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.


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

BRC Sequencing Core at UBC

https://brc.ubc.ca/next-generation-sequencing-at-the-brc/

Located on campus at the Biomedical Research Center, the BRC Sequencing Core (BRC-Seq) brings greater sequencing accessibility to all researchers at UBC and beyond. BRC-Seq provides researchers with quality data — from standardized sample preparation to sequencing to QC to analysis — and a quick turnaround time.

Services include:

  • Bioanalyzer sizing and QC: RNA samples are run on the Agilent Bioanalyzer to ensure RNA is of sufficient quality and quantity for library preparation. DNA libraries are quantified by Qubit, sized on the Agilent Bioanalyzer, and quantified by qPCR using the NEBNext Library Quant Kit for Illumina.
  • Library Preparation: RNA or DNA samples are prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. We offer both poly(A) mRNA and ribodepletion selection.   
  • Single Cell Capture: Using the 10x Genomics Platform, cells are captured using either the 3’ RNA, 5’VDJ, ATAC or Multiome kit, with the option to include Total-Seq or Cite-Seq applications.
  • Sequencing: Depending on experimental requirements, libraries are quantified, pooled and ran on either the Illumina MiSeq or NextSeq2000, with customizable sequencing fragment read length and depth.

Instrumentation:

  • 10X Genomics Chromium Single Cell Controller
  • Illumina NextSeq2000 & Illumina MiSeq
  • Agilent 2100 Bioanalyzer
  • Covaris M220
  • ViiA 7 Real-Time PCR System
  • epMotion 5075t
  • Invitrogen Qubit

Contact:
E: tstach [at] brc.ubc.ca
P: (604) 827-3381

Scientific Director: Dr. Michael T. Underhill
Facility Manager: Tara Stach
Sequencing Technician: Yvonne Chung
Bioinformatic Technician: Bernie Zhao

Address: Biomedical Research Centre – Room 300
2222 Health Sciences Mall, University of British Columbia
Vancouver, BC, V6T 1Z3

Sequencing and Bioinformatics Consortium (SBC)

http://sequencing.ubc.ca/

The Sequencing and Bioinformatics Consortium in the Pharmaceutical Sciences building at UBC provides experimental design consultation, next generation (Illumina) sequencing, Sanger sequencing, genotyping, and bioinformatics analysis. Their expertise and experience allows them to develop and utilize customized solutions for sequencing and bioinformatics analysis with rapid turnaround times. Their website provides clear descriptions of services, costs and turnaround times.

The SBC provides high throughput sequencing on Illumina MiSeq and NextSeq instruments, including sample QC and library preparation (genomic, RNA, 16S, amplicon, and custom protocols), with results provided as FASTQ and/or BAM files. Custom analysis is available for projects with unique needs.

Contacts
David Levy-Booth, PhD, Bioinformatics Specialist
Sunita Sinha, PhD, Research Manager
E: sequencing.centre [at] ubc.ca

Pharmaceutical Sciences Building
University of British Columbia
3124 – 2405 Wesbrook Mall
Vancouver, BC V6T 1Z3

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, and performed on a "first in, first on" basis. All work is put in a queue based on the date of receipt, and turnaround times vary. Please see their terms and conditions or submit inquiries about collaborative services here.

Sequencing services include:

  • Nucleic acid extraction and library construction
  • Whole genome, whole transcriptome, epigenome, ChIP, exome capture, miRNA, long reads, linked reads, customized

Instrumentation:

  • Illumina HiSeqX, HiSeq2500, NextSeq500, MiSeq
  • Oxford Nanopore MinION, PromethION
  • MGI DNBSEQ-G400

Contact

Leslie Alfaro, PhD, PMP, Projects Team Leader
P: (604) 707-5800 x 675244
E: lalfaro [at] bcgsc.ca

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

Laboratory for Advanced Genome Analysis

https://www.prostatecentre.com/node/255

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 next-generation 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 2017, LAGA’s performance has been rewarded by >20 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 for integrative analysis of SNVs and CNVs
  • 16S rRNA genes
  • Target capture sequencing
  • RNA sequencing (gene expression analysis)
  • RNA sequencing (whole transcriptome analysis)
  • Small RNA sequencing
  • ChIP-seq; ATAC-seq
  • 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

Other

GENEWIZ Dropbox

https://www.genewiz.com/

LSI researchers can drop off samples for GENEWIZ in a dropbox in LSC Shipping and Receiving on level B2. GENEWIZ provides services including Next Generation and Sanger Sequencing, gene and oligo synthesis, and many more. Samples from the dropbox are picked up daily between 2:00 - 2:30pm.

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 2018

https://bioinformatics.ca/workshops/2018-informatics-on-high-throughput-sequencing-data/

Video (YouTube) and slide decks (PDF) of lectures from the two-day Canadian Bioinformatics Workshops on Informatics on High Throughput Sequencing Data, May 2018. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Genome Visualization; Genome Alignment; Small-variant calling and annotation; Structural variation; De Novo Assembly.

Informatics for RNA-seq Analysis - CBW 2018

https://bioinformatics.ca/workshops/2018-informatics-for-RNA-seq-analysis/

Video (YouTube) and slide decks (PDF) of lectures from the three-day Canadian Bioinformatics Workshops on Informatics for RNA-seq Analysis, May 2018. 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; Reference free alignment; Genome Guided and Genome-Free Transcriptome Assembly; Functional Annotation and Analysis of Transcripts.

Bioinformatics for Cancer Genomics - CBW 2018

https://bioinformatics.ca/workshops/2018-bioinformatics-for-cancer-genomics/s

Video (YouTube) and slide decks (PDF) of lectures from the six-day Canadian Bioinformatics Workshops on Bioinformatics for Cancer Genomics, March 2018. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Introduction to Cancer Genomics; Ethics of Data Usage and Security; Databases and Visualization Tools; Genome Alignment; Genome Assembly; Somatic Copy Number Changes; Somatic Mutations and Annotations; Gene Expression Profiling; Gene Fusion Discovery and Genomic Rearrangements; Sharing and Scaling a VM; Working Reproducibly in the Cloud; Big Data Analysis in the Cloud; Genes to Pathways; Variants to Networks; Integration of Clinical Data.

Pathway and Network Analysis of -omics Data - CBW 2018

https://bioinformatics.ca/workshops/2018-pathway-and-network-analysis-of-omics-data/

Video (YouTube) and slide decks (PDF) of lectures from the three-day Canadian Bioinformatics Workshops on Pathway and Network Analysis of -omics Data, June 2018. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Introduction to pathway and network analysis; Finding over-represented pathways in gene lists; Network visualization and analysis with Cytoscape; More Depth on Pathway and Network Analysis; Gene Function Prediction; Regulatory Network Analysis.

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

https://www.pcf.msl.ubc.ca

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 - UBC has acquired Sigma’s MISSION shRNA human and mouse whole-genome TRC shRNA libraries, consisting of almost 200,000 pre-cloned shRNA vectors targeting more than 22,000 human and 20,000 mouse genes. See here for details.

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: proteomics [at] msl.ubc.ca

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

NCE Building
University of British Columbia
344-2125 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, Chris Overall, and Lindsay Eltis 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

David Schibli, Associate Director

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

General Inquiries
P: 250-483-3226
E: info@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 (McGill University), 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

https://www.metabolon.com/solutions/

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 2017

https://bioinformatics.ca/workshops/2017-informatics-and-statistics-metabolomics/

Video (YouTube) and slide decks (.ppt and .pdf) of lectures from from the two-day Canadian Bioinformatics Workshops on Metabolomics, June 2017, 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; Metabolite Identification and Annotation; Databases for Chemical, Spectral and Biological Data; Backgrounder in Statistical Methods; MetaboAnalyst; 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

https://github.com/hallamlab/MetaPathways/ or https://github.com/hallamlab/metapathways2

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

Gut4Health Microbiome Core Facility (BC Children’s Hospital)

https://bcchr.ca/gut4health/contact-us

Gut4Health facilitates microbiome studies for researchers at BC Children’s Hospital and at UBC. The facility will receive, process and store biological specimens, perform sequencing and analysis of microbial communities, and provide consultation on study design and sample collection. Services offered include DNA and RNA extraction, sample preparation and sequencing (Illumina MiSeq and HiSeq platforms), and assistance with bioinformatic analysis.

Contact:

Bruce A. Vallance, PhD, Director
E: bvallance [at] cw.bc.ca

Andy Sham, PhD, Project Manager
P: 604-875-2000 ext. 5773
E: andy.sham [at] bcchr.ca

BC Children's Hospital Research Institute
Rm 211 950 W. 28th Avenue
Vancouver, BC
V5Z 4H4

Microbiomics Training and Online Resources

Hallam Lab Video Protocols

https://www.jove.com/author/Steven+J._Hallam

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

Guang Gao, Facility Manager
P: 604-827-3946
E: gaoguang [at] mail.ubc.ca

Life Sciences Institute
University of British Columbia

The Molecular and Advanced Pathology Core (MAPcore)

https://mapcore.med.ubc.ca/

MAPcore provides researchers with access to equipment and services for spatial omics analysis of protein and mRNA from tissue sections, using multiplex Opal immunofluorescence from Akoya and GeoMx Digital Spatial Profiling from NanoString Technologies. In addition to a wide array of technical services for histology, histochemistry, and imaging, MAPcore is committed to furthering the success of omics and other discovery research by helping to translate these findings to clinical utility – offering project consultation and basic research pathology assessment services.

MAPcore is an affiliated core facility with the UBC Department of Pathology & Laboratory Medicine, Vancouver Coastal Health Research Institute, and BC Cancer Research Institute.

Equipment:

  • nanoString GeoMx® Digital Spatial Profiler
  • Zeiss Axio Scan.Z1
  • Leica RM2235 Manual Rotary Microtome
  • Leica Aperio AT2 Digital Whole Slide Scanner
  • Leica BOND RX fully automated research stainer
  • Leica Laser Capture Microdissection Microscope LMD7


Contact

Project/Laboratory Manager: Julie Ho, MHA, CHE
E: map.core [at] ubc.ca
P: 604-875-4111 ext. 68893

MAPcore | Department of Pathology & Laboratory Medicine
Faculty of Medicine
2660 Oak Street
Vancouver, BC Canada V6H 3Z6

Centre for High-Throughput Phenogenomics

https://chtp.ubc.ca/

The Centre for High-Throughput Phenogenomics in the Faculty of Dentistry offers a comprehensive suite of imaging technologies, providing multi-dimensional information and analysis about the fine structure of specimens. The Centre welcomes collaborative, interdisciplinary research projects from across universities, research organizations, and corporate users.

Equipment:

X-Ray Imaging

  • Micro-CT Specimen Scanner
  • Micro-CT In Vivo Scanner

Scanning Electron Microscopy

  • Helios FIB SEM
  • Hitachi SU3500

Light Microscopy

  • Confocal and fluorescence microscopes
  • Zeiss AxioVision/PALM Laser Capture
  • Optical Projection Tomography (OPT)

Sample Preparation

  • Cryostat, Coating System, Critical Point Dryer, Microwave System, Grinding/Polishing Suite

Data Analysis

  • Free access to a variety of image analysis software packages


Contact

Dr. Nancy L. Ford, Director
P: 604-822-6641
E: nlford [at] dentistry.ubc.ca


Faculty of Dentistry
The University of British Columbia
2405 Wesbrook Mall
Vancouver, BC, Canada V6T 1Z3

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, Research Coordinator
hotline: 604-783-0204
BRC: 604-822-7838
LSC: 604-822-0437
E: andew.johnson [at] ubc.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

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

Video (YouTube) 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

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://finder.ubc.ca/

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

Lindsay Eltis, Director
E: leltis [at] mail.ubc.ca
E: finder.communications [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

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

https://www.msl.ubc.ca/people/dr-paul-pavlidis/

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
  • GOTrack, a web-based system to track the history of changes to Gene Ontology (GO) and GO annotations (GOA)
  • ErmineJ, gene set analysis software

Contact

Paul Pavlidis
E: paul [at] msl.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.

Koonkie

http://www.koonkie.com/

Koonkie Inc. is a bioinformatics consulting company spun out of the Hallam lab, that designs and provides scalable algorithmic and data analytics solutions in the cloud. Some of their services include data processing, interpretation, and visualization tools, customized cloud services, or statistical analysis for large data sets. Koonkie team members also provide mentorship to students and researchers and deliver training workshops.

Hallam Lab Software and Resources

https://hallam.microbiology.ubc.ca/

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

Leslie Alfaro, PhD, PMP, Projects Team Leader
P: (604) 707-5800 x 675244
E: lalfaro [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 Resources

https://bioinformatics.ca/resources/

The bioinformatics.ca resources page features links to a bioinformatics jobs board, Canadian experts, bioinformatics activities, and education programs.

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 (2013)
  • Informatics and Statistics for Metabolomics

Past workshop content is available under a Creative Commons License at https://bioinformatics.ca/workshops/workshops-2018/

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.

Applied Statistics and Data Science Group

https://asda.stat.ubc.ca/

The Applied Statistics and Data Science Group (ASDa) is operated by the Department of Statistics at UBC. Services provided cover the spectrum of statistical design and analysis, as well as ancillary areas.

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

Online contact form: https://asda.stat.ubc.ca/contact.html

Contact
P: 604-822-2924
E: asda@stat.ubc.ca

Department of Statistics
Room 3178, Earth Sciences Building
2207 Main Mall
The University of British Columbia
Vancouver BC V6T 1Z4

Statistics Training and Online Resources

R Graph Catalog

Recommended by Stefanie Butland, LSI

The R Graph Catalog repository contains code to make graphs from the excellent book "Creating More Effective Graphs" by Naomi Robbins. This code can be used to reproduce figures 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 from this repository on GitHub: https://github.com/jennybc/r-graph-catalog

The R Graph Catalog was created 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: https://stat545.stat.ubc.ca/

Instructors include Drs. Jenny Bryan, Paul Pavlidis and Gabriela Cohen-Freue (now Keegan Korthauer and Vincenzo Coia). 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 2018

https://bioinformatics.ca/workshops/2018-exploratory-analysis-of-biological-data-using-R/

Video (YouTube) and slide decks (PDF) of lectures from from the two-day Canadian Bioinformatics Workshops on Exploratory Analysis of Biological Data using R, May 2018. 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

https://navigator.innovation.ca/

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 Aryannah Rollinson.

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

BRC Sequencing Core at UBC

https://brc.ubc.ca/next-generation-sequencing-at-the-brc/

Located on campus at the Biomedical Research Center, the BRC Sequencing Core (BRC-Seq) brings greater sequencing accessibility to all researchers at UBC and beyond. BRC-Seq provides researchers with quality data — from standardized sample preparation to sequencing to QC to analysis — and a quick turnaround time.

Services include:

  • Bioanalyzer sizing and QC: RNA samples are run on the Agilent Bioanalyzer to ensure RNA is of sufficient quality and quantity for library preparation. DNA libraries are quantified by Qubit, sized on the Agilent Bioanalyzer, and quantified by qPCR using the NEBNext Library Quant Kit for Illumina.
  • Library Preparation: RNA or DNA samples are prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. We offer both poly(A) mRNA and ribodepletion selection.   
  • Single Cell Capture: Using the 10x Genomics Platform, cells are captured using either the 3’ RNA, 5’VDJ, ATAC or Multiome kit, with the option to include Total-Seq or Cite-Seq applications.
  • Sequencing: Depending on experimental requirements, libraries are quantified, pooled and ran on either the Illumina MiSeq or NextSeq2000, with customizable sequencing fragment read length and depth.

Instrumentation:

  • 10X Genomics Chromium Single Cell Controller
  • Illumina NextSeq2000 & Illumina MiSeq
  • Agilent 2100 Bioanalyzer
  • Covaris M220
  • ViiA 7 Real-Time PCR System
  • epMotion 5075t
  • Invitrogen Qubit

Contact:
E: tstach [at] brc.ubc.ca
P: (604) 827-3381

Scientific Director: Dr. Michael T. Underhill
Facility Manager: Tara Stach
Sequencing Technician: Yvonne Chung
Bioinformatic Technician: Bernie Zhao

Address: Biomedical Research Centre – Room 300
2222 Health Sciences Mall, University of British Columbia
Vancouver, BC, V6T 1Z3

Sequencing and Bioinformatics Consortium (SBC)

http://sequencing.ubc.ca/

The Sequencing and Bioinformatics Consortium in the Pharmaceutical Sciences building at UBC provides experimental design consultation, next generation (Illumina) sequencing, Sanger sequencing, genotyping, and bioinformatics analysis. Their expertise and experience allows them to develop and utilize customized solutions for sequencing and bioinformatics analysis with rapid turnaround times. Their website provides clear descriptions of services, costs and turnaround times.

The SBC provides high throughput sequencing on Illumina MiSeq and NextSeq instruments, including sample QC and library preparation (genomic, RNA, 16S, amplicon, and custom protocols), with results provided as FASTQ and/or BAM files. Custom analysis is available for projects with unique needs.

Contacts
David Levy-Booth, PhD, Bioinformatics Specialist
Sunita Sinha, PhD, Research Manager
E: sequencing.centre [at] ubc.ca

Pharmaceutical Sciences Building
University of British Columbia
3124 – 2405 Wesbrook Mall
Vancouver, BC V6T 1Z3

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, and performed on a "first in, first on" basis. All work is put in a queue based on the date of receipt, and turnaround times vary. Please see their terms and conditions or submit inquiries about collaborative services here.

Sequencing services include:

  • Nucleic acid extraction and library construction
  • Whole genome, whole transcriptome, epigenome, ChIP, exome capture, miRNA, long reads, linked reads, customized

Instrumentation:

  • Illumina HiSeqX, HiSeq2500, NextSeq500, MiSeq
  • Oxford Nanopore MinION, PromethION
  • MGI DNBSEQ-G400

Contact

Leslie Alfaro, PhD, PMP, Projects Team Leader
P: (604) 707-5800 x 675244
E: lalfaro [at] bcgsc.ca

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

Laboratory for Advanced Genome Analysis

https://www.prostatecentre.com/node/255

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 next-generation 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 2017, LAGA’s performance has been rewarded by >20 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 for integrative analysis of SNVs and CNVs
  • 16S rRNA genes
  • Target capture sequencing
  • RNA sequencing (gene expression analysis)
  • RNA sequencing (whole transcriptome analysis)
  • Small RNA sequencing
  • ChIP-seq; ATAC-seq
  • 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

Other

GENEWIZ Dropbox

https://www.genewiz.com/

LSI researchers can drop off samples for GENEWIZ in a dropbox in LSC Shipping and Receiving on level B2. GENEWIZ provides services including Next Generation and Sanger Sequencing, gene and oligo synthesis, and many more. Samples from the dropbox are picked up daily between 2:00 - 2:30pm.

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 2018

https://bioinformatics.ca/workshops/2018-informatics-on-high-throughput-sequencing-data/

Video (YouTube) and slide decks (PDF) of lectures from the two-day Canadian Bioinformatics Workshops on Informatics on High Throughput Sequencing Data, May 2018. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Genome Visualization; Genome Alignment; Small-variant calling and annotation; Structural variation; De Novo Assembly.

Informatics for RNA-seq Analysis - CBW 2018

https://bioinformatics.ca/workshops/2018-informatics-for-RNA-seq-analysis/

Video (YouTube) and slide decks (PDF) of lectures from the three-day Canadian Bioinformatics Workshops on Informatics for RNA-seq Analysis, May 2018. 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; Reference free alignment; Genome Guided and Genome-Free Transcriptome Assembly; Functional Annotation and Analysis of Transcripts.

Bioinformatics for Cancer Genomics - CBW 2018

https://bioinformatics.ca/workshops/2018-bioinformatics-for-cancer-genomics/s

Video (YouTube) and slide decks (PDF) of lectures from the six-day Canadian Bioinformatics Workshops on Bioinformatics for Cancer Genomics, March 2018. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Introduction to Cancer Genomics; Ethics of Data Usage and Security; Databases and Visualization Tools; Genome Alignment; Genome Assembly; Somatic Copy Number Changes; Somatic Mutations and Annotations; Gene Expression Profiling; Gene Fusion Discovery and Genomic Rearrangements; Sharing and Scaling a VM; Working Reproducibly in the Cloud; Big Data Analysis in the Cloud; Genes to Pathways; Variants to Networks; Integration of Clinical Data.

Pathway and Network Analysis of -omics Data - CBW 2018

https://bioinformatics.ca/workshops/2018-pathway-and-network-analysis-of-omics-data/

Video (YouTube) and slide decks (PDF) of lectures from the three-day Canadian Bioinformatics Workshops on Pathway and Network Analysis of -omics Data, June 2018. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.

Lectures include: Introduction to pathway and network analysis; Finding over-represented pathways in gene lists; Network visualization and analysis with Cytoscape; More Depth on Pathway and Network Analysis; Gene Function Prediction; Regulatory Network Analysis.

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

https://www.pcf.msl.ubc.ca

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 - UBC has acquired Sigma’s MISSION shRNA human and mouse whole-genome TRC shRNA libraries, consisting of almost 200,000 pre-cloned shRNA vectors targeting more than 22,000 human and 20,000 mouse genes. See here for details.

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: proteomics [at] msl.ubc.ca

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

NCE Building
University of British Columbia
344-2125 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, Chris Overall, and Lindsay Eltis 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

David Schibli, Associate Director

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

General Inquiries
P: 250-483-3226
E: info@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 (McGill University), 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

https://www.metabolon.com/solutions/

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 2017

https://bioinformatics.ca/workshops/2017-informatics-and-statistics-metabolomics/

Video (YouTube) and slide decks (.ppt and .pdf) of lectures from from the two-day Canadian Bioinformatics Workshops on Metabolomics, June 2017, 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; Metabolite Identification and Annotation; Databases for Chemical, Spectral and Biological Data; Backgrounder in Statistical Methods; MetaboAnalyst; 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

https://github.com/hallamlab/MetaPathways/ or https://github.com/hallamlab/metapathways2

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

Gut4Health Microbiome Core Facility (BC Children’s Hospital)

https://bcchr.ca/gut4health/contact-us

Gut4Health facilitates microbiome studies for researchers at BC Children’s Hospital and at UBC. The facility will receive, process and store biological specimens, perform sequencing and analysis of microbial communities, and provide consultation on study design and sample collection. Services offered include DNA and RNA extraction, sample preparation and sequencing (Illumina MiSeq and HiSeq platforms), and assistance with bioinformatic analysis.

Contact:

Bruce A. Vallance, PhD, Director
E: bvallance [at] cw.bc.ca

Andy Sham, PhD, Project Manager
P: 604-875-2000 ext. 5773
E: andy.sham [at] bcchr.ca

BC Children's Hospital Research Institute
Rm 211 950 W. 28th Avenue
Vancouver, BC
V5Z 4H4

Microbiomics Training and Online Resources

Hallam Lab Video Protocols

https://www.jove.com/author/Steven+J._Hallam

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

Guang Gao, Facility Manager
P: 604-827-3946
E: gaoguang [at] mail.ubc.ca

Life Sciences Institute
University of British Columbia

The Molecular and Advanced Pathology Core (MAPcore)

https://mapcore.med.ubc.ca/

MAPcore provides researchers with access to equipment and services for spatial omics analysis of protein and mRNA from tissue sections, using multiplex Opal immunofluorescence from Akoya and GeoMx Digital Spatial Profiling from NanoString Technologies. In addition to a wide array of technical services for histology, histochemistry, and imaging, MAPcore is committed to furthering the success of omics and other discovery research by helping to translate these findings to clinical utility – offering project consultation and basic research pathology assessment services.

MAPcore is an affiliated core facility with the UBC Department of Pathology & Laboratory Medicine, Vancouver Coastal Health Research Institute, and BC Cancer Research Institute.

Equipment:

  • nanoString GeoMx® Digital Spatial Profiler
  • Zeiss Axio Scan.Z1
  • Leica RM2235 Manual Rotary Microtome
  • Leica Aperio AT2 Digital Whole Slide Scanner
  • Leica BOND RX fully automated research stainer
  • Leica Laser Capture Microdissection Microscope LMD7


Contact

Project/Laboratory Manager: Julie Ho, MHA, CHE
E: map.core [at] ubc.ca
P: 604-875-4111 ext. 68893

MAPcore | Department of Pathology & Laboratory Medicine
Faculty of Medicine
2660 Oak Street
Vancouver, BC Canada V6H 3Z6

Centre for High-Throughput Phenogenomics

https://chtp.ubc.ca/

The Centre for High-Throughput Phenogenomics in the Faculty of Dentistry offers a comprehensive suite of imaging technologies, providing multi-dimensional information and analysis about the fine structure of specimens. The Centre welcomes collaborative, interdisciplinary research projects from across universities, research organizations, and corporate users.

Equipment:

X-Ray Imaging

  • Micro-CT Specimen Scanner
  • Micro-CT In Vivo Scanner

Scanning Electron Microscopy

  • Helios FIB SEM
  • Hitachi SU3500

Light Microscopy

  • Confocal and fluorescence microscopes
  • Zeiss AxioVision/PALM Laser Capture
  • Optical Projection Tomography (OPT)

Sample Preparation

  • Cryostat, Coating System, Critical Point Dryer, Microwave System, Grinding/Polishing Suite

Data Analysis

  • Free access to a variety of image analysis software packages


Contact

Dr. Nancy L. Ford, Director
P: 604-822-6641
E: nlford [at] dentistry.ubc.ca


Faculty of Dentistry
The University of British Columbia
2405 Wesbrook Mall
Vancouver, BC, Canada V6T 1Z3

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, Research Coordinator
hotline: 604-783-0204
BRC: 604-822-7838
LSC: 604-822-0437
E: andew.johnson [at] ubc.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

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

Video (YouTube) 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

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://finder.ubc.ca/

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

Lindsay Eltis, Director
E: leltis [at] mail.ubc.ca
E: finder.communications [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

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

https://www.msl.ubc.ca/people/dr-paul-pavlidis/

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
  • GOTrack, a web-based system to track the history of changes to Gene Ontology (GO) and GO annotations (GOA)
  • ErmineJ, gene set analysis software

Contact

Paul Pavlidis
E: paul [at] msl.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.

Koonkie

http://www.koonkie.com/

Koonkie Inc. is a bioinformatics consulting company spun out of the Hallam lab, that designs and provides scalable algorithmic and data analytics solutions in the cloud. Some of their services include data processing, interpretation, and visualization tools, customized cloud services, or statistical analysis for large data sets. Koonkie team members also provide mentorship to students and researchers and deliver training workshops.

Hallam Lab Software and Resources

https://hallam.microbiology.ubc.ca/

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

Leslie Alfaro, PhD, PMP, Projects Team Leader
P: (604) 707-5800 x 675244
E: lalfaro [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 Resources

https://bioinformatics.ca/resources/

The bioinformatics.ca resources page features links to a bioinformatics jobs board, Canadian experts, bioinformatics activities, and education programs.

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 (2013)
  • Informatics and Statistics for Metabolomics

Past workshop content is available under a Creative Commons License at https://bioinformatics.ca/workshops/workshops-2018/

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.

Applied Statistics and Data Science Group

https://asda.stat.ubc.ca/

The Applied Statistics and Data Science Group (ASDa) is operated by the Department of Statistics at UBC. Services provided cover the spectrum of statistical design and analysis, as well as ancillary areas.

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

Online contact form: https://asda.stat.ubc.ca/contact.html

Contact
P: 604-822-2924
E: asda@stat.ubc.ca

Department of Statistics
Room 3178, Earth Sciences Building
2207 Main Mall
The University of British Columbia
Vancouver BC V6T 1Z4

Statistics Training and Online Resources

R Graph Catalog

Recommended by Stefanie Butland, LSI

The R Graph Catalog repository contains code to make graphs from the excellent book "Creating More Effective Graphs" by Naomi Robbins. This code can be used to reproduce figures 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 from this repository on GitHub: https://github.com/jennybc/r-graph-catalog

The R Graph Catalog was created 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: https://stat545.stat.ubc.ca/

Instructors include Drs. Jenny Bryan, Paul Pavlidis and Gabriela Cohen-Freue (now Keegan Korthauer and Vincenzo Coia). 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 2018

https://bioinformatics.ca/workshops/2018-exploratory-analysis-of-biological-data-using-R/

Video (YouTube) and slide decks (PDF) of lectures from from the two-day Canadian Bioinformatics Workshops on Exploratory Analysis of Biological Data using R, May 2018. 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

https://navigator.innovation.ca/

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