Official and maintained implementation of the paper "Attention-Based Transformers for Instance Segmentation of Cells in Microstructures" [BIBM 2020].

An Artificial Life simulator for Investigating Noogenesis

Modular cloning simulation with the MoClo framework in Python

This repository contains the different resources derived or generated using ComPath

Integration of pathway-related information from Reactome in BEL

SigMat: A Classification Scheme for Gene Signature Matching

Genome scale metabolic model for Ogataea polymorpha NCYC495.

The FALCONET R package enables to build and visualise metabolic maps of GEM automatically with aid of cellDesigner 4.4 and R platform

Calibration of Rule-Based Models

Resources derived from PathMe

pyEnGNet: optimized reconstruction of gene co-expression networks using multi-GPU

Mechanism Enrichment Lab SS2017

Automatic rule-based modeling of metabolism, protein-protein interactions, and regulation of gene expression

This Github repository holds the supporting documents for the paper "Evaluation of search-enabled Pre-trained Large Language Models on retrieval tasks for the PubChem Database"

A repository containing abstract classes that Bio2BEL repos should extend to be adapted to the Compath environment

A rerun of the simulations of a Goldbeter paper

An application of the rational enrichment workflow to ten subgraphs from NeuroMMSig for the Human Brain Pharmacome project (https://pharmacome.scai.fraunhofer.de)

A probabilistic programing library empowered with jax to speed up large simulations (still in progress!)