CSIRO Bioinformatics Server
This server is the informal webpresence of the transformational bioinformatics team; official page.
Our charter is to develop novel bioinformatics solutions for research and industry using the latest in cloud and BigData infrastructure. We specifically focus on population-scale 'omics (genomics, transcriptomics, methylomics) analysis as well as genome engineering applications as the two high impact life science areas.
Our two main software platforms are
- VariantSpark Hadoop/Spark based machine learning framework for insights from population scale 'omics cohort
- GT-Scan2 Cloud based recommender engine for computational guided genome engineering application
for other developments please see the sidebar.
images from previous years
Current members of the team
- Denis Bauer (Senior Research Scientist)
- Oscar Luo (Research Scientist)
- Natalie Twine (PostDoc)
- Kaitao Lai (PostDoc)
- Laurence Wilson (PostDoc)
- Arash Bayat (RA)
- Aidan O'Brien (PhD Student)
- Robert Dunne (deployed in)
- Piotr Szul (deployed in)
- Anita Sathyanarayanan (PhD Student, QUT)
- Sadaf Ilyas (PhD Student, ANU)
Nov/Dec 2017 We will deliver the keynote at YOW! 2017, a software development conference reaching over 15,000 software professionals across Australia and New Zealand.
Sept 18 2017 We delivered the keynote for the 2017 YOW! Data conference in Sydney.
July 26 2017 Databricks featured VariantSpark Breaking the “curse of dimensionality” in Genomics using "wide" Random Forests.
Jun 1 2017 The team won two iAwards for "BigData/Machine learning innovation of the year" and "Industrial & Primary Industries Award" at the 2017 NSW state finals.
Mar 1 2017 Partnering with ANU Bioinformatics Consultancy (ABC) Unit
Dec 8 2016 GT-Scan2 was covered by GenomeWeb, one of the largest online news outlets for genomics and lifescience developments "Australian Team Puts CRISPR Design on Amazon Cloud".
Nov 10 2016 AWS coverd GT-Scan2 on their prestigious Jeff Barr Blog "Genome Engineering Applications: Early Adopters of the Cloud"
April 8 2016 New software added: GT-Scan, finding optimal targets for genome editing or regulatory interference using CRISPR/Cas or zinc-finger nuclease systems.
April 8 2016 New softare added: VariantSpark, a framework for applying Spark-based Machine Learning methods to whole-genome variant information.
April 8 2016 New software added: NGSANE, Analysis Framework for Biological Data from High Throughput Experiments.
August 12 2013 Updates to the sparse.inv.cov software page.
Apr 8 2013 A new web page for Blue: a fast, accurate short-read error-correction tool based on k-mer consensus and context.
Please see the legal notice and disclaimer. If you need access or have an idea for a useful application, contact Denis Bauer.