Capabilities of theVictorian Bioinformatics       ConsortiumTorsten Seemann & Paul Harrison
Outline ●   About us ●   Capabilities ●   Examples ●   Funding model ●   Conclusion ●   Contact details07/08/12           ...
Who are we?           ●   The VBC brings together               researchers from various               backgrounds        ...
Main members             ●   School. Computer Science                 and Software Engineering             ●   Dept. Micro...
Where we were●   Monash University    Clayton Campus    Melbourne●   Until Feb 2007    STRIP1 / B75●   Italian Cafe aromas...
Where we are●   2008●   Micro/Physics B27●   Formaldehyde from    neighbouring labs07/08/12        Victorian Bioinformatic...
Where we will be●   2009+●   STRIP2 / B76●   Aroma of fresh    paint and tile    adhesives?07/08/12           Victorian Bi...
Capabilities           ●   Custom software development           ●   Sequence/genomic analysis           ●   Microarray an...
Sequence assembly ●   Short read assembly ●   Mixed assembly - combine     reads from different sources ●   Isolation of p...
Annotation pipeline                 ●   Predict ORFs                 ●   Annotate function via                     homolog...
Wasabi ●   In-house web-based     system for genome     curation and mining ●   View all your     annotations and     sear...
Microarray analysis           ●   Design oligos/probes               –   redundant / non-redundant sets           ●   Anal...
Microarray storage ●   BASE server ●   BioArray     Software     Environment ●   Web based     interface     –     Apache ...
Software                  development           ●   Experienced software engineers           ●   Perl/Python scripting    ...
Data visualization●   Easy!                                              Main title                                       ...
Gene Spaghetti                                              ●   Ball of string                                            ...
Visualize short reads07/08/12       Victorian Bioinformatics Consortium   17
Alignment to reference●   Identify all SNPs and InDels●   Estimate plasmid copy number07/08/12         Victorian Bioinform...
Computer hardware●    Advice on hardware purchases     for your applications      –   servers      –   large RAM or fast C...
Core strength               ●   Ability to adapt to new                   problems in bioinformatics               ●   Ide...
VBC Funding                         ●   3 funding sources                             for 2 core staff                    ...
Conclusion ●   Have expertise ●   But spread too thin ●   Need more     –     time?     –     staff?     –     funding? ● ...
Contact us                     Web      http://www.vicbioinformatics.com/                            Email      torsten.se...
Upcoming SlideShare
Loading in …5
×

Capabilities of the vbc torsten seemann - csiro - 2 apr 2008

292 views
248 views

Published on

0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
292
On SlideShare
0
From Embeds
0
Number of Embeds
1
Actions
Shares
0
Downloads
2
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Capabilities of the vbc torsten seemann - csiro - 2 apr 2008

  1. 1. Capabilities of theVictorian Bioinformatics ConsortiumTorsten Seemann & Paul Harrison
  2. 2. Outline ● About us ● Capabilities ● Examples ● Funding model ● Conclusion ● Contact details07/08/12 Victorian Bioinformatics Consortium 2
  3. 3. Who are we? ● The VBC brings together researchers from various backgrounds – computer science / statistics – bioinformatics – microbiology / biochemistry / medical – agriculture / vetinary07/08/12 Victorian Bioinformatics Consortium 3
  4. 4. Main members ● School. Computer Science and Software Engineering ● Dept. Microbiology ● Dept. Biochemistry07/08/12 Victorian Bioinformatics Consortium 4
  5. 5. Where we were● Monash University Clayton Campus Melbourne● Until Feb 2007 STRIP1 / B75● Italian Cafe aromas07/08/12 Victorian Bioinformatics Consortium 5
  6. 6. Where we are● 2008● Micro/Physics B27● Formaldehyde from neighbouring labs07/08/12 Victorian Bioinformatics Consortium 6
  7. 7. Where we will be● 2009+● STRIP2 / B76● Aroma of fresh paint and tile adhesives?07/08/12 Victorian Bioinformatics Consortium 7
  8. 8. Capabilities ● Custom software development ● Sequence/genomic analysis ● Microarray analysis/storage ● Protein crystallography/model ● Protease structure/function ● Data mining/visualization ● Computer system architecture07/08/12 Victorian Bioinformatics Consortium 8
  9. 9. Sequence assembly ● Short read assembly ● Mixed assembly - combine reads from different sources ● Isolation of plasmids ● Scaffolding to reference genomes ● Developing tools to manage and mine this new data07/08/12 Victorian Bioinformatics Consortium 9
  10. 10. Annotation pipeline ● Predict ORFs ● Annotate function via homology to known seqs ● Flag pseudogenes or potential mis-assemblies ● Identify rRNA, tRNA, repeats, insertion seq. ● Predict operons, signals, RBS, small RNA07/08/12 Victorian Bioinformatics Consortium 10
  11. 11. Wasabi ● In-house web-based system for genome curation and mining ● View all your annotations and searches together ● Homologs, pathways, NCBI submission files07/08/12 Victorian Bioinformatics Consortium 11
  12. 12. Microarray analysis ● Design oligos/probes – redundant / non-redundant sets ● Analyse data using robust methods – normalization of data – identify significant genes ● Store microarray data securely – can host data on our BASE server07/08/12 Victorian Bioinformatics Consortium 12
  13. 13. Microarray storage ● BASE server ● BioArray Software Environment ● Web based interface – Apache – MySQL – PHP07/08/12 Victorian Bioinformatics Consortium 13
  14. 14. Software development ● Experienced software engineers ● Perl/Python scripting ● Web applications ● SQL databases ● Automation of repetitive tasks ● Bulk web form submission ● Run Unix bioinformatics software07/08/12 Victorian Bioinformatics Consortium 14
  15. 15. Data visualization● Easy! Main title 12 – Just use Excel? 10● May need help to massage into Excel 8 Column 1 Column 2● Sometimes just too 6 Column 3 hard with R or 4 Excel 2 0 Row 1 Row 2 Row 3 Row 407/08/12 Victorian Bioinformatics Consortium 15
  16. 16. Gene Spaghetti ● Ball of string representing DNA sequence ● Use position and colour to visualize nucleotide usage07/08/12 Victorian Bioinformatics Consortium 16
  17. 17. Visualize short reads07/08/12 Victorian Bioinformatics Consortium 17
  18. 18. Alignment to reference● Identify all SNPs and InDels● Estimate plasmid copy number07/08/12 Victorian Bioinformatics Consortium 18
  19. 19. Computer hardware● Advice on hardware purchases for your applications – servers – large RAM or fast CPU? – large disk storage – NAS, SAN● Advice on software – Unix / open source solutions 07/08/12 Victorian Bioinformatics Consortium 19
  20. 20. Core strength ● Ability to adapt to new problems in bioinformatics ● Identify/evaluate existing solutions ● Create our own solutions where necessary ● Network of international peers to get advice from07/08/12 Victorian Bioinformatics Consortium 20
  21. 21. VBC Funding ● 3 funding sources for 2 core staff ● $? ● Want to add 2 staff within 2 years ● CSIRO – Monash linkage programme07/08/12 Victorian Bioinformatics Consortium 21
  22. 22. Conclusion ● Have expertise ● But spread too thin ● Need more – time? – staff? – funding? ● Scope to collaborate07/08/12 Victorian Bioinformatics Consortium 22
  23. 23. Contact us Web http://www.vicbioinformatics.com/ Email torsten.seemann@infotech.monash.edu.au paul.harrison@med.monash.edu.au07/08/12 Victorian Bioinformatics Consortium 23

×