Summer of Working Groups

I am happy to announce that this Summer I will be advising/mentoring two research groups of Google Summer of Code (GSoC) students and applicants. Thanks to INCF for sponsoring our applications and applicants again this year. The first group (DevoWorm), based in the OpenWorm Foundation, is interested in image segmentation and Machine Learning. GSoC applicants Asmit Singh and Ujjwal Singh (currently attending IIT Delhi) are working on extracting quantitative data to construct a digital model for organisms in the diatom genus Bacillaria. The GSoC student (Vinay Varma, currently attending Amrita Vishwa Vidyapeetham University) is working on developing a method for Semantic Segmentation based on microscopy of the embryogenetic process, focusing on the biology of Caenorhabditis elegans.

The other group is based in the Orthogonal Research and Education Laboratory, and is focused on creating a methodology for developmental Braitenberg Vehicles. This involves simulating the formation of a brain (neurons and connectome) in a simple body that continuously interacts with its environment. The GSoC student in this group (Stefan Dvoretskii) is developing such a model using Genetic Algorithms and the open-source SimBrain platform. The GSoC applicants (Ziyi Gong, Jesse Parent, and Ankit Gupta) are working on a variety of unique approaches that will aid in our
understanding of this complex system. These alternative approaches range from biologically-inspired (Ziyi) to a cybernetic architecture based on the Every Good Regulator Theorem (Jesse).

The hybrid education/research working group is something I started with last year's Orthogonal Lab GSoC group. There is a good chance that this Summer's discussions and work periods will produce awesome, cutting-edge science. Follow us on Github (DW group, BV group) and YouTube (DW group, BV group) for more!

Open Leaders 7 is almost finished. Join us for a Sprint!

In a previous post, I mentioned that I was a part of Mozilla's Open Leaders program, which is dedicated to working open and improving the overall health of the internet. Each Open Leader worked on an open project over the duration of the 14 week program, which in my case is an open educational curriculum for the DevoWorm group and the OpenWorm Foundation more generally.

Purpose and Outcomes from the Mozilla's POP (purpose, outcomes, process) standards for project management). Click to enlarge.

The purpose of building this curriculum is twofold: to encourage contributions to the organization, and to create educational opportunities that enrich people's contributions. Therefore, our curriculum combines topical tutorials with course materials focused on interdisciplinary topics (bridging data science, computer science, and biology) and training in niche topical areas. The curriculum has a front-end (managed at Eliademy) and a back-end (managed in a Github repository). You can make contributions to the front-end by either enrolling in the course or making notes in hypothes.is.

Examples of the front-end, back-end, and course content. Click to enlarge.

Another way to contribute is to attend the Sprint for Internet Health. Last year this was referred to as the Global Sprint, and gives people an opportunity to engage in open source creation as well as consumption. Our project already has two contributors (Asmit Singh, Vinay Varma, and Uggwal Singh, who are also Google Summer of Code applicants to the organization) who have been refining the materials by way of pull requests. More details to come!

Details on how to get involved. Click to enlarge.

UPDATE (5/25): An interview with project lead Bradly Alicea (by Robert Schafer) is now available on the Mozilla Open Leaders Medium blog.

April is Documentation Month!

This content is cross-posted from OpenWorm Foundation blog.

Based on popular demand, April will be “Docs Month” within the OpenWorm Foundation. The month will be filled with reevaluating our organizational docs, in addition to putting together a proposal (in conjunction with INCF) for the inaugural Google Season of Docs. 

If you have a technical writing background, we can work on a community contribution, which can include (but is not limited to) the following current organizational needs:

1) building an OpenWorm Wiki, which might reference special topics and within the subprojects. 

2) website redesign so as to make it easy to find key information (e.g. people, how to get to Slack, Github, Docker and Blender models). 

3) help refine a reference document started by Senior Contributor Gopal Sarma. 

4) an inventory of projects and docs that align with current organizational goals. 

5) a reorganization of all project docs, mainly merging DevoWorm, NeuroML, Geppetto, and other assorted docs into one location. 

6) help with the educational curriculum. 

7) find and write specs for “casual contributor-friendly” contributions.

Let's get working! 

UPDATE (4/26): We submitted an application by the deadline that incorporates many of these elements. If you are interested in learning more, please join our Slack team and join the #documentation channel, or contact me via e-mail.

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

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.