Resources

Databases & Tools

Comprehensive Antibiotic Resistance Database : A bioinformatic database of resistance genes, their products and associated phenotypes. Supported by the Canadian Institutes of Health Research.

Resistance Gene Identifier : Software for prediction of antimicrobial resistance genes and mutations from genomes or metagenomic reads. Supported by the Canadian Institutes of Health Research.

Bait Capture Platforms: SARS-CoV-2 bait capture & AMR bait capture.

Auspice – Genomic epidemiology of novel coronavirus – Canada : Representation of SARS-CoV-2 variants in Canada released publicly at GISAID. Work on behalf of CanCOGeN. A collaboration led by Dr. Finlay Maguire of Dalhousie University. Quick link to track Variants of Concern in Canada. Supported by a hardware donation from Cisco Systems Canada, Inc. and loan from Pure Storage. Additional hardware support from Hewlett Packard Enterprise via Canadian Foundation for Innovation (CFI) funding.

Auspice – Genomic epidemiology of novel coronavirus – Ontario : Representation of SARS-CoV-2 variants in Ontario released publicly at GISAID. Work on behalf of ONCoV. A collaboration led by Dr. Finlay Maguire of Dalhousie University. Supported by a hardware donation from Cisco Systems Canada, Inc. and loan from Pure Storage. Additional hardware support from Hewlett Packard Enterprise via Canadian Foundation for Innovation (CFI) funding.

SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL) : Standardized bioinformatics snakemate workflow for assembly and analysis of SARS-CoV-2 sequencing using Illumina platforms. Development supported by rapid hardware donation from Hewlett Packard Enterprise.

Coronavirus Genotyping Tool: Machine learning (UMAP) representation of SARS-CoV-2 genomic diversity & epidemiology. A collaboration led by Hassaan Maan & Dr. Bo Wang of the Vector Institute. Supported by a hardware donation from Cisco Systems Canada, Inc. 

Backend processing support provided to the Canadian VirusSeq Data Portal edition of CoVizu (an open source SARS-CoV-2 genome analysis and visualization system). Hardware support from Hewlett Packard Enterprise via Canadian Foundation for Innovation (CFI) funding.

Computing

The computing environment of the McArthur Lab received financial support from the Canadian Foundation for Innovation, Ontario Research Fund, and Cisco Systems Canada, Inc. We use VMWare Cloud Computing, allowing us to create a wide variety of server, operating system, and software configurations. Our computing resources are part of McMaster’s Service Lab and Repository, hosted by McMaster’s Computer Services Unit.

Git Lab, http://devcard.mcmaster.ca:8888 (requires VPN)

The McArthur Lab uses GIT Lab as a centralized resource for software development, data tracking, project documentation, issue tracking, and collaboration. Git Lab access is provided for registered users only – contact mcarthua@mcmaster.ca to register. Generally speaking, all users of McArthur Lab data and servers join the General Admin Repository so they are able to submit hardware, software, or network requests, reports, and comments.

Are you a Comprehensive Antibiotic Resistance Database curator or Resistance Gene Identifier tester? This Git Lab server is where you submit and track bug reports, data curation issues, software requests, and your questions.

Comprehensive Antibiotic Resistance Database

All active CARD curators must join the Broad Street Repository. RGI testers are additionally advised to join the RGI Release Repository.

Linux Workhorses

The Mcarthur Lab uses the command line for a variety of bioinformatics analyses, with a focus on next-generation sequencing data such as RNA-Seq, ChIP-Seq, etc.

Other Servers & Resources

  • General linux bioinformatics server, uppsala.mcmaster.ca (Ubuntu, 8 processors, 62 GB memory) (SSH, VPN)
  • Restricted bioinformatics server, Chemical-Genetic DB, tingsryd.mcmaster.ca (SSH, VPN)
  • UPSTREAM Promotor Analysis database, http://tingsryd.mcmaster.ca

VPN = McMaster virtual private network access required, SSH = secure shell access required

Seminars, Journal Clubs, Meet-Ups

Microbiome Working Group & Human Microbiome Journal Club

The Microbiome Working Group is held Tuesdays, 3:30 – 4:30 in HSC 1J9A. Researchers working on microbiome projects are encouraged to bring their laptops and get or give help with software tools, R, experiment planning, or whatever else is going on in your microbiome world. This is a drop-in with no presentations or preparation required.

The Human Microbiome Journal Club is held on the fourth Friday of each month from 3 – 4 in HSC 3N10A. One person chooses a paper to present and discuss. HMJC is typically followed up with Bioinformatics and Beer at the Phoenix. If you would like to present a paper at HMJC, please inform Dr. Jen Stearns at stearns@mcmaster.ca

To get updates about either of these groups (paper topics, cancellations, etc.), please add yourself to the (low-traffic) hmjc-l mailing list here: https://mailman.mcmaster.ca/mailman/listinfo/hmjc-l

Structural Biology Journal Club

The Structural Biology Journal Club is hosted by IIDR principal investigator Dr. Sara Andres (andressn@mcmaster.ca) and is open to all IIDR faculty and trainees. Journal Club meetings are held on the second Wednesday of every month in MDCL 2218.

Bio-Data Lunch

Hosted by the Department of Biology, a Friday lunch to discuss all things biological data. Contact Dr. Ben Bolker for details.

Seminars, Work-in-Progress, Rounds

The Farncombe Family Digestive Health Research Institute has weekly Research in Progress and Noon Rounds.

Seminars! Our favourites are in the Department of Biochemistry & Biomedical Sciences, Department of Biology, MacData Institute, and the Michael G. DeGroote Institute for Infectious Disease Research (IIDR). Watch for the monthly IIDR – Infectious Diseases Joint Rounds!

McArthur Lab Meeting

The McArthur Lab has a group lab meeting most weeks in which we discuss our latest research progress. Thinking about joining the lab? Consider sitting in one of our meetings. Contact mcarthua@mcmaster.ca for details.

Suggested Reading & Online Tutorials

Drug Resistance

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Bioinformatics, Computing, Genome Science

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Science in Society, Women in Science, Social Justice

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