates between guides (Imageomics and ABC share some team members on this project). The general structure of the website should be broadly applicable, but see [Personalizing the Guide](#personalizing-the-guide) for suggestions on tailoring it for the particular organization or group's needs.
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## Acknowledgments
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This work was supported by both the [Imageomics Institute](https://imageomics.org) and the [AI and Biodiversity Change (ABC) Global Center](http://abcresearchcenter.org). The Imageomics Institute is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under [Award #2118240](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118240) (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning). The ABC Global Climate Center is funded by the US National Science Foundation under [Award No. 2330423](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2330423&HistoricalAwards=false) and Natural Sciences and Engineering Research Council of Canada under [Award No. 585136](https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=782440). This guide draws on research supported by the Social Sciences and Humanities Research Council. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation, Natural Sciences and Engineering Research Council of Canada, or Social Sciences and Humanities Research Council.
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This work was supported by both the [Imageomics Institute](https://imageomics.org) and the [AI and Biodiversity Change (ABC) Global Center](http://abcresearchcenter.org). The Imageomics Institute is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under [Award #2118240](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118240) (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning). The ABC Global Center is funded by the US National Science Foundation under [Award No. 2330423](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2330423&HistoricalAwards=false) and Natural Sciences and Engineering Research Council of Canada under [Award No. 585136](https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=782440). This guide draws on research supported by the Social Sciences and Humanities Research Council. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation, Natural Sciences and Engineering Research Council of Canada, or Social Sciences and Humanities Research Council.
As members of the Imageomics and ABC communities, we agree to maintain an environment where every participant feels welcome to be their true self and speak from the heart.
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As members of the ABC community, we agree to maintain an environment where every participant feels welcome to be their true self and speak from the heart.
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To this end, we agree as individuals and as a group to:
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-**Respect time.** When a session is over, we need to move on. There is designated time for in-depth follow up and continuing conversations.
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-**Care** for each other. We bring our full selves to the community, and we look out for each other wholeheartedly.
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We abide by these principles in all Imageomics and ABC spaces, including but not limited to digital and in-person meetings, formal and informal gatherings, online discussion forums and chat spaces, and field and lab work.
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We abide by these principles in all ABC spaces, including but not limited to digital and in-person meetings, formal and informal gatherings, online discussion forums and chat spaces, and field and lab work.
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Acts of misconduct are prohibited. Those found to engage in misconduct will be subject to dismissal from the project and further actions as directed by the guidelines of the employers and the place of incidence.
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## Acts of Misconduct
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If you believe you have experienced or witnessed misconduct in an Imageomics or ABC setting, please take these steps:
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It is the responsibility of all members of the ABC Global Center community to eliminate any form of misconduct in science and to build a community that allows all individuals to thrive, learn, and grow. Misconduct includes:
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1. Document the incident;
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2. Tell someone you trust;
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3. Report the incident to Diane Boghrat.
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Privacy will be protected to the greatest extent possible.
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## VALUES
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### TRANSPARENCY
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- Abuse of any person, including, but not limited to, harassment, stalking, bullying, or hazing of any kind, whether the behavior is carried out verbally, physically, electronically, or in written form;
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- Conduct that is unwelcome, offensive, indecent, obscene, or disorderly;
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We ensure our efforts are clear about assumptions, uncertainty, and limits, and provide open sources of information, processes, and discovery.
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Those who experience or witness misconduct in an ABC Center-related on- or off-site work environment are advised to take these steps:
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### ACCOUNTABILITY
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We are responsible, individually and collectively, for the outcomes we produce and ensure, to the best of our abilities, that the methods outcome matches intended use.
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### COLLABORATION
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1. Document the incident;
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2. Report the incident to field leaders and/or ABC Center Management who will offer to connect them to resources (i.e. medical care, police, counseling, etc.) and provide validation of their experience.
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We create and nurture collaborative environments and welcome, value, and affirm all members of our community. We also consider how and for whom solutions are created and promote the heterogeneity of perspectives in the creation process. We actively engage others’ perspectives, recognize everyone’s potential to contribute new ideas, and work together to find creative solutions to complex problems.
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ABC Center Management will investigate all reports of misconduct. Those found to engage in misconduct will be subject to dismissal from the project and further actions as directed by the guidelines of the employers, place of incidence, and relevant federal policies.
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### SAFETY
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**Points of contact:**
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We ensure our practices are ethical and impartial to the best of our ability. We address ethical issues when we discover them and practice good data governance. We strive to enhance practices while openly addressing those that harm people or the environment.
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