Software
Knowledge management for systems biology a general and visually driven framework applied to translational medicine
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* Corresponding author: Dieter Maier dieter.maier@biomax.com
1 Biomax Informatics AG, Planegg, Germany
2 Hospital Clinic-IDIBAPS-CIBERES, Universitat de Barcelona, Barcelona, Spain
3 School of Biosciences and Institute of Biomedical Research (IBR), University of Birmingham, Birmingham, UK
4 Departament de Bioquimica i Biologia Molecular, Institut de Biomedicina at Universitat de Barcelona IBUB and IDIBAPS-Hospital Clinic, Barcelona, Spain
5 Computational Biochemistry and Biophysics lab, Research Unit on Biomedical Informatics (GRIB) of IMIM/UPF, Parc de Recerca Biomdica de Barcelona (PRBB); Barcelona, Spain
BMC Systems Biology 2011, 5:38 doi:10.1186/1752-0509-5-38
Published: 5 March 2011Additional files
Additional file 1:
XML export of the full COPD knowledge base data model containing all semantic objects, annotation and experiment definitions.
Format: XML Size: 611KB Download file
Additional file 2:
Table of existing mapping scripts and wrappers.
Format: CSV Size: 1KB Download file
Additional file 3:
Step-by-step tutorial to access and query the COPD specific BioXM instance set-up as part of the BioBridge project.
Format: PDF Size: 1.6MB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 4:
A set of Affymetrix probes used within the Step-by-step tutorial.
Format: TXT Size: 238KB Download file
Additional file 5:
R script for pathway level principal component analysis of expression data integrated into BioXM and used as part of the analysis described in the Step-by-step tutorial.
Format: R Size: 5KB Download file
Additional file 6:
R script for significance testing of differentially regulated pathways identified by principal component analysis integrated into BioXM and used as part of the analysis described in the Step-by-step tutorial.
Format: R Size: 1KB Download file
Additional file 7:
Analysis of the sub-network connecting inflammation to central metabolism which is derived from the overall COPD knowledge network based on shortest path network search.
Format: PDF Size: 354KB Download file
This file can be viewed with: Adobe Acrobat Reader