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

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

Mechanism Enrichment Lab SS2017

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"

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

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!)