Asmparts: assembly of biological model parts

We propose a new computational tool to produce models of biological systems by assembling models from biological parts. Our software not only takes advantage of modularity, but it also enforces standardisation in part characterisation by considering a model of each part. We have used model parts in SBML to design transcriptional networks. Our software is open source, it works in linux and windows platforms, and it could be used to automatically produce models in a server. Our tool not only facilitates model design, but it will also help to promote the establishment of a registry of model parts.

[1]  L. Hartwell,et al.  Theoretical biology: A robust view of biochemical pathways , 1997, Nature.

[2]  M. Elowitz,et al.  Programming gene expression with combinatorial promoters , 2007, Molecular systems biology.

[3]  Catherine M Lloyd,et al.  CellML: its future, present and past. , 2004, Progress in biophysics and molecular biology.

[4]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[5]  J. Chin,et al.  A network of orthogonal ribosome·mRNA pairs , 2005, Nature chemical biology.

[6]  Barbara M. Bakker,et al.  Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. , 2000, European journal of biochemistry.

[7]  Hiroaki Kitano,et al.  CellDesigner: a process diagram editor for gene-regulatory and biochemical networks , 2003 .

[8]  Daniel Segrè,et al.  From annotated genomes to metabolic flux models and kinetic parameter fitting. , 2003, Omics : a journal of integrative biology.

[9]  J. Heijnen,et al.  Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics. , 2003, Metabolic engineering.

[10]  D. Endy.  Foundations for engineering biology , 2005, Nature.

[11]  Uri Alon,et al.  Simplicity in biology , 2007, Nature.

[12]  Richard Kitney,et al.  Registry of BioBricks models using CellML , 2007, BMC Systems Biology.

[13]  M. Elowitz,et al.  Reconstruction of genetic circuits , 2005, Nature.

[14]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[15]  A. Ninfa,et al.  Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli , 2003, Cell.

[16]  S. Leibler,et al.  Robustness in simple biochemical networks , 1997, Nature.

[17]  Jacky L. Snoep,et al.  BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems , 2005, Nucleic Acids Res..

[18]  Alfonso Jaramillo,et al.  Genetdes: automatic design of transcriptional networks , 2007, Bioinform..