Repositories list

• in_silico_framework

  Public
  An in silico framework for multi-scale modeling and analysis of in vivo neuron-network mechanisms

  pythonneurosciencecomputational-neuroscience+ 5

  pythonneurosciencecomputational-neurosciencebrainin-silicomulti-compartment-modelingneuron-simulatormulti-scale-modeling

  Python

  •

  Apache License 2.0

  •11 fork•77 stars•1616 issues•11 pull request•Updated Apr 27, 2026Apr 27, 2026

• jobstats

  Public
  Jobstats is a job monitoring platform for CPU and GPU clusters

  Python

  •

  GNU General Public License v2.0

  •3535 forks•00 stars•00 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• torch-ddp-poc

  Public
  PyTorch script to reproduce the inconsistent initialization params DDP runtime error when running on a compute node with a faulty CUDA driver.

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 27, 2026Mar 27, 2026

• qos-viewer

  Public
  A formatting tool that uses the parsable raw column output from `scontrol show qos` command and generates a user friendly output.

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 24, 2026Mar 24, 2026

• submitit

  Public
  Python 3.8+ toolbox for submitting jobs to Slurm

  Python

  •

  MIT License

  •148148 forks•00 stars•00 issues•00 pull requests•Updated Feb 24, 2026Feb 24, 2026

• yoru

  Public
  YORU : Your Optimal Recognition Utility (https://www.science.org/doi/10.1126/sciadv.adw2109)

  Python

  •

  GNU Affero General Public License v3.0

  •66 forks•00 stars•00 issues•00 pull requests•Updated Feb 13, 2026Feb 13, 2026

• biscuit-app

  Public
  BISCUIT (BioImage Segmentation Comparison Utility and Interactive Tool) is an open-source platform for visually comparing state-of-the-art cell segmentation mod…

  Jupyter Notebook

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 2, 2026Jan 2, 2026

• gpujob-viewer

  Public
  SLURM GPU job performance monitoring tool.

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 20, 2025Nov 20, 2025

• conda-env-replicator

  Public
  A tool to help replicating existing conda environments in HPC cluster during OS migration.

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 18, 2025Nov 18, 2025

• OpenDay_PoseDemo

  Public
  React Demo with Movenet for Open Day Demonstration

  TypeScript

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 22, 2025Sep 22, 2025

• braid-opto-arena

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 16, 2025Sep 16, 2025

• spermull-bonn

  Public
  Hackaton project for a spermull frontend app.

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 9, 2025Sep 9, 2025

• reportseff

  Public
  Tabular seff

  Python

  •

  MIT License

  •1313 forks•00 stars•00 issues•00 pull requests•Updated Aug 27, 2025Aug 27, 2025

• in_silico_framework_hot_zone

  Public
  An in silico framework for multi-scale modeling and analysis of in vivo neuron-network mechanisms

  Python

  •

  GNU General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jun 6, 2025Jun 6, 2025

• amadeusgpt

  Public
  We turn natural language descriptions of behaviors into machine-executable code

  Python

  •

  Apache License 2.0

  •1313 forks•00 stars•00 issues•00 pull requests•Updated Jun 2, 2025Jun 2, 2025

• ood-amadeus-gpt

  Public
  Configure AmadeusGPT to launch using Open OnDemand

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 2, 2025Jun 2, 2025

• howto-cellpose

  Public
  a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •610610 forks•00 stars•00 issues•00 pull requests•Updated May 29, 2025May 29, 2025

• segment-anything-2

  Public
  The repository provides code for running inference with the Meta Segment Anything Model 2 (SAM 2), links for downloading the trained model checkpoints, and exam…

  Jupyter Notebook

  •

  Apache License 2.0

  •2.4k2.4k forks•00 stars•00 issues•00 pull requests•Updated May 28, 2025May 28, 2025

• jobstats-viewer

  Public
  JavaScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 20, 2025May 20, 2025

• isf-pandas-msgpack

  Public
  In-Silico-Framework Pandas Msgpack

  Python

  •

  Other

  •1919 forks•00 stars•00 issues•00 pull requests•Updated May 14, 2025May 14, 2025

• sleap

  Public
  A deep learning framework for multi-animal pose tracking.

  Python

  •

  Other

  •125125 forks•00 stars•00 issues•00 pull requests•Updated Apr 22, 2025Apr 22, 2025

• bc_ollama_jupyter

  Public
  Ollama + Jupyter OOD Application for SOMA at MPINB

  HTML

  •

  MIT License

  •33 forks•00 stars•00 issues•00 pull requests•Updated Mar 28, 2025Mar 28, 2025

• multi_gpu_training

  Public
  jupyter notebooks discussing multi GPU training and performance profiling

  Python

  •

  MIT License

  •5252 forks•00 stars•00 issues•00 pull requests•Updated Mar 6, 2025Mar 6, 2025

• Kaleido

  Public
  Fast static image export for web-based visualization libraries with zero dependencies

  HTML

  •

  MIT License

  •5757 forks•00 stars•00 issues•00 pull requests•Updated Feb 21, 2025Feb 21, 2025

• alphafold

  Public
  Open source code for AlphaFold 2.

  Python

  •

  Apache License 2.0

  •2.6k2.6k forks•00 stars•00 issues•00 pull requests•Updated Jan 29, 2025Jan 29, 2025

• msemalign

  Public
  serial section multibeam scanning electron microscopy volume alignment

  Python

  •

  GNU General Public License v3.0

  •00 forks•66 stars•00 issues•00 pull requests•Updated Dec 3, 2024Dec 3, 2024

• Augmentor

  Public
  Data augmentation for training 3D convolutional nets

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •77 forks•00 stars•00 issues•00 pull requests•Updated Oct 25, 2024Oct 25, 2024

• swipe-labeler

  Public
  Swipe Labeler is a Graphical User Interface based tool that allows rapid labeling of image data.

  Jupyter Notebook

  •77 forks•00 stars•00 issues•00 pull requests•Updated Oct 23, 2024Oct 23, 2024

• waterz

  Public
  Simple watershed and agglomeration library for affinity graphs.

  C++

  •2828 forks•00 stars•00 issues•00 pull requests•Updated Oct 9, 2024Oct 9, 2024

• sparseANNs

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 30, 2024Sep 30, 2024