BioGranat

BioGranat -
Molecular Biology Graph Visualisation and Analysis Tool

Biogranat Development Team^1,2

¹ University of Applied Sciences and Arts Hannover, Faculty IV, Department of Computer Science, Ricklinger Stadtweg 120, 30459 Hannover, Germany
² King's College London, Department of Medical and Molecular Genetics, 8th floor Guy's Hospital Tower Wing, London SE1 9RT, United Kingdom

About

BioGranat is a molecular biology graph visualisation and analysis tool developed in collaboration by Hochschule Hannover and King's College London. It is based on the Java OSGi bundle architecture and currently provides a graphical user interface, input and output routines for various graph file formats, a facility to use the JUNG library, 2D graph layout routines, 3D visualisation of graphs, JAVA scripting and graph analysis algorithms. Further developments address graphics export (jpeg, vector formats), generation of random graphs and the import of biological meta-information. Biogranat can be used to integrate and analyse large-scale gene networks. BioGranat is available as Open Source Software.

Availability

BioGranat is available via sourceforge.

Funding

We would like to acknowledge funding from the German Academic Exchange Service (DAAD PPP D/07/09921), the British Council (ARC1297) and the Royal Society (RG100252).

Publications

• Lehne B, Barkas N, Dand N, Sutherland R, Tebbe C, Sprengel F, Ahlers V and Schlitt T
  De-novo discovery of disease associated subnetworks using Region Growing Analysis
  submitted
  

• Dand N, Sprengel F, Ahlers V, Schlitt T
  BioGranat-IG: A network analysis tool to suggest mechanisms of genetic heterogeneity from exome sequencing data
  Bioinformatics. 2013,29(6):733-741.
  

• Mendig A, Sprengel F, Schlitt T, Ahlers V
  GPU-beschleunigtes 3D-Layout komplexer Netzwerke
  [GPU-accelerated 3D-Layout of complex networks]
  published in Go-3D 2009: Go for Innovations; Editors von Lukas U, Mahnke EM, Vahl M
  Fraunhofer-Verlag, Stuttgart, 2009
  

BioGranat tools

BioGranat-RGA and BioGranat-IG are tools to identify subnetworks that underlie diseases.

BioGranat-RGA has been developed to find the largest subnetwork that contains as many as possible genes from a given ranked list of genes. This ranked list can for example be derived from GWAS results using methods published by Lehne et al. in PLoS ONE. 2011, 6(6): e20133.

BioGranat-IG used for finding the smallest subnetwork that represents all or most individuals; the input data is usually a biological network and lists of genes carrying sequence variants in indivduals whose exomes have been sequenced.

tool	BioGranat-IG Individuals-Grouping	BioGranat-RGA Region Growing Analysis
application	"oligo"-genic disease	complex disease
typical data	exome sequences	GWAS
input data	network gene lists	network ranked gene list

BioGranat Screenshot. BioGranat is available via sourceforge.