IPP Frequently Asked Questions
Q: What's the difference between IPP and TPP?
The IPP is a performance optimized and regression tested version of the Trans Proteomic Pipeline (TPP) originally created at the Institute for Systems Biology.
- The Windows version of IPP is also different from TPP because it does not use the Cygwin linux emulation environment, which has been
a source of trouble and confusion for many would-be TPP users.
- IPP works with either IIS or Apache without any need for specifying port numbers.
- IPP can read residue modification information from a UNIMOD file, TPP users have to alter the source code and recompile to add new
residue modifications.
- IPP is compatible with X!Tandem, including the ability to use any enzyme specified in the X!Tandem result file without changing source code and recompiling.
- IPP is fully compatable (including quantitation) with Mascot results obtained from Mascot Daemon and Distiller, including results from WIFF files.
Q: I'm having a hard time getting IPP to run on Vista.
Have a look at these notes.
Q: Can I install IPP on a machine that already has TPP on it?
Yes. It won't break your TPP installation, IPP installs alongside TPP.
Q: Didn't you used to charge for the IPP?
Yes, but we're now in the process of adding back our improvements to the main TPP codebase and moving to a pure support business model.
Q: What if Apache is already running on my computer? Do I have to uninstall Apache before installing IPP?
No. You do not have to uninstall Apache before installing IPP. The IPP installer will detect Apache on your computer and configure IPP to use the existing Apache web server.
Q: When I try to look at my results my browser asks for a user name and password. What should I do?
This is a file permissions bug. The IPP installer attempts to set the permissions for the directories that you will use, but because every computer is different there are still some holes in this process. Please contact us and tell us about your system (operating system, web server etc.) if you see this problem. You can fix the problem yourself by doing the following:
- Go to the Control panel under the Start menu.
- Select:
- Administrative tools.
- Internet Information services.
- local computer.
- Web Site.
- Default Web Site.
- Right click ISB and select Properties.
In this view are the Read, Write and Directory browsing boxes checked? Does the Execute Permissions show scripts only? If not please change them.
- Select the Directory Security tab and select Edit under Anonymous access and Authentication control.
Are the Anonymous access box and Integrated Windows authentication boxes checked? If not please check them.
Q: IPP says that it can not find my database. Where should I put the database so that IPP can find it?
For SEQUEST the database location is determined by the location that you choose when you run SEQUEST. This information is saved in the sequest.params file. Sometimes IPP gets confused if you moved the data after running SEQUEST. The SEQUEST params file can me opened in a text editor and altered if necessary.
Q: How do you go about using unimod files allow conversion of pepXML files that contain modifications not contained in the IPP's default list?
Have a look at c:\inetpub\ipp-bin\residue_modifications.cfg for details. You can either put the modifications in that file directly, or use that file to point to your modifications (as in a Mascot installation etc).
Getting Help
If your question is not addressed by the FAQ please contact the IPP discussion group at http://groups.google.com/group/InsilicosIPP or contact Insilicos through our support page.
copyright © 2002-2007, Insilicos LLC
