What is Open Source Brain?
Open Source Brain (http://opensourcebrain.org) is a resource for sharing and collaboratively developing, visualizing and simulating computational models of neuronal systems. Open Source Brain promotes development of models in standard formats such as NeuroML, which ensures transparency, modularity, accessibility and cross-simulator portability.
Users of Open Source Brain can visualize their models, examine their properties and simulate them without ever leaving their web browser. Open Source Brain is developed by the Silver Lab at UCL as part of a Wellcome Trust funded project to encourage collaborative development of models in computational neuroscience.
A number of research groups and organisations from all over the world are actively developing and sharing their neuronal models on OSB. At present, Open Source Brain counts 1,273 members, 53 research groups and 219 projects.
What did MetaCell do for Open Source Brain?
MetaCell has worked with UCL staff at the Silver Lab to build OSB on top of the Geppetto platform (http://geppetto.org) over the span of 5 years. MetaCell has built major functionality of the OSB system. MetaCell's process involved working closely with the Silver Lab to analyse and formalise requirements, coordinating resources inside the Silver lab to orchestrate the development and engineering of the platform.
Development happened in multiple phases using an agile process and incremental rollout of new features. Major functionality built by MetaCell included features for collaborative modeling, web based visualization of computational neuroscience models, launching simulations and in-browser replay of simulation results.
What functionality did MetaCell implement?
- Collaborative model development
- Visualisation and exploration of neuronal model metadata
- 3D visualization of neuronal model morphologies
- Visualization and connectivity exploration of neuronal network models
- Neuronal model in browser simulation for single cells and networks
- Integration of external simulators
- Dynamic replay of recorded simulations
- And much more...
What were the results?
The creation of an interactive online tool – Open Source Brain – a hub for researchers to collaboratively build models, explore them, set parameters, run simulation and replay results without ever having to leave the web browser. The web-based nature of the platform is quite revolutionary in the field as normally complex toolchains must be installed locally by researchers in order to run simulations and explore their computational neuroscience models visually.
What can I do with Open Source Brain?
- Host neuroscience models online and get feedback from the community
- Visualise and explore model metadata in the browser
- Visualise model morphologies in beautiful state of the art 3D right in the browser
- Explore network models and visualize a variety of connectivity graphs
- Set model parameters and run simulations from the browser
- Run simulations with simulators that are the de-facto standard in academia
- Run simulations using selected supercomputing clusters
- Replay recorded simulations with dynamic visualization of single neurons and network dynamics
"We chose to work with MetaCell on the development of Open Source Brain because of their expertise in computational neuroscience and their skills in utilizing the latest web technologies to deliver reliable, high performance solutions. Having completed several fixed term contracts, where the requirements were scoped out and work was agreed in advance, I am pleased to confirm that they have consistently delivered elegant and robust software solutions that have exceeded our expectations."
