The Bioinformatics Innovation Centre (BIC) will continue all aspects of the Innovation Centre activity while working with Genome Canada funded projects from the Applied Genomics and Proteomics Research in Human Health Competition, Project Competition III, and other funded research initiatives. Service for the Bioinformatics Innovation Centre are provided on an as-required, customized basis or through new development on a world-wide scale to diverse teams in research and industry.
Services focus on the areas of:
BioMOBY/SADI Web Services (Mark Wilkinson)
BioMOBY/SADI The Bioinformatics Innovation Centre is a world-leader in the creation of data integration and interoperability technologies, including being the source of the BioMOBY and SADI semantic web service frameworks.
These “invisible” technologies allow Innovation Centre data and analysis services to run seamlessly together with the third-party data and analytical tools worldwide, requiring no custom programming or data manipulation by our end-users. Thus, Innovation Centre users can create and run their own complex analytical pipelines, involving the full spectrum of global bioinformatics data and analytical tools, in minutes, and with only minimal software training.
Help Desk/Tools for Proteomics (David Wishart)
The Help Desk offers access to: Phytochemical and food component databases * Biostatistical support and programming * Metabolomic data interpretation * Proteomic data analysis * Microarray data analysis *Automated and semi-automated plant, animal and microbial genome annotation * Text mining and text extraction * Data mining *Machine learning * Custom Programming and custom tool development * Support for ~40 general use databases and webservers * Laboratory Information Management System (LIMS) development * Scientific Database Management System (SDMS) development *Freely available software (from the HelpDesk’s Software Repository) * Web site development * Software advice and assistance * Learning how to program * Monthly Newsletters * A Bioinformatics Researcher Directory.
The Help Desk offers many software tools and databases to the research community, including *BASys (Bacterial Annotation System) * ThePlasMapper server * BacMap * CGView * DrugBank * T3DB * HMDB * PROSESS * VADAR * GelScape * MetaboAnalyst * MSEA * SMPDB and many other tools.
Large Scale Genome Analysis and Hardware Provision
The Sun Center of Excellence for Visual Genomics (CEO) is the lead site for the BIC located at the University of Calgary’s Faculty of Medicine, providing computational infrastructure support through a unique and extremely powerful combination of hardware and next-gen sequencing
Genome and transcript assembly for traditional and next-gen sequencing
In-depth sequence annotation, controlled access Web presentation, and public database submission
Metagenomics/environmental sample analysis
Taxonomy, comparative genomics, phylogenetics, clustering and visualization
Gene expression and microarray analysis of all kinds
Oligonucleotide design, biomarker development
Advanced 2D and 3D medical image analysis, model construction
Web portal development
Command-line access to high-performance computing resources
Large-scale, archival quality data storage
Training (Brian Fristensky & Christoph Sensen)
The Applied Computational Genomics Course (ACGC) The ACGC provides researchers with entry level skills an opportunity to become empowered and increase their problem-solving skills through provision of a hands-on-course, with lectures and tutorials presented by a panel of experts. The course uses tools and services available through the Bioinformatics Innovation Centre. Most tools used are open-source and can be freely downloaded for use at one’s home institution. Topics include (subject to change): Becoming a power user * Perl Programming * Creating automated data pipelines * High throughput genome annotation * Help Desk Services * Secure user of remote bioinformatics systems.
BIRCH – Desktop bioinformatics tools (Brian Fristensky)
Birch – a comprehensive desktop bioinformatics system which comes with many of the commonly-used bioinformatics programs pre-installed (e.g. NCBI, FASTA, PHYLIP, TIGR, TCOFFE, Jalview). It is also a framework of tools, files, and documentation for organizing and managing a bioinformatics core facility and an expandable system that allows you to merge 3rd party programs and documentation seamlessly into the standard BIRCH distribution.
For additional information on the Bioinformatics Innovation Centre and its services or to discuss how we can be of service to you, please contact: