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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 Average Nucleotide Identity of microbial genomes doi:10.1039/C5AY02550H widdowquinn/pyani webpage

Current Teaching

Module Topic Repository 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]
BM329 Block A Workshop: Microbial Identification [repo] [webpage]
BM329 Block B Workshop: Diseases of the Respiratory Tract [repo] [webpage]
BM432 Data Visualisation Workshop [repo] [webpage]
BM425 Microbial Genomics Workshop

Supplementary Information

Publication Title Repository Webpage
Kiepas et al. (2024) [submitted] 16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces [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]

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 2

  3. 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

  4. workshop-phylogenomics workshop-phylogenomics Public

    Introductory and practical phylogenomics workshop

    1

  5. Kiepas_et_al_2024_16S Kiepas_et_al_2024_16S Public

    1

  6. sipbscompbiol-pda sipbscompbiol-pda Public

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

    CSS 1

Repositories

Showing 10 of 33 repositories
  • 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 0 0 Updated Jul 3, 2024
  • 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 0 CC-BY-SA-4.0 0 0 0 Updated Jun 3, 2024
  • 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 0 0 0 Updated May 17, 2024
  • BM214-Workshop-3 Public

    Bacterial/bacteriophage enumeration bioinformatics workshop for BM214 (Being a Biomolecular Scientist 2)

    sipbs-compbiol/BM214-Workshop-3’s past year of commit activity
    Jupyter Notebook 0 CC-BY-SA-4.0 0 1 0 Updated May 17, 2024
  • .github Public

    Public README.md for sipbs-compbiol

    sipbs-compbiol/.github’s past year of commit activity
    0 0 0 0 Updated May 17, 2024
  • little-data-analysis-book Public

    A little book about data analysis. Continually in progress.

    sipbs-compbiol/little-data-analysis-book’s past year of commit activity
    JavaScript 0 CC-BY-SA-4.0 0 0 0 Updated May 1, 2024
  • Kiepas_et_al_2024_16S Public
    sipbs-compbiol/Kiepas_et_al_2024_16S’s past year of commit activity
    1 0 0 0 Updated Apr 29, 2024
  • StudentResources Public

    library of resources to support student learning in bioinformatics/biological sciences

    sipbs-compbiol/StudentResources’s past year of commit activity
    0 0 1 (1 issue needs help) 0 Updated Apr 8, 2024
  • 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
    CSS 1 CC-BY-SA-4.0 0 0 0 Updated Mar 25, 2024
  • 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 1 0 Updated Mar 19, 2024
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