The Univerisity of Virginia web interface to OMSSA OMSSA is the Open Mass Spectrometry Search Algorithm, created and maintained by the National Center for Biotechnology Information (NCBI). Current version of omssacl: omssa-2.0.0.macos Available databases: nr, human refseq System Version: Mac OS X Server 10.4.x Run OMSSA at UVa OMSSA via a web interface is now running at UVa. The web interface that is easy to use, powerful, secure and confidential. No special software is required on your computer (you only need a web browser). Anyone at UVa is welcome to use this facility. An account is required, email twl8n@virginia.edu The UVa OMSSA Web search home page is OMSSA at UVa (requires a login) The UVa OMSSA Web software package is freely available to be installed on your server. See below. Learn more in the readme. We are running the MacOS version of omssacl on a cluster of XServes. The OMSSA Web package has the ability to split a search across multiple nodes of a cluster, or to run the search on a single server. Install OMSSA Web at your site The following downloads are required if you wish to install UVa's OMSSA Web package on your servers. This package allows web access to your local OMSSA installation, as well as command line scripts suitable as the basis for a high-throughput OMSSA data analysis pipeline. OMSSA Web is a LIMS as well as a front end for OMSSA. Click here to download UVa's OMSSA Web as a tar archive. Early in 2007 the install process was tested by performing several installs from scratch. Many small bugs were found and fixed. This code works well but should be considered late beta-release (pre-production). This software is a front-end (wrapper, user-interface) for the NCBI OMSSA package, as well as serving as a high throughput command line scriptable pipeline to run omssacl. You must download the OMSSA package from the NBCI site. Click here to download a slightly newer version of the UVa OMSSA Web package. This version includes small upgrades to session_lib.pm. The changes were small, and seem to work fine, but this version has not been carefully tested. We suggest that you use this version of OMSSA Web if you are using vela_9.tar. OMSSA ms/ms search at NCBI Click here to download UVa's OMSSA XSLT scripts for making csv (Excel compatible) files from the XML output. This version is from February 2, 2007 Click here to download Vela. Vela is required by UVa's OMSSA Web. Click here to download Vela 9. This has some small improvements and includes the rudiments of a daemon to run Vela jobs on cluster nodes without PBS or Torque. Use this if you are using omssaweb_4_11.tar. We are using this version of Vela, but it has not been carefully tested. OMSSA Web and Vela require Linux or OSX, PostgreSQL, Perl, Apache httpd, NCBI's OMSSA, and NCBI databases (search libraries). See the installation documentation included with OMSSA Web for details. OMSSA Web at UVa Features Login required. Users have security, confidentiality, and results reports Upload now, run later No limits on the number of spectra per dta batch file Re-run previously uploaded dta batch files without uploading again Results are archived on the system, and can be downloaded by their owner at any time. Results include the XML output of OMSSA, a csv file with the peptides, a file with the OMSSA command used, and a log file Runs on a cluster using PBS Optionally pipeline batch runs from the command line with only three commands UVa's OMSSA Web includes LIMS features