Ontology of bioimage informatics operations, topics, types of data, and data formats. EDAM-Bioimaging is an extension of the EDAM ontology (edamontology.org) dedicated to bioimaging data analysis, and developed in an open collaboration including partners from NEUBIAS (neubias.org), COMULIS (comulis.eu), and ELIXIR (elixir-europe.org)..
This issue documents the hints for creating a project timeline for the Outreachy applicants.
The project timeline will start with the onboarding tasks including:
- A chosen set of "good first issues" which the applicant hasn't finished already during the application period
- Getting familiar with the community; getting familiar with the minimum basics of open science, biology, open source bioinformatics (with help from the mentors)
Depending on individual interests, applicants can select a (not too big!) subset of the following tasks to form their project plan, split between main tasks and stretch goals:
- Revising and improving the contents of the EDAM and EDAM-bioimaging ontologies (updates; better and more understandable definitions; links to Wikipedia and elsewhere; missing keywords; fixing errors). The intern can also choose to concentrate on a thematic subset (e.g. machine learning🤖, biodiversity🐢, genomics🧬, image analysis🖼, geosciences|climate🌏, etc.), or on working with a particular open source community (_e.g._ [ELIXIR](https://elixir-europe.org), [Debian](https://wiki.debian.org/DebianMed), [Galaxy](https://galaxyproject.org)).
- Implementing content suggestions from other scientists
- Developing a simple Python package to read and write EDAM in various formats (plus implementing it into the development and release workflows)
- Improving the EDAM webpage (possibly Jekyll-style generation; better UX; better aesthetics; better content)
- Implementing continuous deployment (CD) of the EDAM releases and website
- Improving the documentation of EDAM (moving to the main repo; better UX; updating; critical selection of content)
- Updating and improving the EDAM Popovers plugin for Firefox (if [inkuzmin](https://github.com/inkuzmin) is available to help)
- Contributing to the EDAM Browser improvements (functional and UX testing; improving UX; optional JS|HTML|CSS)
- Improving the Bash shell scripts for client-side validation (Git hooks)
- Improving the continuous integration (CI) validation of the ontology
- Improving various templates for contributing: commit messages, pull requests, issues, concepts (owl:Classes), ...
- Improving Apache web server setup (especially httpd rewrites)
- Applicants do not need add additional tasks into their timeline, but they are welcome to do so if they want (especially if wanting to learn something, experiment with something, get in touch with a specific community, etc.)
It's totally fine if the timeline is brief and high-level! 😸 The most important for us mentors is:
- which weeks the candidate will be unavailable, completely or a big part
- maybe good to have some kind of a main focus or "milestone" each week (can be a couple of words, no details), so that both the intern and the mentors can plan better and see progress. But this is not mandatory.
- it would be excellent if the intern could put the 2 mentioned conferences into the timeplan (GCC and ISMB/BOSC). These will both include a CoFest where intensive work will be done together with a broader community. 🐙 They're exciting, and it's highly recommended to reserve a lot of time & energy during those days 😉🐱🏍
matuskalas
commented
3 years ago
This issue documents the hints for creating a project timeline for the Outreachy applicants.
The project timeline will start with the onboarding tasks including:
Depending on individual interests, applicants can select a (not too big!) subset of the following tasks to form their project plan, split between main tasks and stretch goals:
It's totally fine if the timeline is brief and high-level! 😸 The most important for us mentors is: