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NEWSLETTER

Thede.NBIQuarterlyNewsletterinformsaboutrecentdevelop-ments and current events in theprojectGermanNetwork forBioinformaticsInfrastructure.

Furtherinformationat:https://www.denbi.de/

REVIEWOFTHEde.NBIandELIXIRGERMANYPLENARYMEETINGSINNOVEMBER2018

Incombinationwiththede.NBISABmeeting,theplenarymeet-ingsofthede.NBInetworkandofELIXIRGermanytookplaceatthe Seminaris Campus Hotel in Berlin on 30 November 2018.Around110de.NBImembersparticipatedinthesetwomeetings.Thede.NBIplenarymeetingfocusedonflashtalkspresentedbyservicecentersandspecialinterestgroups.Theseflashtalksrespondedtothedetailedreviewerrecommendationsprovidedduringthede.NBImidtermreviewattheendoftheestablishmentphaseI.TheplenarymeetingofELIXIRGermanytookplaceintheafternoonof30November.ThemainpurposeofthismeetingwasanintroductiontotheELIXIRProgramme2019-2023andadiscussiononthefurthercollaborationbetweende.NBIandELIXIRwithafocusonplatforms,communitiesandimple-mentationprojects.ImpressionsoftheSABconferenceandtheplenarymeetingshavebeensummarizedinavideoclip.

Findthevideoathttps://www.denbi.de/news/560-impressions-of-the-sab-and-plenary-meeting-2018

ANENTHUSIASTICREPORTFROMTHESABONTHEde.NBIDE-VELOPMENTThe3rdScientificAdvisoryBoardMeetingofthenetworktookplaceattheSeminarisCampusHotelinBerlinon29-30November2018.Thede.NBIcoordinatorandthede.NBIAdministrationOfficepreparedthede.NBIStatusReport2018entitled“Thede.NBInetworkin its2ndfundingphase”.Theoralpresentationsfocusedonbenefitsandvisionsof

CONTENT:1)Reviewofthede.NBIandELIXIR-DEplenarymeetings 12)AnenthusiasticreportfromtheSABonthede.NBIdevelopment 12)OliverStegleisanewassociatedpartnerinHD-HuB 23)NewELIXIR-DEtechnicalandtrainingcoordinators 34)PublicationawardformanuscriptonPiGx 35)de.NBILinkedINchannel 36)EuropeanBioconductorMeeting2018 37)3rdMetaproteomeSymposium2018–AReview 48)BeerDEcoded:RBCFreiburgandthestreetsciencecommunity 49)Latestfiguresonde.NBItraining 510)AsuccessfulGalaxyRNA-seqworkshopinBelgrade 511)Recentupdatesofde.NBIservices 612)de.NBI@Conferences 713)Upcomingevents 714)Impressum 8

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human,plant, andmicrobialbioinformatics.Theseweresupplemented by lectures on the service, training anddatamanagement cases aswell asrecentdevelopmentsofthede.NBIcloud,workflowengines,theELIXIRcoop-eration,and,finally,thesustainablecontinuation.Inpar-ticular, the sustainable continuation of the de.NBI net-workwasintensivelydiscussedinaninternalmeetingbe-tweenSABandCCUmembers.TheSABevaluatedthenet-work in a very positive way and summarized their re-sponseasfollows:

OLIVERSTEGLEISANEWASSOCIATEDPARTNERINHD-HUB byUlrikeTrojahn&OliverStegle

InOctober2018,DrOliverStegleappliedtojointhede.NBInetworkasanassociatememberwithintheHeidelbergCenterforHumanBioinformatics(HD-HuB).ThedecisionhasnowbeenratifiedwhentheCCUconvenedinGaterslebenon23January2019.OliverStegleisholdingajointappointmentbetweentheEuropeanMolecularBiologyLaboratory(EMBL),GenomeBiol-ogyUnitandtheGermanCancerResearchCenter(DKFZ),DivisionofComputationalGenomicsandSystemGeneticsinHeidel-berg.

O.Stegle’sworkwillcontributetotheSingleCellDataAnalysisactivitiesthatarepartof theHD-HuBserviceportfolio.Thesecontributionsincludewidely-usedbioinformaticstoolsfor

single-cellRNA-seqanalysis, single-cellepigeneticsandmulti-omicsmethods,aswellas spatialtranscriptomics.

TheSteglelaboratoryisalsoamemberoftheHumanCellAtlasproject,andhencewillbringtherequiredexpertisetoestablishcommunitystandardsandworkflowsforsingle-cellanalytics.• Thegroupwillestablishworkflowsforthefirst-lineanalysisofsingle-cellRNA-seqdata,whichin-

cludesreadalignment,qualitycontrol,datanormalizationandbatchadjustment.Theseworkflowswillleveragetheparallelcomputecapacitiesavailableonthede.NBICloudandsupportcommondataformatsandproto-cols,includingSmartSeq2andthe10XGenomicsChromiumplatform.TheworkflowswillbuildonstandardsestablishedbytheHumanCellAtlasproject,whichwillbeextendedtosupportnon-humandata,aswellasmultiplexedpooledexper-imentaldesigns.Inaddition,O.SteglewillestablishandmaintainelementaryanalysistoolsforscRNA-seqonthede.NBICloud.

• Buildingonhisownpriorworkinthisarea,O.Steglewillprovidemethodsandworkflowsforprocessingsparsesingle-cellDNAmethylationdata(DeepCpG),aswellastoolsforinterpretingandvisualizingsingle-cellepigenomedata(scNMT-seqsoftwaresuite).

• Finally,thegroupwilldeliverbioinformaticsmethodsforemergingdatatypesandnewtechnologies.Theyrecentlyde-velopedthefirstgenerationofanalysismethodsfordatafromspatialsingle-cellexpressionassaysandwillprovideandsupportsoftwaresuchasSpatialDE.

Withinthede.NBItrainingprogram,theSteglelabwillofferatrainingcourseforsingle-celldataanalysis,whichwillberunonanannualbasis.ThesetrainingactivitieswillbecoordinatedwiththenewlyestablishedSingle-cellBiologyCenterHeidelberg.

Findfurtherinformationathttps://single-cell-center-hd.de

TheSABinaninternalmeetingwithPtJrepresentativesandde.NBIcoordination

“Itisourviewthatde.NBIisnowamatureestablishedandfunctionalbioinformaticsnetwork,workingtoraisestandardsandexpertiseinhandling lifesciencesdataandprovidinguser-friendlytools,hardware/softwaresolutions,andaccesstocomputetoscientistsinGermanyandbeyond.Intotaleightservicecentresand37differentprojectsarenowopera-tional,includingthesuccessfulextensionin2016toinclude17newpartnerprojects.Thishascreatedadynamicdistrib-utedinfrastructure,withacommunityofdedicatedscientists,devotedtomakingitworkwell.Wecommendtheachieve-mentsoftheDirector–AlfredPühler,theAdministrativeOfficeandtheCentralCoordinationUnit(CCU)formakingthishappen.de.NBIisnowamaturecommunityprovidingstate-of-theartinfrastructureandservicestothelifesciencecom-munity,inparticularatfourlevels:provisionoftools,communitybuilding,training,andthede.NBICloud.Inaddition,byrunningtheELIXIR-DEoperation,de.NBIiswellintegratedininternationalactivitiesandespeciallythebioinformaticscommunityinEurope.”

Photo:OliverStegle

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NEWELIXIR-DETECHNICALANDTRAININGCOORDINATORS

FromthestartofELIXIRGermanyin2016,RolfBackofen(RBC,Freiburg)andOliverKohlbacher(CIBI,Tübingen)havebeenactiveintheGermanELIXIRNodeastechnicalandtrainingcoordi-nator,respectively.AsbothresignedfromtheirELIXIR-DEpositionthisyear,theCentralCoor-dinationUnit(CCU)ofde.NBIunanimouslyelectednewrepresentativesfromthenationalnodeasmembersofELIXIR‘sTechnicalCoordinatorsGroup (TeCG)and theTrainingCoordinatorsGroup(TrCG).Briefly,theformerdeputieswilltakeover:BjörnGrüning(RBC,Freiburg)isthe

new technical coordinator andthus responsibleto explore technicalopportunities and issues topromote connectionsamongtheELIXIRnodesandplatforms.DanielWibberg(de.NBIAdministrationOffice,Bielefeld)isthenewtrainingco-ordinatorandthusinvolvedincoordinatingandimplementingtheELIXIRtrainingstrategyacrossEurope.NewdeputieswillbeelectedbytheCentralCoordinationUnitlaterthisyear.Inaddition,RolfBackofenandAlexanderGoesmann(BiGi,Gießen)havebeenreappointedasELIXIRBoardmembersbytheGermanFederalMinistryofEducationandResearch.

PUBLICATIONAWARDFORMANUSCRIPTPiGx:REPRODUCIBLEGENOMICSANALYSISPIPELINESWITHGNUGuixbyAltunaAkalin

TheAkalin lab/BioinformaticsPlatformat the BerlinInstitute of Medical Systems Biology (BIMSB), MaxDelbrückCenter(MDC)publishedapaperaboutacol-lectionofreproduciblegenomicspipelinescalledPiGx.TheteamcreatedthesehighlyreproduciblepipelinesfortheanalysisofRNA-seq,ChIP-seq,BS-seq,andsin-gle-cell RNA-seq. All pipelines process raw experi-mentaldataandgeneratereportscontainingpublica-tion-readyplotsandfigures,withinteractivereportel-ementsandstandardobservables.TheirdependenciesaremanagedwithGNUGuix,whichalsoprovidesthehighreproducibility.Allthepipelineshaveasimilarin-

terfaceandinstallableviaonelinecommandincludingalltheirdependencies.ThearticlewononeoftheGigaScienceICG-13Prizes.ICGisayearlygenomicsconferencesorganizedbyBGI.Representingtheauthors,RicardoWurmuswasinvitedtopresenttheworkonPiGxandGNUGuixinShenzhen,ChinaatICG-13andreceivedtheawardonbehalfoftheteam.Findthetoolathttp://bioinformatics.mdc-berlin.de/pigxFindthepublicationathttps://academic.oup.com/gigascience/article/7/12/giy123/5114263

de.NBILINKEDINCHANNELAfterthesuccessofusingtheTwitterchannel@denbiOfficeforpublicrelations,de.NBIisnowalsoactiveviaLinkedIn.Thede.NBIprofilenameisTomDenbi,andacompanypagecalled“de.NBI”hasbeenestablished.ThenewLinkedInchannelcurrentlyfeaturesabout

150followersand100posts.Wewillusethischanneltonetworkwithprofessionalsinacademiaandindustryandwithindus-trial partners, e.g. members of the recently founded de.NBI Industrial Forum. Using LinkedIn, we will announce trainingcoursesandallnewsrelatedtode.NBIevents.Interestedtonetworkwithus?FolloworconnectusonLinkedIn!Thechannelcanbefoundathttps://www.linkedin.com/company/de-nbi

EUROPEANBIOCONDUCTORMEETING2018Withover100participants,theEuropeanBioconductorMeeting2018tookplaceinGarchingnearMunichfrom6–7De-cember2018.BioconductorisabioinformaticssoftwarecollectionfortheRprogramminglanguageandiswidelyusedinLifeScienceresearch.Themeetingaddressedsoftwaredevelopersandusersatthesametime.DeveloperspresentedthelatesttoolsandanalysistechniquesforBioconductor.Usershadtheopportunitytoget incontactwithdevelopersand

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discussedrecenttrendsintheLifeSciences.Theconferencesessionscoveredrecenttopics indatavisualization,epige-nomics,proteomics,multiomicsandRNA.AsmembersoftheBioconductorcoredeveloperteamwerealsopresentatthemeeting,softwaredevelopersanduserswereabletoactivelydiscussandshapethefutureofBioconductor.de.NBIsup-portedthemeetingby invitingthekeynotespeakersKeeganKorthauer(Dana-FaberCancerInstitute,Boston,USA)andFannyPerraudeau(WholeBiome,Inc,USA).Furthermore,BioinformaticiansaswellasLifeScienceResearcherswereabletogethands-onexperienceofthede.NBICloudataconferencestand.Independentlyofthemeetingde.NBIsupportsthedevelopmentandmaintenanceoftheBioconductorpackagesBiocWorkflowToolandProteinArrayAnalyzer(PAA).Readmoreabouttheeventathttps://www.denbi.de/events-archive/514-european-bioconductor-meeting-2018

3rdMETAPROTEOMESYMPOSIUM2018–AREVIEW byDirkBenndorfInDecember2018,about80scientistsfrom14countriesparticipatedinthe3rdInternationalMetaproteomeSymposium.TheleadingeventinthefieldofmetaproteomicswasorganizedbyHelmholtz-CentreforEnvironmentalResearch�UFZandtheGermanNetworkforBioinformaticsInfrastructure-de.NBI*.

The number of publications examining microbiomes iscurrently exploding and results are providing new per-spectivesonhumanhealthandglobalnutrient cycles aswellasontechnicalapplicationofmicrobialcommunitiesinbiotechnology.Multi-omicsanalysisisacceptedasthegoldstandardtoassessthemicrobiomesamples,butthedata integration is still challenging. The symposium of-feredagreatopportunitytobroadenthediscussionontheintegrationofdifferentdatasets.Besidesresults fromallareasofmicrobialecology, firstresultsofcollaborativemulti-omicsstudyofahumangutmicrobiomesampleandofadefinedmicrobial communitywerepresented.First insightsdemonstrated the reliabilityofmetaproteomicsregardingtheassignmentofmajorphylaandfunctions.Theongoinganalysisofdatafrommultiplelabswillprovidemoredetailedknowledgeonreliabilityofmetaproteomicdataobtainedwithdifferent experimental andbioinformaticpipelinesandwillrevealaspectsforfurtherimprovementofthedifferentworkflows.

Thesymposiumprovidedagoodplatformfororalandposterpresentationsofyoungpassionatescientistsintheinterdis-ciplinaryfieldofmicrobiomeresearch.Threepostersrepresentingwelltherangeofscientificcontributionswerepriced.

Data-independentacquisitionmassspectrometryenablesreproduciblecharacterizationofmicrobiotafunction(SamiPietilä,UniversityofTurku)

Exploringnewsmallproteinsinasimplifiedhumangutmicrobiome(HannesPetruschke,Helmholtz-CentreforEnvironmentalResearch�UFZ)

Prediction-basedreductionof the search space leads to increased identifications inmetaproteomicswithoutimpactingsensitivity(TimvandenBossche,VIB-GhentCenterforMedicalBiotechnology)

Thescientificcommitteeofthesymposiumagreedtocontinuethissymposiumseriesatoneandahalfyear.Intervals.ThenextsymposiumwillbetakeplaceinSummer2020inLuxembourg(organizedbyPaulWilmes,UniversityofLuxembourg).

Microbiome researchers interested in the emerging fieldmetaproteomics are invited to join the AppliedMetaproteomicsWorkshop(Magdeburg, June2019)providinghands-ontrainingforthecompleteworkflowstartingfromdesignofexperi-mentsviasamplepreparationtomeasurementandbioinformatics(MetaProteomeAnalyzerSoftware)analysisofhigh-resolu-tionMSdata.Moreinformationontheworkshopat:https://www.denbi.de/training/576-applied-metaproteomics-workshop-2019*de.NBIpartnerprojectMetaProtServ,Otto-von-Guericke-UniversityMagdeburgwithinBiGi-Bielefeld-GießenResourceCenterforMicrobialBioinformat-ics

BeerDEcoded:RBCFREIBURGANDTHESTREETSCIENCECOM-MUNITY bytheStreetScienceCommunityFreiburgTheStreetScienceCommunity(https://streetscience.community/)isavolunteer-basednon-profitgroupthataimstobringsciencetothepublic.Thegrouporganizesworkshopstoteachpupils,studentsandcitizensmolecularbiologyandgenetics,data-analysis,andopensciencebyextracting,sequencingandanalyzingDNA.Thecurrentproject,BeerDEcoded,usesthebeertosensitizethepublictomolecularbiologyandgenome-relatedresearch.BeercontainsDNAthatcomesfromitsingre-dientsandoverhundredsofmicrobes.InFreiburg,thegroupdevelopedafirstprototypeoftheDNAextractionandsequencing

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protocolsusingtheNanoporeMinION,aportablereal-timedeviceforDNAsequencing.Theresultsareverypromising!Thegrouphassuc-cessfully identifiedspecificbrewingyeaststrainsfromtheDNAthatwasextractedoutofbottledbeer.Forthebioinformaticdataanalysis,aworkflowusingGalaxy(https://streetscience.usegalaxy.eu)hasbeencreated.Thisopensource,web-basedandeasytouseplatformmakesreproduciblecomputationalbiologyandbioinformaticsaccessible tointerestedcitizens.Therefore,allproof-of-principlepreparationsarefinishedtostartworkshopsandspreadscience intothe community.The Street Science Community is supported by Bérénice Batut andBjörnGrüningfromRBCFreiburgandreceivedfinancialsupportfromde.NBI.

LATESTFIGURESONde.NBITRAINING Thefourthde.NBIyearwasverysuccessfulinthetrainingarea.In2015,de.NBIstartedwith17trainingcoursesandwith329participantsandin2016(40courseswith882participants)and2017(69courseswith1,489participants)thenumbersin-creaseddramatically.Inthelastyear,wefurtherincreasedthenumbersto77trainingcourseswith1,520participants.Thelargestcoursewasattendedby73,thesmallestonebyfourscientists.Approximately,75%oftheparticipantswerePhDstu-dentsorPostdocs.Theremaining25%werePIs,undergraduates,andparticipantsfromindustry.Thegenderratioofthestu-dentswas59%maleand41%female.About30%oftheparticipantscamefromoutsideGermany.Ingeneral,theusersurveyshowssatisfactionvaluesaround90%withonlyasmallnumberofexceptions.IntheELIXIRcontext,de.NBIbelongstotheleadingprovidersbioinformaticstrainingcoursesinEuropein2018.Already50trainingcoursesareannouncedfor2019.

Furtherinformationisavailableathttps://www.denbi.de/training

AsuccessfulGalaxyRNA-seqworkshopinBelgradebyBéréniceBatutTheFreiburgGalaxyteam(RBC)regularlyorganizestrainingworkshopssuchasthebi-annualGalaxyHTSdataanalysiswork-shopinFreiburg.Inthepastyear,wehavealsobeeninvitedtoteachworldwide:CapeTown,Melbourne,Oslo,etc.

InJanuary,NevenaVeljkovicfromtheInstituteof Nuclear Sciences Vinča in Belgrade, Serbiaorganizedandhosteda2-daycourse.TheFrei-burg Galaxy team offered an introductorycoursetoGalaxyandRNA-seqdataanalysis,us-ingtheonlinetrainingmaterialfromtheGalaxyTraining Network and the European Galaxyserver.Detailsofthescheduleandlinkscanbefoundonourdedicatedeventpage.

With50participants,thisworkshopwasthelarg-estwehavetaughtusinginteractivehands-ontraining,andthemostintenseone:Afullypackedroom,whereitwasdifficulttowalk,ahighheterogeneityoftrainees,fewinternet,andserverissues.Nevertheless,theparticipantsseemtohaveenjoyedthisworkshop,giventhefeedback,whenweaskedthemtowriteapositiveoneongreenandanegativeoneonredstickers.Basedonthispositiveexperienceandthehighdemand(morethan80peopleregistered),moretrainingwillbeorganizedinthenear

PicturesfromBéréniceBatut-CCBYSA

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future inSerbia,probablywithfewerparticipantsandlongerprograms.Wewould liketothankNovenaandVladafortheinvitationandthesightseeing,de.NBIforsupportingthistypeofevent,usegalaxy.euandtheGalaxyTrainingNetwork!

FurtherInformationonthiscourseathttps://galaxyproject.eu/event/2018-12-07-Announcement-Galaxy-course/

RECENTUPDATESOFde.NBISERVICESNewversionsofvariousde.NBIservicesandtoolshavebeenreleasedinthelastmonthsaccompaniedbytherespectivepub-lications:

ViennaRNApackage2.4.11.TheViennaRNAPackageconsistsofaCcodelibraryandseveralstand-alonepro-gramsforthepredictionandcomparisonofRNAsecondarystructures.LatestVersion2.4.11from18December2018.Linktotheservice:https://www.denbi.de/services/361-bioinformatics-leipzig-various-webservices-and-tools-for-transcriptomics

Mitos2.0–NewversionoftheWebserverforAutomatedAnnotationofMetazoanMitochondrialGenomes-multi-plestructure-basedRNAalignmentandfolding.MITOSimplementsapipelinefortheautomatedannotationofMet-azoanmitochondrialgenomes.Themethodisbasedonanautomaticconsistentre-annotationofproteincodinggenesandnon-codingRNAsusingBLASTXandco-variancemodels.https://www.denbi.de/services/361-bioinformatics-leipzig-various-webservices-and-tools-for-transcriptomics,http://mitos.bioinf.uni-leipzig.de/index.py,orhttp://mitos2.bioinf.uni-leipzig.de/index.py

MapMan4andMercator:AredesignedandsignificantlyenhancedMapMan4framework,togetherwitharevisedversionoftheassociatedonlineMercatorannotationtoolhavebeenpublishedin:Mapman4:arefinedproteinclas-sificationandannotationframeworkapplicabletomulti-omicsdataanalysis,R.Schwackeetal.,MolecularPlant,9Jan2019.https://doi.org/10.1016/j.molp.2019.01.003Thenewversionispartofhttp://www.plabipd.de/portal/mercator-sequence-annotation

HiCExplorerVersion2.2:Setofprogramstoprocess,analyzeandvisualizeHi-Cdata.NewversionreleasedinNovember2018,https://github.com/deeptools/HiCExplorer

BacDive:Severalnovelfeaturesaddedtothestraindetailview.Relatedpublication:BacDivein2019:bacterialphenotypic data for High-throughput biodiversity analysis, Reimer LC1 et al., Nucleic Acids Res.2019 Jan8;47(D1):D631-D636,https://doi.org/10.1093/nar/gky879

Publications GCBN:Inaproof-of-conceptstudybasedondeepgenotyping-by-sequencing(GBS)oftheentireIPKbarleycollectionofmorethan20,000accessions,comprehensiveandcoherentinformationhasbeengeneratedongeneticdiversityandpopulationstructure.SystematicvalorizationofthesegenomicsdataisfacilitatedbybuildinganinnovativeandintuitivediversityinformaticsanddatawarehouseinfrastructureforaccommodationandanalysisofBIGDATAsets.BRIDGEportal,http://bridge.ipk-gatersleben.de/ThecorrespondingpaperisGenebankgenomicshighlightsthediversityofaglobalbarleycollection,Naturegenetics,vol2issue2,February2019,https://www.nature.com/articles/s41588-018-0266-x

de.STAIRRostock:Twochaptersonnon-codingRNAbioinformatispublished inComputationalBiologyofNon-CodingRNApp199-214,PartoftheMethodsinMolecularBiologybookseries(MIMB,volume1912),FirstOnline12January2019,https://link.springer.com/book/10.1007%2F978-1-4939-8982-91) WorkflowDevelopmentfortheFunctionalCharacterizationofncRNA,M.Wolfien,D.L.Brauer,A.Bagnacani,O.

Wolkenhauer2) ToolsforUnderstandingmiRNA–mRNAInteractionsforReproducibleRNAAnalysis,A.Bagnacani,M.Wolfien,O.

Wolkenhauer

de.NBIandGFBio:ZweidezentraleInfrastrukturprojekteunterstützenWissenschaftundForschung,BigDatainderBiologie:keinProblemmehr,B.Gemeinholzer,J.Nieschulze,A.Tauch,A.Goesmann,BiologieinunsererZeit,Vol.49,58-67,4February2019,https://doi.org/10.1002/biuz.201910668

SelectedremarksPositive feedback: “Interactive with participants”, “on-hands learning”,“Excellenttutorials,greatpresentationsandexamples/training.Goodjob.THANKYOU”,“Itwasalovely experience. I learned a lot, and had a great time.Love the instructors.”, “Excellent presentation and illus-trativeexplanations”,“Björn’slecturesandexplanation”Negative feedback: “the Internet connection”, “smallergroupstoworkwith”,“sometimesyouweretoofastforbe-ginners”, “Too many people. Should be smaller groups”,“Shouldlastlonger(toointensive)”,“Tooshortcourseforcompletebeginners”

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de.NBI@CONFERENCES

de.NBIWorkshopsatupcomingconferencesde.NBIpartnerswillbeteachingavarietyofworkshopsortutorialsatconferencesinMarch:

DGMS 2019 - 52. Jahrestagung der Deutschen Gesellschaft für Massenspektrometrie, Rostock, 10-13March2019TargetedLipidomicswithSkylineandLipidCreator,R.Ahrends,N.Hoffmann(ISASDortmund).ThecoursewillcoverthechallengesandnecessaryprecautionsofdesigningandconductingatargetedLC-MSlipidomicsexperiment.ItwillbedemonstratedhowtoanalyzesuchdatausingtheSkylinesoftwareandthetargetedlip-idomicspluginLipidCreator.Incombination,thesetoolscanbeusedfortargetedassaydevelopmentandopti-mizationandforcustomizedtargetedlipidomicsstudies,includingidentificationandquantificationoflipids.Furtherinformationat:https://www.denbi.de/training/552-lipidomics-workshop-dgms-2019

ProteomicForum2019,Potsdam24-28March2019Tooltraining forproteomics,M.Turewicz, J.Uszkoreit,K. Schork,T. Sunny,D.Kopczynski (RuhrUnversityBochumand ISASDortmund). Inthisone-day course, fourproteomics softwaretoolswill be introduced,PIA,PeptideShaker,SearchGUIandBIONDA.ThiscourseisacommonteachingeventoftheEuBICinitiativeandthede.NBI/ELIXIRGermanyservicecenterBioInfra.Prot.Furtherinformationat:https://www.denbi.de/training/550-tool-training-for-proteomics-proteomic-forum-2019andhttps://www.eupa2019.org/program/tool-training-for-proteomics/

de.NBIsupportedconferencesde.NBIwillsupportthefollowingconferencesco-organizedbyde.NBIpartners:

15thGaterslebenResearchConferenceonAppliedBioinformaticsinCrops,18–20March2019attheLeibnizInstituteofPlantGeneticsandCropPlantResearch(IPK)inGatersleben.ThisconferencewillbeofinteresttoLifeScientists,Bioinformaticians,ComputerScientists,SystemsBiologists,Syn-theticBiologistsandothersworkingor interestedinthedevelopingareaofAppliedBioinformatics forcrops.Themeetingwillprovideanexcellentenvironmentandarangeofopportuni-ties topresent anddiscussmethods, theoretical approaches, and theirpracticalapplications.Topics:•Image-BasedDataAnalysesandDataVis-ualization,•DistributedComputing,•ToolsandInfrastructures,•Sys-tems Biology andModeling, • Biodiversity and Information Systems, •BreedingInformatics.Twokeynotelectureswillbeinvitedbyde.NBI.

Generalinformationandregistrationat:https://meetings.ipk-gatersleben.de/grc2019-abc/

Galaxycommunityconference,Freiburg,1-6July2019. WearepleasedtoannouncethatGCC2019willbeheldinFreiburg,Germany,1-6July.LikepreviousGalaxyCommunityConferences,GCC2019willfeatureinvitedkeynotes,acceptedtalks,posters,anddemos,birds-of-a-feathergatherings,mul-tipledaysofcollaborativework,andplentyofopportunitiestonetworkwithyourfellowdata-intensiveresearchersandpractitioners. Ifyouareworking indata-intensivelifescience,thereisnobetterplacetobe. Generalinformationandregistrationat:at:https://www.denbi.de/events/12-galaxy-community-conference-2019-gcc2019

UPCOMINGEVENTSThecalendarliststhede.NBItrainingcoursesandeventsscheduledinthenextmonths.Alloffersareaccessibleviathede.NBIwebpage.Anumberoftrainingeventsareinthepipelinebutnotyetscheduled.Pleaseconsultthede.NBItrainingprogramfortheactualdates.

Overviewofupcomingde.NBIevents Date Event City Organizer

12-13Feb2019 LinuxCommandLine&BasicScriptingcourse2019 Heidelberg HD-HuB

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Date Event City Organizer

21Feb2019 GTNCoFestonGalaxyTrainingMaterial Online RBC

25Feb-01Mar

20197thGalaxyworkshoponHTSdataanalysis Freiburg RBC

06-08Mar2019 GalaxyforlinkingbisulfitesequencingwithRNAsequencing Rostock RBC/de.STAIR

10Mar2019TargetedLipidomicswithSkylineandLipidCreator-DGMS2019-DGMS2019 Rostock BioIn-

fra.Prot/LIFS 13-14Mar2019 Miracumwhole-exomesequencingpipelineworkshop Freiburg RBC 18Mar2019 SeqAn&OpenMS(CIBI/de.NBI)IntegrationWorkshop Berlin CIBI

18-22Mar2019SummerschoolonIntegrationofLargeScaleLipidomicsDatainSystemsMedicineResearch(LipoSysMed) Leipzig BioIn-

fra.Prot/LIFS

19Mar2019ToolsforSystemsbiologymodelinganddataexchange:COPASI,CellNetAnalyzer,SABIO-RK,FAIRDOMHub/SEEK Heidelberg de.NBI-SysBio

20-22Mar2019 SpringSchool“ComputationalBiologyStarter” Gatersleben GCBN

22-31Mar2019 SeqAn3DeveloperRetreat2019 Escala CIBI

2019-03-28 Tool-TrainingforProteomics–ProteomicForum2019 Potsdam BioInfra.Prot

01-03Apr2019 de.NBICompMSmetaRbolomicsHackathon LutherstadtWittenberg CIBI/MASH

09April2019 18.CCUMeeting Heidelberg CAU,de.NBI-SysBio

23-26Apr2019 Galaxytrainingandhackathon Roscoff RBC

29Apr–01May

2019ProteomicsandMetabolomicswithOpenMS Boston CIBI

22May2019 Phylogeneticreconstructioncourse Kiel AssociatedPartnerKiel

22May2019 Computationalgenomicscourseforhands-ondataanalysis Berlin RBC

27-29May201912thAnnualInternationalConferenceonSystemsBiologyofHu-manDisease-SBHD2019 Berlin HD-HuB

17-21Jun2019 AppliedMetaproteomicsWorkshop2019 Magdeburg BiGi

01-06Jul2019 GalaxyCommunityConference2019–GCC2019 Freiburg RBC

15-19Jul2019 Combine2019Conference Heidelberg de.NBI-SysBio

03Jul2019 19.CCUMeeting Bremen CAU/BioData

21-26Jul2019 CSAMA2019-StatisticalDataAnalysisforGenome-ScaleBiology Bressanone/Brixen HD-HuB

02-06Sep2019 de.NBISummerSchool2019-(Bio)DataScience Gatersleben GCBNetal.

23-24Oct2019 IntroductiontoBRENDAandEnzymeStructures Braunschweig BioDataFurtherinformationat:http://www.denbi.de/training

IMPRESSUMRESPONSIBLEFORCONTENTSA.Pühler,A.Tauch,T.Dammann-Kalinowskide.NBI-GermanNetworkforBioinformaticsInfrastructurec/oCenterforBiotechnology(CeBiTec)BielefeldUniversity33594BielefeldGermanyPhone:+49-(0)521-106-8750Fax:+49-(0)521-106-89046email:puehler@cebitec.uni-bielefeld.deweb:http://www.denbi.deemail:contact@denbi.detwitter:#denbi,@denbiOfficeForquestionsandremarkspleasecontactcontact@denbi.deThede.NBIissupportedbyBMBFgrantsFKZ031A532-031A540and031L0101-031L0108.

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