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<H3>A. Start servers</H3>
The installation has completed successfully. To start openBIS launch the following script:
${INSTALL_BIN_PATH}/allup.sh
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After the completion of the above command openBIS will be available at
<A href="https://localhost:8443/openbis">https://localhost:8443/openbis</A>
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By now you have a fully functional openBIS instance, but it makes little sense
if it has no data in it.
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Here are the steps to get an example prot.XML into openBIS.
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<LI>Login into <A href="https://localhost:8443/openbis">openBIS</A> as 'admin'.
<LI>Open space browser by clicking on menu item <it>Admin -> Spaces</it>.
<LI>Create a space named TEST by using <it>Add Space</it> button.
<LI>Create a project named PROT inside space TEST by using menu item <it>New -> Project</it>.
<LI>At the console execute the command:
cp -R ${DSS_ROOT_DIR}/examples/test+prot ${DSS_ROOT_DIR}/incoming-ms-search
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It will create an experiment in project /TEST/PROT which shows a list of proteins.
We challenge you to go find it in the running application !
You could import a minimalistic example by executing the command:
cp -R ${DSS_ROOT_DIR}/examples/PLATE1 ${DSS_ROOT_DIR}/incoming-hcs
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It will create a plate <i>PLATE1</i> with images data for one of its wells.
We challenge you to go find it in the running application !
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<h4 class="illumina-ngs">Illumina NGS</h4>
A flow cell with flow lanes is created by executing the command:
mkdir -p ${DSS_ROOT_DIR}/incoming-create-flowcell/120420_SN792_0109_BC0P8LACXX/; cp -R ${DSS_ROOT_DIR}/examples/illumina-ngs/120420_SN792_0109_BC0P8LACXX/*.xml ${DSS_ROOT_DIR}/incoming-create-flowcell/120420_SN792_0109_BC0P8LACXX
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A flow cell output from the HiSeq2000 is registered as a data set of the sample 120420_SN792_0109_BC0P8LACXX:
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cp -R ${DSS_ROOT_DIR}/examples/illumina-ngs/120420_SN792_0109_BC0P8LACXX ${DSS_ROOT_DIR}/incoming-register-flowcell
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<H3>Customizing openBIS</H3>
In the scientific world there is no one-size-fits-them-all solutions.
Your research data is certainly different from our example data. Luckily, openBIS provides
an easy way to script the import process - the Jython Dropboxes. You can learn how to
create your custom-tailored Jython Dropbox <A HREF="https://wiki-bsse.ethz.ch/display/CISDDoc/Jython+Dropboxes">here</A>.