Week 27--36 update
It's been a busy summer, so here's a consolidated post on what went on. I'm sure there's a lot more, but here are the salient points.
Conference: CNS 2024 in July
The annual conference for computational neuroscience, held by the Organization for Computational Neurosciences happens in July every year. It alternates between Europe and non-Europe locations to ensure that it's accessible to as much of the research community as possible. This year, it was organised in Natal, Brazil.
We had a tutorial on NeuroML and a couple of posters accepted at the conference. We also had a couple of posters accepted.
I'm also on the Board of Directors for CNS. As part of my duties, I organised a career development session this year on life "beyond academia" where we had a panel of people who had trained in academia but now had moved on to non-academic careers. The idea was to give students and early career researchers (ECRs) some idea of the "black box" that is industry, given that most of us have never worked in industry and therefore don't quite know much about it, which makes moving from academia to non-academic careers quite a daunting task.
The conference was great. It was nice to see a lot of our colleagues, who we hadn't seen in a while. Natal, and Brazil in general, was a brilliant place to go to too. We had numerous Caipirinhas, delicious food, and enjoyed the warm weather. The days were hectic as always---absorbing information non-stop from 9 o'clock till the end of the day at about six o'clock, but then heading over to the socials and staying out late too.
I had half a day extra or so after the conference, and a few of us drove to Praia de Pipa (Pipa Beach). It was absolutely beautiful. Since I was flying out in the evening and had already checked out of my hotel, I didn't get into the water, but we paddled around for quite a bit before having a scrumptious sea-food lunch.
NeuroML related
NeuroML is a standard and software ecosystem for biophysically detailed neuronal modelling.
Google Summer of Code
Google Summer of Code finished recently. Both Ioannis and Aditya passed their final evaluations, of course. They both did great work and we were very lucky to have them.
Aditya completed implementing the SWC to NeuroML converter. I reviewed his PR and made some tweaks before merging it in. The new converter is now part of the recent PyNeuroML 1.3.9 release. One can convert morphologies, for example from https://neuromorpho.org, using either the API or the command line tool:
pynml-swc2nml <swc file>
It runs a number of tests when loading the SWC file, and then validates the NeuroML once generated.
Now that we can export SWC files to NeuroML, we also can visualise them. We first convert them to NeuroML and use our NeuroML visualisation tools. This means that one can now do:
pynml-plotmorph -i <swc file>
One limitation to keep in mind with our handling of SWC is that each SWC file must only hold one neuron (cell), since this is what the standard that NeuroMorpho.org follows specifies.
Ioannis completed a number of tasks related to the Vispy viewer. Initially, our code was using a small number of meshes with many InstancedMesh objects because my understanding was that this was the most efficient way of going about it. Later though, we realised that instead, we could just use one Mesh that included all our individual shapes (spheres and cylinders) and that would be much more performant. So, I refactored our visualization code to use a single mesh. This really simplified a number of things, including lighting and "picking". We can also store the single mesh to a file so that it can be loaded in other analysis tools and visualisers like Paraview. It opens up a bunch of possibilities of what we can do with the morphology visualisation.
Our viewer can also be used in Jupyter notebooks now, although there's a bug when trying to use multiple visualisations in the same notebook that upstream is looking into.
Paper review responses
A lot of our time went in responding to reviews for our submission to E-Life. As part of the improvements suggested by the reviewers, one was to allow neuronal morphologies to be stored in separate files that could be "included" in other files. We added this functionality too. It had been a long open issue anyway, and this gave us the opportunity to finally implement it. It did require quite a few changes in our Java and Python stacks, but it's all complete now, and our modified paper has been re-submitted for review. The pre-print has also been updated to the latest version.
INCF/OCNS Software Working Group
The working group is ticking along. We hosted another session where Adam Tyson spoke to us about the software tools their group develops.
The Neuroinformatics Unit at the Sainsbury Wellcome Centre develops software tools for systems neuroscience.
We'll organise more sessions now that the summer holidays are over.
Some time off and other things
I took a few days off here and there to relax too; it wasn't all work. Since I'd already been away for the conference, I didn't have another holiday planned this summer, though. A few of our friends got married over the summer and we were lucky enough to be there to share their special day with them. We were also lucky enough to see Shania Twain and Stevie Nicks perform in London at the British Summertime Festival at Hyde Park. Obviously very moving, and great fun.
So, it's been a good couple of months.
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