Systems biology tools made available to LLM agents.

Bioprocessing ontology that builds on IOF process patterns and BFO foundations, with domain-specific extensions that reference OBO ontology classes for measurement, sequencing, and biological entit…

This repository contains the data, Jupyter Notebooks and setup for a workshop on the toolbox ``refineGEMs`` and the workflow collection ``SPECIMEN``.

Provides a unified and flexible Java interface for mathematical optimization using multiple solver backends.

This repository will contain all the programs I will write throughout the Numerical Analysis course

A collection of tools for working with models in SBML format

Rationalized Discovery of Robust antiviral targets Using Genome-scale model Systems

The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Lang…

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.

Client library for the MPServer

Automated pipeline for strain-specific metabolic modeling based on a high-quality template model.

SBOannotator: A Python tool for the automated assignment of Systems Biology Onotology terms

The consensus GEM for Saccharomyces cerevisiae

Draft genome-scale metabolic model of Vibrio natriegens

Java library to read/write/create/manipulate/... CombineArchives

This repository contains data generated in the wet lab need for characterization and validation of strain specific GEMs

Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data

This repository contains all changes made to the strain specific models of Corynebacterium striatum.

refineGEMs is a python package inteded to help with the curation of genome-scale metabolic models (GEMS).

Accelerated BLAST compatible local sequence aligner.

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

A metabolic modeling workflow for communities of organisms in an nasal medium.

Python module to automatically curate the mass and charge assignments for metabolites in a metabolic model.

Easily usable JavaFx-based inSilico module for dynamic Systems Biology Markup Language (SBML) model simulation visualization. Provides an intuitive Graphical User Interface for dynamic processing b…

The BiGG Models website server

Registry of containerized biosimulation tools that support a standard command-line interface

memote – the genome-scale metabolic model test suite

pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.