Date: Feb 16, 2021 1700 UTC (Click here to see your local time).
+
Location (Zoom): (link no longer valid)
+
+
The abstract for the talk is below:
+
NeuroFedora is an initiative to provide a ready to use Fedora based Free/Open source software platform for neuroscience.
+We believe that similar to Free software, science should be free for all to use, share, modify, and study.
+The use of Free software also aids reproducibility, data sharing, and collaboration in the research community.
+By making the tools used in the scientific process easier to use, NeuroFedora aims to take a step to enable this ideal.
+In this session, I will talk about the deliverables of the NeuroFedora project and then go over the complete pipeline that we use to produce, test, and disseminate them.
+
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\ No newline at end of file
diff --git a/2021/02/07/dev-session-marcel-stimberg-brian-simulator.html b/2021/02/07/dev-session-marcel-stimberg-brian-simulator.html
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+ Dev session: Marcel Stimberg: Brian Simulator | INCF/OCNS Software WG
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Marcel Stimberg will introduce the Brian Simulator and discuss its development for the first developer session of the year.
+
+
Date: Feb 11, 2021 1700 UTC (Click here to see your local time).
+
Location (Zoom): (link no longer valid)
+
+
The abstract for the talk is below:
+
The Brian Simulator is a free, open-source simulator for spiking neural networks, written in Python.
+It provides researchers with the means to express any kind of neural model in mathematical notation and takes care of translating these model descriptions into efficient executable code.
+During this dev session I will first give a quick introduction to the simulator itself and its code generation mechanism.
+I will then walk through Brian’s code structure, our automatic systems for tests and documentation, and demonstrate how we work on its development.
+The Brian simulator welcome contributions on many levels, hopefully this dev session will give you an idea where to start.
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diff --git a/2021/02/07/wg-meeting-26-january-2021.html b/2021/02/07/wg-meeting-26-january-2021.html
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+ WG meeting 26 January 2021 | INCF/OCNS Software WG
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+
These are the meeting logs from the Software WG meeting that was held on 26th January 2021 at 1000 UTC using INCF’s BlueJeans account.
+The next progress meeting will be held in ~4 weeks time.
+For any clarifications and suggestions, please feel free to contact the current WG chairs at webmaster AT cnsorg DOT org.
Bluejeans, do we want to record? For SIG meetings, we agreed to use BlueJeans with recordings enabled on for members to refer to later.
+
Do we need breakout rooms? We agreed that breakout rooms may be needed during tutorials/developer sessions and so can be decided on a per-session basis. These are not expected to be needed at regular WG progress meetings.
In general, we agreed that the style of the guidelines should be to advise readers, not to force them to follow listed suggestions. Readers will choose the right practices that suit their project.
+
The first version will contain high level suggestions and will be targeted at beginners. More technical, detailed guidelines will be added later for advanced users.
+
For example, we will mention the presence of PEPs for Python and suggest ones that projects should follow. However, we will stress that not all PEPs are to be followed as rules. Rather, it is more important to adopt a set of relevant PEPs and apply them consistently in the project.
+
+
+
The guidelines will aid readers in choosing the right license for their project.
+
The guidelines will also help readers document their projects, for their users and potential contributors.
+
+
The WG discussed the possibility of taking on more teaching focussed tasks, for example, in collaboration with the Software Carpentry and/or Code Coderefinery projects.
+The INCF training space’s study tracks can also be used for such activities.
+
+
RSE societies & resources for development of research software⋆
+
These are other resources/societies that the WG’s tasks may overlap with:
Community poll to gather information on software development issues?
+
+
+
+
WG presence at INCF Assembly 2021 in April (roll call, enter your details)⋆
+
We will at at minimum hold a WG progress meeting at the INCF assembly.
+The current plan is to host more sessions/tutorials, depending on the members’ workloads/availability.
Caglar Cakan will introduce neurolib and discuss its development in this developer session.
+
+
Date: February 23, 2021. 1700 UTC/ 1800 Berlin time (Click here to see your local time).
+
Location (Zoom): (link no longer valid)
+
+
The abstract for the talk is below:
+
neurolib is a computational framework for whole-brain modelling written in Python.
+It provides a set of neural mass models that represent the average activity of a brain region on a mesoscopic scale.
+In a whole-brain network model, brain regions are connected with each other based on structural connectivity data, i.e. the connectome of the brain.
+neurolib can load structural and functional data sets, set up a whole-brain model, manage its parameters, simulate it, and organize its outputs for later analysis.
+The activity of each brain region can be converted into a simulated BOLD signal in order to calibrate the model to empirical data from functional magnetic resonance imaging (fMRI).
+Extensive model analysis is possible using a parameter exploration module, which allows to characterize the model’s behaviour given a set of changing parameters.
+An optimization module allows for fitting a model to multimodal empirical data using an evolutionary algorithm.
+Besides its included functionality, neurolib is designed to be extendable such that custom neural mass models can be implemented easily.
+neurolib offers a versatile platform for computational neuroscientists for prototyping models, managing large numerical experiments, studying the structure-function relationship of brain networks, and for in-silico optimization of whole-brain models.
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diff --git a/2021/02/26/dev-session-james-knight-thomas-nowotny-genn.html b/2021/02/26/dev-session-james-knight-thomas-nowotny-genn.html
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+ Dev session: James Knight, Thomas Nowotny: GeNN | INCF/OCNS Software WG
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James Knight and Thomas Nowotny will introduce the GeNN simulation environment and discuss its development in this dev session.
+
+
Date: March 9, 2021, 1700 UTC (Click here to see your local time).
+
Location (Zoom): (link no longer valid)
+
+
The abstract for the talk is below:
+
Large-scale numerical simulations of brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility.
+Similarly, spiking neural networks are also gaining traction in machine learning with the promise that neuromorphic hardware will eventually make them much more energy efficient than classical ANNs.
+In this dev session, we will present the GeNN (GPU-enhanced Neuronal Networks) framework [1], which aims to facilitate the use of graphics accelerators for computational models of large-scale spiking neuronal networks to address the challenge of efficient simulations.
+GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs through a flexible and extensible interface, which does not require in-depth technical knowledge from the users.
+GeNN was originally developed as a pure C++ and CUDA library but, subsequently, we have added a Python interface and OpenCL backend.
+The Python interface has enabled us to develop a PyNN [2] frontend and we are also working on a Keras-inspired frontend for spike-based machine learning [3].
+
In the session we will briefly cover the history and basic philosophy of GeNN and show some simple examples of how it is used and how it works inside.
+We will then talk in more depth about its development with a focus on testing for GPU dependent software and some of the further developments such as Brian2GeNN [4].
The next open community meeting for the working group will be at 1200 UTC on 12th May, 2021.
+The primary agenda for this meeting is to plan what tutorials the working group intends to undertake at CNS*2021 in July.
+Please join us via Zoom.
+
You can see the local time for the meeting using this link.
+On Linux style systems, you can also use this command in the terminal:
+
+date--date='TZ="UTC" 1200 this wednesday'
+
+
We hope to see you there.
+
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\ No newline at end of file
diff --git a/2021/06/04/dev-session-rick-gerkin-sciunit.html b/2021/06/04/dev-session-rick-gerkin-sciunit.html
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+ Dev session: Rick Gerkin: SciUnit | INCF/OCNS Software WG
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SciUnit is a discipline-agnostic framework for model validation, handling all of the testing workflow by using a implementation-independent interface to models.
+SciUnit also contains code for visualization of model results, and command line tools for incorporating testing into continuous integration workflows.
+
SciUnit is used in model validation in neuroscience via NeuronUnit, which implements an interface to several simulators and model description languages, handles test calculations according to domain standards, and enables automated construction of tests based on data from several major public data repositories.
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\ No newline at end of file
diff --git a/2021/06/09/software-wg-tutorials-at-cns-2021-online-bash-git-and-python.html b/2021/06/09/software-wg-tutorials-at-cns-2021-online-bash-git-and-python.html
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+ Software WG tutorials at CNS*2021 Online: Bash, Git, and Python | INCF/OCNS Software WG
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The Software Working Group is holding three beginner/intermediate level tutorials at the upcoming CNS*2021 Online conference. These will cover using the command line (Bash), using Git and GitHub, and development in the Python programming language.
+
To attend these, and other tutorials at CNS*2021, please register for the conference here.
The purpose of this tutorial is to introduce participants to the tools they need in order to comfortably and confidently work with a Unix/Linux command line terminal.
+Unlike graphical user interfaces, which are often self-explanatory or have obvious built-in help options, the purely text-based nature of a command line terminal can be intimidating and confusing to novice users.
+Yet, once mastered, the command line offers more flexibility and smoother workflows for many tasks, while being entirely irreplaceable for things such as cluster access.
+
In this tutorial, we aim to introduce participants to the concepts and tools they need to confidently operate within a Unix/Linux command line environment.
+In particular, the tutorial is developed for Bash (as per the title), which should cover most Linux and MacOS* use cases.
+We hope to provide participants with a firm understanding of the basics of using a shell, as well as an understanding of the advantages of working from a command line.
+
The tutorial is aimed not only at novices who have rarely or never used a command line, but also at occasional or even regular users of bash who seek to expand or refresh their repertoire of everyday commands and the kinds of quality-of-life tricks and shortcuts that are rarely covered on StackExchange questions.
+
* While MacOS has switched from bash to zsh as its default shell, zsh‘s operation is sufficiently similar for the purposes of this tutorial.
+
Prerequisites
+
A working copy of bash; participants on Linux and MacOS are all set.
+
Participants on Windows have several options to get hold of a bash environment without leaving familiar territory:
+
+
Install Git for Windows, which includes a Git Bash emulation with most of the standard tools you might expect in a Linux/Unix environment, plus of course Git.
+
Alternatively, enable WSL2 and install Ubuntu as a virtual machine hosted by Windows. Somewhat ironically, this requires at least one use of a command line terminal (though not bash); on the upside, the Linux-on-Windows experience can be a smooth and safe first step into Linux territory.
+
+
Topics
+
+
Basics to refer back to: Operating your bash shell (with key bindings and patience)
+
The grammar of a shell command line
+
Getting around: navigating within and beyond your computer: ~, pwd, cd, pushd/popd, ssh
+
Seeing what’s there: ls, globbing, and strategies for naming your files
Version control is a necessary skill that users writing any amount of code should possess.
+Git is a popular version control tool that is used ubiquitously in software development.
+
This hands-on session is aimed at beginners who have little or no experience with version control systems and Git.
+It will introduce the basics of version control and walk through a common daily Git workflow before moving on to show how Git is used for collaborative development on popular Git forges such as GitHub.
+Finally, it will show some advanced features of Git that aid in debugging code errors.
+
Prerequisites
+
The session is intended to be a hands-on session, so all attendees will be expected to run Git commands.
+A working installation of Git is, therefore, required for this session.
+We will use GitHub as our Git remote for forking and pull/merge requests.
+So a GitHub account will also be required.
+
+
Linux users can generally install Git from their default package manager:
Python is amongst the most widely used programming languages today, and is increasingly popular in the scientific domain.
+A large number of tools and simulators in use currently are either implemented in Python, or offer interfaces for their use via Python.
+Python programming is therefore a very sought after skill in the scientific community.
+
This tutorial is targeted towards people who have some experience with programming languages (e.g. MATLAB, C, C++, etc), but are relatively new to Python.
+It is structured to have you quickly up-and-running, giving you a feel of how things work in Python.
+We shall begin by demonstrating how to setup and manage virtual environments on your system, to help you keep multiple projects isolated.
+We’ll show you how to install Python packages in virtual environments and how to manage them.
+This will be followed by a quick overview of very basic Python constructs, leading finally to a neuroscience-themed project that will give you the opportunity to bring together various programming concepts with some hands-on practice.
+
Prerequisites
+
+
shell (participants on Linux and MacOS are all set; see below for Windows users)
+
Python 3.6.9 or higher (see below for info on installation)
+
+
Participants on Windows have several options to get hold of a shell environment without leaving familiar territory:
+
+
Install Git for Windows, which includes a Git Bash emulation with most of the standard tools you might expect in a Linux/Unix environment, plus of course Git.
+
Alternatively, enable WSL2 and install Ubuntu as a virtual machine hosted by Windows. This Linux-on-Windows experience can be a smooth and safe first step into Linux territory.
Just a quick note that the members of the SoftwareWG will be on vacation until the end of September.
+Our meetings, events, and initiatives will resume when everyone has returned.
+
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\ No newline at end of file
diff --git a/2021/10/28/wg-meeting-21-october-2021.html b/2021/10/28/wg-meeting-21-october-2021.html
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+ WG meeting 21 October 2021 | INCF/OCNS Software WG
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These are the meeting logs from the Software WG meeting that was held on 21st October 2021.
+The next progress meeting will be held in ~4 weeks time.
+For any clarifications and suggestions, please feel free to contact the current WG chairs at webmaster AT cnsorg DOT org.
We will begin working on the next round of Dev sessions: NetPyNE, NeuroML, tools from the NeuralEnsemble project.
+
We agreed that our “Dev sessions” do not necessarily have to be developer centric only.
+It is perfectly fine to also include user oriented information.
+We suggest components of both.
+We would like “Dev sessions” to remain informal where developers do not need to make formal presentations, and they should also remain different from traditional tutorials.
A large proportion of the meeting was dedicated to discussion around how we can ensure that software is correctly cited in research work to ensure that their authors get credit for their work.
+This is especially important in the current scientific climate where publications and citations are used as proxies to gauge performance.
ensuring that tools get enough visibility, for example by making sure they are listed on websites dedicated to collecting Open Source tools for neuroscience, e.g.: https://open-neuroscience.com/
+
also increasing visibility of research software using appropriate channels, e.g.: World Wide Neuro series for software: https://www.world-wide.org/Neuro/
adding RRIDs for research software and using them in publications: https://www.rrids.org/ .
+Some journals make it mandatory to cite software using RRIDs and then automatically link to the tool.
“To help promote the identification, discovery, and reuse of key research resources, we encourage you to include Research Resource Identifiers (RRIDs) within the Materials and Methods section to identify the model organisms, cells lines, antibodies, and tools (such as software or databases) you have used.”
Malin was also kind enough to help us set up a Dev session where Daniel S Katz and Neil Chue Hong from the Force11 Software Citation and Software Citation Implementation Working Groups will speak about these issues.
+Please keep an eye out on the website and the mailing list where this session will be announced.
In general, we agree that there’s limited grant funding for development and maintenance of research software.
+
+
+
The software development guidelines website will be set up as an initial empty template and individual guidelines added to it.
+This will make it easier to add information to it quickly and spread the work.
+
We agreed that the WG needs to work on active initiatives to make us more diverse.
+This will be discussed in detail in the next meeting so we can come up with ideas and action items to pursue.
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diff --git a/2021/11/01/dev-session-daniel-s-katz-neil-chue-hong-software-citation-principles.html b/2021/11/01/dev-session-daniel-s-katz-neil-chue-hong-software-citation-principles.html
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+ Dev session: Daniel S Katz, Neil Chue Hong: Software Citation Principles | INCF/OCNS Software WG
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Date: November 22, 2021, 1600 UTC (Click here to see your local time).
+
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+
The abstract for the talk is below:
+
Today, software is a key part of almost all research, and the development and
+maintenance of this software is done by human beings, often in academia. It’s
+essential that these activities be seen as a valued element of scholarly work
+so that the people who do it have career paths that encourage them to continue
+to do it. One means of accomplishing this is to use the existing scholarly
+citation system.
These are the meeting logs from the Software WG meeting that was held on 10th January, 2022.
+The next progress meeting will be held in February.
+For any clarifications and suggestions, please feel free to open a new ticket.
These are the meeting logs from the Software WG meeting that was held on 14th February, 2022.
+The next progress meeting will be held in March.
+For any clarifications and suggestions, please open a new ticket.
Tutorials at CNS*2022 have been announced, with the submission deadline on 15th of April.
+We discussed what tutorials we, the working group, can organise.
+
+
Malin will speak to Fleur about topics/syllabus for the tutorial.
+
An idea is to keep tutorials tool agnostic, and then feed into different simulator specific tutorials.
We need to figure out what it is we want to teach before we can come up with a syllabus and assign tasks.
+
Ideally, we want to find a sweet spot that avoids both generic computational neuroscience teaching and generic tool basics.
+
+
+
A repeat of last year’s tutorials may be acceptable.
+
+
Additionally:
+
+
We discussed setting up a resource that lists various tools and their use cases/features. The aim is to give users a quick way to find the appropriate tool for their task.
+
There’s the NeuroTech mind map, and we should add a tools section to the CompNeuro bits:
These are the meeting logs from the Software WG meeting that was held on 14th March, 2022.
+The next progress meeting will be held in April.
+For any clarifications and suggestions, please open a new ticket.
We have already received ~60 responses to the survey.
+The survey will be closed a couple of weeks after the next OCNS Newsletter has been sent out to allow the OCNS membership time to submit their responses.
+
The results will then be shared with the community.
Joe Graham will introduce NetPyNE and discuss its development in this dev session.
+
+
Date: April 4, 2022, 1600 UTC (Click here to see your local time).
+
+
+
+
+
+
+
+
The abstract for the talk is below:
+
NetPyNE is an open-source Python package to facilitate the development, parallel simulation, analysis, and optimization of biological neuronal networks using the NEURON simulator. The NetPyNE GUI is available from a variety of resources: Neuroscience Gateway Portal (NSG); Open Source Brain (OSB) ; Human Brain Project (HBP) EBRAINS; and the NIHSPARC initiative. The NetPyNE source code is available on GitHub. More information is available on the NetPyNE website.
+
During this dev session, I will give an overview of NetPyNE, go through an interactive demo using the NetPyNE GUI, describe my personal development workflow using virtual environments, and then go through two big dev projects I worked on: (1) documenting code inline and online using docstrings, Sphinx, Napoleon, and autodocsumm, and (2) separating and standardizing analysis and plotting.
+
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\ No newline at end of file
diff --git a/2022/04/21/wg-meeting-11-april-2022.html b/2022/04/21/wg-meeting-11-april-2022.html
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+ WG meeting 11 April 2022 | INCF/OCNS Software WG
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These are the meeting logs from the Software WG meeting that was held on 11th April, 2022.
+The next progress meeting will be held in May.
+For any clarifications and suggestions, please open a new ticket.
We don’t currently have a way of actively communicating with the WG membership because we don’t have a mailing list sort of thing where any announcements go straight to the members’ inboxes (we don’t even have all your e-mails because we decided not to use mailing lists when we started).
+
The worry, however, is that using GitHub tickets/discussions is passive—-i.e., folks do get notifications, but they still need to come up to the repository to engage.
+
The lack of something like a mailing list also means that we don’t have a way of actively informing the community (outside our membership) of our activities.
+
+
So:
+
+
Do we need a better way of keeping the wg membership in the loop? Are you satisfied with our current way of doing things?
+
Are fixed meeting slots working? (we’ve had a lower than usual turnout recently—-what can we do to help more of our members attend meetings?)
+
+
For communicating with the research community:
+
+
Should we send more updates to the already existing mailing lists (for example, should a note of our meeting be sent there?)
+
Or do we need a new mailing list/newsletter setup that folks can subscribe to? (in case our frequent posts to already existing mailing lists are thought to be an abuse of their policies?)
What steps can we take to encourage more folks to join the WG?
+
Are their incentives we can think of to encourage students to join us for example? Simpler tasks for them to do, for example? (see https://github.com/OCNS/SoftwareWG/issues/63 for example).
Possibility of standardising simulation generated output data (or facilitating conversion to NWB type formats to take advantage of the software/analysis ecosystem).
This ensures that they are early enough to not conflict with attendees’ travel arrangements.
+
Open ticket and let folks comment if it does not work for them.
+
+
+
Software WG will host tutorials on whatever tools/technologies the members are able to take up.
+
For stuff that’s not manageable by WG, we will invite developers and other research community members to deliver tutorials about their tools of choice.
+
We will probably need to set up a single registration form to collect e-mail addresses to send out links/information about the tutorials.
+
The form can include check boxes for each session so we have idea of per session interest/attendance.
Try to get in touch with training focussed communities such as NeuroMatch to recommend that they direct their “students” to these sessions as follow-up.
+
INCF work with Neuromatch, so should be able to get us in touch.
+
+
+
ACTION: need more volunteers to help us keep these going regularly.
+
Start new after summer vacations, near September.
+
Send announcements to lists.
+
Ask developers of new tools to get in touch.
+
Software WG members keep eye on publications on new software (JOSS etc.).
At the meeting in April, members of the working group discussed how we can make it easier for us to keep up with the activities of the working group.
+While we do use GitHub tickets and receive notifications from GitHub for these, given that a lot of working group members have many many projects/repositories on GitHub makes these notifications quite noisy.
+This makes it easy for us to miss notifications related to the working group’s repository.
This mailing list does not replace our GitHub tickets for discussion.
+GitHub tickets work very well for us because they allow us to organise and assign tasks to ourselves using all of GitHub’s features.
+Instead, this new mailing list is for announcements only.
+All announcements for events, or tickets that need input from working group members and the community will be sent here.
+This should ensure that everyone only has one well established channel of communication that needs to be monitored for working group updates.
+
Please subscribe to the mailing list (and join us!).
+
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\ No newline at end of file
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+ WG meeting 09 May 2022 | INCF/OCNS Software WG
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These are the meeting logs (and additional progress notes) from the Software WG meeting that was held on 09th May, 2022.
+The next progress meeting will be held in June.
+For any clarifications and suggestions, please open a new ticket.
Fasttrack: less priority as does not fit comp-neuro theme
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Other tools in the survey:
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Missingno + Pingouin + general analysis visualisation tools: maybe a tutorial later in the year
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MorphIO/MorphTool/NeuroM: session later in the year
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NWB ecosystem: do lots of user days themselves, we can do a specific tutorial later in the year
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NiPy suite: also better to do a specific tutorial later in the year
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PETlink: skip for now, not comp-neuro
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PyElectro: with NeuroML bits
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PyBIDS: maybe neuroimaging tutorial later
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PySpike: separate tutorial later in the year (correct typo elsewhere also: spike not spyke)
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Spiking circus: later (spike train analysis tutorial?)
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Allen tools, BMTK: full day tutorial later on
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BrainScaleS + Spinnaker: reach out for tutorial later (needs access to hardware)
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GENESIS?
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SciUnit/NeuronUnit: tutorial later
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STEPS: dedicated tutorial later
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ACTION: Ankur re-ping Thomas Nowotny about sending out the survey in next communication (check if it has been sent out yet), if no newsletter: being sent out in newsletter, so not required: DONE
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ACTION: Shailesh ping newsletter organisers (tentative newsletter in May): DONE
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ACTION: Ankur/Shailesh check if it was included in the INCF newsletter: was in issue 1: DONE
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ACTION: reach out to confirmed tutorials to ask for (WIP):
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Duration (give slot options)
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preferred time
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web page link for session
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whether they need us to set up zoom meetings for them (preferable that they handle this themselves)
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strongly suggest recording (especially if there isn’t a recording of their tutorial already): we will get these uploaded to the training space
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DEADLINE for confirmation: 20th (2 weeks)
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ACTION: end of next week (20th) send out e-mail to public lists about satellite tutorials (“save the date” with initial information)
These are the meeting logs (and additional progress notes) from the Software WG meeting that was held on 6th July, 2022.
+The next progress meeting will be held in August.
+For any clarifications and suggestions, please open a new ticket.
The primary agenda for the meeting was to discuss the software working group satellite tutorials.
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there were 256 registrants in total
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for each session, more than 85 people had indicated that they would attend, but average turn out was at about 10—20 for each session
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We discussed ideas for the next round of satellite tutorials to increase turn out:
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we could send out daily reminders with links during the tutorial days
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per session e-mails could also be sent out, but would be too much work to do manually (and error prone)
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needs to be automated in a way that e-mails don’t end up in spam: can be scripted using tool such as mailmerge
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also generate and attach an ICS calendar file to e-mails so attendees can add to their calendars
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we could require additional confirmation/cancellation before starting; this will give us better idea of who will attend, but won’t necessarily increase attendance
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we could have a low registration fee: this will filter out people who “just sign up”, but may not increase actual attendance
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could include registration waivers for students
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could make it free for INCF/OCNS members: encourage memberships
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people may not have known enough about tools to know what sessions to attend
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we could have a starting keynote on introduction to comp neuro, and then it gives attendees an idea of what is going to be featured during the tutorials
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it’ll be good to get a high profile speaker who would be happy to do this to increase attendance
we could also have a recording with a few minutes about each tool that’s featured in the satellite tutorials: teaser type video; so that people can watch a quick YouTube video and get an idea of all tutorials
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we could also have a set of slides based on a template showing the features of each tool
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these last few ideas require some extra work from participating tutors
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Spreading the sessions over weeks instead of days in a week may not necessarily increase attendance
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ACTION: Ankur create and send out feedback survey to registrants to gather information on what went well and why people were not able to attend; it’s important to understand if it was because people missed sessions because the information/calendar wasn’t clearly accessible so that we can improve on these
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does it make sense to do it after the conferences to build on the momentum of the conference: can be done, the next ones in ~6 months time will be independent of the conference
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we must push both INCF and OCNS to send out communications about the sessions
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we may repeat this again in 6 months, with improvements: “Simulator week”?
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Depends on how many software WG folks can commit to spending time on helping with organisation
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ACTION: Ankur e-mail all tutors with our discussion and improvements for the next iteration, asking if they’d be happy to re-do sessions if we repeat in 6 months.
These are the meeting logs (and additional progress notes) from the Software WG meeting that was held on 14th June, 2022.
+The next progress meeting will be held in July.
+For any clarifications and suggestions, please open a new ticket.
ACTION: Ankur send reminder to all tutors to record session: they’ll be uploaded to the INCF training space: DONE
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ACTION: Ankur set up simple feedback form up with a simple text box WIP
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ACTION: Ankur update schedule page with recordings as soon as they become available DONE
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ACTION: Ankur add links to OSBv2 repositories/workspaces on schedule page. DONE
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ACTION: Ankur send out reminder e-mail in week before tutorials DONE
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ACTION: Ankur check on slide for working group DONE
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ACTION: Ankur e-mail slide to tutors and request them to introduce the working group: ask WG members to do it for sessions they’d attend, need to get them in touch with tutors. INCOMPLETE
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ACTION: Ankur ask a few WG members to login to hackmd.io and make then co-owners so multiple people can edit the doc and Ankur is not the single point of contact/failure. DONE (added Shailesh)
These are the meeting logs (and additional progress notes) from the Software WG meeting that was held on 11th August, 2022.
+The next progress meeting will be held in September.
+For any clarifications and suggestions, please open a new ticket.
These are the meeting logs (and additional progress notes) from the Software WG meeting that was held on 19th September, 2022.
+The next progress meeting will be held in October.
+For any clarifications and suggestions, please open a new ticket.
Stewart: software showcase very useful (only one showcase this year)
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Showcases: excellent opportunity to quickly introduce tool to community
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Lower turnout at Melbourne
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Will be good to see how next year at Leipzig is attended
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People seem to prefer learning in their own time rather than attend live tutorials—-also because we’re spending more time on documentation and improved video tutorials
These are the meeting logs (and additional progress notes) from the Software WG meeting that was held on 10th October, 2022.
+The next progress meeting will be held in November.
+For any clarifications and suggestions, please open a new ticket.
Denis Alevi will introduce the Brian2CUDA tool in this session, and discuss its development. We will also have a discussion on GPU based simulation in neuroscience after the presentation.
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Date: Thursday, November 3, 2022, 1600 UTC (Click here to see your local time).
Graphics processing units (GPUs) are widely available and have been used with
+great success to accelerate scientific computing in the last decade. These
+advances, however, are often not available to researchers interested in
+simulating spiking neural networks, but lacking the technical knowledge to
+write the necessary low-level code. Writing low-level code is not necessary
+when using the popular Brian simulator, which provides a framework to generate
+efficient CPU code from high-level model definitions in Python. Here, we
+present Brian2CUDA, an open-source software that extends the Brian simulator
+with a GPU backend. Our implementation generates efficient code for the
+numerical integration of neuronal states and for the propagation of synaptic
+events on GPUs, making use of their massively parallel arithmetic capabilities.
+We benchmark the performance improvements of our software for several model
+types and find that it can accelerate simulations by up to three orders of
+magnitude compared to Brian’s CPU backend. Currently, Brian2CUDA is the only
+package that supports Brian’s full feature set on GPUs, including arbitrary
+neuron and synapse models, plasticity rules, and heterogeneous delays. When
+comparing its performance with Brian2GeNN, another GPU-based backend for the
+Brian simulator with fewer features, we find that Brian2CUDA gives comparable
+speedups, while being typically slower for small and faster for large networks.
+By combining the flexibility of the Brian simulator with the simulation speed
+of GPUs, Brian2CUDA enables researchers to efficiently simulate spiking neural
+networks with minimal effort and thereby makes the advancements of GPU
+computing available to a larger audience of neuroscientists.
Current SNNs studies frequently ignore dendrites, the thin membranous extensions of biological neurons that receive and preprocess nearly all synaptic inputs in the brain.
+However, decades of experimental and theoretical research suggest that dendrites possess compelling computational capabilities that greatly influence neuronal and circuit functions.
+Notably, standard point-neuron networks cannot adequately capture most hallmark dendritic properties.
+Meanwhile, biophysically detailed neuron models can be suboptimal for practical applications due to their complexity, and high computational cost.
+For this reason, we introduce Dendrify, a new theoretical framework combined with an open-source Python package (compatible with Brian2) that facilitates the development of bioinspired SNNs. Dendrify allows the creation of reduced compartmental neuron models with simplified yet biologically relevant dendritic and synaptic integrative properties.
+Such models strike a good balance between flexibility, performance, and biological accuracy, allowing us to explore dendritic contributions to network-level functions while paving the way for developing more realistic neuromorphic systems.
These are the meeting logs (and additional progress notes) from the Software WG meeting that was held on 16th January 2023.
+The next progress meeting will be held in February.
+For any clarifications and suggestions, please open a new ticket.
unsure if people are interested in live teaching sessions when they can go through documentation/videos/notebooks at their own pace when required
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if we do a repeat of last year, we will charge a small registration fee to filter out people that are registering for meetings but not necessarily attending: it will be a small fee, that can be waived without requiring documentation (similar to Neuromatch conferences)
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we will use something like Sched to ensure regular reminders are sent to registrants
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we will ask either INCF/OCNS to fund us, and they get whatever registration fees are collected in return
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alternatives
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software wg open day with a mix of user and dev focussed sessions, open to everyone to attend
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short software highlights some time before the conference to give people an idea of the tools (and what to expect from tutorials at CNS): open to everyone
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reproduction projects:
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tutors (tool devs) list some models that they would like reproduced in their simulators
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“students” work with them to reproduce them
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submit to rescience
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Issue: probably not doable in a day, so if done, will be a longer term project requiring multiple meetings
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internships
+- usually require some buy in from institutions, so not easy to do
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ACTION: Ankur put all this in a GitHub issue for discussion
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ACTION: Ankur e-mail tutors from last year to see what they think and what they are ready to do
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+ Software highlight: Kay Robbins: HED (Hierarchical Event Descriptors) | INCF/OCNS Software WG
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In human neuroimaging experiments, a record of what a participant experiences together with a clear understanding of the participant (task) intent are key to interpreting recorded brain dynamics.
+HED (Hierarchical Event Descriptors, https://www.hedtags.org) annotations and supporting infrastructure can provide human-understandable machine-actionable descriptions of events experienced during laboratory and/or real-world time series recordings.
+HED, which is well-integrated into BIDS (Brain Imaging Data Structure) has an ecosystem of tools supporting researchers at various stages including data acquisition, annotation, sharing, and analysis.
+This talk will describe HED principles, focusing on basic representations of an experiment and its design.
+Various tools in the HED ecosystem to support search, summary and analysis will be introduced and demonstrated.
+Finally, we’ll discuss how tool developers can leverage the HED infrastructure to build advanced analysis tools capable of automated analysis in support of machine learning.
+HED is an entirely open-source project, and the HED Working Group welcomes contributors and contributions.
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Papers and resources:
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Capturing the nature of events and event context using Hierarchical Event Descriptors (HED). NeuroImage. Link,
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Building FAIR functionality: Annotating events in time series data using Hierarchical Event Descriptors (HED). Neuroinformatics. Link.
These are the meeting logs (and additional progress notes) from the Software WG meeting that was held on 14th February 2023.
+The next progress meeting will be held in March.
+For any clarifications and suggestions, please open a new ticket.
(Shailesh): about having a new co-chair to replace myself. I have been finding it difficult in recent months to devote much time to the admin activities of the group, and it would therefore be useful to have someone else step-up and help manage the WG. I will naturally continue to contribute as a member of the WG. Forming the task forces (for the two ongoing tasks) was a nice example of how some of the workload could be distributed and managed.
These are the meeting logs (and additional progress notes) from the Software WG meeting that was held on 15th March 2023.
+The next progress meeting will be held in March.
+For any clarifications and suggestions, please open a new ticket.
Defer decision on tutorial/workshops until next meeting so we have information on submissions/scheduling
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Raise question of extra day/dedicated day for community development sessions (student/postdoc related, career, funding, DEI, general training that’s not specific to tools)
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ACTION: Ankur e-mail board to ask if there’s someplace we can feature the SoftwareWG
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ACTION: Ankur e-mail president to suggest Software WG be added to members meeting agenda
These are the meeting logs (and additional progress notes) from the Software WG meeting that was held on 21st April 2023.
+The next progress meeting will be held in October.
+For any clarifications and suggestions, please open a new ticket.
These are the meeting logs (and additional progress notes) from the Software WG meeting that was held on 09th October 2023.
+The next progress meeting will be held in November.
+For any clarifications and suggestions, please open a new ticket.
Hello!
+Sorry, the page you are looking for could not be found.
+Please use a search engine to find the information you are looking for.
+If you cannot still find it, please contact us.
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+ Ankur Sinha Articles | INCF/OCNS Software WG
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+ Denis Alevi will introduce the Brian2CUDA tool in this session, and discuss its development. We will also have a discussion on GPU based simulation in neuroscience after the presentation.
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+ The members of the SoftwareWG will be on vacation until the end of September. Our meetings, events, and initiatives will resume when everyone has returned.
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+ The Software Working Group is holding three beginner/intermediate level tutorials at the upcoming CNS*2021 Online conference. These will cover using the command line (Bash), using Git and GitHub, and development in the Python programming language.
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+ Marcel Stimberg will introduce the Brian Simulator and discuss its development for the first developer session of the year. Please read the full post for the Zoom link.
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+ Denis Alevi will introduce the Brian2CUDA tool in this session, and discuss its development. We will also have a discussion on GPU based simulation in neuroscience after the presentation.
+
+ The members of the SoftwareWG will be on vacation until the end of September. Our meetings, events, and initiatives will resume when everyone has returned.
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+ The Software Working Group is holding three beginner/intermediate level tutorials at the upcoming CNS*2021 Online conference. These will cover using the command line (Bash), using Git and GitHub, and development in the Python programming language.
+
+ Marcel Stimberg will introduce the Brian Simulator and discuss its development for the first developer session of the year. Please read the full post for the Zoom link.
+
+ Denis Alevi will introduce the Brian2CUDA tool in this session, and discuss its development. We will also have a discussion on GPU based simulation in neuroscience after the presentation.
+
+ The Software Working Group is holding three beginner/intermediate level tutorials at the upcoming CNS*2021 Online conference. These will cover using the command line (Bash), using Git and GitHub, and development in the Python programming language.
+
+ Marcel Stimberg will introduce the Brian Simulator and discuss its development for the first developer session of the year. Please read the full post for the Zoom link.
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+ The members of the SoftwareWG will be on vacation until the end of September. Our meetings, events, and initiatives will resume when everyone has returned.
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