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<title>Getting started with openBIS</title>
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<h1> Getting started with openBIS <h1>
<div><img alt="openBIS" id="openbis-logo" name="openbis-logo" src="images/openBIS_Logo.svg" style=
"position: absolute; top: 10px; right: 20px; height: 80px;"></div>
<h3>A. Start servers</h3>The installation has completed successfully. To start openBIS launch the following script:
<div class="sourcecode">
${INSTALL_BIN_PATH}/allup.sh
</div>This command might take several minutes on the inital startup, depending on the performance of your server!<br>
After the completion of the above command openBIS will be available at <a href=
"https://${HOSTNAME}:8443/openbis">https://${HOSTNAME}:8443/openbis</a><br><br>
<div class="text">
Note: by default, openBIS expects to be able to connect your PostgreSQL database as superuser 'postgres' without a password.
This is because openBIS needs to create its database users and schemas.
If this assumption does not hold, the following commands print the SQL scripts that can be used to create the required databases manually:<br>
</div>
openBIS application server database:
<div class="sourcecode">
${INSTALL_BIN_PATH}/init_database.sh openbis_prod openbis
</div>
DSS pathinfo database:
<div class="sourcecode">
${INSTALL_BIN_PATH}/init_database.sh pathinfo_prod openbis
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Imaging database (required only if technology 'microscopy' is enabled)
<div class="sourcecode">
${INSTALL_BIN_PATH}/init_database.sh imaging_prod openbis
</div>
<div class="text">
The first argument of script 'init_database.sh' defines the database name. The second argument defines the username that openBIS will be using to connect the corresponding database.
Again, openBIS expects the user(s) can connect the database without a password. If this is not the case, the password needs to be set to service.properties.
Consult openBIS documentation for details.
</div>
<h3>B. Importing test data</h3>
<p>By now you have a fully functional openBIS instance, but it makes little sense if it has no data in it.</p>
<h4 class="generic">Generic</h4>
<p>Here are the steps to register a file/folder as a data set into openBIS.</p>
<ol>
<li>Open <a href="https://${HOSTNAME}:8444/datastore_server">https://${HOSTNAME}:8444/datastore_server</a> and
accept the self-signed certificate of the server. The site itself will show an error message which can be ignored.
<li>Log in to <a href="https://${HOSTNAME}:8443/openbis">openBIS</a> as admin.
<li>Open the Collection Browser by clicking on the menu item Browse -> Collections and open the default collection. </li>
<li>Click on the Data Set Uploader tab and upload one or several files.</li>
<li>Choose a data set type and press the button 'Create Data Set'.</li>
</ol>
<p></p>
<h4 class="illumina-ngs">Illumina NGS (ETH BSSE Setup)</h4>
<ol>
<li>A flow cell with flow lanes is created reading out two XML files provided by the Illumina sequencer:
<div class="sourcecode">
mkdir -p ${DSS_ROOT_DIR}/create-flowcell-hiseq/120420_SN792_0109_BC0P8LACXX/;<br>
cp -R ${DSS_ROOT_DIR}/examples/illumina-ngs/120420_SN792_0109_BC0P8LACXX/*.xml
${DSS_ROOT_DIR}/create-flowcell-hiseq/120420_SN792_0109_BC0P8LACXX;<br>
touch ${DSS_ROOT_DIR}/create-flowcell-hiseq/.MARKER_is_finished_120420_SN792_0109_BC0P8LACXX<br>
</div>
</li>
<li>A flow cell output from a HiSeq2000 is registered as a data set of the object 120420_SN792_0109_BC0P8LACXX.<br>
Additionally a data set is registered for each flow lane:
<div class="sourcecode">
rsync -a --exclude=Unaligned* ${DSS_ROOT_DIR}/examples/illumina-ngs/120420_SN792_0109_BC0P8LACXX
${DSS_ROOT_DIR}/register-flowcell-hiseq;<br>
touch ${DSS_ROOT_DIR}/register-flowcell-hiseq/.MARKER_is_finished_120420_SN792_0109_BC0P8LACXX;<br>
</div>
</li>
<li>The sequencer is finished and we want to track this automatically. Therefore we sync the RTAComplete.txt in a
drop box:
<div class="sourcecode">
mkdir -p ${DSS_ROOT_DIR}/read-rta-timestamp/120420_SN792_0109_BC0P8LACXX/; rsync
${DSS_ROOT_DIR}/examples/illumina-ngs/120420_SN792_0109_BC0P8LACXX/RTAComplete.txt
${DSS_ROOT_DIR}/read-rta-timestamp/120420_SN792_0109_BC0P8LACXX/RTAComplete.txt; touch
${DSS_ROOT_DIR}/read-rta-timestamp/.MARKER_is_finished_120420_SN792_0109_BC0P8LACXX
</div>
</li>
<li> For creating some objects we use the 'Object Registration'. This is available under the 'Import' menu: <br>
Import -> Object Registration -> Choose object type '(multiple)' and browse to the file:
<div class="sourcecode"> ${DSS_ROOT_DIR}/examples/illumina-ngs/tsv-files/example_samples_with_parents.tsv</div>
Tick 'Update existing'and press the 'Save' button. <br>
This created several objects which can be viewed via Browse -> Objects. You might need to select the Object Type 'all' <br>
Note that the objects are in a parent-/child relationship indicated by the objects shown in the 'Parents' column.
</li>
<br>
<li>After the demultiplexing using the Illumina 'configureBclToFastq.pl' the FASTQ files are created and also some
statistic files are provided.<br>
Let's register them as well in openBIS:
<div class="sourcecode">
mkdir ${DSS_ROOT_DIR}/register-unaligned/120420_SN792_0109_BC0P8LACXX; <br>
rsync -a ${DSS_ROOT_DIR}/examples/illumina-ngs/120420_SN792_0109_BC0P8LACXX/Unaligned* ${DSS_ROOT_DIR}/register-unaligned/120420_SN792_0109_BC0P8LACXX;<br>
touch ${DSS_ROOT_DIR}/register-unaligned/.MARKER_is_finished_120420_SN792_0109_BC0P8LACXX;
</div>
<br>
The demultiplexed FASTQ files are a data set of the objects BSSE-QGF-LIBRARY-1 and BSSE-QGF-LIBRARY-2. Note that lane 1 and two <br>
contained both objects which results in two FASTQ data sets for each object.
</li>
</ol><br>
A short description of all drop boxes is also provided here: <a href=
"https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+for+Illumina+NGS" target="_blank">openBIS for Illumina
NGS<a><br>
<h4 class="eln-lims">ELN-LIMS</h4>
<p>Here are the steps to create your first experimental step and register an image file as preview into the ELN-LIMS interface.</p>
<ol>
<li>Log in to <a href="https://${HOSTNAME}:8443/openbis/webapp/eln-lims">ELN/LIMS</a> interface as admin.</li>
<li>Using the navigation tree on the left hand-side go to <em>Lab Notebook</em> -> <em>Others</em>
-> <em>Default Lab Notebook</em> -> <em>Default Project</em> -> <em>Default Experiment</em></li>
<li>Click on the Upload plus sign on the toolbar and create a new <em>Experimental Step</em>.</li>
<li>Click on the Upload button.</li>
<li>Choose <em>Eln Preview</em> as Data Set Type and drop an image file in the Files Uploader section.</li>
<li>Click the Save button.</li>
<li>Now you have a basic lab notebook with an experiment, experimental step and one image used as preview.</li>
</ol>
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<h4 class="microscopy">Microscopy</h4>
<ol>
<li>At the console execute the command:
<div class="sourcecode">
cp -R ${DSS_ROOT_DIR}/examples/microscopy_example ${DSS_ROOT_DIR}/incoming-microscopy;<br>
touch ${DSS_ROOT_DIR}/incoming-microscopy/.MARKER_is_finished_microscopy_example
</div>
</li>
<li>Log in to <a href="https://${HOSTNAME}:8443/openbis/webapp/eln-lims">ELN/LIMS</a> as admin.</li>
<li>Find the example in project DEFAULT of space DEFAULT.</li>
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</ol>
<h4 class="flow">Flow Cytometry</h4>
<ol>
<li>At the console execute the command:
<div class="sourcecode">
cp -R ${DSS_ROOT_DIR}/examples/flow_cytometry_example ${DSS_ROOT_DIR}/incoming-facsaria;<br>
touch ${DSS_ROOT_DIR}/incoming-facsaria/.MARKER_is_finished_flow_cytometry_example
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</div>
</li>
<li>Log in to <a href="https://${HOSTNAME}:8443/openbis/webapp/eln-lims">ELN/LIMS</a> as admin.</li>
<li>Find the example in project DEFAULT of space DEFAULT.</li>
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</ol>
<h3>Importing example data</h3>
<p></p>
<div class="text">
To import example data please add plugin "[technology]-optional" to core-plugins.properties, where [technology] is
"screening", "illumina-ngs" or "proteomics"
</div>
<p><br></p>
<h3>Customizing openBIS</h3>
<div class="text">
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 dropboxes. You can
learn how to create your custom-tailored dropboxes <a href="https://wiki-bsse.ethz.ch/display/openbisDoc/Dropboxes"