August 27, 2018

Final Google Summer of Code presentations are live!

The final presentation for Google Summer of Code students in the Representational Brains and Phenotypes (Sam and Jim) and DevoWorm (Arnab) groups are now available! The summer went quite well: skills were taught, lessons were imparted, and computing projects were advanced. Here are the links to each project submission and summary video.

Sam's final talk (YouTube) and project repository (Github).

Arnab's final talk (YouTube) and project repository (Github).

Cheng-Hsun (Jim)'s final talk (YouTube) and project repo (Github).

Sam and Jim worked to advance the Contextual Geometric Structures framework (link 1, link 2) using different approaches. Both projects involved a mix of evolutionary algorithms, computational linguistics, hybrid modeling, and representational AI. The Google n-gram database was used to provide a source of training data.

Arnab worked on an XML framework for organizing embryo data at the cellular level. This not only provides the DevoWorm group with a link to more specific XML and simulation frameworks, but also moves us towards network-based representational models of the embryo.

August 20, 2018

Google Summer of Code Experience: Advice for Future Participants

As part of the Google Summer of Code program final project evaluations, I was asked to provide advice to future students and mentors in subsequent years. Here is the advice I gave:

Advice to Students:
I have three pieces of advice: do your research, reach outside of your comfort zone, and keep in communication with your mentor. Doing your research means that you continually reevaluate the big picture of your project. Start with a schematic of the workflow or project vision as outlined in your proposal. If you do not fully understand a set of issues (new algorithm, unfamiliar topical area), look them up or ask around.

Reaching outside of your comfort zone means you need to consider contingency plans for each step of your project in case something does not go as planned. If that requires a deep dive into a new method, then be willing to accommodate this into your project schedule. Do not spend too much time on learning new things, however, as the Summer moves pretty fast.

Finally, regular communication with your mentor on multiple channels helps with scheduling, project reevaluation, and keeping within expectations. I have used a combination of Slack, e-mail, and Google Meet with my mentees. Develop your own rhythm -- weekly Meet and e-mail updates can complement daily Slack communication. Don't be afraid to ask questions or take the initiative, but do be sure to coordinate this with your mentor's needs and expectations.

Advice to Mentors:
This year (2018), I mentored three students in two organizations. How did I do it? Weekly schedules, content management, and flexibility. Let's walk through this past summer to provide examples. The first thing I suggest is to mentor your students through the application process, so that their proposals align with your expectations and programmatic time constraints. During the community period, be sure to plan structured activities such as presentations to the broader community or access to background information on the organization and project.

As the coding period ramps up, be sure to set your weekly plan for communication. In my case, I scheduled a weekly meeting time (0.5 to 1 hour) for each student in Google Meet, set each student up in the appropriate Slack team, and prepared a weekly email newsletter (1-2 paragraphs) covering upcoming milestones. Also, be sure to utilize the link between Github issues and, as the latter serves to make outstanding tasks visually salient.

Our weekly meetings focused on four things:
1) what did you do this week/what will you do next week.
2) any outstanding issues/barriers to discuss in detail (or live demos).
3) upcoming milestones, planning for several weeks out.
4) review Waffle board issues, create new issues.
Finally, be flexible with respect to work style and meeting times. I had students from three different countries on two continents, and we often had to reschedule times. It is also important to let them adopt their own working rhythm (provided it is organized and within the bounds of the organization's needs). If they want to interact more or less on Slack, that is up to them. Just encourage them towards your community standards, and work from there. These things may seem like a lot to ask of a mentor, but I have found that it is worth it.

August 17, 2018

Google Summer of Code Experience: Afonso Pinto

The next Google Summer of Code project I want to highlight involves someone from one of my organizations (OpenWorm Foundation), but whom I did not mentor. Afonso Pinto (mentored by Giovanni Idili and Matteo Cantarelli) spent this summer working on the NWB (Neurodata without Borders): Explorer. Here is Afonso's final project presentation (YouTube) and work product (Github), in which he highlights GSoC-related contributions (a series of work sprints) to the project.

August 13, 2018

Google Summer of Code Experience: Arnab Banerjee

The "Road to GSoC" is paved with learning and fun!

As Organizations are finishing up Google Summer of Code for 2018, I would like to spend a few posts highlighting this Summer's projects at the OpenWorm Foundation and Orthogonal Research and Education Laboratory. In this post, I am reposting Arnab Banerjee's blog post on his experience with open-source development. He worked on a project called "Physics-based XML Model building for mosaic embryogenesis of Caenorhabditis elegans" (project repository, proposal presentation).

          I have recently completed a Google Summer of Code (GSoC) 2018 student project as part of the DevoWorm group and OpenWorm Foundation. Being a newcomer to the world of open source, it might seem a little presumptuous of me to write an article about the stages of becoming an experienced open source developer. But this article has resulted from personal experiences in the Open Source community, and so should be useful to open-source project newcomers and future Summer of Code students alike.

           I would like to begin by sharing a metaphor. Imagine a group of mountain climbers trying to get to the summit of a mountain.

           There are some who are doing it for the first time - the BEGINNERS. They find it difficult to get used to this activity and it is all new to them - from maintaining rations of water and oxygen cylinders to getting used to the physical exhaustion. Then there is the psychological factor - the will power and ability to keep going forward despite setbacks. The psychological and physical factors combine to make this period fraught with unexpected challenges. 

          Then there’s another group who have already done this a few times before. They are definitely more confident in their abilities, but not so good that they can lead an expedition to the top. They know how to maintain the rations like water and oxygen up to the correct levels because they have experienced it a few times before already. Willpower is also a little stronger than the beginners. These are the INTERMEDIATE climbers.

           Finally, the group leading the expedition - the EXPERIENCED - have done mountain climbing dozens of times. They lead the entire movement - from allocating resources to other climbers and deciding course of action in case of disaster. The remaining group looks upto them for directions when they are stuck. The rest of the group draws inspiration from them too, because they are the leaders of the movement. The EXPERIENCED have already been successful at the act of mountain climbing and learned from their failures - but they still keep doing it and training the others to reach higher and better positions.

          I’m sure by now you might have guessed that these grades of expertise parallel the world of open source development. As with mountain-climbing, I believe there are 3 distinct classes of developers in open source:

1. Beginner - A beginner struggles with basic concepts like version control systems. Also diving deep into the code base of an established open source organization seems difficult at first. As with mountain-climbing, the learning curve is steep. But once the initial effort is made, steady progress is seen.

2. Intermediate - Intermediates are ore comfortable with basic issues like using Git or version control system more generally. Intermediates can become familiar with the code base in a shorter amount of time, either due to organizational experience or experience with interpreting code more generally. In working at the intermediate level, time management becomes an important skill to build. Along with contributions to code base in a limited amount of time, other work like collaborating with teams and community bonding become important skills to master.

3. Experienced - The experienced are leaders of their organizations, and decide the overall strategy for these organizations. Experienced open-source contributors allocate new comers to issues to which beginners and intermediates will fit well. Other roles include conflict resolution and making sure that the organization functions with efficiency. Technical expertise (strong coding abilities) and a firm grip on domain-specific knowledge makes them natural leaders. 

          I believe after my GSoC journey, I have almost reached the end of the first 'BEGINNERS' phase. It was both an educational and rewarding experience. The initial weeks were tough to get used to because coding was one of many things I was simultaneously juggling - blog progress, mentor calls, community bonding, documentation, and domain-specific knowledge (learning about embryogenesis and neuroscience). Here is a visual aid in cartoon form (slideshow).

           Prior to my experience with GSoC, I couldn’t have pictured completing such a project with a neuroscience domain organization, but the massive support that I received from the larger OpenWorm Foundation community, Dr. Stephen Larson, and especially my mentor Dr. Bradly Alicea. Bradly introduced me to the DevoWorm Group, and was instrumental in whatever I have been able to achieve this summer. I learned from them that dozens of contributors sitting in 10 different time zones can collaborate to work on a project that has the potential to impact an entire community of researchers and developers.

CONCLUSION - Aiming for a moonshot project

          I hope to keep dedicating myself at least part-time to the cause of OpenWorm. The OpenWorm mantra is “building the world’s first worm-matrix, one line of code at a time”. The project that I worked on has given me a good foothold and introduction to the world of open source - especially the OpenWorm Foundation and DevoWorm Group. Now, there’s no turning back. I have decided that I will contribute to the OpenWorm Foundation by integrating my GSoC project with the Geppetto modeling environment.

          Technically, its a moonshot project and will not be easy to achieve. But HEY! I just participated in GOOGLE SUMMER OF CODE. As they say at Google: "aim for moonshots; its easier to make something 10X better than 10% better". That’s what I’ll aim for - a moonshot. Let’s see where it takes us - me and the OpenWorm Foundation. At worst, I end up contributing some useful code and learning something interesting. At best - well, we integrate DevoWorm with Geppetto!

Until we meet again!
Arnab Banerjee
Student Developer
Google Summer of Code 2018 - INCF (OpenWorm Foundation and DevoWorm Group)

August 1, 2018

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:
See also the Heroku App for extensive curated data on ion channels:

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
  • 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

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.