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 (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)

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