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NAViFluX: A tool that facilitates analyses, refinement and visualizations of Genome Scale Metabolic Models.
Codebase for Flux REaction TArget Prioritization (Flux RETAP) code
An integrated visual environment for metabolic modeling methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock,…
PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
b.next nucleus open-source cell developer kit
CLEAN: a contrastive learning model for high-quality functional prediction of proteins
CheMixHub: Datasets and Benchmarks for Chemical Mixture Property Prediction
✏️ A versatile DNA sequence optimizer
A Granger Causality and Mediation Framework for Inferring Direct Causal Networks in Time-Series Proteomics
Biosynthesis knowledge base using web-crawlers and summerizer agents with RAG validators
A Python package for "classic" Constraint-Based Reconstruction and Analysis (COBRA) and the new COBRA with kinetics (COBRA-k). Link to documentation and tutorials:
StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
FluxGAT introduces a graph neural network (GNN) model designed to predict gene essentiality by utilising graphical representations derived from flux sampling data. This approach effectively bypasse…
A python implementation of FSEOF algorithm for metabolic engineering
FlashFry: The rapid CRISPR target site characterization tool
"Dimensionality-increasing" data visualization tool and interactive WebGL Jupyter widget built for single-cell data.
The Clustergrammer interactive Jupyter notebook widget
Python toolbox for multi-omics data mapping and analysis