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

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

  • Capabilities of theVictorian Bioinformatics ConsortiumTorsten Seemann & Paul Harrison
  • Outline ● About us ● Capabilities ● Examples ● Funding model ● Conclusion ● Contact details07/08/12 Victorian Bioinformatics Consortium 2
  • 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
  • Main members ● School. Computer Science and Software Engineering ● Dept. Microbiology ● Dept. Biochemistry07/08/12 Victorian Bioinformatics Consortium 4
  • Where we were● Monash University Clayton Campus Melbourne● Until Feb 2007 STRIP1 / B75● Italian Cafe aromas07/08/12 Victorian Bioinformatics Consortium 5
  • Where we are● 2008● Micro/Physics B27● Formaldehyde from neighbouring labs07/08/12 Victorian Bioinformatics Consortium 6
  • Where we will be● 2009+● STRIP2 / B76● Aroma of fresh paint and tile adhesives?07/08/12 Victorian Bioinformatics Consortium 7
  • 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
  • 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
  • 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
  • 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
  • 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
  • Microarray storage ● BASE server ● BioArray Software Environment ● Web based interface – Apache – MySQL – PHP07/08/12 Victorian Bioinformatics Consortium 13
  • 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
  • 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
  • Gene Spaghetti ● Ball of string representing DNA sequence ● Use position and colour to visualize nucleotide usage07/08/12 Victorian Bioinformatics Consortium 16
  • Visualize short reads07/08/12 Victorian Bioinformatics Consortium 17
  • Alignment to reference● Identify all SNPs and InDels● Estimate plasmid copy number07/08/12 Victorian Bioinformatics Consortium 18
  • 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
  • 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
  • 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
  • Conclusion ● Have expertise ● But spread too thin ● Need more – time? – staff? – funding? ● Scope to collaborate07/08/12 Victorian Bioinformatics Consortium 22
  • 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