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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 Workshop 1: SARS-CoV-2 Genome Analysis [repo] [webpage]
MP968 Experimental Design Workshop [repo] [webpage]

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

    Jupyter Notebook 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 35 repositories
  • MP968-Workshop_Experimental_Design Public

    MP968 Experimental Design workshop

    sipbs-compbiol/MP968-Workshop_Experimental_Design’s past year of commit activity
    JavaScript 0 CC-BY-SA-4.0 0 0 0 Updated Nov 23, 2024
  • .github Public

    Public README.md for sipbs-compbiol

    sipbs-compbiol/.github’s past year of commit activity
    0 0 0 0 Updated Nov 23, 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 1 0 0 Updated Nov 4, 2024
  • sipbs-internships Public

    Website in support of SIPBS internship matching

    sipbs-compbiol/sipbs-internships’s past year of commit activity
    CSS 0 0 0 0 Updated Nov 1, 2024
  • bm432-datavis_workshop Public

    BM432 data visualisation flipped classroom workshop slides

    sipbs-compbiol/bm432-datavis_workshop’s past year of commit activity
    HTML 0 CC-BY-SA-4.0 0 2 0 Updated Oct 23, 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 Sep 19, 2024
  • 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 Aug 30, 2024
  • Kiepas_et_al_2024_16S Public
    sipbs-compbiol/Kiepas_et_al_2024_16S’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Aug 28, 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 1 0 0 Updated Aug 16, 2024
  • 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
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