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.
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 email@example.com 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.
- CARD Production Server (i.e. public website) (http://card.mcmaster.ca)
- CARD Development & Curation server (VPN, http://devcard.mcmaster.ca)
- CARD*Shark & Staging server, amr.mcmaster.ca
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.
- fhssuperdome.mcmaster.ca SuperDome Flex (Red Hat Enterprise Linux, 144 processors, 3 TB memory) (SSH, VPN). Hardware support from Hewlett Packard Enterprise via Canadian Foundation for Innovation (CFI) funding.
- fhsapollo.mcmaster.ca HPE Apollo 6500 (Red Hat Enterprise Linux, 80 CPU + 8 GPU, 384 GB memory) (SSH, VPN). Hardware support from Hewlett Packard Enterprise via Canadian Foundation for Innovation (CFI) funding.
- ascension.mcmaster.ca (Ubuntu, 88 processors, 1.5 TB memory) (SSH, VPN). Hardware donation from Cisco Systems Canada, Inc.
- upswing.mcmaster.ca (Ubuntu, 88 processors, 1.5 TB memory) (SSH, VPN). Hardware donation from Cisco Systems Canada, Inc.
- galaxylab.mcmaster.ca (Ubuntu, 32 processors, 384 GB memory) (SSH, VPN)
- goteborg2.mcmaster.ca (Ubuntu, 30 processors, 70 GB memory) (SSH, VPN)
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 firstname.lastname@example.org
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 (email@example.com) and is open to all IIDR faculty and trainees. Journal Club meetings are held on the second Wednesday of every month in MDCL 2218.
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 firstname.lastname@example.org for details.
Suggested Reading & Online Tutorials
- Wright & Brown: The greatest threat of our time — antibiotic resistance (National Post 2015)
- 2019 When Antibiotics Fail: The Expert Panel on the Potential Socio-Economic Impacts of Antimicrobial Resistance in Canada
- 2019 CDC AR Threats Report [USA]
- 2018 Progress Report on the 2015 Federal Action Plan on Antimicrobial Resistance and Use [Canada]
- 2017 Tackling Antimicrobial Resistance and Antimicrobial Use: A Pan-Canadian Framework for Action
- 2016 Forum on Genomics and Antimicrobial Resistance – Workshop Report [Canada]
- 2016 UK Review on Antimicrobial Resistance
- 2015 Federal Action Plan on Antimicrobial Resistance and Use in Canada: Building on the Federal Framework for Action
- 2015 Reports of the Auditor General of Canada Report — Antimicrobial Resistance
- 2014 U.S. National Strategy for Combating Antibiotic-Resistant Bacteria
- 2014 Antimicrobial Resistance and Use in Canada: A Federal Framework for Action
- 2014 WHO Antimicrobial Resistance Global Report on Surveillance
Bioinformatics, Computing, Genome Science
- Bioinformatics Goes Back to the Future [Nature]
- Developing Bioinformatics and Programming Skills
- Pick Up Python [Nature]
- Introduction to Shell (command line training)
- Free MIT video lecture series: Introduction to Python
- Rosalind, online bioinformatics problem sets
- Coursera, online courses
- DataCamp, teaches basics of Python and R (tutorials target the Data Sciences)
- Codeacademy, learn coding basics, a good starting point for Python
- Suggested books: Bioinformatics Data Skills, Practical Computing for Biologists
- WikiBooks: Next Generation Sequencing (NGS)
- ISB Biocuration Training Materials
- The Four Vs of Big Data
- Internet of DNA [MIT Tech Review]
- Craft beautiful equations in Word with LaTeX
Science in Society, Women in Science, Social Justice
- Science Culture: Where Canada Stands
- Reflecting on Fifty Years of Progress for Women in Science [DNA and Cell Biology]
- The Henrietta Lacks Legacy Grows [dig deeper: The Immortal Life of Henrietta Lacks]
- The Man Behind the Machine [Nature] [dig deeper: Alan Turing: The Enigma]