2025: Week --37 update
- #Research, #Computational Neuroscience, #Fedora, #NeuroFedora, #Funding, #Grants, #Academic Life, #Post-doc career
The last time I wrote an update was, funnily enough, about a year ago. Also week 37. Clearly a lot has happened since then, but it won't all fit in this one post. I'll limit this post to the higher level details
Job/Research
Work has been extremely busy as always, and also busy enough where my backlog has been growing and growing. There is just so much to do.
Modelling
I have been working on a number of computational models.
We are close to having the full Human L2-3 Cortical Micro-circuit converted to NeuroML. The cells have all been standardised. This includes the ion channels, and the various morphologies and biophysics. What remains is replicating the network behaviour. This is not the hard bit. We have already done all that.
Another model I have been working on is the Golgi cell network that was previously developed in the lab (https://doi.org/10.1016/j.neuron.2021.03.027, model: https://github.com/sanjayankur31/GolgiCellNetwork). There are several predictions about how the Granule cells in the Cerebellum function, and the effect of Golgi cell inhibition on them that will be investigated using this model.
The Golgi cell network model also led to a CookieCutter template, but that merits its own post.
NeuroML
Since the last update, we have publish a NeuroML paper in E-Life after a few rounds of review (https://doi.org/10.7554/eLife.95135.3). This was a great achievement and it did take a lot of work.
Other than that, multiple new releases of the NeuroML libraries have been made. We continue to maintain them and push out improvements and fixes regularly on PyPi under the NeuroML PyPi organisation: https://pypi.org/org/neuroml/.
Google Summer of Code
We participated in Google Summer of Code (GSoC) again this year. Our candidate, Hengye, did an excellent job of converting various bits of the Macaque auditory thalamocortical model to NeuroML. The conversion also lives on GitHub, under the Open Source Brain organisation: https://github.com/OpenSourceBrain/Macaque_auditory_thalamocortical_model_data/tree/feat-neuroml-gsoc. We are going to continue working on this to standardise the full model.
Open Source Brain
Open Source Brain (OSB), an integrated web-platform for neuroscience, continues to tick along. We have made a number of maintenance updates and bug fixes. A new release is ready to be deployed to production after more testing.
We have worked on also integrating the E-BRAINS models into OSBv2. I need to test the E-BRAINS adapter implementation to prepare the PR for merging. This was blocked by some access issues, but they have now been ironed out and this can now proceed.
A paper on OSB is in the works, and should be published as a pre-print in the next coming months.
Grants and funding
This has taken a lot of time since the last update. We have applied for two Wellcome Discovery Awards, two Software Sustainability Institute grants, and are going to apply for several more.
So far, we have not been lucky enough to be accepted even though we were highly rated. Each Wellcome grant application takes about a month of dedicated work. Further, once triaged and accepted for interview, it is another two weeks of preparation. So, it has been a lot of work for no rewards at all.
There just seems to be quite a limited amount of funding, and the intense competition for them means that the success rate for most grant applications has dropped. So, more time spent on writing grants with fewer rewards. It is currently an even tougher time to be a researcher/academic than it already normally is.
Volunteering
I have managed to find time for volunteering, but with the increased work load, this time has reduced.
Software carpentries
I completed my Software Carpentry Instructor Training, and now am a certified instructor. The training was excellent. It pointed out lots of good practices for teaching newcomers/novices computational skills.
I will probably teach a session or two here at UCL this year and if time permits do a couple of classes for the Fedora classrooms.
Fedora
Package maintenance continues. So does the Fedora Join SIG.
We have shifted how we do things in NeuroFedora. We just had too many packages, and it was no longer clear if people were using these. So, we are now testing lots of Python packages directly from PyPi instead of packaging them. You can read more about this post: Packaging changes at NeuroFedora.
The Join SIG is doing well. Quite a few new people are now helping out with onboarding and the Welcome to Fedora process, which means we have so much more human resource at our disposal. There are also more discussions on how we can do better. So we expect tweaks and improvements to make the "Welcome to Fedora" process even better.
OCNS
I remain an elected member of the Board of Directors for the Organization for Computational Neuroscience. I could not get a Schengen visa to attend the annual conference in Florence, though (again). That was quite disappointing, but not a lot can be done about it. Europe is really popular in the summer, and there just aren't enough appointments for visa applications.
Summary
That will do for now. There is certainly a lot happening on multiple fronts, and I have been busy---too busy to write blog posts even. I am going to try to restart regular blog writing, but that's what I said last year before dropping out. So who knows.
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