September 30, 2018

Finding Your Inner Modeler (Part II)

Last year, I attended a workshop at the University of Illinois-Chicago called "Finding Your Inner Modeler". Sponsored by the NSF, FYIM is meant to bring together biologists and modelers and to foster collaborations between the two. There were many interesting talks over the course of two days, including plant biology, biochemical kinetics, and (of course) various types of computational and statistical model [1].

This year was the second installment of FYIM, and this time I was chosen for a platform presentation. The platform presentation (Process as Connectivity: models of interaction in cellular systems) involves a 40-minute discussion between the principal investigator and an expert modeler. For my talk, this expert modeler was Dr. Eric Deeds from the University of Kansas.

The talk features work with several collaborators, features work from the DevoWorm group. In the talk, I described the DevoWorm group as an example of data science biology [2]. As an affiliate of the OpenWorm Foundation [3], the DevoWorm group works with primary and secondary data, and produces secondary and tertiary open datasets that serve as material for publications, student projects, and the wider development/computational biology communities.

The core innovation introduced in this talk is the use of graph theory and complex networks to analyze the organizational structure of the embryonic phenotype. This work is now showcased in a new paper [4] and Github repository.

[1] One example is the Virtual Cell software project, which allows one to model and analyze representations of kinematics, kinetics, geometry, and network interactions at the cellular level.

[2] Alicea, B., Gordon, R., and Portegys, T.E. (2018). DevoWorm: data-theoretical synthesis of C. elegans development. bioRxiv, doi:10.1101/282004.
[3] Sarma, G.P., Lee, C-W., Portegys, T., Ghayoomie, V., Jacobs, T., Alicea, B., Cantarelli, M., Currie, M., Gerkin, R.C., Gingell, S., Gleeson, P., Gordon, R., Hasani, R.M., Idili, G., Khayrulin, S., Lung, D., Palyanov, A., Watts, M., Larson, S.D. (2018). OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans. Philosophical Transactions of the Royal Society B, 373, 20170382. doi:10.1098/rstb.2017.0382.

[4] Alicea, B. and Gordon R. (2018). Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis. BioSystems, doi:10.1016/j.biosystems.2018.09.009.

September 10, 2018

OpenWorm: Royal Society B special issue now live!

Worm images courtesy of the OpenWorm browser (Drs. Christian Grove and Padraig Gleeson)

Regular readers of this blog might recall that the OpenWorm Foundation spearheaded a workshop (From Connectome to Behavior) at the Royal Society (London) in January 2018. This workshop generated a lot of social media content and internal (to OpenWorm Slack) discussion of the presented topics.

Since then, the participants have been hard at work putting together a special issue (now live in Royal Society B) that presents in more detail what was discussed at the meeting. Lots of great papers on interesting topics ranging from network theory to movement models, and from foraging behavior to quantitative phenotyping.

Many of these papers feature ongoing work related to the OpenWorm Foundation, including the Geppetto, c302, and Sibernetic projects. There is also an OpenWorm overview paper that provides a current state of the initiative. Enjoy!

September 4, 2018

September: Movement Validation Month @ OpenWorm

Welcome to Movement Validation month! This content has been cross-posted from the OpenWorm Foundation blog and Chee-Wai Lee's blog.

Movement Motivations
The behavior of C. Elegans is partially captured by their movement characteristics. We develop and work with a number of tools for recording, characterizing, storing, analyzing, and sharing worm movement data.

Our goal is to eventually be able to compare the movement behavior of worms generated via simulation, against real instances of C. Elegans objectively and quantitatively.

The month of September 2018 will see some focus on this activity. We hope you will participate and do stuff that’s interesting to you!

Our Tools
The Database - We work with many others who record the movement activities of real live specimens of C. Elegans. That extended community has generously shared their data via our movement database tool (Github Repo here.)

A Common Data Format - To facilitate the sharing and exchange of data, we have developed the WCON format and accompanying libraries for manipulating data. We are working to support as many languages as we can. Our code repository can be found here.

Tools for Movement Analysis - The code base for our collection of tools to analyze movement is found here.

Activities for the Month
Planning - We have a range of active tool development issues we would like to review, and create tasks for. We expect to discuss this over the course of the first and second weeks. This should happen in our OpenWorm Slack channel #Movement-Analysis. We expect to also discuss new ideas/projects people might like to do, and lay out goals (e.g. integration of production code in OpenWorm’s Docker image.) We will kick this off with an Office Hours presentation in the OpenWorm Slack channel #office-hours on Sep 5th 4pm UTC.

Doing Interesting Stuff - Over the rest of the month, we will break off to work on individual tasks, have discussions, get questions answered. Activities can take many forms over a wide range of skill sets, technical or creative:

1. Create Blog/Art content.
2. Improve code/tool design.
3. Develop new features.
4. Explore new science/analysis techniques.

This will culminate in one or more hackathons over the last week of the month to round off the work. We also expect to create a number of open badges (see for tasks/educational activities that can be built around our results for wider community engagement.

Participate and Share

We encourage both new and experienced volunteers to participate! For newcomers, the best way to do so is filling out our volunteer application form.

After we have had a chance to look at your application, an invite will sent for you to join us in Slack. From there we can work with you to find stuff that you may be interested to work with, and people in the community you can get in touch with.

We look forward to hearing from you!