Shared repository of tools and software (Project if89 on NCI)
ABLeS communities have access to the Australian BioCommons Tools and Workflows project, in project allocation if89. This is a repository of popular tools, containers and workflows that can be used by anyone in the NCI user community. Anyone from an NCI community can contribute to if89 and add more tools that will be shared with others.
if89 Tools
The frequently updated list of tools available through the Australian BioCommons Shared Tools and Workflows repository is available though Tool Finder webpage (Project if89 on GADI-NCI )
module use -a /g/data/if89/apps/modulefiles
After that, you can load any tool then utilising it directly using the following command:
module load $tool/$version
You can list all available modules using the following command:
module available
if89 Workflows
if89 Containers
if89 Tool’s Databases
Some of the databases reqiured by different bioinformatics tools are available through if89 project.
They are located at /g/data/if89/data_library
. You can request other databases to be included by contacting us.
A list of the currently available (25 Jan 2023) databases is below:
Dataset | Source | Download date | Location | Details |
---|---|---|---|---|
Blast | Blast Webpage | 28 Aug 2022 | blast_db/28082022/ |
nr.*.gz: non-redundant protein sequence database with entries from GenPept, Swissprot, PIR, PDF, PDB, and RefSeq. nt.*.gz: nucleotide sequence database, with entries from all traditional divisions of GenBank, EMBL, and DDBJ. |
Alphafold/UniProt | foldseek github pages and AlphaFold Protein Structure Database webpage | 30 Nov 2022 | AlphaFoldDB/aminoacid/UniProt/30112022/ |
Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool. |
Alphafold/UniProt-NO-CA | foldseek github pages and AlphaFold Protein Structure Database webpage | 30 Nov 2022 | AlphaFoldDB/aminoacid/UniProt-NO-CA/30112022/ |
Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool. |
Alphafold/UniProt50 | foldseek github pages and AlphaFold Protein Structure Database webpage | 30 Nov 2022 | AlphaFoldDB/aminoacid/UniProt50/30112022/ |
Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool. |
Alphafold/Proteome | foldseek github pages and AlphaFold Protein Structure Database webpage | 29 Nov 2022 | AlphaFoldDB/aminoacid/Proteome/29112022/ |
Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool. |
Alphafold/Swiss-Prot | foldseek github pages and AlphaFold Protein Structure Database webpage | 30 Nov 2022 | AlphaFoldDB/aminoacid/Swiss-Prot/30112022/ |
Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool. |
if89 Contributors
Andrey Bliznyuk
NCI
Dale Roberts
NCI (at the time of this work), ARC Centre of Excellence for Climate Extremes
Hardip Patel
National Centre for Indigenous Genomics, John Curtin School of Medical Research, The Australian National University
J King Chang
School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney
Javed Shaikh
NCI/ANU
Johan Gustafsson
Australian BioCommons / University of Melbourne
Kyle Drover
Terry Bertozzi
South Australian Museum
Ziad Al Bkhetan
Australian BioCommons / University of Melbourne