GSI is a team of bioinformaticians and software developers at Ontario Institute for Cancer Research that develop, maintain, and operate the core analysis infrastructure, analyze genomic data produced at the institute, and support collaborators and researchers with their bioinformatics analysis.
To support these activities, we have developed a large suite of open-source software that can be found under our Github organizations: oicr-gsi and miso-lims.
For more information and shinier graphics including information about working with us, please visit OICR Genomics and Bioinformatics.
Laboratory tracking
To support our wetlab colleagues, we develop a variety of apps for laboratory tracking that also play nicely with downstream computational tools. For more of our lab tracking software, visit the miso-lims Github organisation.
- MISO LIMS : laboratory information management system specifically for sequencing facilities.
- Run Scanner : web server that monitors output from sequencing instruments (Illumina, PacBio and Oxford Nanopore) and reports their status and metrics
- Visionmate client : Client for accessing a Thermo Scientific VisionMate scanner via TCP/IP
- rawprintserver : Raw Print Server for connecting with network printers (imported and patched)
Pipeline
One of our main goals is to automate as much analysis, validation, and reporting as possible and we’ve built a suite of APIs and software to help.
General Purpose
- server-utils : Java library for creating standard status pages for web servers without real UIs
- drmaaws : A webservice for interacting with DRMAA-based clusters
- node-starter-kit : Basic setup for a new Node project
- queue_use : Calculate the usage and other stats for an SGE queue
Analysis Infrastructure
- Nabu: QC tracking for files via a web service
- Shesmu : Decision-driven action launching system
- Niassa : Bioinformatics workflow engine and analysis provenance system
- Guanyin : Reporting repository and report record keeping
- Pinery : A LIMS abstraction layer to provide generalized LIMS access via a web service.
- Cerberus : Provenance API web service
- Provenance : A Java API for LIMS and analysis metadata
- Acquacotta Shiny Run Report : Interactive and dynamic representation of Run Reports
Bioinformatics Tools
- Debarcer : Debarcer: A package for De-Barcoding and Error Correction of sequencing data containing molecular barcodes
- bamqc : Perl scripts for generating quality control stats from BAM files
- xenoclassify : Classifying short-read sequencing data from xenograft samples
Contact us
Contact us either through the Github issue tracker on any project or in our Gitter room.