hcs openbis : training workshop ethz (hpt b71), august 5, 2010 t. pylak, i. adamczyk & a. bauch
DESCRIPTION
HCS openBIS : Training Workshop ETHZ (HPT B71), August 5, 2010 T. Pylak, I. Adamczyk & A. Bauch ( [email protected] , [email protected] , [email protected] ) -> https://www.infectome.org/openBIS. openBIS : Overview. Data Analysis Pipeline. HCS/ Imaging. openBIS DB. - PowerPoint PPT PresentationTRANSCRIPT
HCS openBIS: Training Workshop
ETHZ (HPT B71), August 5, 2010T. Pylak, I. Adamczyk & A. Bauch ([email protected], [email protected], [email protected])
-> https://www.infectome.org/openBIS
openBISDBExtract, Transform, Load
(ETL)OrganizeSearchShareExport
Visualize
Users
HCS/ Imaging
Mass Spectrometry
Deep Sequencing
Data Analysis Pipeline
openBIS: Overview
DropBox
openBIS: Architecture @ ETHZ
DSSDropBox AS
ScreeningDB
MetaData DB
APIs
1
iBRAIN2DataStore
Web Client
1. Manual (or automated) transfer of images and feature vectors to the drop boxes2. Data loader associated to the drop boxes sends data to the Data Store Server (DSS)3. Data Store Server moves
4. Images to file based Data Store5. Feature vectors to Screening DB
6. Application Server (AS) is a central data hub, facilitating data access and querying functionality7. Metadata - database for annotations, controlled vocabulary, attachments to projects and experiments & samples8. Web client for data management, manual annotations9. APIs for any image analysis pipeline
Images
Feature Vectors
Images Feature Vectors
2 3
4 5
6
7
8
9
CP071-1AA
CP071-1ABCP071-1AC …
CP071-1AACP071-1ABCP071-1AC …
AD3_KY_NEWAD3_MZ_NEW
AD5_KY
Experiment: Empirical approach toacquiring data represented by a set of protocols
CP071-1AACP071-1AB
CP071-1AC …
Sample: Object being observed/measured and comparedto each other
HCS_ImageHCS_Plate_Overview
Image_Analysis_Data
HCS_ImageHCS_Plate_Overview
Image_Analysis_DataDataset: Collection of data containingthe values of the actual observations/measurements
Data Space: Visibility Rules
Pelkmans
Project: A plan for a number of experiments
50 K Drugable Genome
Data Organization
Project
Experiment
Dataset
Sample
Data Space
Attachment
Any kind of file.doc.pdf.xls.ppt etc.
Property Type
Metadata
Project
Experiment
Dataset
Sample
Data Space
Attachment
Any kind of file.pdf.doc.xls.ppt etc.
Attachments
Description of experimental properties:
Exp. Date 2009-05-07Operator Finn McIntyre Protocol Infection Assay
Project
Experiment
Dataset
Sample
Data Space
Attachment
Any kind of file.doc.pdf.xls.ppt etc.
Prop. Type ValueProperty Type
Description of sample properties:
Cell line Hela CNXPerturbation SV40
Description of data set properties:
Microscope cellWoRxData set type HCS_IMAGE
Property Types
Featured Features
1. Browsing of Experiments2. Comparing Images of a list of genes (silenced by RNAi)3. Browsing of Plates (Plate Viewer)4. Accessing Images5. Accessing Analyzed Data6. Visualizing Analyzed Data 7. Customizing Table Views8. Sorting, Filtering of Tables9. Exporting Analyzed Data to Excel10. Sharing Datasets via Cifex11. Add Cell Line Information as a CV to all experiments in 50K
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
Mailing List
[email protected]> announcements of new functionality-> explanations how to use particular features of interest-> user comments and suggestions-> user requests for extensions
If you want be updated about the latest openBIS features, subscribe to the mailing list here:https://sympa.sytemsx.ch/sympa/info/screening-services
Contact person for extension requests: Tomasz Pylak [email protected]
or edit the request wiki page:https://wiki.sytemsx.ch:8443/display/SYBIT/openBIS+for+screening+-+feature+requests
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
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