SE-209 screening: how to import screen data into openBIS

SVN: 14842

screening_tools/dist/readme.txt

-High Content Screening: how to import a library into openBIS
--------------------
+High Content Screening: how to import screen data into openBIS
 
+I. Transform the library file to adhere to openBIS format
+------
 To transform a QIAGEN library (or a file in similar format) you can use the command line tool called "metadata importer".
 
 It takes following parameters:
@@ -14,16 +15,33 @@ e.g:
     metadata-importer.bat master-plate-example.csv /LMC/BLUE-PROJECT/TRAIL-EXPERIMENT 384_WELLS_16X24 LMC
 
 The result of the transformation are 3 files, for genes, oligos and plates.
-You have to register these files manually from the web browser in openBIS in following order:
-- genes: go to "Material -> Import" menu and select material type "GENE". Then select a genes.txt file and click "Save".
-- oligos: as above but select material type "OLIGO"
-- plates: go to "Sample -> Import" and select sample type "(multiple)" - you will register plates and wells at the same time.
+You have to register these files manually from the web browser in openBIS (see next steps).
 
------ Note for Java developers:
+Note for Java developers:
 If your library file format is slightly different you can get the "metadata importer" source code and modify it to fit your needs.
 The source code is available at:
     https://svncisd.ethz.ch/repos/cisd/screening_tools/trunk
 You are interested in this package:
     ch.systemsx.cisd.openbis.metadata
 You can build the package using ant 'metadata-jar' target (build/build.xml).
------ 
\ No newline at end of file
+
+II. Register genes and oligos
+------
+1. Register genes: go to "Material -> Import" menu and select material type "GENE". Then select a genes.txt file and click "Save".
+2. Register oligos: as above but select material type "OLIGO"
+
+III. Register the experiment with plates
+------
+1. Ensure that the appropriate group and project exist
+- you can create a new group in "Administration -> Groups", "Add group"
+- you can create a new project in "Administration -> Project -> New"
+
+2. Register the experiment with the plates
+Go to "Experiment -> New"
+- specify the code of your experiment and choose a project for it
+- select "Samples: register from a file and attach"
+- for "Sample Type" choose "(multiple)"
+- choose a "plates.txt" file generated in the step I.
+- fill other atributes and click "Save". 
+It will take some time to register an experiment if you have a lot of plates in the file. 
+