23 projects
knowledge-chat
A framework to enable retrieval augmented generation (RAG) with knowledge graphs for chat applications.
cobra
COBRApy is a package for constraint-based modeling of metabolic networks.
equilibrator-cache
Cache application for compounds, reactions, and enzymes
optlang
Formulate optimization problems using sympy expressions and solve them using interfaces to third-party optimization software (e.g. GLPK).
taxpasta
TAXonomic Profile Aggregation and STAndardisation
equilibrator-assets
Generate cache assets from MetaNetX content.
equilibrator-api
Calculation of standard thermodynamic potentials of biochemical reactions
component-contribution
A method for estimating the standard reaction Gibbs energy of biochemical reactions
memote
the genome-scale metabolic model test suite
swiglpk
swiglpk - Simple swig bindings for the GNU Linear Programming Kit
depinfo
List any package's direct dependencies and their versions.
equilibrator-cheminfo
Light adapter classes around Open Babel, RDKit, and ChemAxon for the functionality needed in eQulibrator.
conifer-analysis
Post-process conifer output for downstream statistical analysis.
cobra-component-models
SQLAlchemy ORM and pydantic data models for SQL storage and JSON serialization of COBRA components such as reactions, compounds, and compartments.
metanetx-assets
Transform MetaNetX components information and load them into SQL storage.
metanetx-sdk
Parse and clean up information from MetaNetX (https://metanetx.org).
structurizr-python
A Python client package for the Structurizr cloud service and on-premises installation.
dfba
Object-oriented software for dynamic flux-balance simulations.
tag-spy
Identify the latest DD-DeCaF tag on a particular Docker image.
metanetx-post
Enrich the information coming from MetaNetX from additional sources.
searchstringparser
Parse a more general search syntax to conform with a particular SQL dialect.
sanger-sequencing
Semi-automated Sanger sequence analysis for transformation verification.
jinja2-ospath
A Jinja2 extension that introduces the template filters basename and dirname.
