Repositories list

• CellularSenescence

  Public
  Code associated with the paper "Cell-type resolved transcriptional network analysis of in vivo cellular senescence following injury", by Alda Sabalic, Victoria …

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 5, 2026Jun 5, 2026

• C_Elegans_Training

  Public
  Python

  •

  MIT License

  •22 forks•11 star•00 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• dispersion

  Public
  Simulation software corresponding to the paper "Self-generated hydrogel locally ejects cells from a biofilm", by Chou et al (2026)

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 3, 2026Apr 3, 2026

• CellBasedModels.jl

  Public
  Julia package for multicellular modeling

  Julia

  •

  MIT License

  •55 forks•2222 stars•66 issues•00 pull requests•Updated Mar 19, 2026Mar 19, 2026

• GastruloidRobustness

  Public
  TBD

  Python

  •

  MIT License

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

• BlastocystDevERK

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 25, 2026Feb 25, 2026

• qlivecell

  Public
  Python

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Feb 13, 2026Feb 13, 2026

• SignalingOscillators

  Public
  Code for (article information)

  Julia

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 2, 2026Feb 2, 2026

• GastruloidCompetition

  Public
  Python

  •

  MIT License

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

• Autoencoder_analysis

  Public
  Autoencoder analysis of bacterial growth

  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Dec 11, 2025Dec 11, 2025

• ENOMAD

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 4, 2025Dec 4, 2025

• SoftWired-Celegans

  Public
  Code for the paper "Soft-wired long-term memory in a natural recurrent neuronal network".

  Jupyter Notebook

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Nov 12, 2025Nov 12, 2025

• tilesegment

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 24, 2025Oct 24, 2025

• CellularSenescence_v0

  Public
  Code associated with the paper "Cell-type resolved transcriptional networks reveal molecular hallmarks of cellular senescence", by Alda Sabalic, Victoria Moisee…

  Jupyter Notebook

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

• memory-encoding-GRN

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 7, 2025Oct 7, 2025

• LaNMM

  Public
  Codes related to the paper 'Emergence of multifrequency activity in a laminar neural mass model'.

  Fortran

  •

  Creative Commons Zero v1.0 Universal

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

• multilayerAD

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 15, 2025Sep 15, 2025

• risk_paths

  Public
  JavaScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 13, 2025Sep 13, 2025

• networks

  Public
  JavaScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 13, 2025Sep 13, 2025

• multilayer_net

  Public
  JavaScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 13, 2025Sep 13, 2025

• network_paths

  Public
  JavaScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 13, 2025Sep 13, 2025

• Biofilm_PGA

  Public
  Julia

  •

  MIT License

  •55 forks•00 stars•00 issues•00 pull requests•Updated Jul 22, 2025Jul 22, 2025

• GastruloidRegistrationSizeProject

  Public
  Pipeline to analyse time-lapse images and perform non-linear registration.

  Python

  •00 forks•00 stars•33 issues•00 pull requests•Updated May 2, 2025May 2, 2025

• blood_gastruloids

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 25, 2025Apr 25, 2025

• AVEDifferentiation_helper

  Public
  Repository with helper functions for the analysis done in the AVEDifferentiation repository

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 15, 2024Jul 15, 2024

• Docker-single-cell-analysis

  Public
  Shell

  •22 forks•22 stars•00 issues•00 pull requests•Updated Apr 11, 2024Apr 11, 2024

• pyjiyama

  Public
  Python

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Feb 9, 2024Feb 9, 2024

• registration_sitk

  Public
  Script in SimpleITK for the registration of videos.

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 31, 2024Jan 31, 2024

• combo_networks

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Jan 31, 2024Jan 31, 2024

• single_networks

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Jan 31, 2024Jan 31, 2024