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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 )

In order to load any modeules from if89, you need to prepend the directory of if89's modules to the MODULEPATH environment variable using the following command:
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

Please see documentation for more information on this.


if89 Workflows

Will be available soon.


if89 Containers

Will be available soon.


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

AB
If89 contributor

Andrey Bliznyuk

NCI

Dale Roberts If89 contributor

Dale Roberts

NCI (at the time of this work), ARC Centre of Excellence for Climate Extremes

Hardip Patel If89 contributor

Hardip Patel

National Centre for Indigenous Genomics, John Curtin School of Medical Research, The Australian National University

J King Chang If89 contributor

J King Chang

School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney

JS
If89 contributor

Javed Shaikh

NCI/ANU

Johan Gustafsson Engagement

Johan Gustafsson

Australian BioCommons / University of Melbourne

Kyle Drover If89 contributor

Kyle Drover

TB
If89 contributor

Terry Bertozzi

South Australian Museum

Ziad Al Bkhetan Technical/engagement

Ziad Al Bkhetan

Australian BioCommons / University of Melbourne