HCS openBIS: Training Workshop

ETHZ (HPT B71), August 5, 2010T. Pylak, I. Adamczyk & A. Bauch (tpylak@ethz.ch, izabelaa@ethz.ch, baucha@ethz.ch)

-> 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

screening-services@sympa.systemsx.ch-> 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 tomasz.pylak@bsse.ethz.ch

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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