March 6, 2019

March is PyOpenWorm month!

This content is cross-posted from OpenWorm Foundation blog.

PyOpenWorm is a data-access and data sharing library for the OpenWorm project. It is designed to provide the project with a coordinated means for generically describing data in a variety of formats, tracking the origins of said data, and describing various transformations between formats.
This month should see a release for PyOpenWorm and further integration with c302, the neural network model generation tool set. We’re always happy to welcome contributors in this effort! There are, however, a number of other areas where you can help on PyOpenWorm: see the beginner label on PyOpenWorm issue tracker for a listing of issues to start with or else get in touch with Mark Watts, (github:mwatts15) for suggestions.
Also this summer, OpenWorm is again participating in Google Summer of Code (GSoC) under the banner of the INCF. My personal favorite project idea focuses on file sharing (model files, experimental data, etc.) within PyOpenWorm. The file sharing component will have a major role in PyOpenworm going forward, so this is a great project to get involved with now. You can see the list of all OpenWorm projects for 2019 here. Although applications aren’t open until 25 March, you can get in touch with the GSoC mentors and learn more about the problems they’re trying to solve today – so don’t be shy! You can learn more about GSoC in general on their website.
This project of the month kicks off with an “office hours” session on the OpenWorm Slack chat this Wednesday, 6 March at 17:00 UTC where several senior contributors (including me) simultaneously make themselves available for Q&A, discussion, and to talk about current and upcoming activities in the project. You can join by filling out this (short) form.  This is also the best starting place if you’re interested in contributing to OpenWorm more broadly since it will let us know what you’re interested in and what skills you have now so we can help you find which area best fits your interests.
Thanks for reading! Looking forward to hearing from you :-)
Find us on Twitter: @OpenWorm
Link to the OW Contributor form is here

March 1, 2019

Open Data Day 2019: DevoZoo is Live!

Welcome to Open Data Day 2019, sponsored by Orthogonal Research and Education Laboratory! This year we are introducing an open data repository called DevoZoo. Based on work going on in the DevoWorm group, DevoZoo include various primary, secondary, and tertiary datasets from a variety of developing organisms (all characterizing embryogenesis). There are several other tabs on the site, including references on C. elegans developmental biology (the embryo image), a collection of Jupyter notebooks (DevoNotes), methods developed within the DevoWorm group (DevoMethods), and an educational curriculum (DevoWormU).

DevoZoo is based on the "Models for Data Recycling" mini-grant submitted to (but not funded by) Mozilla Science a few months ago. If you want to understand the greater vision for this initiative, please read over the grant proposal document. Feel free to contribute by playing with the datasets, or by proposing new resources by forking our Github repository and submitting a pull request.