Repositories list

• KinRDF

  Public
  Conversion of kinetic data to an RDF model, compatible with WikiPathways PathWayModels

  Python

  •

  MIT License

  •1•0•6•0•Updated Aug 4, 2025Aug 4, 2025

• BridgeDbR

  Public
  BIoconductor R package for BridgeDb

  R

  •8•0•0•0•Updated Aug 2, 2025Aug 2, 2025

• INTOXICOM_Workshop_2

  Public
  TeX

  •

  Creative Commons Attribution 4.0 International

  •1•0•0•0•Updated Jun 24, 2025Jun 24, 2025

• sparql-examples

  Public
  A set of SPARQL examples that are used in different TGX resources

  HTML

  •

  Other

  •22•0•0•0•Updated Jun 20, 2025Jun 20, 2025

• sparql-examples-utils

  Public
  A tool to maintain and test your SPARQL examples

  Java

  •

  Other

  •22•0•0•0•Updated Apr 5, 2025Apr 5, 2025

• PETcourseMetabolomics

  Public
  GitHub repository for the analysis of metabolomics data

  Other

  •14•0•0•0•Updated Mar 11, 2025Mar 11, 2025

• Transcriptomics_Metabolomics_Analysis

  Public
  Automated workflow for Omics integration on IBDs data

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •2•2•0•0•Updated Feb 20, 2025Feb 20, 2025

• WikiPathwaysInteractions

  Public
  Jupyter Notebook SPARQL queries against the WikiPathways SPARQL Endpoint

  Jupyter Notebook

  •4•0•0•0•Updated Jan 18, 2025Jan 18, 2025

• imd-pathway-curation

  Public
  WikiPathways Curation for just the IMD pathways

  Java

  •1•0•2•0•Updated Dec 22, 2024Dec 22, 2024

• bigcat-um.github.io

  Public
  Repository to hold the central sitemap.zml

  Creative Commons Zero v1.0 Universal

  •0•0•0•0•Updated Nov 30, 2024Nov 30, 2024

• INTOXICOM_Workshop_1

  Public
  TeX

  •

  Creative Commons Attribution 4.0 International

  •6•0•0•0•Updated Nov 16, 2024Nov 16, 2024

• PRA3006-SPARQL

  Public
  This ebook has information about life science databases, their SPARQL endpoints, what information they hold, what data models they use, and how to query those.

  sparqlwikidatawikipathways+ 3life-scienceschemblaop-wiki

  Groovy

  •

  Other

  •0•1•2•0•Updated Nov 4, 2024Nov 4, 2024

• MSB1015-Parallel-Programming

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Sep 26, 2024Sep 26, 2024

• PSVD-transcriptomics-workflow

  Public
  Creative Commons Zero v1.0 Universal

  •0•0•0•0•Updated Jun 24, 2024Jun 24, 2024

• ChEMBL-SPARQL-Queries

  Public
  SPARQL queries for the examples panel in https://chemblmirror.rdf.bigcat-bioinformatics.org

  MIT License

  •0•0•0•0•Updated Feb 26, 2024Feb 26, 2024

• IEMPathwayAnalysis

  Public
  R

  •

  MIT License

  •0•0•1•0•Updated Dec 21, 2023Dec 21, 2023

• BridgeDbConfig

  Public
  Java

  •

  Apache License 2.0

  •0•1•2•0•Updated Dec 6, 2023Dec 6, 2023

• pils

  Public
  Programming In the Life Sciences

  javascriptapiwikidata+ 1d3js

  HTML

  •

  Creative Commons Attribution Share Alike 4.0 International

  •6•12•4•0•Updated Nov 17, 2023Nov 17, 2023

• BiGCaT-Teaching

  Public
  Department of Bioinformatics - BiGCaT Teaching Materials

  bioinformaticsoer

  Apache License 2.0

  •1•1•2•0•Updated Nov 12, 2023Nov 12, 2023

• website-monitoring

  Public archive
  Script and configuration for website monitoring

  Shell

  •1•1•0•0•Updated Nov 5, 2023Nov 5, 2023

• org.pathvisio.io.bioschemas

  Public
  biohackeu23

  Java

  •0•1•0•0•Updated Nov 5, 2023Nov 5, 2023

• BLAST-OER

  Public
  Open Educational Resource for first year biomedical sciences students into the world of BLAST.

  bioinformaticsoerblast

  0•0•1•0•Updated Oct 16, 2023Oct 16, 2023

• kubernetes

  Public
  Webpage about the August 2023 Kubernetes workshop

  0•0•0•0•Updated Aug 23, 2023Aug 23, 2023

• Metagenomics_Metabolomics_Analysis

  Public
  HTML

  •0•0•0•0•Updated Jul 17, 2023Jul 17, 2023

• IMD_Curation_Analysis

  Public
  Inherited Metabolic Disorders (IMDs) queries to curate and analyse pathway models

  HTML

  •

  MIT License

  •0•0•0•0•Updated Jun 5, 2023Jun 5, 2023

• Transcriptomics_Metabolomics_Analysis_Rshiny

  Public
  R Shiny application for the multi-omics analysis of inflammatory bowel disease

  multi-omicsshiny-rinflammatory-bowel-disease

  R

  •

  Creative Commons Zero v1.0 Universal

  •0•0•1•0•Updated May 5, 2023May 5, 2023

• AOP-DB-RDF

  Public
  Repository containing setup protocol and jupyter notebook for testing

  Jupyter Notebook

  •

  MIT License

  •0•2•0•0•Updated Apr 7, 2023Apr 7, 2023

• IMD-PUPY

  Public
  Inherited Metabolic Disorders Systems Biology workflow on Purine, Pyrimidine and Urea Cycle disorders

  HTML

  •

  MIT License

  •1•0•0•0•Updated Apr 3, 2023Apr 3, 2023

• PSnpBind-ML-notebook

  Public
  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •3•6•0•0•Updated Feb 6, 2023Feb 6, 2023

• qsar-rdf-sbd4nano

  Public
  Files needed for conversion of nano-QSAR models to RDF

  Jupyter Notebook

  •3•0•0•0•Updated Dec 22, 2022Dec 22, 2022