bimsb/mdc bioinformatics platform overview
TRANSCRIPT
BIMSBBioinforma-csPla2ormOverview
AltunaAkalin@AltunaAkalin
BIOINFORMATICS PLATFORM
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
Scien-ficITsupport
MDCHubsandUCSCGenomebrowserhOp://genome.mdc-berlin.de
hOps://bimsbsta-c.mdc-berlin.net/
Scien-ficSoNwareSupporthOp://guix.mdc-berlin.de
TiredoftryingtoinstallsoNware?Can’tdemul-plex?TryGNUGuix
Galaxy@BIMSB• “Galaxyisanopenweb-basedpla2ormfordata-intensive
biomedicalresearch”(onlyavailablewithincampus)
hOp://galaxy.mdc-berlin.net
DatabasesandVirtualMachines
• BIMSBdatabasesandvirtualmachinesthathostthewebappsanddatabasesaremaintainedbyBIMSBsys.admins.
Training
• Pla2ormprovidestrainingfordevelopmentofbioinforma-csskills
• ~10courses/tutorialsun-lnow– R,computa-onalgenomics,galaxyandunixrelatedcourses
• Yearlycomputa-onalgenomicscourseopentoexternalapplicants
Publictrainings/workshops
MoreinfohOp://bioinforma-cs.mdc-berlin.de/training.html
Learningmaterialproducedbythepla2orm
• Computa-onalgenomicsmaterial– Includesintroductorymaterialforcomputa-onalgenomicsandhands-ondataanalysis
– hOp://compgenomr.github.io/book
• Unix+SGEmaterial– IncludesbasicUnixandSGEcommandsneededtogetstartedonaUnix+SGEenvironment
– hOp://bioinforma-cs.mdc-berlin.de/intro2UnixSGE
BIMSBBioinforma-cswalk-inclinics
Collabora-onNoac-onReferralConsulta-on
Adviseyouhowtoproceedwithyourdataanalysis
Walk-inclinicoutcome
Referyoutoagroupmoreexperiencedinthatpar-cularproblem
Some-mesthereisnothingtobedone
~monthlyeventdedicatedtoprovidingconsulta-onforbioinforma-csproblems
Collabora-on
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.
Moreinfoat…
hOp://bioinforma-cs.mdc-berlin.de