Bioinformatics Tools and Resources for the Life Science Researcher

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Bioinformatics Tools and Resources for the Life
Science Researcher

• Ian J. Forsythe
• Canadian Bioinformatics Help Desk
• September 20, 2005

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Purpose

• To raise awareness locally and across Canada
  about bioinformatics tools and resources
  available to life science researchers
• Increase communication between researchers in
  Canada and the Bioinformatics Platform

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Outline

• What is the Bioinformatics Platform?
• What is the Canadian Bioinformatics Help Desk?
• What is the Canadian Bioinformatics Resource?
• What bioinformatics tools and resources does the
  Bioinformatics Platform offer?

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What is the Bioinformatics Platform?

• Research Bluejay, BioMOBY, Database Analysis,
  Database Bias, Genquire, and Research
  Collaborations
• Bioinformatics Support Facility (Canadian
  Bioinformatics Help Desk) Custom Programming,
  Software Repository, Bioinformatics Newsletter

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What is the Bioinformatics Platform?

• Hardware Platform (Canadian Bioinformatics
  Resource) 14 CBR nodes across Canada, 2 Sun
  Centers (Distributed Bioinformatics and Visual
  Genomics), Generic Accounts
• Bioinformatics Training for Researchers in Canada
  Five so far Next one on February 13-17, 2006
  in Halifax
• Providing platform services to researchers around
  the world

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Bioinformatics Platform Team

• Platform Leader Dr. Christoph Sensen, U.Calgary
• Platform Investigators Dr. David Wishart,
  U.Alberta Dr. Mark Wilkinson, UBC Dr. Brian
  Fristensky, U.Manitoba Dr. Boris Steipe,
  U.Toronto Dr. William Crosby, U.Windsor Terry
  Dalton, NRC's CBR (Halifax)
• Training Coordinator Sophie Chung, U.Calgary
• Platform/Project Manager Marianne Hang, U.Calgary

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Service Across Canada
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Outline

• What is the Bioinformatics Platform?
• What is the Canadian Bioinformatics Help Desk?
• What is the Canadian Bioinformatics Resource?
• What bioinformatics tools and resources does the
  Bioinformatics Platform offer?

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Canadian Bioinformatics Help Desk
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Who are we?

• Director
• Dr. David Wishart
• Bioinformaticians
• Dr. Paul Stothard
• Ian Forsythe
• Savita Shrivastava

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Website

• Our information-rich website is loaded with
  useful links
• Our searchable research directory facilitates
  communication and collaborations between
  researchers
• Our links page provides many important Canadian
  bioinformatics links

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Website
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Research Directory
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Newsletter

• Biweekly (46 issues to date)
• Over 2000 subscribers
• Bioinformatics Profiles
• Software Spotlights
• What's New
• Meetings, Training, Degrees
• Jobs
• Newsletter archive

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Newsletter (Subscribe Today!)
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Web Servers

• 30 web-based applications for
• Plasmid and genome drawing
• Gel analysis/annotation
• cDNA library and lab info. management
• Protein property prediction
• SNP searching
• Medline text mining
• Bacterial genome databases
• Protein structure evaluation and comparison

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Software Repository

• Nearly 70 titles
• Freely downloadable
• Bioinformatics and general data processing
• Many from custom programming requests

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Nearly 70 titles...
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Services

• Telephone support
• (780-492-5969)
• Online support
• Software repository
• Research directory
• Biweekly newsletter
• Software advice
• Programming tutorials
• Custom programming

• LIMS development
• Custom graphics
• Website development
• Database development
• Batch processing
• Data mining
• Data handling
• Data archiving

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CBHD Outreach

• Bioinformatics Platform Rover, since December
  2004
• Responsible for
• Outreach
• Communication
• Bioinformatics Education
• Raise awareness about the Bioinformatics Platform
  for Genome Canada

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CBHD Outreach

• Today's seminar and workshop are experiments
• We have given/will be giving similar
  presentations across Canada
• Edmonton, Calgary, Vancouver
• Montréal (first event in Eastern Canada!)
• We would appreciate your feedback

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Outline

• What is the Bioinformatics Platform?
• What is the Canadian Bioinformatics Help Desk?
• What is the Canadian Bioinformatics Resource?
• What bioinformatics tools and resources does the
  Bioinformatics Platform offer?

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What is the CBR?

• Provide scientists with extensive tools for
  bioinformatics and computational biology
• Over 125 bioinfo software packages
• Over 150 DBs

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Who can use the CBR?

• Most web-based tools freely available
• Registered users
• Full access to all applications and DBs
• Includes command line UNIX access
• Users at member institutions
• Fewer restrictions on disk space, etc.

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www.cbr.nrc.ca
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Outline

• What is the Bioinformatics Platform?
• What is the Canadian Bioinformatics Help Desk?
• What is the Canadian Bioinformatics Resource?
• What bioinformatics tools and resources does the
  Bioinformatics Platform offer?

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Platform Projects

• Bluejay A browser for visualization and
  exploration of biological sequences
• BioMOBY A system for discovery and distribution
  of biological data
• Osprey Oligo design software
• BIRCH Bioinformatics analysis platform
• Genquire Genome annotation workstation

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Platform Projects

• GC-LIMS Laboratory Information Management
  System
• GelScape Gel annotation system
• PlasMapper Automated annotation and drawing of
  plasmid maps
• BacMap An interactive visual database for
  exploring bacterial genomes
• BASys Automated annotation of bacterial genomes

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Visualizing Biological Data
Using Bluejay to Browse Genomic Information
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Bluejay A Biological Sequence Browser

• Expanding on the idea of Internet Browsing
• Graphical display of integrated sequence
  information
• Support of several common data formats
• GenBank XML, FastA, BioML, BSML, Agave XML
• Customizable view of various sequence features
• Genes, introns, exons, repeat regions, promoters,
  markers, etc.
• At the end of the day publication-quality visual
  models
• Scalable Vector Graphics (SVG)

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Bluejay Easy to Use...

• Written in Java
• Operating system independent
• Easy to access
• Web applet or
• Downloadable application
• Point and click interface
• No programming, scripting or
• command line work
• (Great for the Biologist!)

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Bluejay Development

• All of these platform projects are customizable
  (they are not set in stone)
• Customizations are made in response to users
  requests
• e.g. Gene expression visualization tools
  incorporated into Bluejay
• TIGR Multiexperiment Viewer microarray analysis
  package has been incorporated into Bluejay
• Working on linking to pathway maps

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BioMOBYFrom meaningless interoperability to
meaningful integration
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Make sense of this mess!
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Benefits of MOBY

• Little or no programming experience required
• Just a little time with MOBY
• Allow users to create sophisticated tools using
  available web services
• Only limited by the number of programs in the
  registry MOBY Central
• Examples
• Build a high throughput EST pipeline
• Annotate microarray data
• Link to pathway data
• Programs like Taverna have made it even easier

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Taverna
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Osprey
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Osprey

• Calculate optimal oligos for
• Microarrays
• cDNA
• Spotted oligos
• Sequencing
• Contig walking
• Polishing

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Osprey Goals

• Want
• Binding to target sequence with right duplex
  melting temp for the experiment
• Distinguish b/n similar genes
• Avoid
• Oligos that fold back on themselves (hairpins)
• Oligos that fold to other copies of themselves
  (dimers)
• Oligos that bind well to more than one location
  (secondary or off-target binding)

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BIRCH
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What is BIRCH?

• A bioinformatics platform made up of software and
  databases for molecular biology
• Most of the programs have been unified through
  the Genetic Data Environment (GDE, a program that
  runs other programs)
• GDE takes care of the behind the scenes work
  (e.g. interconverting file formats)
• Allows the researcher to concentrate on the
  science

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BIRCH Features

• Bioinformatics programs for
• Sequence analysis
• Database management
• Gene expression analysis
• Building analytical pipelines
• Molecular markers
• Free download fromhttp//home.cc.umanitoba.ca/p
  sgendb/

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BIRCH Features

• Many built in features for customizing to your
  local system
• BIRCH local similar to /usr/local in UNIX
• With BIRCH upgrades, local customizations aren't
  lost
• Easily integrated with local resourcese.g. CBR
  (Halifax), BIRCH installation that calls Paracel
  BLAST via GDE(take advantage of local resources)

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Genquire

• A genome annotation workstation for comparing
  known or predicted gene models and associated
  information
• Facilitates import, viewing, querying, editing,
  and de novo restructuring of features mapped to a
  genome
• Multiple genomes may be viewed simultaneously at
  three levels
• Whole chromosome view
• Zoomable contig view
• Sequence-level view (selected regions)

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Genquire
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Laboratory Information Management System (LIMS)

• Manage and coordinate molecular biology,
  microarray, proteomic, histology, pathology data
• Track samples, monitor results, store data
• Communicate information b/n multiple labs and
  investigators
• Web-based and platform-independent (Java servlets)

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Transplant LIMS Mouse
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Transplant LIMS Analysis
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Transplant LIMS Query
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LIMS Utilities Development

• Customized utilities to support molecular
  biology, microarray, proteomics, pathology, and
  histology studies
• Automated protein/gene annotation
• Online gel analysis/annotation
• Online histology analysis/annotation
• Online microarray analysis

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LIMS Electronic Notebook

• A way of storing lab data in a centralised,
  networked format
• Can enter updates or data from any location with
  web access
• Electronic records/notes instead of paper records

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Transplant LIMS E-Lab Book
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LIMS Summary

• The GC-LIMS provides web-based,
  platform-independent data entry.
• The GC-LIMS provides the basic foundation on to
  which customised utilities to support molecular
  biology, microarray, proteomics, pathology, and
  histology studies can be added.
• The GC-LIMS includes an electronic notebook, that
  stores data in a centralised, networked format.

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GelScape

• Web-enabled gel viewing and annotation system
• Free and platform-independent
• UNIX, Linux, Windows, MacOS
• Browsers IE and Netscape gt 4.5
• Post, share, and compare gels
• Google 'GelScape'

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GelScape Supports ...

• Gel image uploading
• GIF and JPG formats
• 1D gels DNA, protein, Western blots
• 2D gels
• Image resizing
• Band marking and unmarking
• Automatic band detection
• Edge detection algorithm
• User adjustable
• Band annotation
• Swiss-Prot/GenBank ID, mass fingerprint, manual

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Annotate/View Mode
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Click on a Marked Band
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Automatic Spot Detection
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Auto-Annotate Map Plasmids
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PlasMapper Web Server

• Replaces commercial plasmid drawing programs
  (web-based, dont have to buy commercial
  software)
• Automatically draws and annotates plasmid maps
  (user inputs DNA sequence)
• Publication quality plasmid maps
• PNG, JPG, SVG, SVGZ (compressed SVG) formats
• Extensive array of display options including
  user-defined features

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Google 'PlasMapper'
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PlasMapper

• Not set in stone
• Will customize as requested by the scientific
  community
• Currently a 20 kb limit on input sequence
• If users request, we can change this
• If you dont like certain colour schemes, we can
  change them.
• We depend on your input.

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Explore Bacterial Genomes
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BacMap Genome Atlas

• Interactive, visual database containing
• Over 200 fully-labeled, zoomable, and searchable
  maps of bacterial genomes
• Gene labels are hyperlinked to detailed textual
  annotations
• Genomes can be queried using BLAST or keyword
  searches

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Google 'bacmap'
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BacMap
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Text Search Tools
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Sequence Search Tools
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What if Your Organism or Genome isnt in BacMap?
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BASys

• Bacterial Annotation System
• A publicly available web server that performs
  automated annotation of bacterial genomes given
  only the gene sequence of a chromosome or plasmid
• Takes about 24 hrs. for an average genome (4
  megabases)
• Output includes images and annotation text (about
  60 fields for each gene)
• Easily adapted to eukaryotic systems

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Typical BASys Result
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Custom Solutions

• Specific requests from researchers
• Many custom programs in Software Repository
• Examples
• Promoter analysis (custom Perl script)
• Microarray analysis (GeneSpring, GenePublisher)
• Pathway analysis (Ingenuity Pathways Analysis)

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cDNA Library Manager

• Stores/manages sequence trace file data
• Automates/facilitates seq trace file analysis and
  clone ID
• Includes trimming (Phred)
• NCBI BLAST (can choose DB)
• BLAST results added to DB and viewable
• Intra-library BLAST to ID/cluster redundant clones

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Summary

• The Bioinformatics Platform for Genome Canada
  provides many useful bioinformatics tools and
  resources for researchers in Canada and around
  the world
• We are here to meet your bioinformatics needs

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Acknowledgments

• The CBHD, as part of the Integrated and
  Distributed Bioinformatics Platform, is supported
  by Genome Prairie, Genome Canada, and other
  co-funding partners. Genome Canada is a
  not-for-profit corporation which is leading
  Canada's national strategy on genomics with 600
  million in funding from the federal government.

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Acknowledgments

• Dr. David Wishart Leadership
• Dr. Paul Stothard CGView, PlasMapper, BacMap,
  BASys, cDNA Library Manager Development
• Dr. Gary Van Domselaar BacMap, BASys, Help Desk
  website development
• Savita Shrivastava BacMap, BASys development
• Xiaoli Dong Sys Admin, PlasMapper and GC-LIMS
  development
• Nelson Young Sys Admin, GelScape development
• Dr. Christoph Sensen, Paul Gordon, Marianne Hang,
  Dr. Mark Wilkinson, Dr. Brian Fristensky, Terry
  Dalton, and Rob Hutten Bioinformatics Platform
  slides

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Contact Us

• Visit our web sitehttp//gchelpdesk.ualberta.ca
• Send us an emailinfo_at_gchelpdesk.ualberta.ca
• Give us a call 780 492-5969
• We are here to serve your bioinformatics needs