OpenWorm Release 3 Accomplishments

May 2012 - November 2012

Papers

• In Silico Biology publication (Andrey Palyanov, Sergey Khayrulin, Alex Dibert, Stephen Larson)

Presentations

• Modeling C. Elegans: The Open Worm Project, U. Cambridge (Mike Vella)
• Building a Digital Lifeform through an Open Source project: ScienceOnline So Cal (Stephen Larson)
• The NeuroML C. Elegans Connectome, Neuroinformatics 2012 (poster) (Giovanni Idili & Matteo Cantarelli)
• Autonomous Neurodynamics 2012 (slides)(Stephen Larson)
• CNS 2012 (Padraig Gleeson)
• COMBINE 2012 (Padraig Gleeson)

Community building

• Hosted four office hours sessions
• Hosted two online journal clubs on a Whole Cell computational model and on a Large Scale Brain simulation
• Interactions via Twitter, G+, Tumblr, Mailing list

External write-ups / mentions

• Scientific American
• New Yorker
• Long Tail Science blog at U. Cambridge
• Alt 1040 (Spanish)
• i09

Epics

EPIC-1: As a user, I want to be able to mark synapses and have them integrated into the model

• Set up CATMAID server on Amazon EC2 (Gleb Kuznetsov)
• Loaded c. elegans EM data set (Gleb Kuznetsov, Steven Cook)
• Created user accounts (Stephen Larson)
• Created initial orientation tutorial (Steven Cook)
• Parsed existing synapse position data structure (Tim Busbice)
• Wrote Python scaffold to export from synapse position database (Sergey Khayrulin)

EPIC-2: As a developer, I want to launch the simulation engine on Amazon AWS

• Accomplished on an AWS instance (Can be activated on request) (Stephen Larson, Matteo Cantarelli)
• Created a script to pull together the simulation engine into a single package (Stephen Larson)

EPIC-3: As a user, I want to be able to see the body of the worm moving and changing color, driven by activity of the simulation engine (Simplified Worm)

• EPIC-7 was the prerequisite for this and just got accomplished
• NeuroML visualizer being produced for Open Source Brain will be a big help (Matteo Cantarelli)

EPIC-4: As a user, I want to be able to run a simulation that includes muscle cell physics as well as muscle cell membrane excitability

• SPH physics has been implemented with surface tension for both soft bodies and liquids (video2) (Andrey Palyanov, Sergey Khayrulin, Jinze Yu)
• Initial Integration between Pyramidal and the SPH code base has been achieved (Mike Vella)

EPIC-5: As a scientist, I want a detailed written summary of the physiology we intend to include in the model

• Spreadsheet compilation of data from WormAtlas and other sources (Tim Busbice, Stephen Larson)

EPIC-6: As a user, I want to see the optimized data matching the experimental results

• Parsed IGOR data contributed by the Francis Lab (Mike Vella, Denis Turutin)
• Built a NeuroML compatible muscle model (Padraig Gleeson, Mike Vella, Alex Dibert)
• Integrated model with Pyramidal (Alex Dibert, Mike Vella)
• Ran optimization codes for muscle cell against the parsed IGOR data (Mike Vella)

EPIC-7: As a user, I want to see a WebGL visualization of Smoothed Particle Hydrodynamics

• SPH algorithm development (test video)(Sergey Khayrulin, Andrey Palyanov)
• Websockets implementation (Gleb Kuznetsov, Matteo Cantarelli)
• Accomplished on the latest simulation engine demo (Matteo Cantarelli, Giovanni Idili)

Other accomplishments:

• Data collection and exploration of peptides, metabolites, genes (Tim Busbice)
• Further refinement of the c. elegans NeuroML connectome (Padraig Gleeson, Tim Busbice)
• Moved code to GitHub repository (Matteo Cantarelli, Giovanni Idili, Alex Dibert, Sergey Khayrulin)
• Website updates (Giovanni Idili)