Mass spectrometry, Protein Chemistry Facility
Research Institute of Molecular Pathology (IMP)
Institute of molecular biotechnology of the Austrian Academy of Sciences (IMBA)
Gregor Mendel Institute of Molecular Plant Biology (GMI)

PD-Nodes SimpatiQCo Software Tools Publications

SimpatiQCo About Download Installation Manual FAQ's
Installation guide


Please note: If you use or install simpatiQCo, you agree to the licenses in the "Licenses" directory (included in the download).

The installation progress takes some time, but should be no problem for a person with some IT-Knowledge. In short, you will install a PostgreSQL database and a package of an Apache webserver including PHP. You will then copy the SIMPATIQCO site (many PHP scripts and other stuff) to this server and do some minor configuration. We strongly recommend installing SIMPATIQCO on a dedicated PC, rather than on a computer that is also used for other tasks. First, output of server messages make it difficult to perform other tasks. Second, other programs installed on the PC, such as programs "listening" on port 80 which is required by the Apache server, are the main reason for installation problems. If you have any questions, please look at the FAQs or contact us directly.

The following settings must be applied:

Directory tree and Installations

  1. Create the www-directory "www" on your hard drive. E.g.: D:\www. The web documents of Simpatiqco will be stored here.
  2. Create a temp-directory "temp" e.g.: D:\temp. Make sure, that there is enough storage place in this directory to temporally hold your files (several GBs).
  3. Create a directory which will hold ftp-uploaded or directly copied raw files e.g.: D:\temp\ftp. Create another directory for the "hot" folder e.g. D:\temp\hot. Data uploaded to this directory will be processed automatically when the "hot" folder service is active. Make sure that there is enough storage place in these directories to temporally hold your files (several GBs).
  4. Install the Thermo MSFileReader from "Install\MSFileReader64Bit" by executing the .exe file.
  5. If asked, also install additionally needed software.
  6. If your computer does not have the .NET framework installed, or you are unsure about it, install .NET framework 2.0 from Install/dotnetfx.exe. Mascot searches can only be done if the framework is installed, because msconvert from ProteoWizard needs it to run. If the installation programm tells you that this version is not compatible with the currently installed one, cancel the .NET installation and simply continue as you already have a .NET framework installation running. In addition .NET framework 3.5 SP1 needs to be installed as it is required by EasyPHP which is used by SimpatiQCo, and .NET framework 4.0 needs to be installed as it is required by PeakAnalyzer, a component of SimpatiQCo. Therefore install .NET framework 3.5 and .NET framework 4.0 from the Install/ directory or download and install the software from the Microsoft webpage. Using Microsoft "Update" is also an option to ensure that all the required .NET framework components are installed on your system.

PHP & Apache installation

Note: If you already have a PHP/Webserver running and you are familiar with this system, skip the following steps and integrate Simpatiqco there. Please do not install easyPHP on a server where PHP and a webserver is already installed.

  1. Install the easyPHP package from the "Install" directory by executing the setup file.
  2. Launch easyPHP, and apply the settings like in the image below, Right-click -> Configuration -> EasyPHP, click ok to save. The server will now be started automatically with the operating system.
  3. Copy httpd.conf and php.ini from the "Manualy add and edit" directory to your EasyPHP installation path: C:\Program Files\EasyPHP-5.4.0RC4\conf_files. Doing so will overwrite the original files, you can backup them before the operation.
  4. Note: If you use another temp directory than "D:\temp" then after copying you have to open the above mentioned file php.ini and change the following line: upload_tmp_dir="YOUR TEMP DIRECTORY".
  5. Open the above mentioned and copied file "httpd.conf" in a text editor and edit the following lines according to your needs (Server IP-Address, Location of the WWW-Directory):
    • (line 183) ServerName YOUR-IP-SERVER-ADDRESS-HERE
    • (line 190) DocumentRoot "D:/www" -Leave this as it is, if you use D:/www as your servers directory for your websites including SIMPATIQCO.
    • (line 250) <Directory "D:/www"> -Leave this as it is, if you use D:/www as your servers directory for your websites including SIMPATIQCO.
  6. Don't forget to save the files with your settings.
  7. On the EasyPHP frontend, right-click -> Configuration -> PHP Extension: Check the following extensions, uncheck all others.
    • php_curl
    • php_gd2
    • php_mbstring
    • php_pgsql
  8. Click "Apply" and "close".
  9. Click the "Apache" Button on the easyPHP frontend and select "Stop" and then "Restart". Don't use "Restart" only, it might not work.

Copy files

  1. Copy (and therefore keep the subdirectory structure) the files and folders from "Copy to www" to your "www" directory.
  2. Reboot the computer. Really do, please.
  3. Test the connection to your server and the php configuration. Open a browser and navigate to: "localhost/phpinfo.php". A listing of your php configuration should appear, as shown below. If the Apache webserver fails to work properly, please check your PC for any software that might "block" port 80, as this is the most common reason. Such software needs to be uninstalled.
  4. Check for the entry "curl" which should look like this:
  5. Check for the entries mbstring, mcrypt and mhash which should look like this:
  6. Check for the entries "gd" and "hash":
  7. Check the entry for pgsql:
  8. If you see these settings, your PHP and Apache configuration is working!

PostgreSQL database setup

  1. Create a new empty directory for the Database(PostgreSQL)-data with a few GB storage place.
  2. Install PostgreSQL 9.0 from the "Install" directory. During install, use the default settings when asked, set the PostgreSQL data directory to the above mentioned Database(PostgreSQL)-data directory and remember the port number for PostgreSQL, usually 5432. Also carefully remember the root password you choose during installation. Do not launch Stack Builder at the end of the installation.
  3. If it was not already installed during the Postgres installation, install pgAdminIII by executing "Install\pgadmin3.msi". Use the default values.
  4. Start pgAdminIII. If there is not already a default connection, create a connection by clicking Menuebar->File->"add server". Use the following values: Name: "simpatiqco", Host: "localhost", Port: "5432", Maintenance DB: "postgres", Username "postgres". Also provide the root password you used for installation and enable "Store password". Click Ok to save.
  5. Open the connection to the server (Doubleclick) and create a new Login Role (Right click, New Object, New Login Role).
  6. Set the Name and password of the login rule to "simpatiqco" and change the other values according to the images below.
  7. Click Ok to save the login rule.
  8. Right click on "Databases" and create a new database.
  9. For the new database, use the settings according to the images below.
  10. Under the "Privileges" tab, add privileges for role "public" (check "ALL", click "Add/Change"). See image below.
  11. Click "OK" to create the database.
  12. Then goto "right click"->"Properties" on database "simpatiqco" and add privilege "simpatiqco" as shown below (check "ALL", click "Add/Change") and click "OK" again.
  13. In pgAdminIII, select the newly created SIMPATIQCO database and click the SQL button from the menu bar.
  14. Open the simpatiqco.sql file from the "Manualy add and edit" directory.
  15. Press F5. The query will be executed and the database-structure will be created. Ignore NOTICE informations. The last line should look like: "Query returned successfully..."
  16. Close pgAdminIII.

Final tweaks

  1. Open www\SIMPATIQCO\inc\conf.php in a text- or PHP-editor and edit the following lines corresponding to your servers IP address or name in the domain and the directories of your system. Default setting for directories are "D:/temp" and "D:/www". These directory settings should only be changed if you use other locations. In this case, don't forget to also update the "log_dir", "graph_cache_dir", "raw_dir" and "hot_dir" entries.
  2. $conf['root_url'] = "http://YOUR-SERVER/simpatiqco";
    $conf['root_dir'] = "d:/www/simpatiqco";
    $conf['log_dir'] = "d:/temp";
    $conf['logit'] = true; //true is highly recomended
    $conf['raw_dir'] = "d:/temp";
    $conf['ftp_dir'] = "d:/temp/ftp";
    $conf['hot_dir'] = "d:/temp/hot";
  3. Now connect to the Webinterface on the server. Open a browser and navigate to: "localhost/SIMPATIQCO"
  4. Also try to connect to the system from other computers by navigating to: "http://yourServerNameOrIPadress/SIMPATIQCO"
  5. CONGRATULATIONS, you can now start to upload raw files. Click on the default instrument and for the first upload, choose the pre-installed run-type "Raw analysis only" to see if the file upload and raw analysis works. You may have to install Adobe flash (for the upload) but your browser will prompt you anyway if this is the case.
  6. After finishing the installation process completly, visit the Manual to learn how to configure the system to your needs (adding/renaming instruments, etc.).
  7. If you have a running Mascot server in your unit, navigate to the "Settings" page and fill in the Mascot-server address. The Mascot- server address is a URL (including the "http://" entry and all slashes) when typed into a browser gives the welcome screen like in the image below. If the server can be found, you will be able to create run-types including a Mascot search. If no Mascot server is found, every uploaded run will end up as a raw file analysis with no MSn search.
  8. Note that it is not possible to start searches on the matrixscience server, because of the server side size limitation.

Additional notes