Title: Bioinformatics Tools and Resources for the Life Science Researcher
1Bioinformatics Tools and Resources for the Life
Science Researcher
- Ian J. Forsythe
- Canadian Bioinformatics Help Desk
- February and March 11, 2005
2Download Presentation
3Purpose
- To raise awareness locally and across Canada
about bioinformatics tools and resources that are
available to life science researchers. - Increase communication between researchers and
the Help Desk
4Outline
- 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?
5What 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.
6What 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
Four so far Next one on April 30 May 8 in
Calgary. - Providing Platform Services to Researchers around
the world.
7Bioinformatics 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
8Service Across Canada
9Outline
- 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?
10Canadian Bioinformatics Help Desk
11Who are we?
- Director
- Dr. David Wishart
- Bioinformaticians
- Dr. Paul Stothard
- Dr. Gary Van Domselaar
- Ian Forsythe
- Savita Shrivastava
12Website
- 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
13Website
14Research Directory
15Links
16Newsletter
- Biweekly (34 issues to date)
- Over 1600 subscribers
- Bioinformatics Profiles
- Software Spotlights
- What's New
- Upcoming Events
- Jobs
- Newsletter archive
17Newsletter (Subscribe Today!)
18Web Servers
- 26 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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20Software Repository
- Over 60 titles
- Bioinformatics and general data processing
- Many from custom programming requests
21Over 60 titles...
22Services
- Telephone support
- (780-492-5969)
- Online support
- Software repository
- Research directory
- Biweekly newsletter
- Software advice
- Programming tutorials
- Custom programming
- Custom graphics
- Website development
- Database development
- LIMS development
- Batch processing
- Data mining
- Data handling
- Data archiving
23CBHD Outreach
- Bioinformatics Platform Rover, December 2004
- Responsible for
- Outreach
- Communication
- Bioinformatics Education
- Raise awareness about the Bioinformatics Platform
for Genome Canada
24CBHD Outreach
- Today's seminar and workshop are experiments
- We will be giving similar presentations across
Canada - Calgary, Vancouver
- Saskatoon, Toronto, Montreal
- We would appreciate your feedback
25Outline
- 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?
26What is the CBR?
- Provide scientists with extensive tools for
bioinformatics and computational biology - Over 125 bioinfo software packages
- Over 150 DBs
27Who 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.
28www.cbr.nrc.ca
29Outline
- 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?
30Platform Projects
- Bluejay A browser for visualization and
exploration of biological sequences - BioMOBY A system for the discovery and
distribution of biological data - GC-LIMS Laboratory Information Management
- 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
31Visualizing Biological Data
Using Bluejay to Browse Genomic Information
32Bluejay 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)
33Bluejay 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!)
34Bluejay 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 - TIGRs TM4 microarray analysis package has been
incorporated into Bluejay - Working on linking to pathway maps
35BioMOBYFrom meaningless interoperability to
meaningful integration
36Make sense of this mess!
37Benefits 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
- Programs like Taverna have made it even easier
38Laboratory 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)
39Sample Tracking Pathology/cDNA Labeling
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41LIMS 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
42LIMS 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
43LIMS 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.
44GelScape
- 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'
- Young et al., Bioinformatics 20(6)976-8, 2004
45GelScape 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
46Annotate/View Mode
47Click on a Marked Band
48Automatic Spot Detection
49Auto-Annotate Map Plasmids
50PlasMapper 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
51Google 'PlasMapper'
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54PlasMapper
- 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.
55Explore Bacterial Genomes
56BacMap 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
57Google 'bacmap'
58BacMap
59Text Search Tools
60Sequence Search Tools
61What if Your Organism or Genome isnt in BacMap?
62BASys
- 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
63Typical BASys Result
64Custom Solutions
- Specific requests from researchers
- Many custom programs in Software Repository
- Examples
- Promoter analysis (custom Perl script)
- Microarray analysis (GeneSpring, GenePublisher,
TIGR's TM4) - Pathway analysis (Ingenuity Pathways Analysis,
UCSF's GenMAPP)
65Summary
- The Bioinformatics Platform for Genome Canada
provides many useful bioinformatics tools and
resources for researchers in Canada and around
the world. - As University of Alberta researchers, you have
the distinct advantage of having a local resource
(Canadian Bioinformatics Help Desk). - If your needs aren't being met, email
if_at_ualberta.ca to submit a request for assistance.
66Acknowledgments
- The CBHD, as part of the Integrated and
Distributed Bioinformatics Platform, is supported
by Genome Prairie, in part through Genome Canada,
a not-for-profit corporation which is leading a
national strategy on genomics with 375 million
in funding from the Government of Canada.
67Acknowledgments
- 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, Marianne Hang, Dr. Mark
Wilkinson, Terry Dalton, and Rob Hutten
Bioinformatics Platform slides
68Contact 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