BIMSB/MDC Bioinformatics Platform Overview

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