Ankur Sinha "FranciscoD"

Hacked up a new script to update multiple #git repositories (or just the one) non-destructively. Doesn't handle all use cases, of course, but useful for a lot of general cases. It stashes any currently uncommitted work, and updates multiple branches---which can be specified as arguments.

https://github.com/sanjayankur31/100_dotfiles/blob/main/bin/git-update-repo.sh

#Linux #SoftwareDevelopment #Bash #ShellScript

Upgraded another machine to @fedora 44. Upgrade went well, no issues. #Qutebrowser on this machine wouldn't launch. Looks like an issue #QT and GPUs, since this one has an #Nvidia GPU. Workaround seems to be to play with an environment variable. This worked for me: `QTWEBENGINE_FORCE_USE_GBM=1 qutebrowser`

References:

https://github.com/qutebrowser/qutebrowser/issues/8927

#Linux #Fedora44

PSA for #Qutebrowser users (#Qt6 #Webengine based): we need to use this option to enable #kerberos support in `~/.config/qutebrowser/autoconfig.yaml` (for example, if you're a @fedora package maintainer and don't want to have to keep re-logging into Fedora websites):

```
qt.args:
global:
- auth-server-allowlist=*<domain>
```

Used to be `auth-server-whitelist` but changed at some point.

Reference: https://github.com/qutebrowser/qutebrowser/issues/8313

#FOSS #OpenSource

Moved to a new #Syncthing indicator #Gnome #extension that works well:

https://extensions.gnome.org/extension/1070/syncthing-indicator/

(The previous one I was using doesn't support the latest Gnome version)

#Fedora43 #Fedora #Linux #FOSS

Building detailed neuronal models is hard---#NeuroML helps, but there’s still a steep learning curve. We're investigating how #LLMs can be used to create natural language interfaces to improve accessibility:

- #RAG for NeuroML: learn from and query curated information sources
- iterative LLM assisted code/model generation: modelling, validation, and simulation

More details in the post:

https://ankursinha.in/2026/01/30/building-an-ai-assistant-for-computational-modelling-with-neuroml.html

#Neuroscience #ComputationalNeuroscience #AcademicChatter #LangChain

Note to self: use `pre-commit autoupdate` to update pre-commit repositories to their latest versions.

#pre-commit #Git #SoftwareDevelopment

@dzwiedziu

It does allow you to specify what project you want to add the new tasks to. But, please feel free to tweak it for your particular needs.

I am aware of the python libraries. There's `tasklib` that the taskwarrior upstream maintains (and is used by other task related tools I use like #vit) :

https://github.com/GothenburgBitFactory/tasklib

I thought these felt a bit overkill for this simple script, but they can certainly be used. Here I rely on plain parsing of the json export.

How do you manage your task list? If you're not happy with your current setup, give #Taskwarrior a try---it's a really lean, simple yet powerful and extensible tool for managing tasks. It also includes in-built syncing features so that you can use across multiple devices.

https://taskwarrior.org

Recently, I needed to split tasks into smaller tasks. I came up with a quick script:

https://ankursinha.in/2025/07/05/splitting-taskwarrior-tasks-to-sub-tasks.html

#Productivity #TaskTracking #GettingThingsDone

I created a #CookieCutter project template for #ComputationalModelling using #NeuroML

(You can use it for non NeuroML models too, or modify it for your own templates)

More information here:

https://ankursinha.in/2025/09/23/a-cookiecutter-template-to-quickstart-neuroml-modelling-projects.html

#ComputationalNeuroscience #Python #Neuroscience #AcademicChatter

Quick note: if you are using #Duplicity (even via #DejaDup), we're seeing a bug with the new version 3.0.6 where it doesn't recognise the encryption password. Reported upstream here:

https://gitlab.com/duplicity/duplicity/-/issues/901

So, do if you see this issue too, downgrade to 3.0.5. On @fedora , this would be `sudo dnf downgrade duplicity`.

#FOSS #Linux

Reminder to self: listing/opening "recent files" in #Vim : `:oldfiles` or `:History` with fzf.vim

https://stackoverflow.com/q/309723/375067

#fzf

I can't say this enough: time and time again the #NHS has come through to look after people, some that i know and loads that i don't. I know there are issues that we see amd read about, but i am grateful to all the people that work tirelesslely all hours to help strangers that come in for help. So, #ThankYouNHS . We are lucky to have you.

A new release of #PyNeuroML is available. Please update to get the latest fixes and features. #NeuroML #ComputationalModelling #ComputationalNeuroscience

```
pip install --upgrade pyneuroml
```

If you're seeing your #NEST simulator builds fail recently, it's because of a new #Cython release:

https://github.com/nest/nest-simulator/issues/3495

Workaround: fix `cython<3.1.0` for the moment (until new NEST releases with the fix are made)

#ComputationalNeuroscience #ComputationalModelling #Neuroscience #AcademicChatter

Generated a quick plot to see usage trends for Open Source Brain v2 (#OSBv2): an integrated #research platform for #neuroscience that indexes multiple model and data sources (#DANDI, #ModelDB, #Biomodels, #Github) and provides compute resources on the #cloud in "workspaces". It also includes specialist applications: #NWBExplorer for working with data in the NeuroData Without Borders (#NWB) format; #NetPyNE-UI for biophysically detailed #ComputationalModelling and a #JupyterLab environment.

Dendritic arbors structure memories: Synapses on different dendritic domains store distinct types of information

#Neuroscience #SynapticPlasticity #Learning #AcademicChatter

https://www.science.org/doi/10.1126/science.adx0640

Updated #TaskJuggler to the latest version in my #COPR repository for @fedora :

https://copr.fedorainfracloud.org/coprs/ankursinha/rubygem-taskjuggler/

TaskJuggler is an Open Source project management tool. It's full of great features---scheduling, resource allocation, gannt charts, reports and reporting, all of it. See the documentation here: https://taskjuggler.org/documentation.html

I use it to manage all my work projects, and it's a real boon. Give it a go!

#FOSS #ProjectManagement #AcademicChatter

Standardized measurements for monitoring and comparing multiphoton microscope systems | Nature Protocols:

https://www.nature.com/articles/s41596-024-01120-w

#Neuroscience #Microscopy #AcademicChatter #Multiphoton

If you're using a #QT #Webengine based browser like me (@qutebrowser or #Falkon), #Elsevier 's #ScienceDirect website may cause issues because they "only support the last 3 releases" of most browsers. Luckily, they use the user agent to detect the browser. So, a workaround is to use something like this, with a new enough version for the #Chrome version:

Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/6.8.2 Chrome/132.0.0.0 Safari/537.36

#AcademicChatter

Note to self: a #Kanban board is NOT a uni-directional pipeline!! It's OK for stuff to go from "WIP" back to "Ready" or "Backlog" #AcademicChatter #ProjectPlanning

#NeuroML is participating in #GSoC2025 again this year under @INCF . We're looking for people with some experience of #ComputationalNeuroscience to work on developing #standardised biophysically detailed computational models using #NeuroML #PyNN and #OpenSourceBrain.

Please spread the word, especially to students interested in modelling. We will help them learn the NeuroML ecosystem so they can use its standardised pipeline in their work.

https://docs.neuroml.org/NeuroMLOrg/OutreachTraining.html#google-summer-of-code

CC #AcademicChatter

#NeuroML supports all stages of the modelling life-cycle with a vast ecosystem of software tools: creating (#pyNeuroML, #neuroConstruct, #NEURON, #NetPyNE, #PyNN, #N2A), validating (pyNeuroML, #OMV, #SciUnit), visualising (pyNeuroML, #OSB, #NeuroML-DB), simulating (#NEURON, #NetPyNE, #Brian, #PyNN, #NEST, #MOOSE, #EDEN), model fitting/optimisation (#NeuroTune, #BluePyOpt, NetPyNE), sharing and reusing of models (OSB, NeuroML-DB, #NeuroMorpho.org). 7/x

A number of software tools are available for construction and simulation of models: #NEURON, #NetPyNE, #Brian, #PyNN, #NEST, #MOOSE, #EDEN etc. These have their own features, styles, programming interfaces (APIs). This is great but it also means that researchers need to learn each of these individually to use them. It also means that tools and models developed for one don’t necessarily work for others and need to be manually converted. This is often a non-trivial task and limits model reuse. 3/x

We are very happy to provide a consolidated update on the #NeuroML ecosystem in our @eLife paper, “The NeuroML ecosystem for standardized multi-scale modeling in neuroscience”: https://doi.org/10.7554/eLife.95135.3

#NeuroML is a standard and software ecosystem for data-driven biophysically detailed #ComputationalModelling endorsed by the @INCF and CoMBINE, and includes a large community of users and software developers.

#Neuroscience #ComputationalNeuroscience #ComputationalModelling 1/x

Accessing UCL VPN using OpenConnect on Linux systems
https://ankursinha.in/2024/11/25/accessing-ucl-vpn-using-openconnect-on-linux-systems.html
#UCL #VPN #AnyConnect #OpenConnect #Linux #Fedora

Update on what I did from weeks 27-36 this year:

https://ankursinha.in/2024/09/06/week-27-36-update.html

#NeuroML #ComputationalNeuroscience #Fedora #OpenSourceBrain #GoogleSummerOfCode #ComputationalModelling #AcademicChatter #FOSS #OpenScience

#Standardized #NeuroML model of the day (2024-09-11):

Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties, Hay et al 2011

See if on #OpenSourceBrain here:

https://v1.opensourcebrain.org/projects/l5bpyrcellhayetal2011

and on #GitHub here: https://github.com/OpenSourceBrain/L5bPyrCellHayEtAl2011

#ComputationalNeuroscience #ComputationalModelling #Neuroscience #Cortex #Layer5B #FAIR #OpenScience #AcademicChatter

Learn more about NeuroML here: https://docs.neuroml.org

The latest release of #PyNeuroML, 1.3.9, includes `pynml-swc2nml` for conversion of #SWC neuronal morphologies to #NeuroML. Also accessible via the API:

https://pyneuroml.readthedocs.io/en/development/pyneuroml.swc.html#pyneuroml.swc.ExportNML.convert_swc_to_neuroml

Install it using pip:

https://pypi.org/project/pyNeuroML/1.3.9/

#NeuroML #ComputationalNeuroscience #NeuronalModelling #FAIR #Neuroscience #AcademicChatter

Preserved neural dynamics across animals performing similar behaviour | Nature: https://www.nature.com/articles/s41586-023-06714-0

#Neuroscience #NeuralDynamics #MotorCortex

How's Friday going folks? I've been working on standardising the #Purkinje Cell model from Zang et al 2018 to #NeuroML. Exported the morphology already, on to the converting the individual Ion channels next.

You can use the converted bits from here: https://github.com/sanjayankur31/ZangEtAl2018/tree/development

#Neuroscience #ComputationalNeuroscience #Modelling #ComputationalModelling #Cerebellum

https://www.theguardian.com/education/2024/feb/23/daylight-robbery-two-in-five-uk-teachers-work-26-hours-for-free-each-week

‘Daylight robbery’: two in five UK teachers work 26 hours for free each week | Teachers' workload | The Guardian

#UK #Teaching #UKEducation

Version 1.2.0 of #pyNeuroML, the #Python package for working with #NeuroML models, has been released, brings more bugfixes and better support for #SBML

https://github.com/NeuroML/pyNeuroML/releases/tag/v1.2.0

#NeuroML #ComputationalNeuroscience #Neuroscience #Standardisation #FAIR

#Hojlund!! That's it! Get in! #ManchesterUnited

https://www.biorxiv.org/content/10.1101/2023.12.07.570537v1

The #NeuroML ecosystem for standardized multi-scale modeling in neuroscience

#ComputationalNeuroscience #Neuroscience #Modelling #ComputationalModelling #AcademicChatter

Very well said!

Shared from birdsite:

https://x.com/lorraine/status/1727651597142864364?s=20

“I’m tired Lorraine of having to justify my existence by the worth I bring to this country”

DrAmirKhanGP
responds to the immigration and NHS claims made by Nigel Farage in last night’s episode of
imacelebrity

#Lorraine #ImACeleb #Politics #UK #Immigration

I use pushd/popd quite a bit to navigate directories. I've also been using #fzf quite a bit with and without #vim. It's Alt + C mapping for the terminal is awesome. So I went ahead and created a new Alt + P mapping that does the same thing but uses #pushd instead of #cd. Here's the tweak to my `~/.bashrc` if anyone else wants to do it too:

https://github.com/sanjayankur31/100_dotfiles/commit/ae2a168ce18f9c849244e75a0fc94678f760dd0c

#bash #terminal #bashrc #terminal #cli

@fedora Org Chart: Now updated! https://communityblog.fedoraproject.org/fedora-org-chart-now-updated/ #OrgChart

We're looking for candidates to work with us at #GSoC2023 on conversion of published #ComputationalNeuroscience models into #NeuroML and #PyNN standard formats. Please spread the word, and get in touch!

https://neurostars.org/t/gsoc-2023-project-idea-21-1-open-brain-cross-simulator-large-scale-cortical-models-in-neuroml-and-pynn/24921

#INCF #Standardisation #FAIR #Neuroscience #Replication