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Humboldt-Universität zu Berlin - Mathematisch-Naturwissenschaftliche Fakultät - Wissensmanagement in der Bioinformatik

Download PiPa

PiPa is a java-based tool to setup and maintain a database for information on Protein-Protein Interactions and biological Pathways integrated from multiple public databases. The data is stored to a local MySQL database allowing the user SQL-based access to it.

Installation Instructions for PiPa


  1. PiPa binaries (Runnable jar-file)
  2. Java Runtime Environment (Version 1.6 recommended)
  3. MySQL-Server (at least version 5.1.36)
  4. Standard Widget Toolkit (Version 3.7.1 recommended)
  5. SQuirreL, a visual tool for querying databases via JDBC (optional).

Running PiPa

  1. Place the runnable PiPa jar-file to an empty directory
  2. Place the platform-spicific SWT zip-file or swt.jar in the same directory
  3. Run java -jar pipa.jar from the PiPa directory


Arzt, S., Starlinger, J., Arnold, O., Kröger, S., Jaeger, S., and Leser, U. (2011).
PiPa: Custom Integration of Protein Interactions and Pathways
GI-Jahrestagung 2011, Workshop "Daten In den Lebenswissenschaften" (to appear).


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