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sib-swiss

15 indexed repositories · View on GitHub

training-collection
Collection of bioinformatics training materials

Python · 1149 stars
sparql-llm
🦜✨ Chat system, MCP server, and reusable components to improve LLMs capabilities when generating SPARQL queries

Jupyter Notebook · 124 stars
intro-machine-learning-training

Jupyter Notebook · 76 stars
first-steps-with-python-training
repository of the 3-day course "First steps with Python in Life Sciences" from SIB-training

Jupyter Notebook · 71 stars
sparql-examples
A set of SPARQL examples that are used in different SIB resources

HTML · 38 stars
termal
Terminal-based multiple sequence alignment (MSA) viewer designed for remote and HPC bioinformatics workflows.

Rust · 34 stars
sparql-editor
💫 A standard web component to deploy a user-friendly SPARQL query editor for one or more endpoints. Built on the popular YASGUI editor, i...

TypeScript · 24 stars
RNAseq-introduction-training
Webpage of the "Introduction to RNA-Seq: From quality control to pathway analysis - streamed" SIB course.

16 stars
kgsteward
Knowledge Graph Steward - Command line tool to help manage RDF store

Python · 8 stars
sparql-examples-utils
Help maintain your SPARQL examples collection

Java · 7 stars
dsSwissKnifeClient

R · 3 stars
reproducible-analysis-training
SIB course on FAIR analysis with Quarto, GitHub and Zenodo

R · 3 stars
mol-search-sparql-service
🫆 A SPARQL service for finding similar chemicals and substructures using molecular fingerprints with RDKit

Python · 3 stars
training-cookbook

0 stars
swisslipidsreact
Enumerating reactions based on SwissLipids and Rhea DB

Python · 0 stars

Beginner friendly Everything

Open All

Disk caching of some datasets Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

sib-swiss/kgsteward#23 · 1 reaction · Opened Sep 18, 2026
Preserve previous version of some dataset Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 42/100

sib-swiss/kgsteward#22 · Opened Sep 16, 2026
freeze/unfreeze Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

sib-swiss/kgsteward#21 · Opened Sep 11, 2026
Improve the YAML structure Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

sib-swiss/kgsteward#20 · 1 comment · Opened Sep 11, 2026
merge queries into dataset Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

sib-swiss/kgsteward#19 · Opened Sep 11, 2026
Move the file and URL loaders inside the driver definitions Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

sib-swiss/kgsteward#18 · Opened Sep 11, 2026
remove list flattening Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 48/100

sib-swiss/kgsteward#17 · Opened Sep 11, 2026
Update Pydantic Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

sib-swiss/kgsteward#16 · Opened Sep 11, 2026
fb for next course Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

sib-swiss/reproducible-analysis-training#6 · Opened Sep 4, 2026
HEAD might be blocking for kgsteward Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

sib-swiss/kgsteward#15 · 1 comment · Opened Aug 20, 2026
Effect of kgsteward -I on GraphDB Open

good first issue

Difficulty 3/5 1-2 days Newbie friendliness 45/100

sib-swiss/kgsteward#14 · Opened Aug 19, 2026
doc: improve first steps user guide Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

sib-swiss/kgsteward#13 · Opened Aug 4, 2026
`dssPrincomp()` fails on the server with `requires numeric/complex matrix/vector arguments` when a site has more features than samples (p > n) Open

Difficulty 3/5 1-2 days Newbie friendliness 76/100

sib-swiss/dsSwissKnifeClient#5 · Opened Jul 23, 2026
june2026 feedback Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

sib-swiss/intro-machine-learning-training#14 · 2 comments · Opened Jul 16, 2026
Python port of sparql to mermaid Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

sib-swiss/sparql-examples-utils#20 · Opened Jul 15, 2026
List of fingerprints Open

Difficulty 2/5 Under an hour Newbie friendliness 65/100

sib-swiss/mol-search-sparql-service#5 · Opened Jun 4, 2026
I don't know what to do with it Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

sib-swiss/mol-search-sparql-service#4 · Opened Jun 3, 2026
Void description Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

sib-swiss/sparql-editor#32 · Opened May 13, 2026
migrate to zensical + add site tracking Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

sib-swiss/RNAseq-introduction-training#15 · Opened Apr 16, 2026
Option -F does not respect frozen states Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

sib-swiss/kgsteward#12 · Opened Apr 13, 2026
timeout on HEAD Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

sib-swiss/kgsteward#11 · 1 comment · Opened Mar 25, 2026
importing from .rq results in duplicated prefixes Open

sib-swiss/sparql-examples-utils#15 · 1 comment · 1 assignee · Opened Jan 30, 2026
Compute checksum for prefixes and queries Open

enhancement

sib-swiss/kgsteward#8 · 1 comment · 1 assignee · Opened Jan 13, 2026
Issue running kgsteward on windows machine Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

sib-swiss/kgsteward#6 · Opened Dec 15, 2025
Failed to execute 'setItem' on 'Storage': Setting the value of 'yasgui_rmd_output4_config' exceeded the quota. Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

sib-swiss/sparql-editor#30 · 2 comments · Opened Dec 8, 2025
Enabling templated query forms Open

enhancement question

Difficulty 5/5 Over a week Newbie friendliness 25/100

sib-swiss/sparql-editor#29 · Opened Nov 27, 2025
Metadata not loaded from localStorage when `query` or `endpoint` URL params provided Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

sib-swiss/sparql-editor#28 · Opened Nov 25, 2025
Auto limit the number of results/pagination Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

sib-swiss/sparql-editor#27 · 1 comment · Opened Nov 25, 2025
Allow for preventing auto-execution for URLs with 'query' param Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

sib-swiss/sparql-editor#26 · 2 comments · 1 reaction · Opened Nov 6, 2025
Dr. Open

Difficulty 5/5 Over a week Newbie friendliness 1/100

sib-swiss/intro-machine-learning-training#13 · Opened Oct 8, 2025
sep25 self-feedback Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

sib-swiss/RNAseq-introduction-training#13 · 2 comments · Opened Sep 29, 2025
add exam to course materials Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

sib-swiss/RNAseq-introduction-training#12 · Opened Sep 26, 2025
base IRI Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

sib-swiss/swisslipidsreact#2 · 2 comments · Opened Sep 18, 2025
double-bond number not conserved Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

sib-swiss/swisslipidsreact#1 · 6 comments · Opened Sep 18, 2025
reference sequence setting to reduce redundant amino acid representations? Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

sib-swiss/termal#1 · 5 comments · 1 reaction · Opened Sep 16, 2025
Publish Expasy MCP as Python package Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

sib-swiss/sparql-llm#5 · 1 reaction · Opened Sep 9, 2025
Warning: use of `eval` Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

sib-swiss/sparql-editor#22 · Opened Aug 4, 2025
Structure according to the training life cycle Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

sib-swiss/training-cookbook#10 · Opened Jul 29, 2025
Possible enhancement to the round and colored dot Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

sib-swiss/sparql-editor#21 · Opened Jul 18, 2025
Instructions for zoom presence is in there twice Open

Difficulty 1/5 Under an hour Newbie friendliness 45/100

sib-swiss/training-cookbook#9 · Opened Jul 15, 2025
SEPARATOR="\n" Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

sib-swiss/sparql-editor#20 · 2 comments · Opened Jul 14, 2025
make snapquery compatible Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

sib-swiss/sparql-examples-utils#10 · 3 comments · 1 reaction · Opened May 11, 2025
Void generation with SPARQL updates Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

sib-swiss/sparql-editor#18 · Opened May 2, 2025
Add configuration to enable the share query button Open

Difficulty 2/5 1-3 hours Newbie friendliness 62/100

sib-swiss/sparql-editor#17 · Opened Apr 18, 2025
Improve `Add common prefixes` button Open

enhancement good first issue

Difficulty 4/5 3-5 days Newbie friendliness 45/100

sib-swiss/sparql-editor#16 · Opened Apr 18, 2025
Automatically update endpoints metadata in the background Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 30/100

sib-swiss/sparql-editor#15 · Opened Apr 18, 2025
Cluttered IDSM class overview Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

sib-swiss/sparql-editor#14 · 2 comments · Opened Apr 14, 2025
Show of interest Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

sib-swiss/sparql-llm#3 · 2 reactions · Opened Mar 21, 2025
Resolve SPARQL query examples URIs Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

sib-swiss/sparql-editor#11 · Opened Mar 10, 2025
Notes about "Broken" queries and queries with no results Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

sib-swiss/sparql-examples#174 · 1 comment · Opened Mar 6, 2025

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