Computational Tools and Resources for Integrative Modeling in Systems Biology


Mathematical modeling is key for systems level understanding of cellular processes. The development of mathematical models demands advanced computational tools that keep track of heterogeneous data of molecules and their interactions. Especially the integration of experimental data and pre-existing knowledge into computational models of biological systems is of considerable importance. In silico simulations of model behavior under similar conditions as in the experiment give the possibility for model validation regarding specific experimental data. Such an integrative approach leads eventually to a more accurate and consistent description of the observed biological system. We review several resources and computational tools which support the investigation of biological networks and describe several resources and methods for integrative modeling.


Omics data Mathematical modeling Software tools Network analysis Reverse engineering 



Algorithm for the Reconstruction of Accurate Cellular Networks


Adenosine TriPhosphate


Biological Pathway Exchange


BRaunschweig ENzyme Database


Cancer Cell Line Excyclopedia


Cell Markup Language


Chemical Entities of Biological Interest


Chromatin immunoprecipitation


COmplex PAthway Simulator


Deoxyribonucleic Acid




Dialogue on Reverse Engineering Assessment and Methods


Flux-Balance Analysis


Gene Expression Data Analysis Suite


Gene Expression database of Normal and Tumor tissues


Gene Expression Omnibus


Gene Ontology


Gene eXpression Database


HUGO Gene Nomenclature Committee


Human Metabolite DataBase


Human Genome Organisation


Kyoto Encyclopedia of Genes and Genomes


Metaboloc Control Analysis


Methylated DNA immunoprecipitation


Mouse Multiple tissue Metabolome DataBase


Model Organism Protein Expression Database


messenger RNA


Mass Spectrometry


Neighborhood-based Entity SeT


Nuclear Magentic Resonace


Ordinary Differential Equation


Protein Abundance across organisms DataBase


Principal Component Analysis


Ribonucleic Acid


System for the Analysis of Biochemical Pathways - Reaction Kinetics)


Systems Biology Graphical Notation


Systems Biology Markup Language


Stanford Microarray Database


Support Vector Machine


The Cancer Genome Atlas


Transcriptional Regulatory Element Database


Visualization and Analysis of Networks containing Experimental Data


eXtensible Markup Language


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Max Planck Institute for Molecular GeneticsBerlinGermany

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