High-throughput equipment of the Slovenian Consortium for Bio-Chips

ModelManufacturerInstitutionDepartmentPerson responsible for the equipmentLocationYear of purchaseResearch fieldAvailabilityMaintenanceTechnical supportData storage supportSoftware licensing for data storageStorage typeData accessStorage software manufacturere, software name and versionNumber of usersTotal quantity of data [in gigabytes]Expected quantity of data per year [in gigabytes]Do you use any international data guidelinesIf you annotate your data in a standard way, please name standard ontologies, controlled vocabularies and terminologiesData analysis supportSoftware licensing for data analysisSofware typeAnalysis software manufacturere, software name and versionFull namePhoneEmailWeb page
n/a (robotic manipulator)Adept plusInstitut "Jožef Stefan"Odsek za molekularne in biomedicinske znanostidr. Uroš PetrovičIJS, Jamova 39, Lj., B4062006phenotypingWith support of trained personnelOccasionally (upon need)Both, in-house and externalPartiallyOpen-source software, In-house developed software or solutionLocal computerLocal computern/a51000100NePartiallyOpen-source software, In-house developed softwareInstalled on a local computer (single-user)n/aUroš Petrovič01/4773250uros.petrovic@ijs.si
mass spectrometer LTQ Orbitrap Velos ETDThermo ScientificInstitut "Jožef Stefan"Odsek za biokemijo in molekularno in strukturno biologijoMarko FonovićIJS, Jamova cesta 392010ProteomicsAuthorized personnel onlyRegularlyboth, in-house and externalNoNo operational softwareLocal server (within LAN)Within LANnone360001000nonedata is annotated by the date and sample originYes, fullyManufacturer's proprietary software and open sourceInstalled on a local computerThermo Scientific, Matrix Science, PEAKSMarko Fonovic38614773215Marko.fonovic@ijs.si
ÄKTA Protein Purification Systems GE HealthcareUniversity of Nova GoricaCenter for biomedical sciences and engineeringArio de MarcoLanthieri Palace, Glavni trg 8, SI-5271 Vipava, Slovenia. 2014protein purification With support of trained personnelRegularlyBoth, in-house and externalYes, fullyManufacturer's proprietary softwareLocal computerLocal computerÄKTA30,10,1//Yes, fullyManufacturer's proprietary softwareInstalled on a local computer (single-user)ÄKTAArio de Marco 00386 5 9099700ario.demarco@ung.sihttp://www.ung.si/en/research/center-for-biomedical-sciences-and-engineering/
LS200 laser scannerTecanMF ULCFGBCPeter JuvanCFGBC2005Proteomics, Transcriptomics, Genomics, ImagingWith support of trained personnelOccasionally (upon need)Yes, external (manufacturer or its representative)Yes, fullyOpen-source softwareLocal computer, Local server (within LAN), External server (WAN)Local computer, Within LAN, From InternetBASE15801MIAMEnoneYes, fullyManufacturer's proprietary software, Open-source softwareInstalled on a local computer (single-user), Installed on a server (multiple users)Tecan, R/BioconductorPeter Juvan+386 1 543 7593peter.juvan@mf.uni-lj.sihttp://cfgbc.mf.uni-lj.si/equipment/tecan_scanner
GenePix 4100A scannerMolecular DevicesMF ULCFGBCPeter JuvanCFGBC2007Proteomics, Transcriptomics, GenomicsWith support of trained personnelOccasionally (upon need)Yes, external (manufacturer or its representative)Yes, fullyOpen-source softwareLocal computer, Local server (within LAN), External server (WAN)Local computer, Within LAN, From InternetBASE15142MIAMEnoneYes, fullyManufacturer's proprietary software, Open-source softwareInstalled on a local computer (single-user), Installed on a server (multiple users)"GenePix Pro 6.1; R/Bioconductor"Peter Juvan+386 1 543 7593peter.juvan@mf.uni-lj.sihttp://cfgbc.mf.uni-lj.si/equipment/genepix_scanner
Hybridization Oven 645, Fluidics Station 450, Scanner GCS 3000 7GAffymetrixMF ULCFGBCRok KoširCFGBC2007Transcriptomics, GenomicsWith support of trained personnelRegularlyYes, external (manufacturer or its representative)Yes, fullyOpen-source softwareLocal computer, Local server (within LAN), External server (WAN)Local computer, Within LAN, From InternetBASE157410MIAMEnoneYes, fullyManufacturer's proprietary software, Open-source softwareInstalled on a local computer (single-user), Installed on a server (multiple users)"Affymetrix Command/Expression Console; R/Bioconductor"Rok Košir+386 1 543 7592rok.kosir@mf.uni-lj.sihttp://cfgbc.mf.uni-lj.si/equipment/affy_system
LightCycler 480RocheMF ULCFGBCRok KoširCFGBC2008Transcriptomics, GenomicsWith support of trained personnelRegularlyYes, external (manufacturer or its representative)Yes, fullyManufacturer's proprietary softwareLocal computer, Local server (within LAN)Local computer, Within LANRoche Exor database1651nonenoneYes, fullyManufacturer's proprietary software, Open-source softwareInstalled on a local computer (single-user), Installed on a server (multiple users)Roche LightCycler 480 software release 1.5.0Rok Košir+386 1 543 7592rok.kosir@mf.uni-lj.sihttp://cfgbc.mf.uni-lj.si/equipment/roche_lc480
GS Junior sequencerRocheMF ULCFGBCRok KoširCFGBC2011Transcriptomics, Genomics, MetagenomicsWith support of trained personnelRegularlyYes, external (manufacturer or its representative)NoNo operational softwareLocal computer, Local server (within LAN)Local computer, Within LANnone5300100nonenoneYes, fullyManufacturer's proprietary softwareInstalled on a local computer (single-user)Roche 454 Sequencing ApplicationsRok Košir+386 1 543 7592rok.kosir@mf.uni-lj.sihttp://cfgbc.mf.uni-lj.si/equipment/roche_gs_junior
Ion Torent PGMLifeTechnologiesVeterinary FacultyInstitute of Microbiology and Parasitologydr. Matjaž OcepekVeterinary Faculty, Gerbičeva 60, 1000 Ljubljana, Inštitute of Microbiology and Parasitology2014GenomicsAuthorized personnel onlyRegularlyYes, external (manufacturer or its representative)Yes, fullyManufacturer's proprietary softwareLocal server (within LAN)Within LANLife technologies10603000PartiallyManufacturer's proprietary software, Open-source softwareInstalled on a server (multiple users)IGV, DNAstardr. Matjaž Ocepek+386 1 4779252matjaz.ocepek@vf.uni-lj.si
QuantStudio 3D dPCRLifeTechnologiesVeterinary FacultyInstitute of Microbiology and Parasitologydr. Matjaž OcepekVeterinary Faculty, Gerbičeva 60, 1000 Ljubljana, Inštitute of Microbiology and Parasitology2014Transcriptomics, GenomicsWith support of trained personnelRegularlyYes, external (manufacturer or its representative)Yes, fullyManufacturer's proprietary softwareLocal computer, Free cloud-based storageLocal computer, From InternetQuantStudio 3D660500Yes, fullyManufacturer's proprietary softwareInstalled on a local computer (single-user), Web-based application (no installation required)DNAstardr. Matjaž Ocepek+386 1 4779252matjaz.ocepek@vf.uni-lj.si
3200 Qtrap - LC MS/MSAB SciexUniverstity Medical CentreUnit for Special laboratory diagnosticsBarbka Repič LampretVrazov trg 12009MetabolomicsAuthorized personnel onlyRegularlyBoth, in-house and externalNoNo operational softwareLocal computerLocal computer-111--Yes, fullyManufacturer's proprietary softwareInstalled on a local computer (single-user)AB Sciex, Chemowiev, AnalistBarbka Repič Lampret15224775barbka.repic@kclj.si
MiSeqDxIlluminaInstitute of Oncology LjubljanaDept of Molecular Diagnosticsdr. Srdjan NovakovićZaloska 5, stavba B2015Genomicsdiagnostic use onlyRegularlyNoNo operational softwarenone000PartiallyManufacturer's proprietary softwareInstalled on a local computer (single-user)"Illumina MiSeq Reporter; VariantStudio"Srdjan Novaković15879546snovakovic@onko-i.si
Genetic Analyzer 3500AppliedBiosystemsInstitute of Oncology LjubljanaDept. of Molecular Diagnosticsprof. Srdjan NovakovićZaloska 5, 1000 Ljubljana, Slovenia, building B2010Genomicsdiagnostic use onlyRegularlyNo operational softwarenone000PartiallyManufacturer's proprietary softwareInstalled on a local computer (single-user)"AppliedBiosystems Sequencing Analysis v5.4; GeneMapper v4.1."prof. Srdjan Novaković15879546snovakovic@onko-i.si
7900HT Fast Real Time PCR SystemAppliedBiosystemsInstitute of Oncology LjubljanaDept. of Molecular Diagnosticsprof. Srdjan NovakovićZaloška 5, 1000 Ljubljana, Slovenia, building B2010Genomicsdiagnostic use onlyOccasionally (upon need)NoNo operational softwarenonenonenone000PartiallyManufacturer's proprietary softwareInstalled on a local computer (single-user)AppliedBiosystems SDS 2.4prof. Srdjan Novaković15879546snovakovic@onko-i.si
QX100BioRadNIBDepartment for Biotechnology and Systems BiologyDejan ŠtebihNIB-FITO lab, Večna pot 111, 1000 Ljubljana2012Transcriptomics, GenomicsAuthorized personnel onlyRegularlyBoth, in-house and externalNo 000Yes, fullyManufacturer's proprietary softwareInstalled on a local computer (single-user)QuantaSoftŠpela Baebler059 232 825 spela.baebler@nib.sihttp://www.nib.si/eng/index.php/departments/infrastructural-centre-planta/description-of-large-equipment#biorad
BioMark HDFluidigmNIBDepartment for Biotechnology and Systems BiologyDejan ŠtebihNIB-FITO lab, Večna pot 111, 1000 Ljubljana2012Transcriptomics, GenomicsAuthorized personnel onlyRegularlyBoth, in-house and externalNo 000Yes, fullyManufacturer's proprietary software, In-house developed softwareInstalled on a local computer (single-user), Web-based application (no installation required)"Fluidigm Biomark HD Data Collection Software v3; qPCRcalculator (http://qPCRcalculator.nib.si)"Špela Baebler059 232 825spela.baebler@nib.sihttp://www.nib.si/eng/index.php/departments/infrastructural-centre-planta/description-of-large-equipment#fluidigm
TCS LSI confocal stereomicroscopeLeica NIBDepartment for Biotechnology and Systems BiologyDavid DobnikNIB-FITO lab, Večna pot 111, 1000 Ljubljana2014ImagingAuthorized personnel onlyRegularlyBoth, in-house and externalNo 000Yes, fullyManufacturer's proprietary softwareInstalled on a local computer (single-user)Leica Application Suite X v1.0.00Špela Baebler059 232 825spela.baebler@nib.sihttp://www.nib.si/eng/index.php/departments/infrastructural-centre-planta/description-of-large-equipment#stereomikroskop
QIACubeQiagenUniverstity Medical CentreUnit for Special laboratory diagnosticsTinka HovnikVrazov trg 12009Proteomics, Transcriptomics, GenomicsWith support of trained personnelOccasionally (upon need)Both, in-house and externalNoNo operational softwareLocal computerLocal computer-110NoNo operational softwareNo operational software-Tinka Hovnik15224025tinka.hovnik@kclj.si
MiSeqIlluminaUniversity Medical Centre Ljubljana, Division of PaediatricsUnit of Special Laboratory DiagnosticsJernej KovačVrazov trg 1, 1000 Ljubljana2014GenomicsFor diagnostic use onlyRegularlyYes, in-housePartiallyIn-house developed software or solutionLocal computer, Local server (within LAN)Local computer01025002000Yes, fullyManufacturer's proprietary software, Third-party proprietary software, Open-source softwareInstalled on a local computer (single-user), Installed on a server (multiple users), Web-based application (no installation required)"Illumina; SoftGenetics; Galaxy; Microsoft"Jernej Kovač38615224023jernej.kovac@kclj.si
ViiA 7 Real-Time PCR SystemApplied BiosystemsBlood Transfusion Centre of SloveniaDept. of ImunohematologyTadeja Dovč DrnovšekŠlajmerjeva 6, 1000 Ljubljana2012Genomicsdiagnostic use onlyRegularlyBoth, in-house and externalYes, fullyManufacturer's proprietary softwareLocal computer, Local server (within LAN)Local computer, Local server (within LAN)Applied Biosystems, ViiA 7 Software v1.2Yes, partiallyManufacturer's proprietary softwareInstalled on a local computer (muliple-users)Applied Biosystems, ViiA 7 Software v1.2Tadeja Dovč Drnovšek01 5438 195tadeja.dovc-drnovsek@ztm.si
EZ1 BioRobotQiagenBlood Transfusion Centre of SloveniaDept. of ImunohematologyTadeja Dovč DrnovšekŠlajmerjeva 6, 1000 Ljubljana2006Nucleic Acid Isolationdiagnostic use onlyRegularlyYes, in-houseNoNo operational softwareTadeja Dovč Drnovšek01 5438 195tadeja.dovc-drnovsek@ztm.si
Genetic Analyzer ABI 3500Applied BiosystemsBlood Transfusion Centre of SloveniaTissue Typing CenterIrena KemperleŠlajmerjeva 6, 1000 Ljubljana2014Genomicsdiagnostic use onlyRegularly
LABScan3DLuminexBlood Transfusion Centre of SloveniaTissue Typing CenterSabina Kunilo JamnikŠlajmerjeva 6, 1000 Ljubljana2012Genomicsdiagnostic use onlyRegularly