[[PageOutline]] = Proteios SE server administration = Some configuration of the Proteios SE server is needed to enable all features. Furthermore, the administrator also needs to create user accounts and activate plug-ins, see the administration part of the [wiki:UserGuide user guide]. == Tomcat memory settings == Tomcat by defaults run with little memory allocated to the Java Virtual Machine. Some Proteios SE plug-ins will require more memory, as will multiple concurrent users. It is thus recommended that you change the memory allocation to at least 512Mb. Depending on Tomcat version and base system, this can be done in different ways. Basically you'd like to set the environment variable JAVA_OPTS for tomcat to -Xmx512m (or higher). [[BR]] - On a SuSE Linux 10.x system with tomcat55 as a service, you can edit JAVA_OPTS in /srv/www/tomcat55/base/conf/tomcat55.conf.[[BR]] - If running Tomcat as a Windows service you can access the Java memory settings by the `Monitor Tomcat` tray icon. [[BR]] - Also see: [http://wiki.apache.org/tomcat/FAQ/Memory Tomcat wiki]. == Web server security == If you have Internet access to your Proteios SE server, it is advisable to use SSL encryptation of the connection, since passwords and settings are otherwise sent without encryptation. This is discussed [wiki:TomcatApacheSSLConfigurationHints here]. Also see [http://tomcat.apache.org/tomcat-6.0-doc/ssl-howto.html ssl-howto] for Tomcat. == FTP Server == The integrated Proteios SE ftp server needs to be started separately, [wiki:FTPServer see]. == Search Engine configuration == There are several search engines that can be accessed directly from Proteios SE. The server administrator needs to edit the configuration files of these to point to the right URLs. Furthermore, for the Proteios SE results combination of multiple search engines, exactly the same databases need to be installed for the different search engines, with a random/reverse part that has a specific prefix for all the random entries. [http://www.matrixscience.com/help/decoy_help.html Matrix Science] provides a free script to generate such a database. [attachment:decoy_IPI.pl Here] you can download a modified script which will name modified IPI:IPI entries IPI:IPRNDx.x or IPI:IPREVx.x for easy parsing of accession numbers. Other entries will have a ###RND### or ###REV### prefix. The script should be run with the --append option so that the decoy database is added at the end of the existing database. If you plan to do PMF searches or 'no enzyme' searches, the --random option is preferable. If you use local reference (.dat) files for Mascot IPI databases, the .dat will also need to be expanded using [attachment:expand_IPI_dat_random.pl this script] === X!Tandem configuration === Locate the Proteios X!Tandem search properties file `xtandem.properties`, which can be found under WEB-INF/classes in your installation. If not existing, locate the Proteios X!Tandem search properties file template `xtandem.properties.in`, and copy it to a file named `xtandem.properties` in the same directory. Edit the `xtandem.properties` file by setting the value of the following parameters (more information and examples can be found in the file): 1. Set the value of `xtandem.gpm.server.url` to the URL for the GPM web site to use for the search. 1. Set the value of `xtandem.gpm.result.filename.prefix` to the prefix used for result files. 1. Set the value of `xtandem.gpm.server.timediff.hours` to the time difference in hours of a GPM server in another time zone. 1. Set the value of `xtandem.gpm.server.timediff.correction.minutes` to the difference in system clock settings. The other settings can normally be used with their default values. For a local GPM install the commented settings in the `xtandem.properties` file can be used. If you are not sure about the GPM result filename prefix, just "`GPM`" should work in most cases. Otherwise, run a search through the web interface and check how the result is named. === OMSSA configuration === Install OMSSA according to the instructions at [http://pubchem.ncbi.nlm.nih.gov/omssa/download.htm OMSSA download pages]. Process your fasta databases using `formatdb` from the [ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/ Blast distribution]. The output files from formatdb should all be located in the same directory. Locate the Proteios OMSSA search properties file `omssa.properties`. If not existing, locate the Proteios OMSSA search properties file template `omssa.properties.in`, and copy it to a file named `omssa.properties` in the same directory. Edit the `omssa.properties` file by setting the value of the following parameters (more information and examples can be found in the file): 1. Set the value of `omssa.local.install.path` to the path for the locally installed OMSSA search engine. 1. Set the value of `omssa.local.program.name` to the name of the OMSSA search program (normally "`omssacl`"). 1. Set the value of `omssa.local.database.directory.path` to the path of the local directory, where the sequence libraries (databases) are installed. 1. Set the value of `omssa.local.input.basename` to base name of the created OMSSA input files (a time stamp will be added to make the final name). The default choice is "`omssa_input.xml`". The settings above concern a locally installed OMSSA search engine, which is currently supported. === Mascot configuration === Mascot searches can be conducted in batch from Proteios SE similarily to X!tandem searches, and search results from Mascot Daemon searches can be retrieved in batch. For this to work, you need to edit the mascot server settings in the file `mascot.properties`, which can be found under WEB-INF/classes in your Proteios SE installation. After editing the file you need to restart Tomcat. === PIKE configuration === Proteios SE can access a PIKE web site to fetch information for input protein list files, and upload the result files. The PIKE server settings are stored in file `pike.properties`, which can be found under WEB-INF/classes in your Proteios SE installation. The default settings can normally be used, but the file may be edited if you want to access another PIKE web site. After editing the file you need to restart Tomcat. == Retrieval of remote files == Remote files can be registered by their URI and used in Proteios as if they were located on the Proteios server. [wiki:HttpsRemoteFiles Click here] to read about how to configure your server to access files via https using certificates (needed for BILS).