Project Application Details

ARCHIE Project title: ≈5GB
Project PI: 161 Cathedral Street
Department: 2021-07-12
Address: 161 Cathedral Street, , open-source software, G4 0RE
Relevant industrial collaborations:
Existing relevant KTP activities:
Does the PI require to run calculations? 1
Number of users involved in the project: 26 months
User 1 details:

Angelika Kiepas – xmb20196

The user is a Strathclyde-funded REA PhD student in SIPBS, studying bioinformatics/computational biology. There is no associated budget, so subscription will be paid from the PI’s general fund.

Service level requested:
ARCHIE Project description: ≈5GB
Potential output of the project:

We have already produced the largest, most comprehensive 16S phylogenetic tree of the Streptomyces genus (important for antibiotic discovery and industrial production), to aid classification and comparative genomic analysis. Being able to use ARCHIE-West will enable:

– efficient refinement of this tree to take into account variable evolutionary influences across the length of the sequence
– extension of the approach to multigene trees (more precise)
– pangenomic analysis within coherent organism groups identified using these trees
– metabolic modelling and comparisons between and within these groups

The phylogenetic analysis and (re)classification of Streptomyces is expected to lead to publications in journals such as Microbial Genomics and Molecular Biology and Evolution; pangenomic analyses are expected to be published in mBio or Microbial Genomics; metabolic modelling outputs are targeted at Molecular Systems Biology.

Project start date: 2021-07-12
Duration of the project: 26 months
Total CPU time required (in hours): <≈500,000
CPU hours required by typical job: 1
Approximate amount of data created per job (in GB):
Approximate amount of data created per project: ≈5GB
Funding Agency Grant Reference No: n/a
pFact ID: n/a
RKES ID: n/a
Software required for the project: open-source software
Software required to be installed for the project: conda, with bioconda channel (all packages used should be available through this medium)
Experience in using software package 1: 8
Software required to be installed for the project:
Experience in using software package 2: 1
Software required to be installed for the project:
Experience in using software package 3: 1
Training required: Basic of using HPC
Other training required:
Experience in using HPC: 1