Bioinformatics: Difference between revisions

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==Introduction== <!--T:1-->


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=Software= <!--T:8-->
While the bioinformatics community has matured substantially in recent years, rapid development is required to keep pace with massive increases in data volume and generation. Specifically, there is still much room for improvement in the optimization of computational resources, discovery of and access to analytical tools, and training and general dissemination of bioinformatics best practices. Furthermore, privacy and data protection policies often present major obstacles for bioinformaticians, particularly those in the realm of health informatics. To address these needs, the Compute Canada Bioinformatics National Team (BNT) is committed to a strategy that includes leveraging existing Compute Canada resources as well as developing new resources and practices where necessary.


==Who we are== <!--T:3-->
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The BNT's members are bioinformatics professionals from Compute Canada, the BC Genome Sciences Centre, and the Canadian Centre for Computational Genomics.
See [[Available_software#List_of_globally-installed_modules|Available software]] for a list of bioinformatics applications on our systems.
=== Team members ===
You can sort on <i>Type</i>, where bioinformatics software is categorized as <i>bio</i>.
Jose Sergio Hleap (Team interim Lead), University of Guelph<br/>
Arun Ramani (Bioinformatic Software Specialist), University of Toronto<br/>
Brian McConeghy (Bioinformatic, Software Specialist), University of British Columbia<br/>
David Anderson de Lima Morais (Bioinformatic Software Specialist), Université de Sherbrooke<br/>
François Lefebvre (Canadian Bioinformatics Helpdesk coordinator), McGill University<br/>
Gemma Hoad (Bioinformatic Software Specialist), Simon Fraser University<br/>
Jean-François Lucier (Bioinformatic Software Specialist), Université de Sherbrooke<br/>
Jiarui Li (Bioinformatic Software Specialist), University of British Columbia<br/>
José Héctor Gálvez (Bioinformatic Software Specialist), McGill University<br/>
Neke Ibeh (Bioinformatic Software Specialist), University Health Network<br/>
Pascale Marquis (Bioinformatic Software Specialist), McGill University<br/>
Richard Corbett (Bioinformatic Software Specialist), British Columbia Genome Sciences Centre <br/>
Robert Syme (Data repository coordinator), McGill University<br/>
Shadi Khalifa (Bioinformatic Software Specialist), Queen's University<br/>
Steven Handy (Bioinformatic Software Specialist) Queen's University<br/>
Viswateja Nelakuditi (Bioinformatic Software Specialist), SickKids<br/>
Wade Klaver (Bioinformatic Software Specialist), University of British Columbia<br/>
Zhibin Lu (Bioinformatic Software Specialist), University Health Network<


==Access to Compute Canada resources== <!--T:4-->
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Compute Canada's digital research infrastructure is available free-of-charge to eligible researchers.
Some bioinformatics software is available as [[Python]] packages, which do not appear on the list mentioned above.  
For more information, see [https://www.computecanada.ca/research-portal/account-management/apply-for-an-account/ apply for an account]
See [[Available Python wheels]] for a list of Python <i>wheels</i> customized for our clusters.


==Bioinformatics support== <!--T:5-->
=Data= <!--T:9-->
If you have a bioinformatics or sequencing question, and would like to access our experts from across the country, please visit the [https://bioinformatics.computecanada.ca/ Canadian Bioinformatics Helpdesk].  You can browse the existing solutions in our forum, or simply register and post your query.  One-on-one sessions are also available to eligible users in case posting a question just won't cut it.


==General support== <!--T:6-->
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If you are experiencing a general issue working on Compute Canada systems, please email [[Technical support]].
Some genome databases are available on our clusters, provided by [https://genpipes.readthedocs.io/en/latest/c3gres/cvmfs_genomes.html MUGQIC].


==Training and education== <!--T:7-->
If you're interested in bioinformatics workshops and seminars, please see our page [https://bioinformatics.computecanada.ca/events/ here]
Or, if you don't see what you're looking for, please [mailto:bioinformatics@computecanada.ca let us know] your idea and we'll do our best to make it happen.
==Software== <!--T:8-->
[[Available_software#List_of_modules|Click here]] to see a list of available bioinformatics software on Compute Canada systems.
You can sort on 'Type', where bioinformatics software is categorized as 'bio'.
==Genome database== <!--T:9-->
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In partnership with [http://www.computationalgenomics.ca C3G], we maintain several genome databases on Cedar and Graham as well as Guillimin and Mammouth. In addition to the fasta sequence, many genomes include aligner indices and annotation files. For more information about the available data [[Genomics_data | click here]]


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Latest revision as of 18:49, 27 June 2023


This article is a draft

This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.



Other languages:


Software

See Available software for a list of bioinformatics applications on our systems. You can sort on Type, where bioinformatics software is categorized as bio.

Some bioinformatics software is available as Python packages, which do not appear on the list mentioned above. See Available Python wheels for a list of Python wheels customized for our clusters.

Data

Some genome databases are available on our clusters, provided by MUGQIC.


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