Repositories list

• training_repos_traffic_tracker

  Public
  some code to track the traffic on multiple github repos beyond the 15 days limit

  Python

  •1•0•0•0•Updated Jan 7, 2026Jan 7, 2026

• first-steps-with-python-training

  Public
  repository of the 3-day course "First steps with Python in Life Sciences" from SIB-training

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •16•65•2•0•Updated Jan 6, 2026Jan 6, 2026

• easybuild-easyconfigs

  Public
  A collection of easyconfig files that describe which software to build using which build options with EasyBuild.

  Python

  •

  GNU General Public License v2.0

  •773•3•0•0•Updated Jan 6, 2026Jan 6, 2026

• kgsteward

  Public
  Knowledge Graph Steward - Command line tool to help manage RDF store

  Python

  •

  GNU General Public License v3.0

  •2•6•1•0•Updated Jan 5, 2026Jan 5, 2026

• Introduction-to-statistics-with-R

  Public
  Other

  •3•4•1•3•Updated Jan 5, 2026Jan 5, 2026

• sparql-llm

  Public
  🦜✨ Chat system, MCP server, and reusable components to improve LLMs capabilities when generating SPARQL queries

  sparqlmcpsparql-query-builder+ 3expasyllmmcp-server

  Jupyter Notebook

  •

  MIT License

  •12•83•3•0•Updated Jan 5, 2026Jan 5, 2026

• intro-machine-learning-training

  Public
  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •21•59•1•0•Updated Jan 5, 2026Jan 5, 2026

• single-cell-python-training

  Public
  HTML

  •

  Creative Commons Attribution 4.0 International

  •1•5•0•0•Updated Jan 4, 2026Jan 4, 2026

• spatial-transcriptomics-training

  Public
  R

  •

  Creative Commons Attribution 4.0 International

  •2•5•1•0•Updated Jan 4, 2026Jan 4, 2026

• glittr-stats

  Public
  General statistics of Glittr.org. Comes with the manuscript.

  PostScript

  •0•2•0•0•Updated Jan 4, 2026Jan 4, 2026

• cancer-variants-training

  Public
  HTML

  •

  Creative Commons Attribution 4.0 International

  •4•9•0•0•Updated Jan 4, 2026Jan 4, 2026

• training-collection

  Public
  Collection of bioinformatics training materials

  Python

  •

  Other

  •196•1.1k•1•0•Updated Dec 28, 2025Dec 28, 2025

• constraint-based-modeling-in-R

  Public
  COnstraint-based Reconstruction and Analysis (COBRA) of metabolic networks in R

  R

  •

  GNU General Public License v3.0

  •5•0•5•0•Updated Dec 19, 2025Dec 19, 2025

• sparqlr

  Public
  R package to query SPARQL endpoints

  R

  •

  GNU General Public License v3.0

  •0•2•2•0•Updated Dec 18, 2025Dec 18, 2025

• sib-software-stack

  Public
  Scripts and documentation to deploy the SIB software stack

  Perl

  •0•1•0•0•Updated Dec 17, 2025Dec 17, 2025

• open-data-registry

  Public
  A registry of publicly available datasets on AWS

  Python

  •

  Apache License 2.0

  •1.1k•0•0•0•Updated Dec 15, 2025Dec 15, 2025

• seq-spatial-transcriptomics-training

  Public
  Introduction to Sequencing-based Spatial Transcriptomics Data Analysis

  R

  •

  Creative Commons Attribution 4.0 International

  •3•2•1•0•Updated Dec 12, 2025Dec 12, 2025

• sparql-examples

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

  HTML

  •

  Other

  •28•29•5•5•Updated Dec 11, 2025Dec 11, 2025

• sparql-examples-utils

  Public
  Help maintain your SPARQL examples collection

  sparqljunit5

  Java

  •

  Other

  •5•5•2•0•Updated Dec 10, 2025Dec 10, 2025

• sparql-editor

  Public
  💫 A standard web component to deploy a user-friendly SPARQL query editor for one or more endpoints. Built on the popular YASGUI editor, it provides context-aware autocomplete for classes and predicates based on the content of the endpoints.

  sparqlsparql-querysparql-query-builder+ 2sparql-editoryasgui

  TypeScript

  •

  MIT License

  •6•20•22•0•Updated Dec 9, 2025Dec 9, 2025

• termal

  Public
  Terminal-based multiple sequence alignment (MSA) viewer designed for remote and HPC bioinformatics workflows.

  rustbioinformaticsterminal+ 4hpctuimsamultiple-sequence-alignement

  Rust

  •

  MIT License

  •2•23•1•0•Updated Dec 6, 2025Dec 6, 2025

• training-cookbook

  Public
  Other

  •0•0•2•0•Updated Dec 5, 2025Dec 5, 2025

• pytorch-practical-training

  Public
  pratrical crash course on pytorch by reproducing some published biology-related deep-learning models

  bioinformaticsdeep-learningpytorch+ 1training-materials

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •5•29•3•0•Updated Dec 3, 2025Dec 3, 2025

• enrichment-analysis-training

  Public
  Course material for Enrichment analysis course by SIB

  enrichmentrenrichment-analysis+ 2gseatutorial-course

  Other

  •9•11•5•0•Updated Dec 2, 2025Dec 2, 2025

• shell-scripting-training

  Public
  UNIX shell scripting - course material

  Shell

  •1•3•0•0•Updated Nov 28, 2025Nov 28, 2025

• EPD

  Public
  The Eukaryotic Promoter Database (EPD) website

  promoterstranscription-start-siteeukaryotic+ 1eukaryotic-transcription-signal

  JavaScript

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 28, 2025Nov 28, 2025

• sequencing-data-analysis-training

  Public
  SIB course that introduces analysis of NGS data

  trainingtutorialcourse+ 2teachingngs-analysis

  Shell

  •

  Creative Commons Attribution 4.0 International

  •14•16•4•0•Updated Nov 21, 2025Nov 21, 2025

• BEAt_DKD

  Public
  R

  •0•1•0•0•Updated Nov 20, 2025Nov 20, 2025

• intermediate-machine-learning-training

  Public
  Intermediate Machine Learning course of the Swiss Institute of Bioinformatics

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •2•7•2•0•Updated Nov 20, 2025Nov 20, 2025

• intermediate-python-training

  Public
  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •31•82•2•0•Updated Nov 20, 2025Nov 20, 2025