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BIMSB/MDC Bioinformatics Platform Overview
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Transcript of BIMSB/MDC Bioinformatics Platform Overview
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BIMSBBioinforma-csPla2ormOverview
AltunaAkalin@AltunaAkalin
BIOINFORMATICS PLATFORM
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Bioinforma-csPla2ormatMDC/BIMSB
-Generegula-on-Comp.(Epi)genomics:diseaseanddevelopment
Data-intensivecomputa-onalmethodstoinferbiologicalknowledge
Research
Collabora-on
Training
Scien-ficITSupport
BIOINFORMATICS PLATFORM
-Maintaindatabases- Maintainscien-ficsoNware
hOp://bioinforma-cs.mdc-berlin.de
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Scien-ficITsupport
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MDCHubsandUCSCGenomebrowserhOp://genome.mdc-berlin.de
hOps://bimsbsta-c.mdc-berlin.net/
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Scien-ficSoNwareSupporthOp://guix.mdc-berlin.de
TiredoftryingtoinstallsoNware?Can’tdemul-plex?TryGNUGuix
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Galaxy@BIMSB• “Galaxyisanopenweb-basedpla2ormfordata-intensive
biomedicalresearch”(onlyavailablewithincampus)
hOp://galaxy.mdc-berlin.net
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DatabasesandVirtualMachines
• BIMSBdatabasesandvirtualmachinesthathostthewebappsanddatabasesaremaintainedbyBIMSBsys.admins.
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Training
• Pla2ormprovidestrainingfordevelopmentofbioinforma-csskills
• ~10courses/tutorialsun-lnow– R,computa-onalgenomics,galaxyandunixrelatedcourses
• Yearlycomputa-onalgenomicscourseopentoexternalapplicants
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Publictrainings/workshops
MoreinfohOp://bioinforma-cs.mdc-berlin.de/training.html
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Learningmaterialproducedbythepla2orm
• Computa-onalgenomicsmaterial– Includesintroductorymaterialforcomputa-onalgenomicsandhands-ondataanalysis
– hOp://compgenomr.github.io/book
• Unix+SGEmaterial– IncludesbasicUnixandSGEcommandsneededtogetstartedonaUnix+SGEenvironment
– hOp://bioinforma-cs.mdc-berlin.de/intro2UnixSGE
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BIMSBBioinforma-cswalk-inclinics
Collabora-onNoac-onReferralConsulta-on
Adviseyouhowtoproceedwithyourdataanalysis
Walk-inclinicoutcome
Referyoutoagroupmoreexperiencedinthatpar-cularproblem
Some-mesthereisnothingtobedone
~monthlyeventdedicatedtoprovidingconsulta-onforbioinforma-csproblems
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Collabora-on
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Maincollabora-onstructures• Smallscale
– Runningworkflowsweestablishedoutpudngpredefinedreports(currently:RNA-seq,BS-seq,ChIP-seq,SNP/CNVcalling)
– Sta-s-calmodelingwithalreadyprocesseddata– Dependson:
• availableman-hours• Largescale
– Needsintegra-onandanalysisoflargenumberofsamples– Needsdevelopmentofnewworkflows– Dependson:
• Overlapwithpla2ormresearchobjec-ves• Availableman-hours
• Inallcases,authorshipstatusmustbediscussedinadvance.
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Moreinfoat…
hOp://bioinforma-cs.mdc-berlin.de