Omics & Phenotyping Portal

Omics & Phenotyping Portal


The Life Sciences Institute curates a directory of services and resources for Omics, Phenotyping, and other Core technologies to enable research. We provide links under Genomics, Proteomics, Metabolomics, Microbiomics, Imaging, Phenotyping, Data Management & Analysis and Other Portals.


Contents

Genomics

Genomics includes assessment of genome-wide phenomena involving DNA, RNA and epigenetic marks. Applications of high throughput sequencing include: sequencing or resequencing of whole or targeted regions of genomes from a single cell to microbial communities to whole organisms (genomics); capturing the complete expression profile of protein-coding genes as well as noncoding RNAs by RNA-sequencing (transcriptomics); genome-wide profiling of DNA-protein interactions (ChIP-Seq), epigenetic marks, and chromatin structure (epigenomics); and analysis of microbiome genetic potential and gene expression.

LSI Genomics Directors Don Moerman & Corey Nislow

High Throughput Sequencing

UBCSeq

http://sequencing.ubc.ca/

The UBC Sequencing Centre at Pharmaceutical Sciences is an end-to-end genetic analysis pipeline designed to enable a broad range of research. Their state-of-the-art technology allows them to develop and utilize customized solutions for sequencing, bioinformatic analysis and clinical applications with rapid turnaround times. Their website provides clear descriptions of services, costs and turnaround times.

UBCSeq provides high throughput sequencing on Illumina MiSeq and HiSeq, including library preparation; results are provided as FASTQ files. UBCSeq has the first Canadian installation of the KnoSYS Human Genome Interpretation Platform, which provides the capacity to interpret variant lists from human genome, exome and targeted sequencing data with integrated hardware and software.

Contact

Corey Nislow, Director
Sunita Sinha, Manager
P: 604-827-0310
E: sequencing.centre [at] ubc.ca

Pharmaceutical Sciences Building
University of British Columbia
6204 – 2405 Wesbrook Mall
Vancouver, BC V6T 1Z3

LSI Collaborators and Key Users

The Director of UBCSeq, Corey Nislow, is a Director of the Genomics Suite in the LSI's 2014 application to the Canada Foundation for Innovation. LSI Principal Investigators Don Moerman, Pieter Cullis, Steven Hallam, Bill Mohn, Jim Johnson, and Chris Overall have ongoing collaborations with Nislow. Leonard Foster is a key user of UBCSeq.

Genome Sciences Centre - Sequencing

http://www.bcgsc.ca/services

The GSC, Canada's Michael Smith Genome Sciences Centre, is the largest capacity genomics centre of its type in Canada. The GSC specializes in high-throughput, large-scale genome research activities encompassing cancer genetics, bioinformatics, LIMS, DNA sequencing, data analysis, genome mapping, gene expression profiling, proteomics and technology development. The GSC has services available for sequencing, bioinformatics platform services, proteomics and in-silico drug design.

GSC services are in high demand. Consult the Terms of service and the Queue for estimated turnaround times.

Sequencing services include:

  • Second generation sequencing - Illumina HiSeq 2000/2500
  • High-throughput DNA sequencing - AB 3730XL
  • T-cell and B-cell receptor profiling

Contact

Diane Miller, Project Manager
P: (604) 707-5808
F: (604) 877-6085
E: dmiller [at] bcgsc.ca

Genome Sciences Centre, BC Cancer Agency
Suite 100, 570 West 7th Ave
Vancouver, BC, V5Z 4S6

Macrogen

http://www.macrogen.com/eng/business/ngs_overview.html

recommended by Brett Finlay, UBC, for Microbiome sequencing

4 to 8 week turnaround time with competitive pricing.

Biodiversity Research Centre NextGen Sequencing Facility

https://sites.google.com/site/biodiversitynextgensequencing/

We have highly competitive turnaround times of two months, including DNA or RNA library preparation. Results are provided as FASTQ or raw data files. Our services are accessible to first-time users of next-gen sequencing as well as experienced users who wish to prepare their own libraries. Projects are conducted on a first-come first-served basis. We encourage you to contact us if you are considering a sequencing experiment as we offer project design guidance and support free of charge.

Contact
Anastasia Kuzmin
P: 604-822-6438
E: kuzmin [at] zoology.ubc.ca

Biodiversity Research Centre
University of British Columbia
260-2212 Main Mall
Vancouver, BC

Laboratory for Advanced Genome Analysis

http://www.pctriadd.com/genomic-analysis/overview

Vancouver Prostate Centre genomics core facility

Expertise: The Laboratory for Advanced Genome Analysis (LAGA) specializes in the acquisition, processing, statistical analysis, integration, and visualization of high-density sequencing and microarray data. Our highly trained technicians interpret complex data and offer important recommendations for the best possible use of genomics and transcriptomics technology. LAGA prides itself on providing clients with solutions that are rapid, economical and tailored to their needs. From 2011 to 2014, LAGA’s performance has been rewarded by 17 peer-reviewed publications arising directly from work performed by Dr. Collins’ group and close collaborators.

LAGA has unique capabilities in the following areas:

  • Translational genomics, where genomics, computer science, and clinical science converge in diagnostics and therapeutics
  • Combined use of microarray and sequencing technologies
  • Advanced bioinformatics and data visualization
  • Comparative oncogenomics, where tumours from different organ sites converge on common genome structures as they progress toward metastasis

Services: PC-TRiADD’s Laboratory for Advanced Genome Analysis supports small and large-scale projects across Canada and internationally for the following applications:

Microarray Platform

  • Agilent catalog and custom design microarray

Microarray Applications As a Certified Service Provider, all Agilent microarray applications are supported; LAGA specializes in:

  • Gene, exons and non-coding expression
  • Array Comparative Genomic Hybridization with CGH probes for genome-wide DNA copy number variation and SNP probes for copy neutral aberrations

Next Generation Sequencing Platforms

  • Life Technologies Ion Proton
  • Illumina MiSeq

Next Generation Sequencing Applications

  • Exome sequencing
  • Amplicon sequencing including 16S rRNA genes
  • Target capture sequencing
  • RNA sequencing (Quantitation)
  • RNA sequencing (Transcriptome)
  • Small RNA sequencing
  • Microbial and viral whole genome sequencing, including metagenomics

Bioinformatics

  • Acquisition, processing, statistical analysis, integration, and visualization of high-density genomic and transcriptome data from simple to complex experimental designs using one of several platforms
  • Utilization of software that allows seamless cross-platform integration and analysis of expression, genomic, and next generations sequence data making possible extremely powerful and comprehensive studies

Contact

Research:
Colin Collins, PhD
Professor, Dept. Urological Sciences
University of British Columbia
Senior Research Scientist
Director, LAGA and BGI@VPC
P: 604-779-9287
E: ccollins [at] prostatecentre.com

Services:
Stéphane LeBihan, PhD
Manager, LAGA and BGI@VPC
P: 604-875-4506
E: slebihan [at] prostatecentre.com

Vancouver Prostate Centre
2660 Oak Street
Vancouver, BC, Canada V6H 3Z6

Single Cell Genomics

Bigelow Laboratory Single Cell Genomics Center

https://scgc.bigelow.org/

The Single Cell Genomics Center (SCGC) is a nonprofit research and service center at Bigelow Laboratory for Ocean Sciences, with its primary focus on microbial single cell genomics for applications in microbial ecology, evolution, bioprospecting and human health. SCGC offers a comprehensive suite of single cell genomics services, from single cell separation through genome sequencing and bioinformatics and can provide advice on environmental sample collection and storage protocols and post-sequencing analyses.

Contact

Ramunas Stepanauskas, Director
Brian Thompson, Manager
P: 207-315-2567, ext. 517
F: 207-315-2329
E: bthompson [at] bigelow.org

Single Cell Genomics Center
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive
East Boothbay, Maine 04544-0380 USA

Expression Analysis

For RNASeq expression analysis see Genomics > High Throughput Sequencing

CDRD - Target Validation

http://www.cdrd.ca/about-us/facilities-and-expertise/target-validation/

Recommended by Suheda Erener, Kieffer Lab, LSI, for fair pricing and fast straightforward service.

The Centre for Drug Research and Development (CDRD) offers global transcriptional analysis using the Affymetrix Microarray platform. Consult their website for listings of a wide range of other facilities and expertise.

Contact

T. Michael Underhill, Division Chair
Edie Dullaghan, Head
P: 604-827-1147
F: 604-827-1299
E: edullaghan [at] cdrd.ca

Pharmaceutical Sciences Building
University of British Columbia
2405 Wesbrook Mall (corner of Wesbrook and Agronomy Rd.), Fourth Floor
Vancouver, BC V6T 1Z3

Other

NAPS

http://naps.msl.ubc.ca

The NAPS Unit at UBC is a core facility providing DNA sequencing and genotyping services to both academic and commercial researchers. Generating 1,000+ bases per run, data is available within 24hrs through an on-line dnaLIMS (Laboratory Information Management System). Highly trained staff, comprising >20 years of sequencing expertise, provide personalized service to assist with experimental design, data interpretation, and troubleshooting difficult templates.

The facility also operates a NAPS-IDT portal, an Applied Biosystems On-Site Freezer Program and a QIAstock cabinet, providing easily accessible custom oligonucleotides and molecular biology reagents to the scientific community.

Contact

Debbie Adam, Director
P: 604-822-9769
F: 604-822-9174
E: dna_lab [at] interchange.ubc.ca

Lyndsey
P: 604-822-4570

NAPS Unit
University of British Columbia
Room 419 - NCE Building
2125 East Mall
Vancouver, BC, CANADA V6T 1Z4

Genomics Training and Online Resources

SEQanswers Forum

http://seqanswers.com/forums/index.php

SEQanswers was founded to be an information resource and user-driven community focused on all aspects of next-generation genomics including next generation sequencing technology discussion and education. The site attempts to cater to everyone, regardless of scientific background or knowledge.

Informatics on High Throughput Sequencing Data - CBW 2014

http://bioinformatics.ca/workshops/2014/informatics-high-throughput-sequencing-data-2014

Video (.mp4) and slide decks (.pptx and .pdf) of lectures from from the two-day Canadian Bioinformatics Workshops on Informatics on High Throughput Sequencing Data, June 2014. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Visualization Tools; Reference-guided Genome Alignment; Small-variant calling and annotation; Structural variant calling (includes CNVs); Visual Analysis, Bringing it all together: Galaxy; De Novo Assembly.

Informatics for RNA-sequence Analysis - CBW 2014

http://bioinformatics.ca/workshops/2014/informatics-rna-sequence-analysis-bc-2014

Video (.mp4) and slide decks (.pptx and .pdf) of lectures from from the two-day Canadian Bioinformatics Workshops on Informatics for RNA-sequence Analysis, June 2014. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Introduction to RNA sequencing and analysis; RNA-seq alignment and visualization; Expression and differential expression; Isoform discovery and alternative expression.

Bioinformatics for Cancer Genomics - CBW 2014

http://bioinformatics.ca/workshops/2014/bioinformatics-cancer-genomics-bicg-2014

Video (.mp4) and slide decks (.pptx and .pdf) of lectures from from the five-day Canadian Bioinformatics Workshops on Bioinformatics for Cancer Genomics, May 2014. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Introduction to Cancer Genomics; Databases and Visualization Tools; Alignment & Genome rearrangements; Gene Fusion Discovery; Copy Number Alterations; Somatic Mutations; Variants to Networks; Gene Expression Profiling; Integration of Clinical Data.

Pathway and Network Analysis of -omics Data - CBW 2014

http://bioinformatics.ca/workshops/2014/pathway-and-network-analysis-omics-data-2014

Video (.mp4) and slide decks (.pptx and .pdf) of lectures from from the 2.5-day Canadian Bioinformatics Workshops on Pathway and Network Analysis of -omics Data, June 2014. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Brief introduction to gene lists; Regulatory Network Analysis; Finding over-represented pathways in gene lists; Pathway and Network Analysis; Network Visualization; Gene Function Prediction.

Proteomics

Proteomics is the large-scale study of proteins, including their abundance, modifications, structures, functions, interacting partners and complexes.

LSI Proteomics Directors Chris Overall & Leonard Foster

UBC Proteomics Core Facility

http://www.chibi.ubc.ca/facilities-2/proteomics-core-facility-3/proteomics-core-facility/

The Proteomics Core Facility (PCF) offers a broad range of services, from mass confirmations to large-scale quantitative proteomic screens, along with all the associated bioinformatics. Basically, if it involves characterizing polypeptides, we can probably do it. Some of the services we provide most commonly include:

  • Measure the mass and identity of a protein or peptide you may have (e.g., to confirm successful synthesis of a peptide or the purity of a recombinant protein
  • Identify unknown bands from a gel
  • Characterize post-translational modifications on your favourite protein
  • Identify the protein interacting partners of a ligand
  • Measure global changes in protein levels or post-translational modifications (e.g., phosphoproteomics)
  • Monitor the global interaction landscape of cells

We are also open to collaborative projects on a case-by-case basis. Staff in the PCF are available for project planning and sample preparation in addition to general mass spectrometry scientific advice and consulting on a walk-in basis.

New resource - Expected availability November 1, 2014 Whole genome shRNA libraries for human & mouse available to UBC community (for testing 1 to 20,000 genes) - through UBC PCF or through #NAPS

Comment from Stefanie Butland, LSI: The UBC Proteomics Core Facility site provides rich details for new users such as pre-reading, how to prepare samples, how to read results.

Contact
Jason Rogalski, Operations Manager
P: 604-827-5209
F: 604-827-2603
E: rogy [at] mail.ubc.ca

Leonard Foster, Director
P: 604-822-8311
F: 604-827-2603
E: foster [at] chibi.ubc.ca

NCE Building
University of British Columbia
416-2125 East Mall
Vancouver, BC V6T 1Z4 CANADA


LSI Collaborators and Key Users

The Director of the UBC Proteomics Core Facility, Leonard Foster, is a Director of the Proteomics Suite in the LSI's 2014 application to the Canada Foundation for Innovation. LSI Principal Investigators Pieter Cullis, Paul Pavlidis, Chris Overall, Lindsay Eltis and Brett Finlay have ongoing collaborations with Foster.

University of Victoria GenomeBC Proteomics Centre

http://www.proteincentre.com/

Featured Services:

  • Biomarker Discovery and Validation
  • Quantitative Proteomics
  • MRM Assays
  • Structural Proteomics
  • MALDI Imaging
  • Protein Characterization
  • Protein Identification
  • Peptide Synthesis
  • Bioinformatics
  • Metabolomics through #TMIC - The Metabolomics Innovation Centre

Contact

Christoph Borchers, Director
P: 250-483-3221
E: christoph [at] proteincentre.com

Derek Smith, Technical Operations Manager, Project Manager
P: 250-483-3224
E: derek [at] proteincentre.com

University of Victoria - Genome BC Proteomics Centre
Vancouver Island Technology Park
3101-4464 Markham St
Victoria, BC V8Z 7X8

ASTRID

http://astrid-lsi.sites.olt.ubc.ca/infrastructure/

The ASTRID - Advanced Structural Biology for Re-emerging Infectious Diseases - infrastructure platform includes an NMR Spectroscopy Unit, an X-ray Crystallography Unit and a Bio-analytical Unit. ASTRID was established with support from the Canadian Foundation for Innovation and the BC Knowledge Development Fund.

Contact

Lawrence McIntosh
E: mcintosh [at] chem.ubc.ca

Metabolomics

Metabolomics involves the the near global analysis of small molecule metabolites (< 1500 Daltons, including carbohydrates, amino acids, lipids, nucleotides). The metabolome is the complete set of metabolites within a cell, tissue or biological sample at any given time point.

LSI Metabolomics Directors James Johnson & Lindsay Eltis

TMIC - The Metabolomics Innovation Centre

http://www.metabolomicscentre.ca/

recommended by Brett Finlay, UBC

The Metabolomics Innovation Centre (TMIC) is a nationally-funded research and core facility that supports a wide range of metabolomic studies for clinical trials research, biomedical studies, bioproducts studies, nutrient profiling and environmental testing. Methods include: NMR, GC-MS, DI-MS, HPLC, LC-MS, MALDI Imaging, Lipidomics, ICP-MS. The TMIC website provides detailed descriptions of services provided, types of metabolomics assays, equipment, software and databases.

TMIC is led by Dr. David Wishart (University of Alberta), Dr. Christoph Borchers (University of Victoria), Dr. Liang Li (University of Alberta), and Dr. James Harynuk (University of Alberta).

Contact
http://www.metabolomicscentre.ca/contact

Rupasri Mandal, Project Manager
P: 780-492-8574
E: rmandal [at] ualberta.ca


LSI Collaborators and Key Users

TMIC leads, David Wishart and Christoph Borchers are partners in the LSI's 2014 application to the Canada Foundation for Innovation. Brett Finlay is a key user of TMIC.

Metabolon

http://www.metabolon.com/research-services.aspx

Metabolon, Inc., is a pioneer in outcome-based metabolomics providing high-throughput metabolite identification, quantification and analysis of nearly any sample type. Metabolon’s expert biochemists, molecular biologists and nutritionists work directly with collaborators to understand investigator research goals, design well-powered metabolomics studies, and interpret the data output from small and large sample sets to yield meaningful results. A publication-ready report and other deliverables convey study outcomes, provide statistical and biological interpretation and identify candidate biomarkers.

Metabolon offers metabolomic profiling services on hundreds of different sample types from most species. The number of metabolites identified depends on the sample type, but typically ranges from 500-1000 metabolites in common sample types such as urine or plasma. Samples are processed in either Metabolon’s biomarker discovery lab or its CLIA-certified and CAP-accredited clinical diagnostics lab using a multi-platform approach incorporating GC/MS, GC-FID and UPLC/MS/MS. Metabolon’s proprietary software and extensive biochemical reference library of 14000+ known and novel metabolites (including complex lipids) allow them to offer broad global metabolic profiling, metabolite class-specific focused panels, and custom-built targeted assays. Interpreted study results and deliverables are provided via a secure, interactive client portal featuring a suite of statistical and bioinformatics tools allowing investigators an ability to explore, visualize and share study results. Global profiling results are typically returned within 6-8 weeks.

Contact

Jeff Buckthal, Sr. Director, Science Development
P: 919-802-6244
E: jbuckthal [at] metabolon.com

Metabolomics Training and Online Resources

Informatics and Statistics for Metabolomics - CBW 2014

http://bioinformatics.ca/workshops/2014/informatics-and-statistics-metabolomics-2014

Video (.mp4) and slide decks (.ppt and .pdf) of lectures from from the two-day Canadian Bioinformatics Workshops on Metabolomics, June 2014, delivered by David Wishart, Canadian Metabolomics expert and co-lead of #TMIC - The Metabolomics Innovation Centre - The Metabolomics Innovation Centre. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Introduction to Metabolomics; Software for Metabolite Identification and Quantification; Metabolite Identification and Annotation; Databases for Chemical, Spectral and Biological Data; LC-MS spectra processing using XCMS; Backgrounder in Statistical Methods; Metabolomic Data Analysis using MetaboAnalyst; Data Integration, and Applications and the Future of Metabolomics.

Introduction to Metabolomics - EBI

http://www.ebi.ac.uk/training/online/course/introduction-metabolomics

The EBI Introduction to Metabolomics provides a very clear basic introduction and takes 30-60 minutes to click through.
Learning objectives:

  • Comprehend the purpose and importance of the field of metabolomics
  • Describe some principles of metabolomic study design
  • Evaluate advantages and limitations of some analytical techniques used in metabolomics studies
  • Discuss some of the modern-day applications of metabolomics
  • Access metabolomics resources at the EBI

Microbiomics

Microbiomics is the study of complex communities of microbiota and the interactions between microbiome and host. High-throughput sequencing platforms are integrated into microbiomics workflows.

LSI Microbiomics Directors Bill Mohn & Steven Hallam

MetaPathways

http://hallam.microbiology.ubc.ca/MetaPathways/

MetaPathways is a modular software pipeline for integrated analysis of environmental sequence information, developed by the Hallam Laboratory. It takes an assembled or unassembled genomic sequence file (.fasta), predicts open reading frames (ORFs), and systematically produces a series of data products using the MEGAN, ML-TreeMap, tRNA-scan, and 16S SSU rRNA methods and software. The pipeline culminates in the production of an environmental pathway/genome database (ePGDB), inferring metabolic potential using the Pathway Tools software.

Contact

Steven Hallam
P: 604-827-3420
F: 604-822-6041
E: shallam@mail.ubc.ca

Life Sciences Institute
2.552 - 2350 Health Sciences Mall
University of British Columbia
Vancouver, BC V6T 1Z3
Canada

MetaMixis

http://www.metamixis.com/

MetaMixis is an integrated synthetic biology company that uses a platform that screens environmental DNA for the synthesis and secretion of targeted small molecules to engineer microbes in an iterative and high throughput manner. MetaMixis Inc. was established by LSI researcher Dr. Steven Hallam.

Contact

P: (604) 827-3420
F: (604) 822-6041
E: contact [at] metamixis.com

Microbiomics Training and Online Resources

Hallam Lab Video Protocols

http://hallam.microbiology.ubc.ca/LabResources/Protocols.html

The Hallam Laboratory provides 8 Jove video protocols that are 5 to 20 minutes long:

  1. Seawater Sampling and Collection
  2. Large Volume (20L+) Filtration of Coastal Seawater Samples
  3. Small Volume (1-3L) Filtration of Coastal Seawater Samples
  4. DNA Extraction from 0.22 μM Sterivex Filters and Cesium Chloride Density Gradient Centrifugation
  5. Large Insert Environmental Genomic Library Production
  6. Extraction of High Molecular Weight Genomic DNA from Soils and Sediments
  7. Expression of Recombinant Proteins in the Methylotrophic Yeast Pichia pastoris
  8. A High Throughput Screen for Biomining Cellulase Activity from Metagenomic Libraries


Contact

Steven Hallam
P: 604-827-3420
F: 604-822-6041
E: shallam@mail.ubc.ca

Life Sciences Institute
2.552 - 2350 Health Sciences Mall
University of British Columbia
Vancouver, BC V6T 1Z3
Canada

Imaging

LSI Imaging Core

http://lsi.ubc.ca/resources/facilities/imaging/

LSI Imaging is a core research imaging facility of the Life Sciences Institute with state of the art fluorescence microscopy equipment. Applications include FRET, FRAP, TIRF and high throughput content screening (small molecule and siRNA). It provides access, user training and technical assistance for super-resolution microscopy, confocal microscopy (point laser scanning or spinning disk), high throughput imaging and image deconvolution, 3D reconstruction and quantitative analysis.

Contact

I. Robert Nabi, Director
P: 604-822-7000
E: ivan.robert.nabi [at] ubc.ca

Fanrui Meng (Ray), Manager
P: 604-827-3946
E: frui.meng [at] gmail.com

Life Sciences Institute
University of British Columbia

LSI TEM Facility

http://lsi.ubc.ca/resources/facilities/tem/

The LSI Transmission Electron Microscopy (TEM) facility houses the TEM and ultramicrotome purchased from a Canada Foundation for Innovation grant received by Drs. Robert Molday, Wayne Vogl and Nelly Pante. The TEM has a high level of automation and is suitable for applications like 3D-imaging using tomography and/or cryo-electron microscopy.

Contact

Wayne Vogl
E: wayne.vogl [at] ubc.ca
Life Sciences Institute
University of British Columbia

Phenotyping

Phenotyping is a broad category that includes Cell Phenotyping, Model Organisms and Functional Screening.

LSI Phenotyping Directors Tim Kieffer & Robert Nabi

Cell Phenotyping

ubcFLOW Cytometry Facility

http://www.ubcflow.ca/

The UBC Flow Cytometry Facility offers a state of the art facility with a wide range of instruments at two locations on the UBC Vancouver Campus open to industry, academia and government agencies. We have multicolour, high throughput and clinical specific analysers, combined with cell sorters and a CyTOF; enabling you to analyse the characteristics of any cell that you might be interested in and define more than 30 simultaneous parameters relating to it.

ubcFLOW also offers cell isolation technologies that enable researchers to isolate pure populations of cells, such as stem cells or bacterial cells, from heterogeneous samples including tissues, blood or environmental samples, to interrogate their biological processes, assess for heterogeneity, and to test therapeutics.

ubcFLOW provides full training, application development and support, allowing someone new to flow cytometry to take their idea from an initial hypothesis through to publication. We would like people to send data that they have acquired by flow cytometry and are considering to submit for a grant application or publication. This would allow the facility to review your figures and make sure that you are sending out the correct message in the data. Only the flow component and figure will be analyzed and possibly improved to give you a strengthened application or manuscript.

Contact

Pauline Johnson & Fabio Rossi, Directors
Andy Johnson, Facility Manager
Justin Wong, Co-ordinator
hotline: 604-783-0204
BRC: 604-822-7838
LSC: 604-822-0437
E: andy [at] ubcflow.ca

Locations

The Life Sciences Centre
University of British Columbia
2350 Health Sciences Mall

The Biomedical Research Centre
University of British Columbia
2222 Health Sciences Mall

Flow Cytometry Data Analysis using R - CBW 2013

http://bioinformatics.ca/workshops/2013/flow-cytometry-data-analysis-using-r-2013#material

Video (.mp4) and slide decks (.pdf) of lectures from from the two-day Canadian Bioinformatics Workshops on Flow Cytometry Data Analysis using R, June 2013. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Introduction to Flow Cytometry Analysis in R, Exploring FCM data in R, Preprocessing and Quality Assurance of FCM Data, 1D Static gating, 1D Dynamic gating, Clustering and Additional FCM Tools.

AbLab - UBC Antibody Lab

http://www.AbLab.ca

Recommended by Andy Johnson, ubcFLOW

The AbLab supplies the research community with high quality in-house antibody reagents at cost. The AbLab can assist you throughout the entire process from production and down-stream processing to modification including labelling, conjugation and fragmentation. This includes custom conjugation for use in flow cytometry including CYTOF. Our production systems provide high batch-to-batch reproducibility. You provide us your hybridoma and we do the rest. The AbLab also maintains an extensive inventory of commonly used monoclonal antibodies conjugated to multiple fluorophores for your convenience and serves as a repository for researchers' hybridomas, ensuring a reliable consistent supply and simplifying the handling of requests for clones and antibodies.

Contact

Michael Williams, Facility Manager
AbLab (UBC Antibody Lab)
Front Desk: 604-822-7810
Direct: 604-822-8060
E: info [at] ablab.ca

AbLab (UBC Antibody Lab)
The Biomedical Research Centre
University of British Columbia
2222 Health Sciences Mall
Vancouver BC

Model Organisms

Expertise in Model Organisms research in the Life Sciences Institute includes Yeast (Christopher Loewen), Drosophila (Vanessa Auld, Doug Allan), C. elegans (Don Moerman), zebrafish (Tim Kieffer) and rodents.

Centre for Disease Modelling

http://www.cdm.ubc.ca/contact.html

The Centre for Disease Modelling (CDM) aspires to be recognized as a leader in animal science. The CDM provides direct access to flow cytometry and imaging systems within and outside the pathogen-free containment barrier.

Contact

P: 604.827.3425
F: 604.827.5906
E: cdm.reception [at] ubc.ca

Centre for Disease Modelling
2350 Health Sciences Mall
University of British Columbia
Vancouver, BC, Canada V6T 1Z3

FINDER - Facility for Infectious Disease and Epidemic Research

https://www.finder.ubc.ca/about#resources

The Facility for Infectious Disease and Epidemic Research (FINDER) is dedicated to discovering new avenues for antimicrobial and antiviral drugs and to developing new vaccines that combat infectious human diseases. FINDER is one of the largest and most comprehensive facilities of its kind in the world, and offers a state-of-the-art BSL-3 laboratory to researchers from across Canada and internationally.

Contact

Francois Jean, Director
E: francois.jean [at] ubc.ca
E: finder.admin [at] ubc.ca

Life Sciences Institute
University of British Columbia

COPAS Biosorter for Large Particle Flow Cytometry - Worm Sorter

The “worm” Sorter is used to place individual nematodes, or any number you desire, into individual wells and we can work with formats up to 96-well microtiter plates. On average, placing a single worm per well in a 96 well format takes less than two minutes. The sorter can be used to size-select worms for different developmental stages. It has fluorescence detection capabilities as well so that one can sort based on GFP expression screening. Applications include functional screening of sorted worms (e.g. drug screening).

Note that the flow cell size on this model is not suitable for flies or zebrafish.

See http://www.unionbio.com/copas/

Contact

Don Moerman
E: moerman [at] zoology.ubc.ca

Life Sciences Institute
University of British Columbia
2350 Health Sciences Mall
Vancouver, BC V6T 1Z3

The Million Mutation Project

http://genome.sfu.ca/mmp/search.html

The Million Mutation Project (MMP), a joint project by Don Moerman's (LSI UBC) and Bob Waterston's (University of Washington) labs, has exploited whole genome resequencing to identify multiple mutations in virtually every C. elegans gene in a collection of 2,000 mutagenized strains. The web interface allows users to search using identifiers for human genes in order to identify the C. elegans phenotype that results from mutation of that gene.

Contact

Don Moerman
E: moerman [at] zoology.ubc.ca

Biomedical Research Centre Genotyping Facility

http://brc.ubc.ca/genotyping/

Recommended by Andy Johnson, ubcFLOW

Contact
Taka Murakami
P: 604-822-9491
E: taka [at] brc.ubc.ca

The Biomedical Research Centre
University of British Columbia
2222 Health Sciences Mall
Vancouver, BC Canada V6T 1Z3

Other

LSI Tissue Processing Facility

http://lsi.ubc.ca/resources/facilities/tissue-processing/

The Tissue Processing Facility is suitable for performing immunohistochemical and immunofluorescence analysis of tissue slices (e.g. lymphoid organs, pancreas). The facility has a high quality semi-electronic cryostat as well as an Olympus BX61 motorized fluorescence microscope.

Contact

Cal Roskelly, Director
Megan Gilmour, Manager
P: 604-822-1781
E: meg.gilmour [at] gmail.com

Rm 3435, Life Sciences Centre
University of British Columbia
2350 Health Sciences Mall
Vancouver BC

Centre for Biothermodynamics

http://www.lmb.ubc.ca/BT-main.html

The Centre for Biothermodynamics (CBT) is part of the Laboratory for Molecular Biophysics and the Michael Smith Laboratories at UBC. The CBT provides academic scientists and biotechnology corporations access to and training on a suite of high-precision instruments for biophysical measurements and is the only such service available in Canada. The Centre includes high sensitivity isothermal titration calorimeters (ITC) and differential scanning calorimeters (DSC). Thermodynamic sample analysis is available with a fee-for-service structure. The CBT also includes a Biacore surface plasmon resonance detector for binding kinetic and thermodynamic studies and an analytical ultracentrifuge for macromolecule characterization.

Contact

Louise Creagh, Manager
P: 604-827-5210
F: 604-822-2114
E: alcreagh [at] chbe.ubc.ca

Laboratory
P: 604-822-3179
F: 604-822-2114

Michael Smith Laboratories
University of British Columbia
001-2185 East Mall
Vancouver, BC, CANADA V6T 1Z4

Data Management and Analysis

Bioinformatics

Life science is rapidly evolving into a data-intensive information science. A biological understanding of health and disease requires bioinformatics for integrated data generation, data management, interpretation and communication.

LSI Bioinformatics Directors: Steven Hallam & Paul Pavlidis

Pavlidis Lab Software and Resources

http://www.chibi.ubc.ca/faculty/paul-pavlidis/pavlidis-lab/software-and-resources/

Software and databases developed in the Pavlidis lab for integrated genotype and phenotype data include:

  • Gemma, a system for analyzing genomic data using meta-analysis techniques. Gemma permits researchers to compare and combine gene expression data sets with other datatypes including proteomics and genetics, and neuroscience-domain-specific data such as neuroanatomy and neuropharmacology.
  • ASPIREdb, a web-based software system for the analysis of genomic variants (CNVs, SNVs, and Indels) and phenotypes
  • Phenocarta, a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations

Contact

Paul Pavlidis
E: paul [at] chibi.ubc.ca
P: 604-827-4157

LSI Collaborators and Key Users

Paul Pavlidis is a Director of the Bioinformatics Suite in the LSI's 2014 application to the Canada Foundation for Innovation. LSI Principal Investigators Jim Johnson, Chris Overall and Shernaz Bamji have ongoing collaborations with Pavlidis.

Hallam Lab Software and Resources

http://hallam.microbiology.ubc.ca/LabResources/Software.html

KnoSYS Human Genome Interpretation Platform

http://sequencing.ubc.ca/tech/knome/

UBCSeq, the UBC Sequencing Centre at Pharmaceutical Sciences, has the first Canadian installation of the KnoSYS Human Genome Interpretation Platform. This provides the capacity to interpret variant lists from human genome, exome and targeted sequencing data with integrated hardware and software.

Contact

Corey Nislow, Director
Sunita Sinha, Manager
P: 604-827-0310
E: sequencing.centre [at] ubc.ca

Pharmaceutical Sciences Building
University of British Columbia
6204 – 2405 Wesbrook Mall
Vancouver, BC V6T 1Z3

Genome Sciences Centre - Bioinformatics

http://www.bcgsc.ca/services

The GSC, Canada's Michael Smith Genome Sciences Centre, is the largest capacity genomics centre of its type in Canada. The GSC specializes in high-throughput, large-scale genome research activities encompassing cancer genetics, bioinformatics, LIMS, DNA sequencing, data analysis, genome mapping, gene expression profiling, proteomics and technology development. The GSC has services available for sequencing, bioinformatics platform services, proteomics and in-silico drug design.

The GSC Bioinformatics Platform offers services in:

  • Genome Annotation
  • High-throughput PCR primer prediction
  • Regulatory element prediction
  • Laboratory information management systems (LIMS)
  • Data dissemination (e.g. web/ftp sites, submission to official repositories)
  • Development and maintenance of biological databases
  • Other Custom Services

The GSC Drug Discovery Platform offers in-silico drug design using Molsoft ICM software for molecular docking on a 400 CPU compute cluster to screen 1+ million compounds per day.

Specific bioinformatics analysis modules for sequence data are associated with their Sequencing services.

Contact

Diane Miller, Project Manager
P: (604) 707-5808
F: (604) 877-6085
E: dmiller [at] bcgsc.ca

Genome Sciences Centre, BC Cancer Agency
Suite 100, 570 West 7th Ave
Vancouver, BC, V5Z 4S6

Bioinformatics Training and Online Resources

Bioinformatics Links Directory

http://bioinformatics.ca/links_directory/

The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. The links listed in this directory are selected on the basis of recommendations from bioinformatics experts in the field. We also rely on input from our community of bioinformatics users for suggestions. Starting in 2003, we have also started listing all links contained in the NAR Webserver issue.

Canadian Bioinformatics Workshops

http://bioinformatics.ca/

The Canadian Bioinformatics Workshops are an annual series of specialized two to five-day hands-on workshops delivered by researchers active in the areas being taught.

  • Exploratory Analysis of Biological Data using R
  • Bioinformatics for Cancer Genomics
  • Informatics for RNA-sequence Analysis
  • Informatics on High Throughput Sequencing Data
  • Pathway and Network Analysis of -omics Data
  • Flow Cytometry Data Analysis using R
  • Informatics and Statistics for Metabolomics

Past workshop content is available under a Creative Commons License at http://bioinformatics.ca/workshops/2014

Bioinformatics Networking

VanBUG - Vancouver Bioinformatics Users Group

http://vanbug.org/

VanBUG is an association of researchers, other professionals and students in the B.C. Lower Mainland who have an interest in the field of bioinformatics. VanBUG meets on the second Thursday of every month from September through April. Research presentations by bioinformatics leaders, students and industry representatives are followed by networking over pizza and refreshments.

Subscribe to VanBUG mailing list (low volume, moderated) at http://www.vanbug.org/mailing-list/

Statistics

LSI researchers are encouraged to consult with statisticians at the earliest possible stages of experimental design for Omics or large cohort studies. This will ensure that experimental results can be analyzed appropriately and statistically rigorous conclusions can be drawn.

UBC Statistical Consulting and Research Laboratory (SCARL)

http://www.stat.ubc.ca/SCARL/

The Statistical Consulting and Research Laboratory (SCARL) is operated by the Department of Statistics. Services provided cover the spectrum of statistical design and analysis, as well as ancillary areas.

How can SCARL help? provides details on the range of services available.

SCARL offers one hour of free statistical consulting to UBC graduate students through the Statistical Opportunity for Students (SOS) program.

Contact

Rick White, Director
P: 604-822-2479
F: 604-822-6960
E: rickw [at] stat.ubc.ca

Department of Statistics
Room 3102, Earth Sciences Building
2207 Main Mall
The University of British Columbia
Vancouver BC V6T 1Z4

Statistics Training and Online Resources

R Graph Catalog

http://shinyapps.stat.ubc.ca/r-graph-catalog/

Recommended by Stefanie Butland, LSI

The R Graph Catalog is a visual index of over 100 graphs from the excellent book "Creating More Effective Graphs" by Naomi Robbins. Click on a graph thumbnail and you'll see the figure AND all the code necessary to reproduce the figure exactly with ggplot2, the R package written by Hadley Wickham. This is a resource for people who want to make a good graph and kind of know what it should look like … but they could really use an example to get started!

You can get the code for ALL figures and the infrastructure that makes the app from this repository on GitHub: https://github.com/jennybc/r-graph-catalog

The R Graph Catalog is maintained by Dr Jennifer Bryan, UBC Department of Statistics, and the initial work was facilitated by an NSERC Undergraduate Student Research Award to Joanna Zhao.

UBC Graduate Courses in Data Analysis

Recommended by Nikolas Fortelny, Overall Lab, LSI

STAT540 Statistical methods for high dimensional biology: http://www.ugrad.stat.ubc.ca/~stat540/
STAT 545A Exploratory Data Analysis and STAT 547M Basic Training for Data Science: http://stat545-ubc.github.io

Instructors include Drs. Jenny Bryan, Paul Pavlidis and Gabriela Cohen-Freue. These are very good courses for people serious about working with Omics data. Much of the course content can be found on GitHub. Follow the links above.

Exploratory Analysis of Biological Data using R - CBW 2014

http://bioinformatics.ca/workshops/2014/exploratory-analysis-biological-data-using-r-2014

Video (.mp4) and slide decks (.ppt and .pdf) of lectures from from the two-day Canadian Bioinformatics Workshops on Exploratory Analysis of Biological Data using R, May 2014. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: The R Landscape; Exploratory data analysis for biological data; Regression Analysis; Data reduction; Clustering Analysis; Hypothesis testing for EDA

Other Portals

Canada Foundation for Innovation Research Facilities Navigator

http://www.innovation.ca/en/navigator

The CFI Research Facilities Navigator is a searchable online directory of participating research labs and facilities in universities, colleges and research hospitals across Canada that are open to working with business. The Navigator was created by the Canada Foundation for Innovation (CFI) to help businesses and other organizations find the cutting-edge facilities, equipment and expertise they require to meet their research and innovation needs. For institutions and researchers, the Navigator offers an effective way to promote their labs and expertise to potential research partners in the private sector. All labs and facilities listed in this directory have received funding from the CFI or use CFI-funded infrastructure.

Science Exchange

https://www.scienceexchange.com

Search for a service, compare qualified providers, request a quote from one or more providers, select a provider. The Science Exchange allows users to compare service pricing, turn-around time, past client feedback and recommendations of expert service providers at core research and commercial facilities.

source: http://wiki.ubc.ca/Sandbox:LSI_Omics_Portal


To recommend or comment on a listing, contact A.J. Dhalla, ajdhalla [at] mail.ubc.ca

Facilities that are part of the Life Sciences Institute will have “LSI” in the description.

Genomics

Genomics includes assessment of genome-wide phenomena involving DNA, RNA and epigenetic marks. Applications of high throughput sequencing include: sequencing or resequencing of whole or targeted regions of genomes from a single cell to microbial communities to whole organisms (genomics); capturing the complete expression profile of protein-coding genes as well as noncoding RNAs by RNA-sequencing (transcriptomics); genome-wide profiling of DNA-protein interactions (ChIP-Seq), epigenetic marks, and chromatin structure (epigenomics); and analysis of microbiome genetic potential and gene expression.

LSI Genomics Directors Don Moerman & Corey Nislow

High Throughput Sequencing

UBCSeq

http://sequencing.ubc.ca/

The UBC Sequencing Centre at Pharmaceutical Sciences is an end-to-end genetic analysis pipeline designed to enable a broad range of research. Their state-of-the-art technology allows them to develop and utilize customized solutions for sequencing, bioinformatic analysis and clinical applications with rapid turnaround times. Their website provides clear descriptions of services, costs and turnaround times.

UBCSeq provides high throughput sequencing on Illumina MiSeq and HiSeq, including library preparation; results are provided as FASTQ files. UBCSeq has the first Canadian installation of the KnoSYS Human Genome Interpretation Platform, which provides the capacity to interpret variant lists from human genome, exome and targeted sequencing data with integrated hardware and software.

Contact

Corey Nislow, Director
Sunita Sinha, Manager
P: 604-827-0310
E: sequencing.centre [at] ubc.ca

Pharmaceutical Sciences Building
University of British Columbia
6204 – 2405 Wesbrook Mall
Vancouver, BC V6T 1Z3

LSI Collaborators and Key Users

The Director of UBCSeq, Corey Nislow, is a Director of the Genomics Suite in the LSI's 2014 application to the Canada Foundation for Innovation. LSI Principal Investigators Don Moerman, Pieter Cullis, Steven Hallam, Bill Mohn, Jim Johnson, and Chris Overall have ongoing collaborations with Nislow. Leonard Foster is a key user of UBCSeq.

Genome Sciences Centre - Sequencing

http://www.bcgsc.ca/services

The GSC, Canada's Michael Smith Genome Sciences Centre, is the largest capacity genomics centre of its type in Canada. The GSC specializes in high-throughput, large-scale genome research activities encompassing cancer genetics, bioinformatics, LIMS, DNA sequencing, data analysis, genome mapping, gene expression profiling, proteomics and technology development. The GSC has services available for sequencing, bioinformatics platform services, proteomics and in-silico drug design.

GSC services are in high demand. Consult the Terms of service and the Queue for estimated turnaround times.

Sequencing services include:

  • Second generation sequencing - Illumina HiSeq 2000/2500
  • High-throughput DNA sequencing - AB 3730XL
  • T-cell and B-cell receptor profiling

Contact

Diane Miller, Project Manager
P: (604) 707-5808
F: (604) 877-6085
E: dmiller [at] bcgsc.ca

Genome Sciences Centre, BC Cancer Agency
Suite 100, 570 West 7th Ave
Vancouver, BC, V5Z 4S6

Macrogen

http://www.macrogen.com/eng/business/ngs_overview.html

recommended by Brett Finlay, UBC, for Microbiome sequencing

4 to 8 week turnaround time with competitive pricing.

Biodiversity Research Centre NextGen Sequencing Facility

https://sites.google.com/site/biodiversitynextgensequencing/

We have highly competitive turnaround times of two months, including DNA or RNA library preparation. Results are provided as FASTQ or raw data files. Our services are accessible to first-time users of next-gen sequencing as well as experienced users who wish to prepare their own libraries. Projects are conducted on a first-come first-served basis. We encourage you to contact us if you are considering a sequencing experiment as we offer project design guidance and support free of charge.

Contact
Anastasia Kuzmin
P: 604-822-6438
E: kuzmin [at] zoology.ubc.ca

Biodiversity Research Centre
University of British Columbia
260-2212 Main Mall
Vancouver, BC

Laboratory for Advanced Genome Analysis

http://www.pctriadd.com/genomic-analysis/overview

Vancouver Prostate Centre genomics core facility

Expertise: The Laboratory for Advanced Genome Analysis (LAGA) specializes in the acquisition, processing, statistical analysis, integration, and visualization of high-density sequencing and microarray data. Our highly trained technicians interpret complex data and offer important recommendations for the best possible use of genomics and transcriptomics technology. LAGA prides itself on providing clients with solutions that are rapid, economical and tailored to their needs. From 2011 to 2014, LAGA’s performance has been rewarded by 17 peer-reviewed publications arising directly from work performed by Dr. Collins’ group and close collaborators.

LAGA has unique capabilities in the following areas:

  • Translational genomics, where genomics, computer science, and clinical science converge in diagnostics and therapeutics
  • Combined use of microarray and sequencing technologies
  • Advanced bioinformatics and data visualization
  • Comparative oncogenomics, where tumours from different organ sites converge on common genome structures as they progress toward metastasis

Services: PC-TRiADD’s Laboratory for Advanced Genome Analysis supports small and large-scale projects across Canada and internationally for the following applications:

Microarray Platform

  • Agilent catalog and custom design microarray

Microarray Applications As a Certified Service Provider, all Agilent microarray applications are supported; LAGA specializes in:

  • Gene, exons and non-coding expression
  • Array Comparative Genomic Hybridization with CGH probes for genome-wide DNA copy number variation and SNP probes for copy neutral aberrations

Next Generation Sequencing Platforms

  • Life Technologies Ion Proton
  • Illumina MiSeq

Next Generation Sequencing Applications

  • Exome sequencing
  • Amplicon sequencing including 16S rRNA genes
  • Target capture sequencing
  • RNA sequencing (Quantitation)
  • RNA sequencing (Transcriptome)
  • Small RNA sequencing
  • Microbial and viral whole genome sequencing, including metagenomics

Bioinformatics

  • Acquisition, processing, statistical analysis, integration, and visualization of high-density genomic and transcriptome data from simple to complex experimental designs using one of several platforms
  • Utilization of software that allows seamless cross-platform integration and analysis of expression, genomic, and next generations sequence data making possible extremely powerful and comprehensive studies

Contact

Research:
Colin Collins, PhD
Professor, Dept. Urological Sciences
University of British Columbia
Senior Research Scientist
Director, LAGA and BGI@VPC
P: 604-779-9287
E: ccollins [at] prostatecentre.com

Services:
Stéphane LeBihan, PhD
Manager, LAGA and BGI@VPC
P: 604-875-4506
E: slebihan [at] prostatecentre.com

Vancouver Prostate Centre
2660 Oak Street
Vancouver, BC, Canada V6H 3Z6

Single Cell Genomics

Bigelow Laboratory Single Cell Genomics Center

https://scgc.bigelow.org/

The Single Cell Genomics Center (SCGC) is a nonprofit research and service center at Bigelow Laboratory for Ocean Sciences, with its primary focus on microbial single cell genomics for applications in microbial ecology, evolution, bioprospecting and human health. SCGC offers a comprehensive suite of single cell genomics services, from single cell separation through genome sequencing and bioinformatics and can provide advice on environmental sample collection and storage protocols and post-sequencing analyses.

Contact

Ramunas Stepanauskas, Director
Brian Thompson, Manager
P: 207-315-2567, ext. 517
F: 207-315-2329
E: bthompson [at] bigelow.org

Single Cell Genomics Center
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive
East Boothbay, Maine 04544-0380 USA

Expression Analysis

For RNASeq expression analysis see Genomics > High Throughput Sequencing

CDRD - Target Validation

http://www.cdrd.ca/about-us/facilities-and-expertise/target-validation/

Recommended by Suheda Erener, Kieffer Lab, LSI, for fair pricing and fast straightforward service.

The Centre for Drug Research and Development (CDRD) offers global transcriptional analysis using the Affymetrix Microarray platform. Consult their website for listings of a wide range of other facilities and expertise.

Contact

T. Michael Underhill, Division Chair
Edie Dullaghan, Head
P: 604-827-1147
F: 604-827-1299
E: edullaghan [at] cdrd.ca

Pharmaceutical Sciences Building
University of British Columbia
2405 Wesbrook Mall (corner of Wesbrook and Agronomy Rd.), Fourth Floor
Vancouver, BC V6T 1Z3

Other

NAPS

http://naps.msl.ubc.ca

The NAPS Unit at UBC is a core facility providing DNA sequencing and genotyping services to both academic and commercial researchers. Generating 1,000+ bases per run, data is available within 24hrs through an on-line dnaLIMS (Laboratory Information Management System). Highly trained staff, comprising >20 years of sequencing expertise, provide personalized service to assist with experimental design, data interpretation, and troubleshooting difficult templates.

The facility also operates a NAPS-IDT portal, an Applied Biosystems On-Site Freezer Program and a QIAstock cabinet, providing easily accessible custom oligonucleotides and molecular biology reagents to the scientific community.

Contact

Debbie Adam, Director
P: 604-822-9769
F: 604-822-9174
E: dna_lab [at] interchange.ubc.ca

Lyndsey
P: 604-822-4570

NAPS Unit
University of British Columbia
Room 419 - NCE Building
2125 East Mall
Vancouver, BC, CANADA V6T 1Z4

Genomics Training and Online Resources

SEQanswers Forum

http://seqanswers.com/forums/index.php

SEQanswers was founded to be an information resource and user-driven community focused on all aspects of next-generation genomics including next generation sequencing technology discussion and education. The site attempts to cater to everyone, regardless of scientific background or knowledge.

Informatics on High Throughput Sequencing Data - CBW 2014

http://bioinformatics.ca/workshops/2014/informatics-high-throughput-sequencing-data-2014

Video (.mp4) and slide decks (.pptx and .pdf) of lectures from from the two-day Canadian Bioinformatics Workshops on Informatics on High Throughput Sequencing Data, June 2014. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Visualization Tools; Reference-guided Genome Alignment; Small-variant calling and annotation; Structural variant calling (includes CNVs); Visual Analysis, Bringing it all together: Galaxy; De Novo Assembly.

Informatics for RNA-sequence Analysis - CBW 2014

http://bioinformatics.ca/workshops/2014/informatics-rna-sequence-analysis-bc-2014

Video (.mp4) and slide decks (.pptx and .pdf) of lectures from from the two-day Canadian Bioinformatics Workshops on Informatics for RNA-sequence Analysis, June 2014. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Introduction to RNA sequencing and analysis; RNA-seq alignment and visualization; Expression and differential expression; Isoform discovery and alternative expression.

Bioinformatics for Cancer Genomics - CBW 2014

http://bioinformatics.ca/workshops/2014/bioinformatics-cancer-genomics-bicg-2014

Video (.mp4) and slide decks (.pptx and .pdf) of lectures from from the five-day Canadian Bioinformatics Workshops on Bioinformatics for Cancer Genomics, May 2014. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Introduction to Cancer Genomics; Databases and Visualization Tools; Alignment & Genome rearrangements; Gene Fusion Discovery; Copy Number Alterations; Somatic Mutations; Variants to Networks; Gene Expression Profiling; Integration of Clinical Data.

Pathway and Network Analysis of -omics Data - CBW 2014

http://bioinformatics.ca/workshops/2014/pathway-and-network-analysis-omics-data-2014

Video (.mp4) and slide decks (.pptx and .pdf) of lectures from from the 2.5-day Canadian Bioinformatics Workshops on Pathway and Network Analysis of -omics Data, June 2014. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Brief introduction to gene lists; Regulatory Network Analysis; Finding over-represented pathways in gene lists; Pathway and Network Analysis; Network Visualization; Gene Function Prediction.

Proteomics

Proteomics is the large-scale study of proteins, including their abundance, modifications, structures, functions, interacting partners and complexes.

LSI Proteomics Directors Chris Overall & Leonard Foster

UBC Proteomics Core Facility

http://www.chibi.ubc.ca/facilities-2/proteomics-core-facility-3/proteomics-core-facility/

The Proteomics Core Facility (PCF) offers a broad range of services, from mass confirmations to large-scale quantitative proteomic screens, along with all the associated bioinformatics. Basically, if it involves characterizing polypeptides, we can probably do it. Some of the services we provide most commonly include:

  • Measure the mass and identity of a protein or peptide you may have (e.g., to confirm successful synthesis of a peptide or the purity of a recombinant protein
  • Identify unknown bands from a gel
  • Characterize post-translational modifications on your favourite protein
  • Identify the protein interacting partners of a ligand
  • Measure global changes in protein levels or post-translational modifications (e.g., phosphoproteomics)
  • Monitor the global interaction landscape of cells

We are also open to collaborative projects on a case-by-case basis. Staff in the PCF are available for project planning and sample preparation in addition to general mass spectrometry scientific advice and consulting on a walk-in basis.

New resource - Expected availability November 1, 2014 Whole genome shRNA libraries for human & mouse available to UBC community (for testing 1 to 20,000 genes) - through UBC PCF or through #NAPS

Comment from Stefanie Butland, LSI: The UBC Proteomics Core Facility site provides rich details for new users such as pre-reading, how to prepare samples, how to read results.

Contact
Jason Rogalski, Operations Manager
P: 604-827-5209
F: 604-827-2603
E: rogy [at] mail.ubc.ca

Leonard Foster, Director
P: 604-822-8311
F: 604-827-2603
E: foster [at] chibi.ubc.ca

NCE Building
University of British Columbia
416-2125 East Mall
Vancouver, BC V6T 1Z4 CANADA


LSI Collaborators and Key Users

The Director of the UBC Proteomics Core Facility, Leonard Foster, is a Director of the Proteomics Suite in the LSI's 2014 application to the Canada Foundation for Innovation. LSI Principal Investigators Pieter Cullis, Paul Pavlidis, Chris Overall, Lindsay Eltis and Brett Finlay have ongoing collaborations with Foster.

University of Victoria GenomeBC Proteomics Centre

http://www.proteincentre.com/

Featured Services:

  • Biomarker Discovery and Validation
  • Quantitative Proteomics
  • MRM Assays
  • Structural Proteomics
  • MALDI Imaging
  • Protein Characterization
  • Protein Identification
  • Peptide Synthesis
  • Bioinformatics
  • Metabolomics through #TMIC - The Metabolomics Innovation Centre

Contact

Christoph Borchers, Director
P: 250-483-3221
E: christoph [at] proteincentre.com

Derek Smith, Technical Operations Manager, Project Manager
P: 250-483-3224
E: derek [at] proteincentre.com

University of Victoria - Genome BC Proteomics Centre
Vancouver Island Technology Park
3101-4464 Markham St
Victoria, BC V8Z 7X8

ASTRID

http://astrid-lsi.sites.olt.ubc.ca/infrastructure/

The ASTRID - Advanced Structural Biology for Re-emerging Infectious Diseases - infrastructure platform includes an NMR Spectroscopy Unit, an X-ray Crystallography Unit and a Bio-analytical Unit. ASTRID was established with support from the Canadian Foundation for Innovation and the BC Knowledge Development Fund.

Contact

Lawrence McIntosh
E: mcintosh [at] chem.ubc.ca

Metabolomics

Metabolomics involves the the near global analysis of small molecule metabolites (< 1500 Daltons, including carbohydrates, amino acids, lipids, nucleotides). The metabolome is the complete set of metabolites within a cell, tissue or biological sample at any given time point.

LSI Metabolomics Directors James Johnson & Lindsay Eltis

TMIC - The Metabolomics Innovation Centre

http://www.metabolomicscentre.ca/

recommended by Brett Finlay, UBC

The Metabolomics Innovation Centre (TMIC) is a nationally-funded research and core facility that supports a wide range of metabolomic studies for clinical trials research, biomedical studies, bioproducts studies, nutrient profiling and environmental testing. Methods include: NMR, GC-MS, DI-MS, HPLC, LC-MS, MALDI Imaging, Lipidomics, ICP-MS. The TMIC website provides detailed descriptions of services provided, types of metabolomics assays, equipment, software and databases.

TMIC is led by Dr. David Wishart (University of Alberta), Dr. Christoph Borchers (University of Victoria), Dr. Liang Li (University of Alberta), and Dr. James Harynuk (University of Alberta).

Contact
http://www.metabolomicscentre.ca/contact

Rupasri Mandal, Project Manager
P: 780-492-8574
E: rmandal [at] ualberta.ca


LSI Collaborators and Key Users

TMIC leads, David Wishart and Christoph Borchers are partners in the LSI's 2014 application to the Canada Foundation for Innovation. Brett Finlay is a key user of TMIC.

Metabolon

http://www.metabolon.com/research-services.aspx

Metabolon, Inc., is a pioneer in outcome-based metabolomics providing high-throughput metabolite identification, quantification and analysis of nearly any sample type. Metabolon’s expert biochemists, molecular biologists and nutritionists work directly with collaborators to understand investigator research goals, design well-powered metabolomics studies, and interpret the data output from small and large sample sets to yield meaningful results. A publication-ready report and other deliverables convey study outcomes, provide statistical and biological interpretation and identify candidate biomarkers.

Metabolon offers metabolomic profiling services on hundreds of different sample types from most species. The number of metabolites identified depends on the sample type, but typically ranges from 500-1000 metabolites in common sample types such as urine or plasma. Samples are processed in either Metabolon’s biomarker discovery lab or its CLIA-certified and CAP-accredited clinical diagnostics lab using a multi-platform approach incorporating GC/MS, GC-FID and UPLC/MS/MS. Metabolon’s proprietary software and extensive biochemical reference library of 14000+ known and novel metabolites (including complex lipids) allow them to offer broad global metabolic profiling, metabolite class-specific focused panels, and custom-built targeted assays. Interpreted study results and deliverables are provided via a secure, interactive client portal featuring a suite of statistical and bioinformatics tools allowing investigators an ability to explore, visualize and share study results. Global profiling results are typically returned within 6-8 weeks.

Contact

Jeff Buckthal, Sr. Director, Science Development
P: 919-802-6244
E: jbuckthal [at] metabolon.com

Metabolomics Training and Online Resources

Informatics and Statistics for Metabolomics - CBW 2014

http://bioinformatics.ca/workshops/2014/informatics-and-statistics-metabolomics-2014

Video (.mp4) and slide decks (.ppt and .pdf) of lectures from from the two-day Canadian Bioinformatics Workshops on Metabolomics, June 2014, delivered by David Wishart, Canadian Metabolomics expert and co-lead of #TMIC - The Metabolomics Innovation Centre - The Metabolomics Innovation Centre. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Introduction to Metabolomics; Software for Metabolite Identification and Quantification; Metabolite Identification and Annotation; Databases for Chemical, Spectral and Biological Data; LC-MS spectra processing using XCMS; Backgrounder in Statistical Methods; Metabolomic Data Analysis using MetaboAnalyst; Data Integration, and Applications and the Future of Metabolomics.

Introduction to Metabolomics - EBI

http://www.ebi.ac.uk/training/online/course/introduction-metabolomics

The EBI Introduction to Metabolomics provides a very clear basic introduction and takes 30-60 minutes to click through.
Learning objectives:

  • Comprehend the purpose and importance of the field of metabolomics
  • Describe some principles of metabolomic study design
  • Evaluate advantages and limitations of some analytical techniques used in metabolomics studies
  • Discuss some of the modern-day applications of metabolomics
  • Access metabolomics resources at the EBI

Microbiomics

Microbiomics is the study of complex communities of microbiota and the interactions between microbiome and host. High-throughput sequencing platforms are integrated into microbiomics workflows.

LSI Microbiomics Directors Bill Mohn & Steven Hallam

MetaPathways

http://hallam.microbiology.ubc.ca/MetaPathways/

MetaPathways is a modular software pipeline for integrated analysis of environmental sequence information, developed by the Hallam Laboratory. It takes an assembled or unassembled genomic sequence file (.fasta), predicts open reading frames (ORFs), and systematically produces a series of data products using the MEGAN, ML-TreeMap, tRNA-scan, and 16S SSU rRNA methods and software. The pipeline culminates in the production of an environmental pathway/genome database (ePGDB), inferring metabolic potential using the Pathway Tools software.

Contact

Steven Hallam
P: 604-827-3420
F: 604-822-6041
E: shallam@mail.ubc.ca

Life Sciences Institute
2.552 - 2350 Health Sciences Mall
University of British Columbia
Vancouver, BC V6T 1Z3
Canada

MetaMixis

http://www.metamixis.com/

MetaMixis is an integrated synthetic biology company that uses a platform that screens environmental DNA for the synthesis and secretion of targeted small molecules to engineer microbes in an iterative and high throughput manner. MetaMixis Inc. was established by LSI researcher Dr. Steven Hallam.

Contact

P: (604) 827-3420
F: (604) 822-6041
E: contact [at] metamixis.com

Microbiomics Training and Online Resources

Hallam Lab Video Protocols

http://hallam.microbiology.ubc.ca/LabResources/Protocols.html

The Hallam Laboratory provides 8 Jove video protocols that are 5 to 20 minutes long:

  1. Seawater Sampling and Collection
  2. Large Volume (20L+) Filtration of Coastal Seawater Samples
  3. Small Volume (1-3L) Filtration of Coastal Seawater Samples
  4. DNA Extraction from 0.22 μM Sterivex Filters and Cesium Chloride Density Gradient Centrifugation
  5. Large Insert Environmental Genomic Library Production
  6. Extraction of High Molecular Weight Genomic DNA from Soils and Sediments
  7. Expression of Recombinant Proteins in the Methylotrophic Yeast Pichia pastoris
  8. A High Throughput Screen for Biomining Cellulase Activity from Metagenomic Libraries


Contact

Steven Hallam
P: 604-827-3420
F: 604-822-6041
E: shallam@mail.ubc.ca

Life Sciences Institute
2.552 - 2350 Health Sciences Mall
University of British Columbia
Vancouver, BC V6T 1Z3
Canada

Imaging

LSI Imaging Core

http://lsi.ubc.ca/resources/facilities/imaging/

LSI Imaging is a core research imaging facility of the Life Sciences Institute with state of the art fluorescence microscopy equipment. Applications include FRET, FRAP, TIRF and high throughput content screening (small molecule and siRNA). It provides access, user training and technical assistance for super-resolution microscopy, confocal microscopy (point laser scanning or spinning disk), high throughput imaging and image deconvolution, 3D reconstruction and quantitative analysis.

Contact

I. Robert Nabi, Director
P: 604-822-7000
E: ivan.robert.nabi [at] ubc.ca

Fanrui Meng (Ray), Manager
P: 604-827-3946
E: frui.meng [at] gmail.com

Life Sciences Institute
University of British Columbia

LSI TEM Facility

http://lsi.ubc.ca/resources/facilities/tem/

The LSI Transmission Electron Microscopy (TEM) facility houses the TEM and ultramicrotome purchased from a Canada Foundation for Innovation grant received by Drs. Robert Molday, Wayne Vogl and Nelly Pante. The TEM has a high level of automation and is suitable for applications like 3D-imaging using tomography and/or cryo-electron microscopy.

Contact

Wayne Vogl
E: wayne.vogl [at] ubc.ca
Life Sciences Institute
University of British Columbia

Phenotyping

Phenotyping is a broad category that includes Cell Phenotyping, Model Organisms and Functional Screening.

LSI Phenotyping Directors Tim Kieffer & Robert Nabi

Cell Phenotyping

ubcFLOW Cytometry Facility

http://www.ubcflow.ca/

The UBC Flow Cytometry Facility offers a state of the art facility with a wide range of instruments at two locations on the UBC Vancouver Campus open to industry, academia and government agencies. We have multicolour, high throughput and clinical specific analysers, combined with cell sorters and a CyTOF; enabling you to analyse the characteristics of any cell that you might be interested in and define more than 30 simultaneous parameters relating to it.

ubcFLOW also offers cell isolation technologies that enable researchers to isolate pure populations of cells, such as stem cells or bacterial cells, from heterogeneous samples including tissues, blood or environmental samples, to interrogate their biological processes, assess for heterogeneity, and to test therapeutics.

ubcFLOW provides full training, application development and support, allowing someone new to flow cytometry to take their idea from an initial hypothesis through to publication. We would like people to send data that they have acquired by flow cytometry and are considering to submit for a grant application or publication. This would allow the facility to review your figures and make sure that you are sending out the correct message in the data. Only the flow component and figure will be analyzed and possibly improved to give you a strengthened application or manuscript.

Contact

Pauline Johnson & Fabio Rossi, Directors
Andy Johnson, Facility Manager
Justin Wong, Co-ordinator
hotline: 604-783-0204
BRC: 604-822-7838
LSC: 604-822-0437
E: andy [at] ubcflow.ca

Locations

The Life Sciences Centre
University of British Columbia
2350 Health Sciences Mall

The Biomedical Research Centre
University of British Columbia
2222 Health Sciences Mall

Flow Cytometry Data Analysis using R - CBW 2013

http://bioinformatics.ca/workshops/2013/flow-cytometry-data-analysis-using-r-2013#material

Video (.mp4) and slide decks (.pdf) of lectures from from the two-day Canadian Bioinformatics Workshops on Flow Cytometry Data Analysis using R, June 2013. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Introduction to Flow Cytometry Analysis in R, Exploring FCM data in R, Preprocessing and Quality Assurance of FCM Data, 1D Static gating, 1D Dynamic gating, Clustering and Additional FCM Tools.

AbLab - UBC Antibody Lab

http://www.AbLab.ca

Recommended by Andy Johnson, ubcFLOW

The AbLab supplies the research community with high quality in-house antibody reagents at cost. The AbLab can assist you throughout the entire process from production and down-stream processing to modification including labelling, conjugation and fragmentation. This includes custom conjugation for use in flow cytometry including CYTOF. Our production systems provide high batch-to-batch reproducibility. You provide us your hybridoma and we do the rest. The AbLab also maintains an extensive inventory of commonly used monoclonal antibodies conjugated to multiple fluorophores for your convenience and serves as a repository for researchers' hybridomas, ensuring a reliable consistent supply and simplifying the handling of requests for clones and antibodies.

Contact

Michael Williams, Facility Manager
AbLab (UBC Antibody Lab)
Front Desk: 604-822-7810
Direct: 604-822-8060
E: info [at] ablab.ca

AbLab (UBC Antibody Lab)
The Biomedical Research Centre
University of British Columbia
2222 Health Sciences Mall
Vancouver BC

Model Organisms

Expertise in Model Organisms research in the Life Sciences Institute includes Yeast (Christopher Loewen), Drosophila (Vanessa Auld, Doug Allan), C. elegans (Don Moerman), zebrafish (Tim Kieffer) and rodents.

Centre for Disease Modelling

http://www.cdm.ubc.ca/contact.html

The Centre for Disease Modelling (CDM) aspires to be recognized as a leader in animal science. The CDM provides direct access to flow cytometry and imaging systems within and outside the pathogen-free containment barrier.

Contact

P: 604.827.3425
F: 604.827.5906
E: cdm.reception [at] ubc.ca

Centre for Disease Modelling
2350 Health Sciences Mall
University of British Columbia
Vancouver, BC, Canada V6T 1Z3

FINDER - Facility for Infectious Disease and Epidemic Research

https://www.finder.ubc.ca/about#resources

The Facility for Infectious Disease and Epidemic Research (FINDER) is dedicated to discovering new avenues for antimicrobial and antiviral drugs and to developing new vaccines that combat infectious human diseases. FINDER is one of the largest and most comprehensive facilities of its kind in the world, and offers a state-of-the-art BSL-3 laboratory to researchers from across Canada and internationally.

Contact

Francois Jean, Director
E: francois.jean [at] ubc.ca
E: finder.admin [at] ubc.ca

Life Sciences Institute
University of British Columbia

COPAS Biosorter for Large Particle Flow Cytometry - Worm Sorter

The “worm” Sorter is used to place individual nematodes, or any number you desire, into individual wells and we can work with formats up to 96-well microtiter plates. On average, placing a single worm per well in a 96 well format takes less than two minutes. The sorter can be used to size-select worms for different developmental stages. It has fluorescence detection capabilities as well so that one can sort based on GFP expression screening. Applications include functional screening of sorted worms (e.g. drug screening).

Note that the flow cell size on this model is not suitable for flies or zebrafish.

See http://www.unionbio.com/copas/

Contact

Don Moerman
E: moerman [at] zoology.ubc.ca

Life Sciences Institute
University of British Columbia
2350 Health Sciences Mall
Vancouver, BC V6T 1Z3

The Million Mutation Project

http://genome.sfu.ca/mmp/search.html

The Million Mutation Project (MMP), a joint project by Don Moerman's (LSI UBC) and Bob Waterston's (University of Washington) labs, has exploited whole genome resequencing to identify multiple mutations in virtually every C. elegans gene in a collection of 2,000 mutagenized strains. The web interface allows users to search using identifiers for human genes in order to identify the C. elegans phenotype that results from mutation of that gene.

Contact

Don Moerman
E: moerman [at] zoology.ubc.ca

Biomedical Research Centre Genotyping Facility

http://brc.ubc.ca/genotyping/

Recommended by Andy Johnson, ubcFLOW

Contact
Taka Murakami
P: 604-822-9491
E: taka [at] brc.ubc.ca

The Biomedical Research Centre
University of British Columbia
2222 Health Sciences Mall
Vancouver, BC Canada V6T 1Z3

Other

LSI Tissue Processing Facility

http://lsi.ubc.ca/resources/facilities/tissue-processing/

The Tissue Processing Facility is suitable for performing immunohistochemical and immunofluorescence analysis of tissue slices (e.g. lymphoid organs, pancreas). The facility has a high quality semi-electronic cryostat as well as an Olympus BX61 motorized fluorescence microscope.

Contact

Cal Roskelly, Director
Megan Gilmour, Manager
P: 604-822-1781
E: meg.gilmour [at] gmail.com

Rm 3435, Life Sciences Centre
University of British Columbia
2350 Health Sciences Mall
Vancouver BC

Centre for Biothermodynamics

http://www.lmb.ubc.ca/BT-main.html

The Centre for Biothermodynamics (CBT) is part of the Laboratory for Molecular Biophysics and the Michael Smith Laboratories at UBC. The CBT provides academic scientists and biotechnology corporations access to and training on a suite of high-precision instruments for biophysical measurements and is the only such service available in Canada. The Centre includes high sensitivity isothermal titration calorimeters (ITC) and differential scanning calorimeters (DSC). Thermodynamic sample analysis is available with a fee-for-service structure. The CBT also includes a Biacore surface plasmon resonance detector for binding kinetic and thermodynamic studies and an analytical ultracentrifuge for macromolecule characterization.

Contact

Louise Creagh, Manager
P: 604-827-5210
F: 604-822-2114
E: alcreagh [at] chbe.ubc.ca

Laboratory
P: 604-822-3179
F: 604-822-2114

Michael Smith Laboratories
University of British Columbia
001-2185 East Mall
Vancouver, BC, CANADA V6T 1Z4

Data Management and Analysis

Bioinformatics

Life science is rapidly evolving into a data-intensive information science. A biological understanding of health and disease requires bioinformatics for integrated data generation, data management, interpretation and communication.

LSI Bioinformatics Directors: Steven Hallam & Paul Pavlidis

Pavlidis Lab Software and Resources

http://www.chibi.ubc.ca/faculty/paul-pavlidis/pavlidis-lab/software-and-resources/

Software and databases developed in the Pavlidis lab for integrated genotype and phenotype data include:

  • Gemma, a system for analyzing genomic data using meta-analysis techniques. Gemma permits researchers to compare and combine gene expression data sets with other datatypes including proteomics and genetics, and neuroscience-domain-specific data such as neuroanatomy and neuropharmacology.
  • ASPIREdb, a web-based software system for the analysis of genomic variants (CNVs, SNVs, and Indels) and phenotypes
  • Phenocarta, a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations

Contact

Paul Pavlidis
E: paul [at] chibi.ubc.ca
P: 604-827-4157

LSI Collaborators and Key Users

Paul Pavlidis is a Director of the Bioinformatics Suite in the LSI's 2014 application to the Canada Foundation for Innovation. LSI Principal Investigators Jim Johnson, Chris Overall and Shernaz Bamji have ongoing collaborations with Pavlidis.

Hallam Lab Software and Resources

http://hallam.microbiology.ubc.ca/LabResources/Software.html

KnoSYS Human Genome Interpretation Platform

http://sequencing.ubc.ca/tech/knome/

UBCSeq, the UBC Sequencing Centre at Pharmaceutical Sciences, has the first Canadian installation of the KnoSYS Human Genome Interpretation Platform. This provides the capacity to interpret variant lists from human genome, exome and targeted sequencing data with integrated hardware and software.

Contact

Corey Nislow, Director
Sunita Sinha, Manager
P: 604-827-0310
E: sequencing.centre [at] ubc.ca

Pharmaceutical Sciences Building
University of British Columbia
6204 – 2405 Wesbrook Mall
Vancouver, BC V6T 1Z3

Genome Sciences Centre - Bioinformatics

http://www.bcgsc.ca/services

The GSC, Canada's Michael Smith Genome Sciences Centre, is the largest capacity genomics centre of its type in Canada. The GSC specializes in high-throughput, large-scale genome research activities encompassing cancer genetics, bioinformatics, LIMS, DNA sequencing, data analysis, genome mapping, gene expression profiling, proteomics and technology development. The GSC has services available for sequencing, bioinformatics platform services, proteomics and in-silico drug design.

The GSC Bioinformatics Platform offers services in:

  • Genome Annotation
  • High-throughput PCR primer prediction
  • Regulatory element prediction
  • Laboratory information management systems (LIMS)
  • Data dissemination (e.g. web/ftp sites, submission to official repositories)
  • Development and maintenance of biological databases
  • Other Custom Services

The GSC Drug Discovery Platform offers in-silico drug design using Molsoft ICM software for molecular docking on a 400 CPU compute cluster to screen 1+ million compounds per day.

Specific bioinformatics analysis modules for sequence data are associated with their Sequencing services.

Contact

Diane Miller, Project Manager
P: (604) 707-5808
F: (604) 877-6085
E: dmiller [at] bcgsc.ca

Genome Sciences Centre, BC Cancer Agency
Suite 100, 570 West 7th Ave
Vancouver, BC, V5Z 4S6

Bioinformatics Training and Online Resources

Bioinformatics Links Directory

http://bioinformatics.ca/links_directory/

The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. The links listed in this directory are selected on the basis of recommendations from bioinformatics experts in the field. We also rely on input from our community of bioinformatics users for suggestions. Starting in 2003, we have also started listing all links contained in the NAR Webserver issue.

Canadian Bioinformatics Workshops

http://bioinformatics.ca/

The Canadian Bioinformatics Workshops are an annual series of specialized two to five-day hands-on workshops delivered by researchers active in the areas being taught.

  • Exploratory Analysis of Biological Data using R
  • Bioinformatics for Cancer Genomics
  • Informatics for RNA-sequence Analysis
  • Informatics on High Throughput Sequencing Data
  • Pathway and Network Analysis of -omics Data
  • Flow Cytometry Data Analysis using R
  • Informatics and Statistics for Metabolomics

Past workshop content is available under a Creative Commons License at http://bioinformatics.ca/workshops/2014

Bioinformatics Networking

VanBUG - Vancouver Bioinformatics Users Group

http://vanbug.org/

VanBUG is an association of researchers, other professionals and students in the B.C. Lower Mainland who have an interest in the field of bioinformatics. VanBUG meets on the second Thursday of every month from September through April. Research presentations by bioinformatics leaders, students and industry representatives are followed by networking over pizza and refreshments.

Subscribe to VanBUG mailing list (low volume, moderated) at http://www.vanbug.org/mailing-list/

Statistics

LSI researchers are encouraged to consult with statisticians at the earliest possible stages of experimental design for Omics or large cohort studies. This will ensure that experimental results can be analyzed appropriately and statistically rigorous conclusions can be drawn.

UBC Statistical Consulting and Research Laboratory (SCARL)

http://www.stat.ubc.ca/SCARL/

The Statistical Consulting and Research Laboratory (SCARL) is operated by the Department of Statistics. Services provided cover the spectrum of statistical design and analysis, as well as ancillary areas.

How can SCARL help? provides details on the range of services available.

SCARL offers one hour of free statistical consulting to UBC graduate students through the Statistical Opportunity for Students (SOS) program.

Contact

Rick White, Director
P: 604-822-2479
F: 604-822-6960
E: rickw [at] stat.ubc.ca

Department of Statistics
Room 3102, Earth Sciences Building
2207 Main Mall
The University of British Columbia
Vancouver BC V6T 1Z4

Statistics Training and Online Resources

R Graph Catalog

http://shinyapps.stat.ubc.ca/r-graph-catalog/

Recommended by Stefanie Butland, LSI

The R Graph Catalog is a visual index of over 100 graphs from the excellent book "Creating More Effective Graphs" by Naomi Robbins. Click on a graph thumbnail and you'll see the figure AND all the code necessary to reproduce the figure exactly with ggplot2, the R package written by Hadley Wickham. This is a resource for people who want to make a good graph and kind of know what it should look like … but they could really use an example to get started!

You can get the code for ALL figures and the infrastructure that makes the app from this repository on GitHub: https://github.com/jennybc/r-graph-catalog

The R Graph Catalog is maintained by Dr Jennifer Bryan, UBC Department of Statistics, and the initial work was facilitated by an NSERC Undergraduate Student Research Award to Joanna Zhao.

UBC Graduate Courses in Data Analysis

Recommended by Nikolas Fortelny, Overall Lab, LSI

STAT540 Statistical methods for high dimensional biology: http://www.ugrad.stat.ubc.ca/~stat540/
STAT 545A Exploratory Data Analysis and STAT 547M Basic Training for Data Science: http://stat545-ubc.github.io

Instructors include Drs. Jenny Bryan, Paul Pavlidis and Gabriela Cohen-Freue. These are very good courses for people serious about working with Omics data. Much of the course content can be found on GitHub. Follow the links above.

Exploratory Analysis of Biological Data using R - CBW 2014

http://bioinformatics.ca/workshops/2014/exploratory-analysis-biological-data-using-r-2014

Video (.mp4) and slide decks (.ppt and .pdf) of lectures from from the two-day Canadian Bioinformatics Workshops on Exploratory Analysis of Biological Data using R, May 2014. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: The R Landscape; Exploratory data analysis for biological data; Regression Analysis; Data reduction; Clustering Analysis; Hypothesis testing for EDA

Other Portals

Canada Foundation for Innovation Research Facilities Navigator

http://www.innovation.ca/en/navigator

The CFI Research Facilities Navigator is a searchable online directory of participating research labs and facilities in universities, colleges and research hospitals across Canada that are open to working with business. The Navigator was created by the Canada Foundation for Innovation (CFI) to help businesses and other organizations find the cutting-edge facilities, equipment and expertise they require to meet their research and innovation needs. For institutions and researchers, the Navigator offers an effective way to promote their labs and expertise to potential research partners in the private sector. All labs and facilities listed in this directory have received funding from the CFI or use CFI-funded infrastructure.

Science Exchange

https://www.scienceexchange.com

Search for a service, compare qualified providers, request a quote from one or more providers, select a provider. The Science Exchange allows users to compare service pricing, turn-around time, past client feedback and recommendations of expert service providers at core research and commercial facilities.

source: http://wiki.ubc.ca/Sandbox:LSI_Omics_Portal