GEOMI

GEOMI is a network visualisation and analysis platform originally developed at National ICT Australia (NICTA). The program and its source code are released under the LGPL licence. For more information, please click here.

The SBI version of GEOMI enables visualisation of protein-protein interaction data in four-dimensions, and mapped with proteomic data as described in:

• Li SS, Xu K, Wilkins MR (2011). Visualisation and analysis of the complexome network of Saccharomyces cerevisiae. Journal of Proteome Research, 10: 4744-56. [abstract]
• Goel A, Li SS, Wilkins MR (2010). Four-Dimensional Visualisation and Analysis of Protein-Protein Interaction Networks. Proteomics, 11: 2672-82. [abstract]
• Ho E, Webber R, Wilkins MR (2008). Interactive three-dimensional visualization and contextual analysis of protein interaction networks. Journal of Proteome Research, 7: 104-12. [abstract]

Download GEOMI (SBI version) [zip]
Requires Java and at least Java 3D 1.5.

GEOMI User Guide [pdf]

4-D Visualisation of Protein-Protein Interaction Networks

More videos can be viewed on our Youtube channel.

DNA mismatch repair proteins

Cell cycle gene expression data has been mapped onto DNA mismatch repair proteins MLH1, MSH2, MSH6, PMS1 and nearby interacting proteins in yeast. Green: down regulation, Red: up regulation, Black: no change in expression. Colour intensity indicates level of expression change.

Histones in the cell cycle

Cell cycle expression data mapped onto histone proteins and nearby interacting partners in yeast. Green: down regulation, Red: up regulation, Black: no change in expression. Colour intensity indicates level of expression change.

XWG Files

The XWG (XML Wilma Graph) file format is used by GEOMI to visualise networks. To view these files, move the downloaded files to the data directory in GEOMI. Make sure the directory also contains the WilmaGraph.dtd file.