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Asmparts: assembly of biological model parts.

Rodrigo G, Carrera J, Jaramillo A - Syst Synth Biol (2008)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: IBMCP, CSIC-UPV, Camino de Vera s/n, 46022, Valencia, Spain.

ABSTRACT
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.

No MeSH data available.


Diagram showing how to build a synthetic network by assembling different model parts from a library
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Fig1: Diagram showing how to build a synthetic network by assembling different model parts from a library

Mentions: We consider that a promoter has as inputs its regulating transcription factors and also POPS (e.g., from a TT or from another promoter), and as output POPS and mRNA. With the variable POPS we can calculate the mRNA dynamics. We do not consider RNA-polymerase as an input for a promoter because we assume that its amount in the medium is enough for transcription and it does not affect in the dynamics of the network. In fact, we consider that the amount of cellular resources, such as RNAPs, ribosomes, nucleotides or amino-acids, is sufficient to sustain a foreign system. Thus, RIPS only depends on the amount of mRNA. For the RBS we consider as input POPS and mRNA, and as output POPS and RIPS. The CDS has as input POPS and RIPS, and as output POPS and protein. Finally, the TT has POPS as input and output (see Fig. 1). This choice allows generating arbitrary complex transcriptional circuits using models for promoters and TF from the registry of parts.Fig. 1


Asmparts: assembly of biological model parts.

Rodrigo G, Carrera J, Jaramillo A - Syst Synth Biol (2008)

Diagram showing how to build a synthetic network by assembling different model parts from a library
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2553328&req=5

Fig1: Diagram showing how to build a synthetic network by assembling different model parts from a library
Mentions: We consider that a promoter has as inputs its regulating transcription factors and also POPS (e.g., from a TT or from another promoter), and as output POPS and mRNA. With the variable POPS we can calculate the mRNA dynamics. We do not consider RNA-polymerase as an input for a promoter because we assume that its amount in the medium is enough for transcription and it does not affect in the dynamics of the network. In fact, we consider that the amount of cellular resources, such as RNAPs, ribosomes, nucleotides or amino-acids, is sufficient to sustain a foreign system. Thus, RIPS only depends on the amount of mRNA. For the RBS we consider as input POPS and mRNA, and as output POPS and RIPS. The CDS has as input POPS and RIPS, and as output POPS and protein. Finally, the TT has POPS as input and output (see Fig. 1). This choice allows generating arbitrary complex transcriptional circuits using models for promoters and TF from the registry of parts.Fig. 1

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: IBMCP, CSIC-UPV, Camino de Vera s/n, 46022, Valencia, Spain.

ABSTRACT
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.

No MeSH data available.