capabilities of the vbc torsten seemann - csiro - 2 apr 2008
TRANSCRIPT
Capabilities of the Capabilities of the Victorian Bioinformatics Victorian Bioinformatics
ConsortiumConsortium
Torsten Seemann & Paul Harrison
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Outline
● About us● Capabilities● Examples● Funding model● Conclusion● Contact details
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Who are we?
● The VBC brings together researchers from various backgrounds– computer science / statistics– bioinformatics– microbiology / biochemistry / medical– agriculture / vetinary
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Main members
● School. Computer Scienceand Software Engineering
● Dept. Microbiology
● Dept. Biochemistry
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Where we were
● Monash UniversityClayton CampusMelbourne
● Until Feb 2007STRIP1 / B75
● Italian Cafe aromas
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Where we are
● 2008
● Micro/Physics B27
● Formaldehyde from neighbouring labs
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Where we will be
● 2009+
● STRIP2 / B76
● Aroma of freshpaint and tile adhesives?
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Capabilities
● Custom software development● Sequence/genomic analysis● Microarray analysis/storage● Protein crystallography/model● Protease structure/function● Data mining/visualization● Computer system architecture
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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 data
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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 RNA
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Wasabi
● In-house web-based system for genome curation and mining
● View all your annotations and searches together
● Homologs, pathways, NCBI submission files
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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 server
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Microarray storage
● BASE server● BioArray
SoftwareEnvironment
● Web based interface– Apache– MySQL– PHP
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Software development
● Experienced software engineers● Perl/Python scripting● Web applications● SQL databases● Automation of repetitive tasks● Bulk web form submission● Run Unix bioinformatics software
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Data visualization
● Easy!– Just use Excel?
● May need help to massage into Excel
● Sometimes just too hard with R or Excel
Row 1 Row 2 Row 3 Row 40
2
4
6
8
10
12
Main title
Column 1 Column 2
Column 3
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Gene Spaghetti
● Ball of string representing DNA sequence
● Use position and colour to visualize nucleotide usage
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Visualize short reads
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Alignment to reference
● Identify all SNPs and InDels● Estimate plasmid copy number
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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
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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 from
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VBC Funding
● 3 funding sources for 2 core staff
● $ ?
● Want to add 2 staff within 2 years
● CSIRO – Monash linkage programme
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Conclusion
● Have expertise● But spread too thin● Need more
– time?– staff?– funding?
● Scope to collaborate
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Contact us
Webhttp://www.vicbioinformatics.com/