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

LLM based multi agent system for automated MorpheusML model generation from scientific papers using Model Context Protocol (MCP).

Genome scale metabolic model for Ogataea polymorpha NCYC495.

Convert proteomics data from ppm to cellular concentrations (g/gDCW) for enzyme constrained modeling

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

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

Calibration of Rule-Based Models

Resources derived from PathMe

Bioinformatics Dependencies Platform - A better way to manage your bioinformatics data sources, search and query across multiple bioinformatics databases, tooling. Properly version and reproduce your research, generate citation and data acessibility statement.

Public summary of my MSc thesis on metabolic flux prediction via Deep Learning

A Python simulator for modeling gene expression perturbations using a recursive, depth-limited path summation model.

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

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