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Resources  Everything you wanted to know about NGSactivities in Victoria but were too busy to ask!     Andrew Lonie, Clare...
Bioinformatics Groups●   WEHI (20? - Bioinformatics Division - res and applied)●   VLSCI (12-15 - applied)●   Petermac (6?...
Instruments in Vic: last year 2011 AGRF                                   PeterMac 4x Illumina HiSeq2000                  ...
(Some) Victorian sequencing machines
Instruments in Vic: 2012 losing count! AGRF                                     PeterMac 4x Illumina HiSeq2000            ...
Compute Infrastructure 2012VLSCI     1000 core cluster (148GB) + 700 core cluster (up to 48GB 1TB)          8000 core Blue...
Compute Infrastructure accessVLSCI      http://www.vlsci.org.au/page/rasVPAC       http://vpac.org - not sure how access w...
Education/CoursesUnimelb MSc (Bioinformatics):http://graduate.science.unimelb.edu.au/master-of-science-bioinformaticsRMIT ...
Regular Seminars/MeetingsAGRF NGS SIGs (bimonthly @ Tue 4:00pm)  Applications, technology, methodsWEHI Bioinformatics (wee...
SchoolsWinter School in Computational Biology  Annually in July for 5 days  IMB, UQ, Brisbane (Organized by Nick Hamilton ...
Conferences (national)AMATA -  Australasian Genomics Technologies Association    Rotates between capital cities - Annually...
Conferences (international)ISMB - International Society Molecular Biology   Has excellent satellite meetings and informati...
Mailing ListsVLSCI News (vlsci-news@lists.vlsci.org.au)LSCC Event List (cf. Andrew Lonie)WEHI Seminars (seminars@wehi.edu....
WebsitesSeqAnswers.com  Forums on NGS, Bioinformatics, ToolsBioStars.org  Forums on NGS, Bioinformatics, ToolsAustralianBi...
Blogshttp://omicsomics.blogspot.com/                       http://SEQanswers.comhttp://pathogenomics.bham.ac.uk/blog      ...
TwitterFollowing the right tweeters allows you to find out new ideas, goodpapers, and discover things you would have misse...
Corporate technical contactsIllumina (MiSeq, HiSeq)   Gareth (ex Illumina UK)   Gabe Kolle (ex IMB/UQ)LifeTech (SOLiD / PG...
InitiativesNeCTAR: National eResearch Collaboration Tools and Resources●   Research Cloud: Like Amazon cloud, 25000 cores ...
Initiatives: NeCTAR and RDSI  Research Cloud  node  RDSI node
Initiatives: NeCTAR and RDSI  Research Cloud  node  RDSI node  Coming 2013....  "Additional node" (?)
Initiatives: NeCTAR and RDSI  Research Cloud  node  RDSI node                                                  QCIF       ...
Initiatives: Genomics Virtual Lab  Research Cloud  node  RDSI node                                                  QCIF  ...
Genomics Virtual Lab                   Mature workflows for common tasksInteractive                                       ...
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Genomics resources in Victoria Australia

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Genomics resources in Victoria Australia

  1. 1. Resources Everything you wanted to know about NGSactivities in Victoria but were too busy to ask! Andrew Lonie, Clare Slogget, Torsten Seemann : December 2012
  2. 2. Bioinformatics Groups● WEHI (20? - Bioinformatics Division - res and applied)● VLSCI (12-15 - applied)● Petermac (6? - applied)● NICTA  (5 - application res and dev, some applied)● MCRI (5 - res and applied)● Baker (4? - applied)● Monash: VBC (5 - research & applied)● Monash: Uni+MIMR+AMReP (4 - research & applied)● Uni Melb (various)● DPI (1 + lots of statisticians - applied)● Ludwig (3 - applied)● SVI (?)
  3. 3. Instruments in Vic: last year 2011 AGRF PeterMac 4x Illumina HiSeq2000 1x Illumina GAIIx 4x Illumina GAIIx 1x HiSeq2000 Unimelb Baker 1x ABI SOLiD4 1x Illumina GAII 3x Ion Torrent [Path,Micro,Genetics] 1x MiSeq [Pathology] Monash 1x Illumina GAIIx, 1x MiSeq Bio21 1x Ion Torrent DPI 1x GAIIx LaTrobe 1x 454 1x Ion Torrent 1x HiSeq2000 CSIRO  1x 454 [AAHL, Geelong]
  4. 4. (Some) Victorian sequencing machines
  5. 5. Instruments in Vic: 2012 losing count! AGRF PeterMac 4x Illumina HiSeq2000 1x Illumina GAIIx 4x Illumina GAIIx 1x HiSeq2000/2500 2x PGM Baker Unimelb 1x Illumina GAIIx 1x ABI SOLiD4 [Pathology] 3x PGM [Path,Genetics,Micro] Monash 2x MiSeq [Pathology, Micro] 1x Illumina GAIIx, 1x MiSeq [Micromon] 1x HiSeq2500 [Pathology] 1x ABI SOLiD5, 1x PGM [MIMR] Bio21 DPI 1x PGM 1x GAIIx 1x 454 LaTrobe 1x HiSeq2000 1x Ion Torrent 1x Miseq CSIRO  1x Hiseq2000 (soon) 1x 454 [AAHL, Geelong] Legend: GREEN => new in last 12 months
  6. 6. Compute Infrastructure 2012VLSCI 1000 core cluster (148GB) + 700 core cluster (up to 48GB 1TB) 8000 core BlueGene/P 65000 core BlueGene/Q 2PB HSM data store [merit-based access Vic researchers]NCI/APAC 1492 node Sun Constellation cluster 57500 core Fujitsu cluster [merit-based access thru NCI]VPAC 888 core cluster; GPU cluster; Power5 cluster [ACCESS?] Merged with VeRSIUoM 768 core Linux cluster [UoM researchers]Monash CPU bound: grid of 1500 cores, 5 TB RAM total RAM bound: 4 x Dell R910 w/ 1 TB RAM + 64 cores eachWEHI medium Linux cluster [WEHI researchers]Massive 1200 cores + 84 GPU cluster [merit-based all researchers thru NCI]Nectar 3000 (?) core research cloud @ UoM - available to all researchers
  7. 7. Compute Infrastructure accessVLSCI http://www.vlsci.org.au/page/rasVPAC http://vpac.org - not sure how access works nowNCI/APAC http://nci.org.au/facilities-and-services/national-facility/UoM https://its.unimelb.edu.au/research/hpc/Monash http://www.monash.edu.au/eresearch/services/mcg/index.htmlWEHI Not for general access - contact WEHI Bioinf groupMassive http://massive.org.auNectar http://nectar.org.au/research-cloud
  8. 8. Education/CoursesUnimelb MSc (Bioinformatics):http://graduate.science.unimelb.edu.au/master-of-science-bioinformaticsRMIT Grad Dip (Bioinf):http://www.rmit.edu.au/programs/gd152LaTrobe Master of Biotech and Bioinf:http://www.latrobe.edu.au/handbook/2012/postgraduate/science-tech/coursework/shmbb.htm LSCC workshops: Genomics, programming, software tool use, toolsetupBioPlatforms Australia EMBL training workshops:http://www.bioplatforms.com.au/special-initiatives/bioinformatics/bpa-ebi-training-workshopsVLSCI / VPAC / MeRC: Regular MPI, PBS, GPU coursesMicromon RecDNA course - 6 days, Nov, annualhttp://www.micromon.monash.org/dnacourse.html
  9. 9. Regular Seminars/MeetingsAGRF NGS SIGs (bimonthly @ Tue 4:00pm) Applications, technology, methodsWEHI Bioinformatics (weekly @ Tue 10:45am) Research advances in bioinformatics, algorithm developmentLSCC Capacity Seminars (fortnightly @ Fri 2:30pm) Open lab meeting, student presentations, technology discussions, pipelines, best practice, problems
  10. 10. SchoolsWinter School in Computational Biology Annually in July for 5 days IMB, UQ, Brisbane (Organized by Nick Hamilton - formerly Mark Ragan)BioInfo Summer Annually in Nov/Dec for 5 days Adelaide 2012AGRF/EMBL The trained-trainers toured Australia in 2012LSCC Workshops 1 day workshops RNA-Seq, variant calling, Intro to NGS
  11. 11. Conferences (national)AMATA -  Australasian Genomics Technologies Association Rotates between capital cities - Annually in Sept/Oct for 4 days Adelaide 2012, Gold Coast 2013, Melbourne 2014BA - Bioinformatics Australia    Has been part of AusBioTech - Biennial for 2 days (defunct?)Lorne Genome/Cancer/Proteomics     Has an informatics presence - Annually in Jan/FebASM - Australian Society of Microbiology     Has an NGS SIG session - Annually in July for 5 daysLSCC Conference - possible future event?    Covering all 3 themes: Genomics, Imaging, Systems Biology
  12. 12. Conferences (international)ISMB - International Society Molecular Biology Has excellent satellite meetings and informatics sessions (Berlin 2013)BOSC - Bioinformatics Open Source Conference Pre satellite session to ISMB (Berlin 2013)ECCB - European Conference on Computation Biology Partners with ISMB biennially in Europe (Berlin 2013)APBC - Asia Pacific Bioinformatics Conference Held in Melbourne, Jan 2012, will be in Vancouver 2013EHGC - European Human Genetics Conference (EU)ABPHM - Applied Bioinf. in Public Health Microbiology (UK)GCC - Galaxy Community Conference (Oslo 2013)BioIT Asia - 2012 first event in Singapore, looking to raise profile
  13. 13. Mailing ListsVLSCI News (vlsci-news@lists.vlsci.org.au)LSCC Event List (cf. Andrew Lonie)WEHI Seminars (seminars@wehi.edu.au)Melbourne Bioinformatics Alliance (cf. Torsten Seemann)IMB Bioinformatics List (cf. Mark Ragan)
  14. 14. WebsitesSeqAnswers.com Forums on NGS, Bioinformatics, ToolsBioStars.org Forums on NGS, Bioinformatics, ToolsAustralianBioinformatics.net Jobs, event calendar, resources, blog (David Lovell will cover in his talk)
  15. 15. Blogshttp://omicsomics.blogspot.com/ http://SEQanswers.comhttp://pathogenomics.bham.ac.uk/blog http://dskernel.blogspot.com/http://bacpathgenomics.wordpress.com/ http://ensembl.blogspot.com/http://contig.wordpress.com http://genome.wustl.edu/news/http://blog.malde.org http://themindwobbles.wordpress.comhttp://bioinforuby.blogspot.com/ http://thenaturefallacy.blogspot.com/http://bcbio.wordpress.com http://phylogenomics.blogspot.com/http://bytesizebio.net http://www.vlsci.org.au/newshttp://selab.janelia.org/people/eddys/blog http://nsaunders.wordpress.comhttp://finchtalk.geospiza.com/ http://xfam.wordpress.comhttp://genehack.org http://flxlexblog.wordpress.com/http://www.genomeweb.com/magazine/genome-technologyhttp://www.homolog.us/blogshttp://blog.jcuff.net/http://igotgenes.blogspot.com/ Blogs are a rich source ofhttp://microbialgenomics.blogspot.com/http://microbialmodus.wordpress.com cutting edge information, tips,http://microbiology.sehttp://kevinl.wordpress.com and tricks. Many NGShttp://www.clcngs.comhttp://wiki.nodalpoint.org/ practitioners have blogged orhttp://www.null-hypothesis.co.uk//http://rna-seqblog.com tweeted information or linkshttp://robertedgar.wordpress.com long before mainstream newshttp://seqanswers.com/forums/ sources get to them.
  16. 16. TwitterFollowing the right tweeters allows you to find out new ideas, goodpapers, and discover things you would have missed. Twitter ~ RNA-Seq <=> Journal feeds ~ MicroarraysSome examples of good tweeters: @ausbionet Australian BioinfmaticsNetwork @pathogenomick Nick Loman @genetics_blog Stephen Turner @BioMickWatson Mick Watson @phylogenomics Jonathan Eisen
  17. 17. Corporate technical contactsIllumina (MiSeq, HiSeq) Gareth (ex Illumina UK) Gabe Kolle (ex IMB/UQ)LifeTech (SOLiD / PGM / Proton) Fabrice Odefey (ex UOM) IonCommunity web siteRoche (454) Anyone know? (VIDRL has a 454 Jr)PacBio None in Australian. Hopefully AGRF buys one!
  18. 18. InitiativesNeCTAR: National eResearch Collaboration Tools and Resources● Research Cloud: Like Amazon cloud, 25000 cores across Oz● Virtual Laboratories: Online research platforms on the Res Cloud● National Server Program: Persistent reliable virtual servers for hosting important applicationsRDSI: Research Data Storage Initiative● Data Nodes● Research Data Services: development and hosting of (community advocated) data sets of national significance.● Data Sharing: moving data around between nodes?EMBL Australia: Ensembl mirror, data mirrors, other resourceshttp://ebi.edu.au
  19. 19. Initiatives: NeCTAR and RDSI Research Cloud node RDSI node
  20. 20. Initiatives: NeCTAR and RDSI Research Cloud node RDSI node Coming 2013.... "Additional node" (?)
  21. 21. Initiatives: NeCTAR and RDSI Research Cloud node RDSI node QCIF Murdoch U eResearchSA Coming 2013.... Intersect Unimelb ANU "Additional node" Monash UTas
  22. 22. Initiatives: Genomics Virtual Lab Research Cloud node RDSI node QCIF GVL Murdoch U eResearchSA Coming 2013.... Intersect GVL Unimelb ANU "Additional node" Monash UTas
  23. 23. Genomics Virtual Lab Mature workflows for common tasksInteractive Interactive researcher-led Training analysis analysis Interactive analysis, workflow developmentPython, perl Ruffus Galaxy BioLinux bespoke Python-based workflow Interactive web-based workflow Cloud-based bioinf solutions framework framework tools Genomics Virtual Laboratory "Mezzanine-level" NeCTAR Research Cloud compute cluster Data RDSI

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