Home

Network Biology, 2012, 2(1): 26-37
[XML] [EndNote Tagged] [BibTex] [ Full PDF (145K)] [Comment Article]

Article

GKIN: a tool for drawing genetic networks

Jonathan Arnold11 , Thiab R. Taha2, Leonidas Deligiannidis3
1Genetics Department, The University of Georgia, Athens, GA 30602-0001, USA
2Computer Science Department, The University of Georgia, Athens, GA 30602-0001, USA
3Computer Science Department, Wentworth Institute of Technology, Boston, MA 02115, USA

Received 20 October 2011;Accepted 30 November 2011;Published online 1 March 2012
IAEES

Abstract
We present GKIN, a simulator and a comprehensive graphical interface where one can draw the model specification of reactions between hypothesized molecular participants in a gene regulatory and biochemical reaction network (or genetic network for short). The solver is written in C++ in a nearly platform independent manner to simulate large ensembles of models, which can run on PCs, Macintoshes, and UNIX machines, and its graphical user interface is written in Java which can run as a standalone or WebStart application. The drawing capability for rendering a network significantly enhances the ease of use of other reaction network simulators, such as KINSOLVER (Aleman-Meza et al., 2009) and enforces a correct semantic specification of the network. In a usability study with novice users, drawing the network with GKIN was preferred and faster in comparison with entry with a dialog-box guided interface in COPASI (Hoops, et al., 2006) with no difference in error rates between GKIN and COPASI in specifying the network. GKIN is freely available at http://faculty.cs.wit.edu/~ldeligia/PROJECTS/GKIN/.

Keywords GKIN; genetic network; drawing tool; Java; GUI.


International Academy of Ecology and Environmental Sciences. E-mail: office@iaees.org
Copyright © 2009-2024 International Academy of Ecology and Environmental Sciences. All rights reserved.
Web administrator: office@iaees.org, website@iaees.org; Last modified: 2024/4/18


Translate page to: