Plug-Ins for Omix

Input & Output

Model In- and Output

Many plug-ins are available building a compatibility layer between Omix and simulators as well as databases:

• The KEGG Database Plug-In allows to search and download reactions, pathways and entire organisms from the KEGG® databases directly into Omix.
• In a similar manner, the BioCyc Database Plug-In allows to load network from the BioCyc database collection.
• With the Reaction Equation Import Plug-In, networks can be assembled from reaction equations as they are frequently published in scientific publications.
• The SBML Import/Export Plug-In allows to import and export to the popular SBML® model exchange format.
• The SBGN-ML Import/Export Plug-In allows to import and export file in SBGN format.
• The BioPAX Import Plug-In allows to import BioPAX files.
• With the FluxML Plug-In models for 13CFLUX2 can be imported and exported.
• The Stoichiometry Matrix Exporter allows to export network stoichiometries to CSV spreadsheets as well as MATLAB® code.

Data Input

For data visualization, Omix provides a central window component, the data manager. The user can create own visualization approaches defining how data from the data manager shall be represented in the diagram. Since data might be available in specific file formats, a number of plugins exist, that allow to load different file formats into the data manager:

• By default, Omix can load CSV spreadsheets.
• The plug-ins Excel Plug-In, ODF Plug-In and HDF5 Plug-In allow to load data from Microsoft Excel®, OpenDocument format (Apache OpenOffice, LibreOffice) and HDF5, respectively.
• The 13CFLUX2 FWDSIM Import Plug-In allows to load results from the 13CFLUX2 simulator.

Visualization Output

Network diagrams can be exported to various visual output formats:

• By default, Omix can export following image formats^*:
  • BMP - Windows Bitmap
  • JPG - Joint Photographic Experts Group
  • PNG - Portable Network Graphics
  • PPM - Portable Pixmap
  • TIFF - Tagged Image File Format
  • XPM - X11 Pixmap
  Furthermore, diagrams can be exported to the vector-based SVG format and the page-based PDF format.
• With the Powerpoint Export Plug-In network diagrams can be exported to Powerpoint® slides.
• The SWF Export Plug-In allows to export Flash animations.
• With the MVideo Plug-In Omix has capabilities to export animated data visualization to AVI videos.

* The set of supported image formats can be extended depending on the platform because Omix is able to find and utilize additional image processing libraries of the operation system.

File Access

The SSH Access and the CIFS Access plug-ins allow to load remote documents via SSH and the CIFS (Windows file share) protocol, respectively.