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HCS openBIS : Training Workshop ETHZ (HPT B71), August 5, 2010 T. Pylak, I. Adamczyk & A. Bauch

HCS openBIS : Training Workshop ETHZ (HPT B71), August 5, 2010 T. Pylak, I. Adamczyk & A. Bauch ( tpylak@ethz.ch , izabelaa@ethz.ch , baucha@ethz.ch ) -> https://www.infectome.org/openBIS. openBIS : Overview. Data Analysis Pipeline. HCS/ Imaging. openBIS DB.

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HCS openBIS : Training Workshop ETHZ (HPT B71), August 5, 2010 T. Pylak, I. Adamczyk & A. Bauch

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  1. HCS openBIS: Training Workshop ETHZ (HPT B71), August 5, 2010 T. Pylak, I. Adamczyk & A. Bauch (tpylak@ethz.ch, izabelaa@ethz.ch, baucha@ethz.ch) -> https://www.infectome.org/openBIS

  2. openBIS: Overview Data Analysis Pipeline HCS/ Imaging openBIS DB Extract, Transform, Load (ETL) Organize Search Share Export Visualize Users MassSpectrometry DeepSequencing

  3. openBIS: Architecture @ ETHZ MetaData DB Images DropBox DSS AS DropBox Feature Vectors Web Client ScreeningDB Data Store iBRAIN2 APIs Images Feature Vectors • Manual (or automated) transfer of images and feature vectors to the drop boxes • Data loader associated to the drop boxes sends data to the Data Store Server (DSS) • Data Store Server moves • Images to file based Data Store • Feature vectors to Screening DB • Application Server (AS) is a central data hub, facilitating data access and querying functionality • Metadata - database for annotations, controlled vocabulary, attachments to projects and experiments & samples • Web client for data management, manual annotations • APIs for any image analysis pipeline 1 2 3 4 5 6 7 8 9

  4. Data Organization Data Space: Visibility Rules Pelkmans HCS_Image Project: A plan for a number ofexperiments 50 K Drugable Genome HCS_Plate_Overview Image_Analysis_Data Experiment: Empiricalapproachto acquiringdatarepresented bya setofprotocols AD3_KY_NEW AD3_MZ_NEW AD5_KY CP071-1AA CP071-1AA CP071-1AA Sample: Objectbeingobserved/ measuredandcompared toeachother HCS_Image CP071-1AB CP071-1AB CP071-1AB HCS_Plate_Overview CP071-1AC … CP071-1AC … CP071-1AC … Image_Analysis_Data Dataset: Collectionofdatacontaining thevaluesoftheactual observations/measurements

  5. Metadata Data Space Project Experiment Property Type Attachment Anykindoffile .doc .pdf .xls .ppt etc. Sample Dataset

  6. Attachments Data Space Project Experiment Attachment Anykindoffile .pdf .doc .xls .ppt etc. Sample Dataset

  7. Description of sample properties: CelllineHela CNX Perturbation SV40 Description of data set properties: MicroscopecellWoRx Data set type HCS_IMAGE Property Types Data Space Project Prop. Type Value Property Type Description of experimental properties: Experiment Exp. Date 2009-05-07 Operator Finn McIntyre Protocol Infection Assay Attachment Anykindoffile .doc .pdf .xls .ppt etc. Sample Dataset

  8. Featured Features Browsing of Experiments Comparing Images of a list of genes (silenced by RNAi) Browsing of Plates (Plate Viewer) Accessing Images Accessing Analyzed Data Visualizing Analyzed Data Customizing Table Views Sorting, Filtering of Tables Exporting Analyzed Data to Excel Sharing Datasets via Cifex Add Cell Line Information as a CV to all experiments in 50K

  9. Exercises • 1. Find all images for ABL1, ARAF, CAMK4, CAMK2D, MAPK8, • MAPK14, CSF1R in Experiment AD3_KY_NEW • 2. Share 3 datasets of your choice generated in Experiment • SV40_CNX with a colleague • 3. Export in an Excel sheet all genes where the infection index • in Experiment VSV_CNX is bigger than 27% • 4. Show Image analysis data as graphs for all plates in • Experiment SV40_ CNX • 5. Find the apoptotic index for TAOK1 in Experiment SV40 _CNX

  10. Mailing List screening-services@sympa.systemsx.ch -> announcementsofnewfunctionality -> explanationshowtouseparticularfeaturesofinterest -> usercommentsandsuggestions -> userrequestsforextensions IfyouwantbeupdatedaboutthelatestopenBISfeatures, subscribetothemailinglisthere: https://sympa.sytemsx.ch/sympa/info/screening-services Contactpersonforextensionrequests: Tomasz Pylak tomasz.pylak@bsse.ethz.ch oredittherequestwikipage: https://wiki.sytemsx.ch:8443/display/SYBIT/openBIS+for+screening+-+feature+requests

  11. For developers: API • list all screening experiments • list names of all features in an experiment • list plates • all • in a selected experiment • fetch features for every well where a given gene has been suppressed • all or selected features • in a selected experiment • in all experiments • load images • for the given well • for all or selected channels • save in temporary files • open the image automatically Download resources

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