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 firstname.lastname@example.org 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, Resistance Gene Identifier tester, or Galaxy user? This Git Lab server is where you submit and track bug reports, data curation issues, software requests, and your questions.
Comprehensive Antibiotic Resistance Database
- CARD version 1 (VPN, http://legacycard.mcmaster.ca)
- CARD version 2 (http://card.mcmaster.ca)
- CARD development & curation server (VPN, http://devcard.mcmaster.ca)
Relion Electron Cryo-Microscopy Image Analysis
Cryo-EM analysis is led by the laboratory of Dr. Joaquin Ortega (Department of Biochemistry & Biomedical Sciences, McMaster University), email@example.com.
- cryoem.mcmaster.ca (SSH, VPN) [Galaxy instance]
Linux Workhorses & Galaxy Instances
The Mcarthur Lab uses both command line and Galaxy for a variety of bioinformatics analyses, with a focus on next-generation sequencing data such as RNA-Seq, ChIP-Seq, etc. Collaborators and members of the McMaster research community are welcome to use our Galaxy server for their analyses. Galaxy access is provided for registered users only – contact firstname.lastname@example.org to register. All Galaxy users must join the Galaxy Repository as this is the central resource for bug reports, issue tracking, documentation, and data/software requests.
- galaxylab.mcmaster.ca (ubuntu, 38 processors, 384 GB memory) (SSH, VPN) [Galaxy instance]
- goteborg.mcmaster.ca (ubuntu, 32 processors, 256 GB memory) (SSH, VPN)
- goteborg2.mcmaster.ca (ubuntu, 30 processors, 128 GB memory) (SSH, VPN)
- General linux bioinformatics server (various FHS researchers), uppsala.mcmaster.ca (SSH, VPN)
- Restricted linux bioinformatics server, Chemical-Genetic DB, tingsryd.mcmaster.ca (SSH, VPN)
- BIGSdb interface (coming soon) (VPN)
- AMR Discussion Forums (http://amr.mcmaster.ca)
- UPSTREAM Promotor Analysis database (login required, http://tingsryd.mcmaster.ca)
- ClinicalDB (pathogen genome sequencing) (coming soon) (VPN)
VPN = McMaster virtual private network access required, SSH = secure shell access required