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BioNetCAD: design,
simulation and experimental validation of synthetic
biochemical networks

Author(s):

Rialle, S
(Rialle, Stephanie)
1
;
Felicori, L
(Felicori, Liza)
1
;
Dias
-
Lopes, C
(Dias
-
Lopes, Camila)
1
;
Peres,
S
(Peres, Sabine)
1
;
El Atia, S
(El Atia, Sanaa)
1
;
Thierry, AR
(Thierry, Alain R.)
1
;
Amar, P
(
Amar, Patrick)
2
;
Molina,
F

(Molina, Franck)
1


Source:
BIOINFORMATICS


Volume:

26


Issue:

18


Pages:

2298
-
2304


DOI:

10.1093/bioinformatics/btq409


Published:

SEP 2010

Times

Cited:

4

(from Web of Science)

Cited References:

34

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Citation Map






Abstract:

Motivation: Synthetic biology studies how

to design and construct biological systems with functions that
do not exist in nature. Biochemical networks, although easier to control, have been used less frequently than
genetic

networks as a base to build a synthetic system. To date, no clear
engineer
ing

principles exist to design
such cell
-
free biochemical networks.


Results: We describe a methodology for the construction of synthetic biochemical networks based on three main
steps: design, simulation and experimental validation. We developed BioNetCA
D to help users to go through
these steps. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB,
a
database

of parts for synthetic biology. BioNetCAD enables also simulations with the HSim software and the
classical
Ordinary Differential Equations (ODE). We demonstrate with a case study that BioNetCAD can
rationalize and reduce further experimental validation during the construction of a biochemical network.

Accession Number:

WOS:000281714100048

Document Type:

Article

Language:

English

KeyWords Plus:

ELEMENTARY BRICKS; BUILDING
-
BLOCKS; BIOLOGY; SYSTEMS; REPRESENTATION;
STANDARD

Reprint Address:

Rialle, S (reprint author), SysDiag, UMR 3145, CNRS Biorad, Cap Delta Parc Euromed,1682
Rue Valsiere
,CS 61003, F
-
34184 Montpellier 4, France.

Addresses:


1. SysDiag, UMR 3145, CNRS Biorad, F
-
34184 Montpellier 4, France

2. Univ Paris 11, Rech Informat Lab, CNRS, UMR 8623, F
-
91405 Orsay, France

E
-
mail Address:

stephanie.rialle@sysdiag.cnrs.fr
;
franck.molina@sysdiag.cnrs.fr


ResearcherID Numbers: [
?

]

[ 1 researcher(s) included this record in their ResearcherID My Publication List. Click to view. ]
Molina, Franck


E
-
8419
-
2011

[ View profile at Resear
cherID.com ]


Funding:

Funding Agency

Grant Number

Centre National de la Recherche Scientifique (CNRS)




Languedoc
-
Roussillon region




EU




Conselho Nacional de Desenvolvimento Cientifico e Tecnologico, Brazil (CNPq)




Institut National de la
Sante Et de la Recherche Medicale (INSERM)





[Show funding text]





Publisher:

OXFORD UNIV PRESS, GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND

Web of Science Categories:

Biochemical Research Methods; Biotechnology & Applied Microbiology; Computer
Science, Interdisciplinary Applications; Mathematica
l & Computational Biology; Statistics & Probability

Research Areas:

Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Computer Science;
Mathematical & Computational Biology; Mathematics

IDS Number:

648SK

ISSN:

1367
-
4803