OmicBrowseManager – Tutorial for Beginners
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OmicBrowseManager – Tutorial for Beginners

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7/13/2007 OmicBrowseManager – Tutorial for Beginners Install OmicBrowse Server before using OmicBrowseManager Please make sure OmicBrowse is installed before beginning this tutorial. You can find detailed instructions on downloading and installing OmicBrowse from: http://omicspace.riken.jp/omicBrowse/OmicBrowseRegister.html Install OmicBrowse file transfer servlet OmicBrowseManager is comprised of two components: a Java application program running on your local PC and a Java servlet program running on the OmicBrowse server. The servlet program makes it easier to retrieve the files necessary for configuration of your OmicBrowse services. For security reasons we recommend only using the file transfer servlet on intranets. This tutorial gives simple instructions for performing the following common tasks: Configuration workflow 1. Get config files from the OmicBrowse server. 2. Configure the server to subscribe to other external OmicBrowse servers. 3. subscribe to external DAS1 Services. 4. Put your updated config files back on the OmicBrowse server. 1. Get config files from Server 2, 3. Edit config files with OmicBrowseManager to alter the config files for the 4. Put config files to Server Server OmicBrowseManager OmicBrowse Server Browsing data OmicBrowse FLASH clients Config files comprising gps/xml/init/init.xml containing species’ genomes and server information gps/WEB-INF/MenuConfig.xml list ...

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7/13/2007 OmicBrowseManager – Tutorial for Beginners Install OmicBrowse Server before using OmicBrowseManager Please make sure OmicBrowse is installed before beginning this tutorial. You can find detailed instructions on downloading and installing OmicBrowse from: http://omicspace.riken.jp/omicBrowse/OmicBrowseRegister.htmlInstall OmicBrowse file transfer servlet OmicBrowseManager is comprised of two components: a Java application program running on your local PC and a Java servlet program running on the OmicBrowse server. The servlet program makes it easier to retrieve the files necessary for configuration of your OmicBrowse services. For security reasons we recommend only using the file transfer servlet on intranets. This tutorial gives simple instructions for performing the following common tasks: Configuration workflow 1.Get config files from the OmicBrowse server. 2.Configure the server to subscribe to other external OmicBrowse servers. 3.Configure the server to subscribe to external DAS1 Services. 4.Put your updated config files back on the OmicBrowse server. 1. Get config files from Server 2, 3. Edit config files with OmicBrowseManager to alter the config files for the 4. Put config files to Server r OmicBrowseManager OmicBrowse Server Browsing data  OmicBrowse FLASH clients Config files comprising  gps/xml/init/init.xml containing species’ genomes and server information gps/WEB-INF/MenuConfig.xml list of each menu file for a species and version gps/WEB-INF/MenuList/ the location of the menu files listed in MenuConfig.xml gps/WEB-INF/classes/Action/lineMode/defDataSource.xml details of each service gps/WEB-INF/classes/Action/lineMode/defObject.xml the dataset details
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Copyright © Riken, 2006-2007
7/13/2007 1. Get files from the OmicBrowse server. This section shows how to get config files from the OmicBrowse server and save them to your local PC. By editing the files on your local PC, you can easily modify the server’s configuration, by subscribing to other external servers, subscribing to external DAS1 servers, adding your private datasets and utilizing other useful functions. First, selectGet from Serverfrom theFilemenu.
Enter theServer Namein theGet from Serverdialog. Please enter the host name of the OmicBrowse server whose configuration you want to modify, and click the OKbutton.
If the server is successfully found on the network, the following dialog appears. Please click theOKbutton to start downloading the config files from the server.
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7/13/2007 To download the config files to your local PC, you will be asked to select a directory in which to save the files. If you want you can create a new directory and then select that. Please note, only one group of files can be saved in each directory.
This button creates a new directory
Specify the directory to save the config files
If the config files have been successfully downloaded from the server into the directory, the following dialog will appear. Please click theYesbutton to begin editing the files.
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7/13/2007 Please make sure that the title includes your server URL.
You have now finished getting the files from the OmicBrowse server. Please go on to the next section of the tutorial for more information on using the OmicBrowseManager.
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7/13/2007 2. Set your Server to subscribe to other external OmicBrowse servers. We previously downloaded files from your OmicBrowse server to your local PC. Now we can update the list of external servers we are subscribed to. When the OmicBrowse server is first installed it is automatically subscribed to RIKEN’somicspaceOnce youwill see how to change your list of subscriptions. server. We have subscribed to a new server any available service for the current species and version will be available from theServercombo box. Make sure you have loaded the config files from the previous step. If they were not loaded after getting them from the server selectOpenfrom theFilemenu and open the directory you stored them in. SelectRegister other servers to subscribe tofrom theServermenu.
ClickRegister new serverin theOther Servers to Subscribe todialog.
Enter theServer Nameof the external OmicBrowse server you wish to subscribe to and click theRegisterbutton in theRegister a New Serverdialog. If “omicspace.riken.jp” does not appear on your list and you want your server subscribed to it, please enter “omicspace.riken.jp” and clickRegister.
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Please make sure that the server is added to the list of servers in theOther Servers to Subscribe todialog and then click “OK”.
The OmicBrowseManager will now attempt to connect to the server and provide you with details of its services whenever a Species and Version is selected. When the server is found, the following dialog appears.
However, if there is no connection to a server, the following dialog appears. If you choose to register this server a connection error message will be shown each time you select a new species and version.
You can now save your changes, but you will also need to follow step 4 before your OmicBrowse server will be updated with the changes.
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7/13/2007 3. Set your Server to subscribe to external DAS1 Services. We will now go through the steps of adding a DAS1 service to your OmicBrowse server. To add a DAS1 service we need to provide the following three pieces of information: 1.Definition of the dataset that the DAS1 service is providing 2.Original source of the dataset 3.URL and properties of the DAS1 server providing the dataset In the example shown below we will use the following information: 1. Definition of the dataset that the DAS1 service is providing The dataset’s Unique Name used in the OmicBrowse Server:ensembl1834 Brief and understandable description of the dataset:The human genome from EnsemblVersion of the dataset:18.34 2. Original source of the dataset Organization that created the data:Ensembl The dataset’s name officially used by the organization:Ensembl 18.34Link to the organization/data source URL:http://www.ensembl.org 3. URL and properties of the DAS1 server providing the dataset Server URL:http://das.ensembl.org/das/ensembl1834/features Limit window size for a data retrieval:200,000 bp Select theSpeciesandVersionfrom the combo-boxes on the top-right side of OmicBrowseManager to specify the genome coordinate axis. Click theDefine New Datasetbutton from theDataset Definitionpanel on the left-hand side of OmicBrowseManager and fill out the text boxes in theDefine New Datasetpane.
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TheAssign to servicebutton should be enabled, if not please see below. Select theAssign to servicebutton to assign the dataset information to the DAS1 service and specify relevant information about the service. Steps for how to fill in theAssign dataset as a servicepanel that will appear are given further below. If theAssign to servicebutton is disabled please perform the following steps: Click theOKnew dataset will be successfully registered, unless the Unique Name of thebutton. The dataset was registered previously. The dataset’s Unique Name will appear on theDataset Definitionpanel on the left-side of OmicBrowseManager.
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Select aSpeciesandVersionfrom the combo-boxes on the top-right of OmicBrowseManager
Please confirm that the dataset you have just registered is selected on theDataset Definitionpanel, and click the button.
Copyright © Riken, 2006-2007
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TheAssign dataset as a serviceform should now be shown.
Make sure to selectDAS1from theService Protocolcombo box. The panel will change and display the DAS URLtext field. The DAS URL we have used in this tutorial is: http://das.ensembl.org/das/ensembl1834/features
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Enter theDAS URLin theRequired Informationsection and press theOKbutton. You have now added aDAS1service to yourOmicBrowsecan confirm that DAS1 has beenserver. You successfully configured by following step 4 of the tutorial and then viewing the service through your browser.
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7/13/2007 4. Put your updated files back on the OmicBrowse Server Now that you have modified the configuration, we need to put the modified config files back onto the OmicBrowse server. Once you have done this and restarted the server you will be able to see the results of updating your OmicBrowse server. SelectPut to Serverfrom theFilemenu.
Enter theServer Namein the next dialog. The default server name is that of the server you have downloaded the config file from.
In the next dialog select “yes”.
In theLogin Serverdialog, input the user name and password for the OmicBrowse Administrator, and click “OK”.
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