Welcome to our Google Summer of Code scholars for 2025!

 

The Orthogonal Research and Education Laboratory is pleased to welcome three students to the lab as Google Summer of Code (GSoC) scholars. Two (Lalith Baru and Jayadratha Gayen) will be joining the DevoWorm group and one (Vidhi Rohira) will be joining the Open-source Sustainability project.

Lalith and Jayadratha will be working on different aspects of our DevoGraph project (Github). Lalith’s successful project proposal is called “NDP-HNN: Modelling Neural Developmental Programs of C. elegans Using Growing Hypergraph Neural Networks”, while Jayadratha’s successful project proposal is called “DevoTG: Dynamic Graph Neural Networks for Modeling C. elegans Development”. Good luck to both of them! They will be working with the DevoWorm group and active in our weekly meetings. They will also be hosted by the OpenWorm Foundation and contributing to their mission.

Vidhi will be contributing to OREL's Open-source Sustainability project (Github) by working at the intersection of Reinforcement Learning and Agent-based Modeling. Vidhi’s successful project proposal is called “SustainHub: Adaptive Agent-Based Model for Open-Source Community Sustainability”. Check out her updates as part of the Saturday Morning NeuroSim meeting series.

We have also invited our unsuccessful candidates to join our Open-source interest group. We host this meeting every Friday at 12 Noon Eastern time, and cover promoting open-source practices, project development, and project management education.

Google Summer of Code 2024

 

Welcome to the new Google Summer of Code scholars for 2024! INCF is sponsoring four students for which I (Bradly Alicea) am acting as mentor: two students for the DevoWorm group (via the OpenWorm Foundation community) and two students for the Orthogonal Research and Education Laboratory. 

D-GNNs (sponsored by the DevoWorm group)

Congratulations to Pakhi Banchalia and Mehul Arora for being accepted to work on the Developmental Graph Neural Networks (D-GNNs) project. Pakhi will be working on incorporating Neural Developmental Programs (NDPs) into GNN models. Mehul will be working on hypergraph techniques for developmental lineage trees and embryogenesis [1]. Himanshu Chougule (Google Summer of Code scholar) is a co-mentor for this project.

Virtual Reality for Research and Open-source Sustainability (sponsored by the Orthogonal Research and Education Lab)

Congratulations to Sarrah Bastawala for being accepted to work on the Open-source Sustainability project [2]. Sarrah is incorporating Large Language Models (LLMs) into the collection of agent-based approaches for this project. Jesse Parent is a co-mentor for this project.

We also have two Open-source Development scholars for Summer 2024: Adama Koita and Shubham Soni. They will be participating in the Orthogonal Lab's open-source weekly meetings in addition to projects based around Virtual Reality and Open-source Sustainability, respectively. 

OpenWorm Annual Meeting 2023 (DevoWorm update)

It's that time again -- time for the OpenWorm Annual meeting. Below are the slides I presented on progress and the latest activities in the DevoWorm group. If anything looks interesting to you, and you would like to contribute, please let me know. Click on any slide to enlarge.

Google Summer of Code 2023

Welcome to the new Google Summer of Code scholars for 2023! INCF is sponsoring four students for which I (Bradly Alicea) am acting as mentor: two students for the DevoWorm group (via the OpenWorm Foundation community) and two students for the Orthogonal Research and Education Laboratory. These four students are pursuing three projects.

D-GNNs and DevoLearn (sponsored by the DevoWorm group)

Congratulations to Himanshu Chougule and Sushmanth Reddy Mereddy for being accepted to work on the Developmental Graph Neural Networks (D-GNNs) project. Sushmanth has been contributing to the DevoLearn platform for quite some time and will spend this summer working on improving the image segmentation to GNN embedding pipeline. Himanshu was a part of last Summer's GSoC cohort in the Orthogonal Research and Education Laboratory, working on the Open-source Sustainability project. His work resulted in developing Agent-based Model-Reinforcement Learning hybrid models. This year, he will be working on building Topological Data Analytic capabilities into the D-GNN pipeline. 

Mayukh Deb and Jiahang Li are co-mentors for this project.

Virtual Reality for Research and Open-source Sustainability (sponsored by the Orthogonal Research and Education Lab)

Congratulations to Vrushali Nandurkar and R.V. Rajagopalan for being accepted to work on the projects Virtual Reality for Research and Open-source Sustainability, respectively. Vrushali is enthusiastic about working on creating open-source virtual world assets for scientific research and educational initiatives. R.V. will be working on a continuation of the Open-source Sustainability project, helping to augment the existing models and web interface.

Jesse Parent is a co-mentor for both projects, while Brian McCorkle is a co-mentor for the Open-source Sustainability project. 

DevoLearn (Open-source) Maintenance and Evangelism

 2021 has been a busy year for the DevoLearn initiative. Not only has Mayukh Deb been busy maintaining and generating new versions of the DevoLearn pre-trained model, but I (Bradly Alicea) has been engaging in technology evangelism to advance awareness and involvement in the initiative.  The DevoLearn pre-trained model software (for C. elegans embryogenesis) is now at version 0.3.0, and has garnered 12 contributors making 165 commits (largely since January 2021). Our involvement in Google Summer of Code has bolstered many of these contributions. While our popularity is currently limited, we are trying to spread the word.

To that end, we have presented two versions of a promotional talk on using DevoLearn for facilitating Computational Developmental Biology research and education. The first presentation (DevoLearn: Engaging learners with Computational Developmental Biology) is a flash talk given to the OSF Education Un-conference on Open Scholarship Practices in Education Research, held in February. The second presentation was a longer (15-minute) presentation to the INCF Assembly (DevoLearn: a platform for open Developmental Data Science, Machine Learning, and Education), held in April.

As for developing the broader platform, Ujjwal Singh and I will be working this Summer to develop algorithms for colony morphogenesis and behavior in the Diatom genus Bacillaria. This will be added to the platform in a manner similar to the DevoLearn pre-trained model. In addition to the software development activities, Mayukh, myself, and Krishna Katyal have been the main contributors to the DevoWorm Onboarding Guide. Looking forward to an exciting future!

Update, 8/19:

All of this work has paid off! From the #devolearn Slack channel (OpenWorm Slack team).

Welcome, Summer of Coders (2020)!

The Google Summer of Code selections for 2020 have been made! Congratulations to Ujjwal Singh and Mayukh Deb, who will be joining the OpenWorm Foundation and the DevoWorm group for a summer of community engagement and code. Ujjwal's project is called OpenDevoCell Integration, and here is the description:

This project will focus on improving the data science and machine learning infrastructure of the DevoWorm group. The work will focus on an extension of the Summer of Code projects completed in 2017 and 2019. The first two aims are to improve upon the OpenDevoCell web interface and to improve segmentation techniques overall. While the OpenDevoCell interface has been implemented as a Heroku app, we would like to develop a dashboard for interpretation as well as tighter integration with DevoZoo's collection of open-source microscopy data. The third aim is to deploy the code package as a unified Python library, which would be done in concert with the improvement of segmentation techniques.The priority for this Summer is to improve the web interface both in terms of interactivity and functionality. Ideally, we would like to provide users with multiple options for analysis. This includes the ability to incorporate new forms of analysis as well as algorithms for new types of data. Currently, our web app is optimized for microscopy images acquired using the SPIM technique. However, we would also like to segment microscopy images acquired using a wide range of technologies. Feeding into this is the ability to segment and obtain features for the data in our DevoZoo. The ability to extract quantitative data from these movie images is key to conducting the comparative and time-series analysis. The development of a dashboard would ideally enable users to employ various machine learning and simulation techniques in one place.These improvements are meant to increase participation in our open science initiative and make sophisticated analytical techniques more accessible to students and potential collaborators alike. 

Mayukh's project is called Pre-trained Models for Developmental Neuroscience, and is based on previous work done in the group during the DevoWormML course [1]. This project is described thusly:

This project will center around building a pre-trained model for shapes and processes related to Developmental Biology and Neurobiology and extracted from image data. Our organization's Machine Learning interest group (DevoWormML) has published a blog post [1] on the advantages and need for pre-trained models in this area. In short, biological development is characterized by characteristic shapes, movements, changes in shape, and temporal processes that define important features. Pre-trained models are used in NLP and Deep Learning for the domains of sequence discovery in language processing (GPT-2) and bounding box methods for segmenting complex images (DeepLabv3). Models specialized for biology, however, do not exist. A suitable pre-trained model would greatly reduce the need for input data without sacrificing the ability to generalize to different contexts.Our main interest is in extracting spatiotemporal features from image data. We will focus on microscopy data such as that found in the DevoZoo or from more specialized sources [2]. For a typical pre-trained model, the network is pre-trained with non-random weights that approximate the generalized versions of the features we would like to discover. However, we are also interested in a semantic component, particularly the ability to incorporate elements such as meaning assigned to static knowledge (semantics) and multiple meanings for a single feature (polysemy). This will enable relational modeling and the mapping of segmented image data to lineage trees and taxonomies. This will enable relational modeling and the mapping of segmented image data to lineage trees and taxonomies. Our model, tentatively called DevLearningv1, should be applicable to a wide range of neural network and deep learning techniques.

Thanks to INCF for sponsoring our activities once again this year. Thanks also go to Vinay Varma, who will be providing support on all things mentorship this summer. Vinay was a GSoC student last summer, and will be sharing his wisdom with this year's students. I would also like to invite all those who applied for these projects to contribute to the Organization in some other way. Often, interaction with the community now can lead to additional opportunities down the road. 

As for the Orthogonal Research and Education Lab project (Contextual Neurodevelopmental Dynamics), we unfortunately did not get any slots this year. Thanks to Ankit Gupta and Jesse Parent for their excellent proposals. But I would like to continue pursuing the initiative as an open-source effort, hopefully leading to other avenues for development and funding. The same community interaction advice given for OpenWorm applies to Orthogonal Lab as well. 

We are going to be developing in the Meta-Brain repository on Github. Be sure to check out our Saturday Morning NeuroSim meetings for more information on this project (join our mailing list!). And register for the Neuromatch Summer School if you have not already, as it will be quite relevant to what we will be doing.

A sample of Saturday Morning NeuroSim (with a recap of the ICLR conference). Click to enlarge.

UPDATE (5/5): One of our regular meeting attendees (Devansh Batra) has also received a Google Summer of Code position with the OpenCV organization. Congrats!

NOTES:

[1] Alicea, B., Gordon, R., Kohrmann, A., Parent, J., and Varma, V. (2019). Pre-trained Machine Learning Models for Developmental Biology. The Node blog, October 29.

Work With Me in 2020

The Google Summer of Code (GSoC) is once again accepting applications from students to work on a range of programming-oriented projects over the Summer of 2020. Orthogonal Research and Education Laboratory and the OpenWorm Foundation have contributed a number of projects to the list. Here are links to the project descriptions (login to INCF Neurostars required):

DevoWorm Group:

Project #14: Pre-trained models for Developmental Neuroscience

Project  #15: OpenDevoCell Integration

Orthogonal Laboratory:

Project #16: Contextual Neurodevelopmental Dynamics

I am the contact person for both the Orthogonal Laboratory and DevoWorm Group projects. If you have any questions about the application process or want to have be review your application before submission, please feel free do so. According to this year's schedule, the proposal deadline is March 31, and the community bonding period starts on April 27. Stay tuned!

Join us once again on the "Road to GSoC"!

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!

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!

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.

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 Waffle.io, 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.

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.

 

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)

Ready to Start to Google Summer of Code 2018!

Currently at the red roadhouse on the left-hand side of the road.

On your mark, get set, go! We are quickly traveling down the Google Summer of Code (GSoC) road! First, a welcome to the three students I will be mentoring: Arnab Banerjee (Pune University), Sam Felder (University of Illinois Urbana-Champaign), and Cheng-Hsun Hsueh (National Yang-Ming University).

Arnab will be working within the OpenWorm Foundation on "Physics-based XML Model-building for the Mosaic Embryo", while Sam and Cheng-Hsun will be working on "Contextual Geometric Structures of Cultural Behavior ".

This tweet says it all. Check in on the DevoWorm and Representational Brains and Phenotypes group activities throughout the Summer for updates.

We are currently in the Community Period, which lasts until the coding period begins (May 14). Towards the end of Community Period, each student will present a 15-20 minute presentation on their accepted proposal, including additional insights on what will make their project successful. Stay tuned! 

Google Summer of Code Application Deadline is Approaching!

A quick reminder as to what is near. Nothing to fear -- except that applications for Google Summer of Code 2018 are due on March 27th (in a little more than a week). Thanks to all the applicants to our projects so far. I am the mentor for the following projects (all sponsored by INCF):

Contextual Geometric Structures (Project 8)

Towards a k-D embryo (Project 10.2)

Physics-based XML (Project 10.1)

Apply to work work either the Orthogonal Research Lab community (Project 8) or the OpenWorm Foundation community (Projects 10.1, 10.2). Please contact me (Bradly Alicea) for more information.

There are several other projects hosted by the OpenWorm Foundation that combine work with Neuroscientific data and Computational Modeling. These include:

Advanced Neuron Dynamics in WormSim (Project 10.3)

Mobile application to explore C. elegans nervous system dynamics (Project 10.4)

Add support for Neurodata Without Borders 2.0 to Geppetto (Project 10.5)

All three of these projects are based in the OpenWorm Foundation community, and are lead by mentors Matteo Cantarelli, Giovanni Idili, and Stephen Larson.

Work With Me, the Orthogonal Laboratory, and the OpenWorm Foundation This Summer!

The Google Summer of Code (GSoC) is once again accepting applications from students to work on a range of programming-oriented projects over the Summer of 2018. Orthogonal Laboratory and the OpenWorm Foundation have contributed a number of projects to the list. Here are links to the project descriptions (login required):

Orthogonal Laboratory:

Project #8: Contextual Geometric Representations of Cultural Behavior

DevoWorm Group:

Project #10.1: Physics-based XML Model-building for the Mosaic Embryo

Project #10.2: Digital Morphogenesis: towards a k-D embryo

OpenWorm Foundation:

Project #10.3: Advanced Neuron Dynamics in WormSim

Project #10.4: Mobile application to explore C. elegans nervous system dynamics

Project #10.5: Add support for Neurodata Without Borders 2.0 to Geppetto

I am the contact person for the Orthogonal Laboratory and DevoWorm Group projects, and Matteo Cantarelli is the contact person for the other projects. If you have any questions about the application process or want to have be review your application before submission, please feel free do so. The deadline for application submission is tentatively in late March/early April. Stay tuned!

Join us on "The Road to GSoC"!