OpenWorm Blog: August is ChannelWorm Month!

Content is being cross-posted from OpenWorm Foundation blog

August is ChannelWorm Month at OpenWorm!

As we make steady progress on our goal of building the world’s first detailed simulation of C. elegans, we’ve been brainstorming ways to systematically draw attention to each of the components of OpenWorm's platform.

Our scientific and outreach committees have decided that each month will be dedicated to a specific repository that will be designated “Project of the Month.”

This coming month (August 2018) will be dedicated to ChannelWorm, a repository aimed at constructing quantitative models of ion channel behavior.

Visit our Github repo and take a look for yourself: https://github.com/openworm/ChannelWorm
See also the Heroku App for extensive curated data on ion channels: https://chopen.herokuapp.com

WHAT ARE ION CHANNELS? Ion channels are pore-forming proteins which facilitate the movement of charged particles (ions) between the extracellular space and the cytoplasm.  All cells contain ion channels and play a central role in normal cellular function.  However, their role in the nervous system is much more significant.  In particular, ion channels in the nervous system mediate the generation of action potentials, the fundamental mechanism by which a network of neurons processes information. 

HOW THIS CONTRIBUTES TO THE OPENWORM VISION: Ion channels are the most granular level of detail in OpenWorm.  In other words, we abstract away the many complexities of intra-cellular function and treat the organism as an information processing system which uses electrical signals to mediate body movement.  Incorporating additional levels of biological detail is certainly a possibility but is not currently on our scientific roadmap.
BRIEF OVERVIEW OF CHANNELWORM: The aim of ChannelWorm is to build quantitative models of ion channel function.  To that end, we use the following workflow:

• Create a database of information about C. elegans ion channels specifying channel type and location in the nervous system (i.e. name of neuron) where the channel is expressed. 
• Identify relevant scientific papers which contain experimental recordings of ion channel behavior.
• Extract plots from the corresponding papers and add them to the database of ion channels. (This data is currently available at https://chopen.herokuapp.com)
• Digitize plots to extract data points.
• Use parameter fitting techniques to determine numerical values of parameters for quantitative models.
• Export ion channel models in the NeuroML (NML) format to be stored in PyOpenWorm.

SHARE IN THE COMMUNITY! We very much encourage both new and experienced volunteers to turn their attention to ChannelWorm and find areas that might be of interest to them.  The best way to get involved is to first fill out our volunteer application form.

In the meantime, we recommend taking a look at the Github repository for ChannelWorm for open issues the project is currently tackling.  Some of the issues are specifically marked as being appropriate for beginners.  We will add to this list over the next few weeks.

WHAT HAPPENS AFTER THE APPLICATION: After we look at your application, you’ll receive an invitation to join our workspace on Slack.  From there, you can contact other volunteers who can help find a project to match your skills and interests.

WHAT IF I’M NOT A PROGRAMMER? Even if you are not a computer programmer, you can still contribute! Here are some of the ways:

• Author a blog post: we’d love to have informative scientific blog posts on anything relevant to ion channel function and modeling. Submit a draft and we will host it on the OpenWorm blog.

• Literature search and data re-evaluation: we’d also like to support basic science in this area. If you have experience with conducting research, please get in touch!

• Create educational content: we can support educational initiatives such as the creation of digital badges and video tutorials. Pitch an idea and become part of the conversation!

• Something original: if you have an idea for something that no one has thought of, we’d love to hear your proposal!  Artwork, animations, popular scientific articles, etc. are all welcome.  

At the end of August, we’ll be organizing a distributed hackathon for the community to get together and work on tackling open items on our to-do list. We’ll announce more details towards the second week of August.

OW Science Committee is held at 3:00pm UTC, link provided in Slack #science channel. Hackathon Time/Date: TBA. Digital badges are located at badgelist.com/openworm.

We hope you can join us!

Please fill out our volunteer application form and contact us on Slack for more information!

ChannelWorm is currently building upon the work featured in this publication:

Gurkiewicz, M. and Korngreen, A. (2007). A Numerical Approach to Ion Channel Modelling Using Whole-Cell Voltage-Clamp Recordings and a Genetic Algorithm. PLoS Computation Biology, 3(8), e169. https://doi.org/10.1371/journal.pcbi.0030169