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Automated Proteomics Pipeline

A front end for several popular open source proteomics tools

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APP automates and allows distributed computing of common proteomics tasks using a java-front end to provide both GUI and server parts. It is highly recommended for use with the Trans Proteomic Pipeline but this is not a requirement.

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  • Please note that APP server demands Java 7 for monitoring of folders
  • Easily distribute and monitor execution of dozens of proteomics tools. Including: OMSSA,Myrimatch,X!Tandem, MSGF-+ Peptide, Protein and iProphet + more.
  • Add computers as nodes to a simple distributed cluster. Set up APP on an amazon image and easily scale your infrastructure within a few minutes.
  • Quick screencast of setup and task submission:
  • Major update released, including new dokumentation, have a look. Linux installer and source to follow in a day or two.
  • Quick fix done to add missing unimod.xml file. For those that have had problems with tthe search plugin, please redownload.


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