Embed Size (px)
DESCRIPTION
Citation preview
Everything you wanted to know about NGS activities in Victoria but were too busy to ask!
Resources
Andrew Lonie, Clare Slogget, Torsten Seemann : December 2012
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 (?)
Instruments in Vic: last year 2011
AGRF4x Illumina HiSeq20004x Illumina GAIIx
Unimelb1x ABI SOLiD43x Ion Torrent [Path,Micro,Genetics]1x MiSeq [Pathology]
Bio211x Ion Torrent
LaTrobe1x Ion Torrent
PeterMac1x Illumina GAIIx1x HiSeq2000
Baker1x Illumina GAII
Monash1x Illumina GAIIx, 1x MiSeq
DPI1x GAIIx1x 4541x HiSeq2000
CSIRO 1x 454 [AAHL, Geelong]
(Some) Victorian sequencing machines
Instruments in Vic: 2012 losing count!AGRF4x Illumina HiSeq20004x Illumina GAIIx2x PGM
Unimelb1x ABI SOLiD4 [Pathology]3x PGM [Path,Genetics,Micro]2x MiSeq [Pathology, Micro]1x HiSeq2500 [Pathology]
Bio211x PGM
LaTrobe1x Ion Torrent1x Miseq1x Hiseq2000 (soon)
Legend: GREEN => new in last 12 months
PeterMac1x Illumina GAIIx1x HiSeq2000/2500
Baker1x Illumina GAIIx
Monash1x Illumina GAIIx, 1x MiSeq [Micromon]1x ABI SOLiD5, 1x PGM [MIMR]
DPI1x GAIIx1x 4541x HiSeq2000
CSIRO 1x 454 [AAHL, Geelong]
Compute Infrastructure 2012VLSCI 1000 core cluster (148GB) + 700 core cluster (up to 48GB 1TB)
8000 core BlueGene/P 65000 core BlueGene/Q2PB HSM data store [merit-based access Vic researchers]
NCI/APAC 1492 node Sun Constellation cluster57500 core Fujitsu cluster [merit-based access thru NCI]
VPAC 888 core cluster; GPU cluster; Power5 cluster [ACCESS?]Merged with VeRSI
UoM 768 core Linux cluster [UoM researchers]
Monash CPU bound: grid of 1500 cores, 5 TB RAM totalRAM bound: 4 x Dell R910 w/ 1 TB RAM + 64 cores each
WEHI 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
Compute Infrastructure accessVLSCI http://www.vlsci.org.au/page/ras
VPAC http://vpac.org - not sure how access works now
NCI/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.html
WEHI Not for general access - contact WEHI Bioinf group
Massive http://massive.org.au
Nectar http://nectar.org.au/research-cloud
Education/CoursesUnimelb MSc (Bioinformatics):http://graduate.science.unimelb.edu.au/master-of-science-bioinformatics
RMIT Grad Dip (Bioinf):http://www.rmit.edu.au/programs/gd152
LaTrobe 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, tool setup
BioPlatforms Australia EMBL training workshops:http://www.bioplatforms.com.au/special-initiatives/bioinformatics/bpa-ebi-training-workshops
VLSCI / VPAC / MeRC: Regular MPI, PBS, GPU courses
Micromon RecDNA course - 6 days, Nov, annualhttp://www.micromon.monash.org/dnacourse.html
Regular Seminars/Meetings
AGRF NGS SIGs (bimonthly @ Tue 4:00pm)Applications, technology, methods
WEHI Bioinformatics (weekly @ Tue 10:45am)Research advances in bioinformatics, algorithm development
LSCC Capacity Seminars (fortnightly @ Fri 2:30pm)Open lab meeting, student presentations, technology discussions, pipelines, best practice, problems
Schools
Winter School in Computational BiologyAnnually in July for 5 daysIMB, UQ, Brisbane (Organized by Nick Hamilton - formerly Mark Ragan)
BioInfo SummerAnnually in Nov/Dec for 5 daysAdelaide 2012
AGRF/EMBLThe trained-trainers toured Australia in 2012
LSCC Workshops1 day workshops RNA-Seq, variant calling, Intro to NGS
Conferences (national)
AMATA - Australasian Genomics Technologies AssociationRotates between capital cities - Annually in Sept/Oct for 4 daysAdelaide 2012, Gold Coast 2013, Melbourne 2014
BA - Bioinformatics Australia Has been part of AusBioTech - Biennial for 2 days (defunct?)
Lorne Genome/Cancer/Proteomics Has an informatics presence - Annually in Jan/Feb
ASM - Australian Society of Microbiology Has an NGS SIG session - Annually in July for 5 days
LSCC Conference - possible future event? Covering all 3 themes: Genomics, Imaging, Systems Biology
Conferences (international)ISMB - International Society Molecular Biology
Has excellent satellite meetings and informatics sessions (Berlin 2013)
BOSC - Bioinformatics Open Source ConferencePre satellite session to ISMB (Berlin 2013)
ECCB - European Conference on Computation BiologyPartners with ISMB biennially in Europe (Berlin 2013)
APBC - Asia Pacific Bioinformatics ConferenceHeld in Melbourne, Jan 2012, will be in Vancouver 2013
EHGC - 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
VLSCI News ([email protected])
LSCC Event List (cf. Andrew Lonie)
WEHI Seminars ([email protected])
Melbourne Bioinformatics Alliance (cf. Torsten Seemann)
IMB Bioinformatics List (cf. Mark Ragan)
Mailing Lists
SeqAnswers.comForums on NGS, Bioinformatics, Tools
BioStars.orgForums on NGS, Bioinformatics, Tools
AustralianBioinformatics.netJobs, event calendar, resources, blog(David Lovell will cover in his talk)
Websites
Blogs
http://omicsomics.blogspot.com/http://pathogenomics.bham.ac.uk/bloghttp://bacpathgenomics.wordpress.com/http://contig.wordpress.comhttp://blog.malde.orghttp://bioinforuby.blogspot.com/http://bcbio.wordpress.comhttp://bytesizebio.nethttp://selab.janelia.org/people/eddys/bloghttp://finchtalk.geospiza.com/http://genehack.orghttp://www.genomeweb.com/magazine/genome-technologyhttp://www.homolog.us/blogshttp://blog.jcuff.net/http://igotgenes.blogspot.com/http://microbialgenomics.blogspot.com/http://microbialmodus.wordpress.comhttp://microbiology.sehttp://kevinl.wordpress.comhttp://www.clcngs.comhttp://wiki.nodalpoint.org/http://www.null-hypothesis.co.uk//http://rna-seqblog.comhttp://robertedgar.wordpress.comhttp://seqanswers.com/forums/
http://SEQanswers.comhttp://dskernel.blogspot.com/http://ensembl.blogspot.com/http://genome.wustl.edu/news/http://themindwobbles.wordpress.comhttp://thenaturefallacy.blogspot.com/http://phylogenomics.blogspot.com/http://www.vlsci.org.au/newshttp://nsaunders.wordpress.comhttp://xfam.wordpress.comhttp://flxlexblog.wordpress.com/
Blogs are a rich source of cutting edge information, tips, and tricks. Many NGS practitioners have blogged or tweeted information or links long before mainstream news sources get to them.
TwitterFollowing the right tweeters allows you to find out new ideas, good papers, and discover things you would have missed.
Twitter ~ RNA-Seq <=> Journal feeds ~ Microarrays
Some examples of good tweeters:@ausbionet Australian Bioinfmatics
Network@pathogenomick Nick Loman@genetics_blog Stephen Turner@BioMickWatson Mick Watson@phylogenomics Jonathan Eisen
Corporate technical contactsIllumina (MiSeq, HiSeq)
Gareth (ex Illumina UK)Gabe Kolle (ex IMB/UQ)
LifeTech (SOLiD / PGM / Proton)Fabrice Odefey (ex UOM)IonCommunity web site
Roche (454)Anyone know? (VIDRL has a 454 Jr)
PacBioNone in Australian. Hopefully AGRF buys one!
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 applications
RDSI: 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
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
Coming 2013....eResearchSA
QCIF
Intersect
Unimelb
Monash
UTas
Murdoch U
ANU"Additional node"
Initiatives: Genomics Virtual Lab
Research Cloud node
RDSI node
Coming 2013....eResearchSA
QCIF
Intersect
Unimelb
Monash
UTas
Murdoch U
ANU"Additional node"
GVL
GVL
Genomics Virtual Lab
NeCTAR Research Cloud"Mezzanine-level" compute cluster
Ruffus
Python-based workflow framework
Galaxy
Interactive web-based workflow framework
Mature workflows for common tasks
Python, perl
bespoke solutions
Interactive analysis Interactive analysis, workflow
development
Genomics Virtual Laboratory
Interactive researcher-led analysisTraining
Data
BioLinux
Cloud-based bioinf tools
RDSI
