Getting Started with IPP
You should have received an IPP executable (IPP.exe) To install IPP, just double click the IPP executable. Read the license and continue if you agree. The IPP installer will set up the pipeline and the web server that will be used to interact with the pipeline. The installer will also give you the option of installing InsilicosViewer. InsilicosViewer is an agile data viewer for mass spectrometric proteomics experiments. InsilicosViewer can be very useful for publishing MS data and trouble shooting the analytical process. The installation could take a few minutes and you may see a blank black window during the installation depending on your system. Please be patient during installation. After installation a shortcut to the Insilicos Proteomics Pipeline will be placed on your desktop.
The IPP GUI is a web application that calls a set of command line utilities that generate results in XML format for viewing in a web browser. Thus, it's necessary to have a web server installed on the computer that IPP is installed on. If you don't have a web server, the IPP installer will install one for you. You do not need to do any extra setup, but you should be aware that a web server is part of IPP installation.
For security reasons, web servers are particular about what directories they allow web applications to read and write. Thus, you must place your data to be analyzed on the web server computer at or below the c:\Inetpub\wwwroot\ISB directory level.
IPP licenses are sold as yearly subscriptions. Academic discounts are available. Quotes are available by writing to getipp@insilicos.com. When you install and run the IPP you will notice language about sending a code to Insilicos at getipp@insilicos.com. You can do this at your convenience, the IPP will operate without a license, but to get the full benefit of the Insilicos performance enhancements and extra features you will need a license.
When a new version of IPP becomes available install it over the older version. You do not need to first uninstall the old version. The new version will not alter the data that you have processed. The new version will find your license key and transfer it to the new version. IPP can be completely removed from your computer by selecting "uninstall" from the "Insilicos Proteomics Pipeline" menu under programs in the Windows start menu. Uninstalling IPP will not remove your data.
A great way to learn how to use IPP is to follow the IPP tutorial. The IPP tutorial is a .pdf document that takes you through the IPP analysis of ICAT labeled MudPIT data.
If you have a question regarding the IPP, please first look at the list of IPP FAQ. If your question is not addressed by the FAQ contact the IPP discussion group at http://groups.google.com/group/InsilicosIPP or contact Insilicos through our support page.
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