Agreed. I would like to see a list of computational neuroscience tools too. The SIG could play an important role in dissemination. There may be some overlap with INCF in that regard. Does anybody know?
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Of course you can. SIGs are just a bunch of people with common interests who “hang out” together to do different things that match common interests/goals. No prior knowledge of anything is required. Everyone is welcome. A primary goal of SIGs is to enable “knowledge exchange” 
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There already are lists of computational neuroscience tools. This list is a great one:
The primary issue with taking on the task of maintaining one is that it needs to remain up to date to be useful, and that of course requires an active team of “curators”. Aiding existing lists may be more useful (and less work)?
I have a slightly different idea where the SIG comes up with a checklist of best-practices for software and then members of the SIG use this checklist to review tools we use. We will then get in touch with the developers with suggestions on improving bits that didn’t pass our checklist and where possible, we’ll help them do it. I’m not aware of a group doing this at the moment.
Most Linux distributions have software guidelines, so we can derive ours from them. Fedora (RedHat based) has quite exhaustive guidelines here (since software in Fedora ends up in later releases of RedHat Enterprise Linux) for example:
https://docs.fedoraproject.org/en-US/packaging-guidelines/
https://docs.fedoraproject.org/en-US/packaging-guidelines/ReviewGuidelines/
A review is just a peer-review. Here’s one I’d submitted for Neuron as an example (this can all be done over GitHub):
https://bugzilla.redhat.com/show_bug.cgi?id=1662526
We should timebox things now. I’ll poke the OCNS Board about e-mailing all our members, and I’ll e-mail the mailing lists today.
The primary task at the moment is to set up our communication channels. So:
- for asynchronous discussion: is Neurostars OK, or do we want a mailing list (infra-sig@cnsorg.org can be set up easily for example)
- for synchronous discussion: what do people think of a Gitter channel? It’s open, public, and can manage large numbers of people chatting. (I’d like to avoid Slack: it’s proprietary, and is invite only).
This is something we need to look into. The hope is that someone that works with INCF will also work with us, and thus serve as a bridge between the two.
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The Center for Reproducible Biomedical Modeling have similar aims. PLOS Computational Biology are piloting them as part of manuscript reviews. https://reproduciblebiomodels.org/
https://biologue.plos.org/2020/05/05/improving-reproducibility-of-computational-models/
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Happy to hear that. Let me know the probable procedure.
Moreover, I forgot to mention my research interest: I’m passionate about time function in the brain and also neurofeedback (enhancement of this techniques by working on its feedback modalities and also finding neuromarkers for disorders like depression and anxiety, ADHD subtypes and …).
Thank you for gathering us together.
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I like your idea about reviewing tools based on best practices, and having developers looped in on how things can be improved. Alongside, a good part of our focus should also be directed towards publicizing existing tools, and educating the community about these. A listing such as the GitHub page (https://github.com/asoplata/open-computational-neuroscience-resources) is useful in what it does, but very limited in what if offers. For sure, we would require a lot of volunteers/curators to keep any of this upto date. So we would need to see how many signup to be a part of the SIG. I would be very keen to see the SIG help disseminate tools by conducting periodic events, such as bi-weekly online sessions where the authors of a particular tool have a short (~30 mins) presentation and demo about their tool. The recordings of these can then be made available on a OCNS SIG YouTube channel for even future users to get a quick glimpse of the various tools.
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Periodic meetings is certainly something we should try to do.
Just FYI: I mailed the comp-neuro, systems neuroscience, and connectionists mailing lists about the SIG today.
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Hi ! I’d like to join the group too.
My name is Amelie Aussel and I’m currently a postdoc at Boston University. I’ve been using Brian2 for Python for about 4 years (since I started my PhD in France), mainly to build Hodgkin-Huxley based neural networks. My current project aims at modeling attentional processes. I also have an engineering background.
I’d be very happy to learn more about the many tools available and how they were developed, and discuss potential new features
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Hi, I am Chaitree Baradkar. This looks like a great initiative. I am not sure how can I contribute though as I am not from computational neuroscience background. I have been working in Machine Learning for 4 years and very interested in interplay between machine learning and computational neuroscience. Please let me know if I can be of any help.
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Hello everyone,
Just an update: the OCNS VP has drafted up an e-mail to send out to all members, so hopefully it’ll be sent out next week. That’ll give all the members a chance to get in touch too, and then we can start planning the first meeting etc.
Hello all. I’m Robert. My Ph.D. was in mathematics, and I also have a master’s in computational biology and bioinformatics. I did postdoctoral work in computer science, neuroscience, and medical informatics. I’m currently biostatistics faculty.
I have been a developer for the NEURON simulator for about 9 years, and for the ModelDB repository for about 7.5 years. Feel free to contact me if you’d like to get involved in either of these projects.
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Hello everyone! I’m Brent, product owner of Arbor, a relatively new morphologically-detailed simulator. Arbor simulates single cell models, very large networks and everything in between, and was written from the ground up with with many-cpu and gpu architectures in mind.
We’re very interested in getting new users and user feedback on Arbor, and we’re very interested in open standards and integrations with other tools. This forum would be a good avenue for discussing the latter things in particular, so me and my team are curious to see this SIG develop!
Feel free to approach me directly if you’re interested in working with Arbor.
Cheers,
Brent
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Hi everyone! I’m Marcel, a research engineer in computational neuroscience at the Vision Institute / Sorbonne University in Paris. In the last couple of years my work has been mainly on the Brian simulator, but I am also very interested in more general questions around the use of software in research, reproducibility, etc. Would be happy to join the group!
PS: @sanjayankur31 I’m on the comp-neuro mailing list, but I did not see any message about the SIG. Maybe worth sending another one (apologies if I simply missed it)?
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Hello @mstimberg. I did send one out on the 4th of August to the systems-neuroscience, comp-neuro, and connectionist lists. They’re all moderated though, so perhaps it didn’t make it through the moderation process. (I don’t see it in the archives here: http://www.tnb.ua.ac.be/pipermail/comp-neuro/2020-August/thread.html)
It did go through to the other two, fortunately:
- https://groups.google.com/g/systems-neuroscience/c/vVA1suM4D1U
- https://mailman.srv.cs.cmu.edu/pipermail/connectionists/2020-August/034689.html
I’ll go see about posting to the comp-neuro list again.
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Hi Guys
I am Max and I am mostly working on in-vivo electrophysiology recordings and this year set up a standardised pipeline for training, recoding and stirring of ephys data for my lab. I was trained as an engineer/physicists and feel that neuroscience can profit immensely from moving to standardised tools and pipelines. I am also here due to selfish reasons because I feel that there is a more efficient way of doing analysis compared to how I have been doing it where I got the feeling of always reinventing the wheel.
I think it would be awesome to have a dedicated platform for discussion and fostering the community for software tools
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Hello all, I am Malin Sandström, Community Engagement Officer at INCF. Part of my work role is to interface with the INCF community and especially ’our’ computational neuroscientists, INCF SIGs and Working Groups. I have a background in Computational Neuroscience (as a PhD student with Anders Lansner at KTH) and have worked with the INCF Multiscale Modelling Taskforce when it was active.
I’d be happy to join this SIG and serve as a link between OCNS and INCF.
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I am Jim Perlewitz, the webmaster of Computational Neuroscience on the Web. If some of you are still looking for a listing of tools, you might check the relevant page on my site:
https://compneuroweb.com/sftwr.html
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Hi I am Daniele Avitabile from VU Amsterdam, and I would be very interested in taking part. I work on numerical methods for bifurcation analysis in PDEs and integro-differential equations, with applications in mathematical neuroscience.
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Thanks everyone! I think we’ve waited enough and have a core group of folks who are interested here. So, the first task is to brainstorm what kind of activities we want to take up. This is what I had in mind when I proposed the SIG. Please add/comment on them as necessary:
Improving awareness of current tools
The idea here is to provide a platform for developers of the many many tools to showcase their tools. So, an example activity would be regular (web?) sessions targeting end-users. These sessions will show how to install and use tools, where to get help and discuss issues, how to file bugs and feature requests.
Improving the maintenance of current tools
The idea here is to help developers improve their tools, and build communities around them to help maintain them in the long term. So, I was thinking of regular sessions targeting prospective contributors. These would encompass, for example:
- overview of the dev team and the dev pipeline (the contributing guidelines, PR review steps and so on),
- short and long term goals from a dev perspective,
- tasks where the dev team are looking for help,
- an example walk through of setting up the dev environment and perhaps making a contribution (a PR for example)
Reviewing tools
Another task that I thought would improve the maintenance + standard of current tools was for us to review them periodically. So,
- we come up with a review checklist of best practices in software development for Free/Open Source software
- members of the SIG review tools they’re interested in. (a good way to go is for dev teams to swap reviews. I.e, the team for software 1 reviews software 2 and vice versa.)
This helps different teams engage with each other and share their tips and tricks on improving tools, and it also helps devs identify areas for improvement. It’ll also help us form consensuses over best practices and so on—so the community will have a starting point when they look to contribute or start writing new tools.
The checklist will remain a living document, and perhaps each tool can be reviewed once annually (or at another frequency that can be decided on later).
Examples of checklists/reviews that we use while including software in NeuroFedora:
Here’s another example of a review: the one we did for Brian:
https://bugzilla.redhat.com/show_bug.cgi?id=1649127
You’ll see that we check quite a few things, and in lots of cases, we file issues and patches with the dev teams.
As @Shailesh_Appukuttan and other suggested, we can maintain a list of tools and their review reports as a useful source of information for the research community. It will also encourage dev teams to seek review.
Improving technical knowledge
This is simply us holding workshops to teach general technical skills/tools independent from tools. For example, on git, version control, different programming languages. While the tool related sessions would be short—an hour or two each—these can be multiple sessions over a few weeks if necessary.
There’s a lot of information out there on general computing already, so this is slightly low priority for me. I think if we work on improving the dev environments, that’ll improve general computing skills itself.
I can’t think of anything else at the moment. Thoughts/comments/additions/removals?
Hello all! I’m Joe Graham, and I am a NetPyNE developer (www.netpyne.org). NetPyNE (Network simulations using Python and NEURON) is an open-source Python package to facilitate the development, simulation, parallelization, analysis, and optimization of biological neuronal networks using the NEURON simulator. The NetPyNE source code is available on GitHub.
To make NetPyNE more accessible, we have released a (beta version) graphical user interface (GUI). The GUI is freely available at www.netpyne.org/gui with documentation here.
My background is in bioengineering and neuroscience, originally mostly experimental (spinal cord and locomotion) but now completely computational. My long-term goal is to develop neuro-musculo-skeletal models of motor control. I’d love to join a software interest group.
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