Welcome to the Imageomics Guide!
Just joining or starting a new project? Check out the Imageomics Guide for guidance on conventions and best practices.
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. 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.
Please feel free to open an issue with any questions regarding the content of this guide.
If you'd like to contribute to this guide, please read our Contributing Guidelines for information about our standards, development workflow, and submission process.
To test this site locally, first clone this repository, then create an environment with requirements.txt
pip install -r requirements.txt
and run mkdocs serve:
mkdocs serve
Then the site will run at http://127.0.0.1:8000/Imageomics-guide/.
This guide 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 or adjacent fields of computer and data science, and it is tailored to help domain scientists bridging that gap. We further expanded development to include a more general template guide, the Collaborative Distributed Science Guide, for others wishing to develop a similar organization-specific guide (please see the template repository for more information). This solution was born out of the desire to do so for the AI and Biodiversity Change (ABC) Global Center while limiting duplicative updates between guides (Imageomics and ABC share some team members on this project).
This work was supported by both the Imageomics Institute and the AI and Biodiversity Change (ABC) Global Center. The Imageomics Institute is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under Award #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 and Natural Sciences and Engineering Research Council of Canada under Award No. 585136. 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.