January is DevoWorm month!

Blossoms or fireworks to ring in the New Year?

Welcome to 2019! And welcome to OpenWorm Foundation’s project of the month for January, featuring DevoWorm. Here I will briefly go over progress in the DevoWorm group over the last year and a half. If you would like to know more, we have a group Slack channel (#devoworm) in the OpenWorm team, a group website, and a Github repository.

For the uninitiated, the DevoWorm group has a multifaceted set of interests. We are interested in simulating and analyzing data related to worm development, but have an interest in the development of other model organisms as well. In terms of results, we have focused mostly on publications and open datasets, but as you will see from the website, we have also been involved in the creation of unique demos and software development.

The DevoWorm group is also interested in education. Our educational efforts have largely spread out over four types of pedagogy: digital badges, tutorials via interactive notebooks, public lectures, and one-on-one mentorship through the Google Summer of Code (GSoC) program. The OpenWorm Foundation has hosted a DevoWorm GSoC student for the past two years (2017 and 2018), and will be offering a third opportunity this year (2019).

This is the 15th anniversary for the GSoC program, and it is always an excellent experience. The application process begins on February 25th. If you are interested in a mixture of computational biology, image processing, and machine learning, please contact us for more information.

COURTESY: Image from "One, Two, Three,....GSoC!" by Vipal Gupta

While GSoC is well-compensated opportunity to participate in DevoWorm, there are also less formal ways through which one can collaborate. One of these ways is through a conventional research pathway such as analyzing data, building a simulation, or curating a dataset. Another way to collaborate is to help create new types of educational content. We are particularly interested in creating virtual reality-based offerings in the near future. If you enjoy creating educational content, or simply enjoy learning, please get in touch!

Another new initiative is called DevoZoo. The DevoZoo site aggregates open datasets, methods, and techniques relevant to computational developmental biology and data science biology. We currently host open datasets for the following model organisms: C. elegans, Drosophila, Zebrafish, Ascidians, and Mouse. DevoZoo also hosts raw microscopy data in the form of movies for many of these model organisms as well as Spiders. As if this were not enough, we also try to engage learners and open scientists with artificial life models. The DevoZoo presents three: Morphozoans, developmental Braitenberg Vehicles, and Multicell Systems. The artificial life models in particular could use some further development. Check out the DevoZoo webpage or ask us if you would like to learn more.

Finally, you can participate by collaborating on a publication. The DevoWorm group has been featured in four publications in the past year. The OpenWorm article in the “Connectome to Behavior” special issue of Royal Society B provides a succinct description of the project and its current course. Some of our members served as editors and contributors to a special issue of BioSystems in honor of Dr. Lev Beloussov. This issue features 32 articles that provide a very broad and innovative look at the topic of morphogenesis. Our set of contributions (peer-reviewed papers) spanned from network models of the embryo to the developmental emergence of the connectome and quantitative approaches to organogenesis in the eye imaginal disc.

If you are interested in joining in on the discussion, we hold group meetings online every Monday at 9pm UTC. We are also starting to host hackathons on Fridays during the late morning/early afternoon North American time. Check out our scheduling page for more information. Hope to encounter you soon, and have a great month!

Posted by Bradly Alicea