Software
Dynamic simulation of regulatory networks using SQUAD
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* Corresponding authors: Ioannis Xenarios Ioannis.Xenarios@merckserono.net - Luis Mendoza lmendoza@biomedicas.unam.mx
1 Merck Serono, Geneva, 9 Chemin des Mines, Switzerland
2 EPFL, Lausanne, Building INF 341, Switzerland
3 Swiss Institute of Bioinformatics, Vital-IT Group, Quartier Sorge – Batiment Genopode, CH-1015 Lausanne, Switzerland
4 Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP04510, México
BMC Bioinformatics 2007, 8:462 doi:10.1186/1471-2105-8-462
Published: 26 November 2007Additional files
Additional file 1:
Description of SQUAD input formats. Description of the file formats used for loading network topology data into SQUAD.
Format: PDF Size: 124KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 2:
T-helper regulatory network in CellDesigner SBML format. Representation of the T-helper regulatory network using the CellDesigner SBML format. The file can be viewed using CellDesigner [15] and imported directly into SQUAD for the analysis.
Format: XML Size: 67KB Download file
Additional file 3:
Network file. A sample network file containing a network of 111 nodes and 116 edges.
Format: NET Size: 1KB Download file
Additional file 4:
Perturbation protocol. Example of perturbation protocol file used to perform the simulations. The file describes two perturbations. The first one on the Th0 state with IL-4, the second on the Th0 state with IL-4 and subsequent IFN-γ addition. The file can be loaded from the Perturbation tool in SQUAD. The file also contains three different perturbations of the IL-18 node aimed at demonstrating the use of the different pulse types: "constant", "range" and "single".
Format: PRT Size: 4KB Download file
Additional file 5:
SQUAD software. Compressed Zip file containing the binaries of SQUAD. To run SQUAD: Unzip the folder, in linux type chmod +x Squad2 and run it with ./Squad, or in windows click on Squad2.bat. A quick-start guide and a more detailed tutorial can be found on the SQUAD home page [30]. The zip file encloses a samples folder containing all the files described in this manuscript.
Format: ZIP Size: 6.4MB Download file