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.

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

Calibration of Rule-Based Models

Phenorewire is a henotype-aware metabolomics network rewiring analysis pipeline: it identifies metabolites that change how they co-regulate across biological states.

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

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.

Resources derived from PathMe

LLM-assisted orchestration and evaluation workflow for genetic circuit design using Cello-based CAD pipelines.

Mechanism Enrichment Lab SS2017

Unsupervised clustering of common human diseases based on GWAS and WGS data, with a focus on Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

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