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@sipbs-compbiol

SIPBS Computational Biology

Computational Biology in the Strathclyde Instititute for Pharmacy and Biomedical Sciences
README.md

sipbs-compbiol

Hi there! 👋

This is the GitHub home of the sipbs-compbiol SIPBS Computational Biology group. We conduct research and teaching in bioinformatics and computational biology at the University of Strathclyde.

Areas of Interest

  • Microbiology and microbial genomics (taxonomy and classification, host-microbe interactions, functional annotation, etc.)
  • Industrial biotechnology (protein engineering, improving industrial strains, etc.)
  • Biostatistics and modelling (metabolic modelling, experimental design, etc.)

If you'd like to know more, please visit our group pages

Group Repositories

This GitHub organisation hosts software and teaching material written by group members. We have some convenient shortcuts below.

Software

Name Summary Publication Repository Webpage
cazy_webscraper make a local, extensible, version of CAZy doi:10.1099/mgen.0.001086 HobnobMancer/cazy_webscraper webpage
ncfp download coding sequences and backthread proteins n/a widdowquinn/ncfp webpage
pyani-plus Average Nucleotide Identity of microbial genomes n/a pyani-plus/pyani-plus webpage
pyani (archived) doi:10.1039/C5AY02550H widdowquinn/pyani webpage

Current Teaching

Module Topic Repository Webpage
BM110 Microbiology Lab Statistics Support [repo] [webpage]
BM211 Workshop 1: Microbial Ecology [repo] [webpage]
BM211 Workshop 5: Phylogenetic Trees [repo] [webpage]
BM214 Workshop 2: Sequence Searching [repo] [webpage]
BM214 Workshop 3: Data Interpretation [repo] [webpage]
BM327 Workshop 1: Hospital Infection [repo] [webpage]
BM327 Workshop 2: UTI Pathogen Adherence [repo] [webpage]
BM329 Block A Workshop: Microbial Identification [repo] [webpage]
BM329 Block D Workshop: Diseases of the Respiratory Tract [repo] [webpage]
BM432 Data Visualisation Workshop [repo] [webpage]
BM425 Workshop 1: SARS-CoV-2 Genome Analysis [repo] [webpage]
MP968 Experimental Design Workshop [repo] [webpage]
MP968 Experimental Design Workshop Slides [repo] [webpage]

Supplementary Information

Publication Title Repository Webpage
Kiepas et al. (2024) Microbial genomics doi:10.1099/mgen.0.001287 16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces [repo] [webpage]
Bizior et al. (2026) bioRxiv doi:10.64898/2026.09.24.754001 A bacterial Rhesus transporter retunes a structurally conserved ammonium pore into a reversible nitrogen valve [repo] [webpage]

Pages for Students

Topic Repository Webpage
BM432 UG Final Year Project Guidance [repo] [webpage]
BM432 UG Final Year Project GitHub Template [repo] [webpage]
BM954 MSc Project Guidance [repo] [webpage]
PDA Student Guidance [repo] [webpage]
SIPBS Internships [repo] [webpage]

Former Teaching

Module Topic Repository Webpage
BM432 UG Final Year Project Workshops [repo] [webpage]
BM425 Carpentries for UG Projects [repo] [webpage]
MP429 Introduction to Statistics [repo] [webpage]
CPD Carpentries for IBioIC 2021-05-04 [repo] [webpage]
CPD Carpentries for IBioIC 2021-05-11 [repo] [webpage]
CPD Carpentries for IBioIC 2025-11-04 [repo] [webpage]

Popular repositories Loading

  1. BM432 BM432 Public

    Online reading material for BM432 course workshops in data management, analysis and visualisation, delivered at University of Strathclyde

    HTML 2 1

  2. template_bioinformatics_project template_bioinformatics_project Public template

    Starting template for UG/PG bioinformatics projects using git

    2 6

  3. Kiepas_et_al_2024_16S Kiepas_et_al_2024_16S Public

    Jupyter Notebook 2 1

  4. 2021-05-11-strathclyde-online 2021-05-11-strathclyde-online Public

    Webpage for the 11th-12th March online Carpentries course presentation for IBioIC at the University of Strathclyde

    HTML 1 1

  5. workshop-phylogenomics workshop-phylogenomics Public

    Introductory and practical phylogenomics workshop

    1

  6. bm432-project bm432-project Public

    Support for BM432 students doing their final year project in the SIPBS CompBiol Group

    CSS 1 1

Repositories

Showing 10 of 43 repositories
  • .github Public

    Public README.md for sipbs-compbiol

    sipbs-compbiol/.github's past year of commit activity
    0 0 0 0 Updated Sep 24, 2026
  • SI_Bizior_et_al_2026_Amt Public

    Supplementary Information for Henderson et al. (2026)

    sipbs-compbiol/SI_Bizior_et_al_2026_Amt's past year of commit activity
    R 0 0 0 0 Updated Sep 24, 2026
  • bm432-project Public

    Support for BM432 students doing their final year project in the SIPBS CompBiol Group

    sipbs-compbiol/bm432-project's past year of commit activity
    CSS 1 CC-BY-SA-4.0 1 1 0 Updated Sep 21, 2026
  • BM425-Workshop-1 Public

    SARS-CoV-2 genomics bioinformatics workshop for BM425 (Advanced Microbiology)

    sipbs-compbiol/BM425-Workshop-1's past year of commit activity
    JavaScript 0 CC-BY-SA-4.0 0 2 0 Updated Sep 18, 2026
  • sipbscompbiol-pda Public

    GitHub Pages site to support PDAs mentored by the SIPBS Computational Biology group

    sipbs-compbiol/sipbscompbiol-pda's past year of commit activity
    HTML 1 CC-BY-SA-4.0 0 1 0 Updated Sep 17, 2026
  • BM110-Microbiology-Lab Public

    Statistical support for the BM110 microbiology laboratory

    sipbs-compbiol/BM110-Microbiology-Lab's past year of commit activity
    JavaScript 0 CC-BY-SA-4.0 0 0 0 Updated Aug 13, 2026
  • sipbs-compbiol-book-template Public template

    GitHub repository template for SIPBS CompBiol-formatted Quarto books

    sipbs-compbiol/sipbs-compbiol-book-template's past year of commit activity
    JavaScript 0 CC-BY-SA-4.0 1 2 0 Updated Aug 11, 2026
  • BM954-Project Public

    This repository provides a website to support MSc students in the SIPBSCompBiol group

    sipbs-compbiol/BM954-Project's past year of commit activity
    CSS 0 CC-BY-SA-4.0 0 1 0 Updated Jun 5, 2026
  • BM327-Workshop-2 Public

    Bioinformatics Workshop 2 for BM327 Microbiology

    sipbs-compbiol/BM327-Workshop-2's past year of commit activity
    Lua 0 CC-BY-SA-4.0 0 3 0 Updated Mar 20, 2026
  • BM211-Workshop-5 Public

    Materials for the BM211 phylogenetics workshop

    sipbs-compbiol/BM211-Workshop-5's past year of commit activity
    JavaScript 0 CC-BY-SA-4.0 0 4 (1 issue needs help) 0 Updated Mar 10, 2026
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