Omix

Omix is a highly customizable editor for manually drawing biochemical network diagrams developed by Dr. Peter Droste. The software is equipped with extensive data visualization features. High quality vector graphics can be generated with Omix that are ideally suited for scientific presentation and publication.

Features

Omix' unique features include (but are not limited to):
  • Drawing stylish network diagrams with extensive annotation potential.
  • Interactive visualization of data from experiment as well as simulation in metabolic networks.
  • Different levels of detail to decrease complexity and flexibly highlight different aspects of the network structure.
  • Support of the drawing process by semi-automatic drawing features.
  • Extensible by plug-ins.
  • Visual analysis of time-dependent data by animations.
  • Visualization of chemical structures.
  • 3D visualization of data and network topologies.
  • Network analysis: elementary flux modes, network dependencies, flux balances...
Omix has extensive import and export capabilities, e.g.:
  • Import and export of SBML documents.
  • Import of network models in spreadsheet files (Excel) as well as from reaction equations.
  • Import of network models from KEGG database.
  • Import of data from Excel spreadsheets ans HDF5 files.
  • Export of the drawings into bitmap and vector graphic formats like PNG, JPG and SVG as well as animations (SWF Flash) and movie files (AVI).
Particularly for newcomers a simple and fast access to Omix is warranted. Comprehensive manuals and an elaborated tutorial are provided. Many example applications are made available.

Programmability

One outstanding feature of Omix is OVL, an object-oriented scripting engine that allows programming of network diagrams. Here, programming networks means for example definition of event-driven user interaction and dynamic modification of all invidual attributes of graphical elements in a drawing. This way, time-dependent numerical data are animated in the context of network diagrams with ease.

Usability

Although Omix has been developed having primarily drawings of biochemical networks in mind, the software is actually a fairly general vector-based network drawing program: nodes may be arbitrary polygons or image maps and the line type and stroke of edges can be chosen freely.

Tour

Sample Applications

The 2010 TU Delft iGEM team uses Omix to interactively visualize flux maps resulting from MFA calculations.

Availability

Omix is available for Windows, Linux and Mac OS X. Additionally, user manuals, tutorial courses and many example applications are available. Licenses for non-commercial academic and non-commercial scientific research purposes can be obtained for free by universities and research institutes. Commercial licensing is in preparation.

Software Download

Omix can be downloaded as 90-days trial version. The trial version can be activated with a valid license key.
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