Mon 20 May 2024

Week 20 update

Posted by ankur in Life (1023 words, approximately a 5 minute read)

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Open Source Brain

Open Source Brain (OSB) is a web platform for neuroscientists. Version 1 was focussed on the sharing and archival of biophysically detailed models, standardised in NeuroML. There are a number of published models on the platform that one can visualise and study there already:

A screenshot of Open Source Brain version 1.

A screenshot of Open Source Brain version 1.

The newer version, version 2 takes it a step further. Its goal is to be a cloud based integrated research environment where people can store their data and their code in "workspaces", and work in the cloud, requesting as many resources as they need. This means that people no longer have to set up their own computers/lab servers---the platform will provide the computing infrastructure and the required tools in a web browser. OSBv2 also indexes a number of data sources to make it easier for researchers to find data and models, such as:

A screenshot of Open Source Brain version 2.

A screenshot of Open Source Brain version 2.

OSBv2 also integrates a number of web applications for users:

We're working on integrating as another data source now. This requires adding an adapter to the back end that understands the API so that it can use it to pull information from there to index. An initial version has already been implemented. We now need to test it.

OSBv2: dev environment

Since OSBv2 is cloud based (currently deployed on Google Cloud), it makes use of containers and Kubernetes (our software partners, MetaCell manage our infrastructure and a majority of the development/maintenance of OSB). The complete platform is also broken down into a number of services. To test changes and develop, therefore, one has to run a local deployment. We've documented the steps in our readme, and I've got a script to automate the various steps.

Of course, it's never that simple. While my script had worked the last time I had tinkered with OSBv2, it didn't work last week and I spent hours trying to figure out why. I need to continue with that this week too.

Software Working Group

The Software Working Group is an open community working group about all things software. It's shared by the International Neuroinformatics Co-ordinating Facility and the Organization for Computational Neuroscience. The idea is simply to have a community for exchange of ideas related to research/neuroscience software development. The working group is based on GitHub, and open to anyone at all.

Last week, we had a session on SpikeInterface where Pierre Yger presented the tool to the community. It was recorded, and the recordings should be on the INCF YouTube channel soon.


I worked on a few Neuro SIG packages--updates, Fails to Build From Source (FTBFS) issues, and so on. Not much to report in detail here.

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