Advancing precision medicine
We develop and disseminate a variety of software, the vast majority of which is open source.
Below are links to software developed or co-developed by Digital Metabolic Twin Centre members.
Software | Description | Website | Repository | Tracking Issues | Technical lead |
|---|---|---|---|---|---|
AutoDoc | AI assisted tool designed to turn repository structure, docstring coverage, and code context into a publishable documentation site. | https://autodoc.humanmetabolism.org/ | https://github.com/Digital-Metabolic-Twin-Centre/autodoc | https://github.com/Digital-Metabolic-Twin-Centre/autodoc/issues | Chidi Egwu |
COBRA Toolbox | Software suite for quantitative prediction of cellular and multicellular biochemical networks with constraint-based modelling. | https://opencobra.github.io/cobratoolbox/stable/index.html | https://github.com/opencobra/cobratoolbox | https://github.com/opencobra/cobratoolbox/issues | Farid Zare |
COBRA Tutorials | Collection of tutorials explaining how to use COBRA tools | https://opencobra.github.io/cobratoolbox/stable/tutorials/ | https://github.com/opencobra/COBRA.tutorials | https://github.com/opencobra/COBRA.tutorials/issues | Farid Zare |
ChatRD | An AI-assisted, fully transparent clinical decision support tool that delivers expert-level rare disease diagnosis suggestions from unstructured patient descriptions | https://chatrd.org/ | https://github.com/Unsaif/chatimd_interface | https://linear.app/chatimdrocks/team/CHA/active | Tim Hulshof |
Constructor | Open-source interface for metabolic network reaction-by-reaction curation and validation | https://constructor.humanmetabolism.org/ | https://github.com/opencobra/reconstructor | https://github.com/opencobra/reconstructor/issues | Saleh Alwer |
Headless Feedback | Secure feedback management backend for collecting, tracking, and managing user feedback through APIs and threaded conversations. | https://github.com/Digital-Metabolic-Twin-Centre/feedback | https://github.com/Digital-Metabolic-Twin-Centre/feedback | https://github.com/Digital-Metabolic-Twin-Centre/feedback/issues | Chidi Egwu |
Ethicalizer | AI-driven tool that drafts ethics application responses and performs structured reviews for consistency with study documents and regulatory standards. | https://ethicalizer.humanmetabolism.org | https://gitlab.com/recon4imd/ethicalizer-website | https://gitlab.com/recon4imd/ethicalizer-website/-/issues | Mukundhan Ramesh |
IMDhub | Data management platform that supports research in Inherited Metabolic Diseases (IMDs) | https://imdhub.org | https://gitlab.com/recon4imd/imdhub-frontend | https://gitlab.com/recon4imd/imdhub-frontend/-/issues | Chidi Egwu |
Keycloak | Privately hosted open source identity and access management solution | https://auth.imdhub.org | https://github.com/keycloak/keycloak | https://gitlab.com/recon4imd/king-issues-reporting/-/issues | Chidi Egwu |
KineticXPredictor | Open-source interface for data validation and generation of kinetic parameter predictions of enzyme-catalysed reactions using state of the art methods | https://kineticxpredictor.humanmetabolism.org/ | https://github.com/Digital-Metabolic-Twin-Centre/webKinPred | https://github.com/Digital-Metabolic-Twin-Centre/webKinPred/issues | Saleh Alwer |
OptArrow | OptArrow is an optimization integration engine designed to connect optimization clients and solver backends through a stable, high-performance transport layer. | https://optarrow.github.io/optArrow/ | https://github.com/optArrow/optArrow | https://github.com/optArrow/optArrow/issues | Farid Zare |
StereoMapper | StereoMapper is a stereochemistry-aware pipeline that compares molecular structures to identify relationships such as equivalent molecules, enantiomers, and diastereomers etc. It generates explicit stereochemical mappings between metabolites to support improved cross-resource reconciliation and annotation. | https://github.com/Digital-Metabolic-Twin-Centre/stereomapper | https://github.com/Digital-Metabolic-Twin-Centre/stereomapper | https://github.com/Digital-Metabolic-Twin-Centre/stereomapper/issues | Jack McGoldrick |
VMH | A comprehensive database of curated human and gut microbial metabolic models linking metabolism with disease and nutrition | https://delta.vmh.life/ | https://gitlab.com/recon4imd/vmh_revamped | https://linear.app/vmh-revamped/team/VMH/all | Sandeep Chenna |
Uptime Kuma | Privately hosted open source monitoring tool for tracking availability and website performance | https://monitor.imdhub.org | https://github.com/louislam/uptime-kuma | https://gitlab.com/recon4imd/king-issues-reporting/-/issues | Chidi Egwu |