Systems Biology ORIGINAL PAPER
Standard Virtual Biological Parts: A Repository of Modular Model-
ing Components for Synthetic Biology
M. T. Cooling1,*,V. Rouilly3, G. Misirli2, J. Lawson1, T. Yu1, J. Hallinan2 and A. Wipat2
1Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
2School of Computing Science, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
3Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
Motivation: Fabrication of synthetic biological systems is greatly
enhanced by incorporating engineering design principles and tech-
niques such as computer-aided design. To this end, the ongoing
standardization of biological parts presents an opportunity to de-
velop libraries of standard virtual parts in the form of mathematical
models that can be combined to inform system design.
Results: We present an online Repository, populated with a collec-
tion of standardized models that can readily be recombined to model
different biological systems using the inherent modularity support of
the CellML 1.1 model exchange format. The applicability of this ap-
proach is demonstrated by modeling gold-medal winning iGEM ma-
Availability and Implementation: The Repository is available on-
line as part of http://models.cellml.org. We hope to stimulate the
worldwide community to reuse and extend the models therein, and
contribute to the Repository of Standard Virtual Parts thus founded.
Supplementary Information: Systems Model architecture informa-
tion for the Systems Model described here, along with an additional
example and a tutorial, is also available as Supplementary Informa-
The example Systems Model from this manuscript can be found at
The Template models used in the example can be found at
Since the discovery of recombinant DNA technology, scientists
have manipulated living organisms in order to produce biofuels,
drugs, or other biomaterials. Over the years, a biotechnology in-
dustry has emerged exploiting this technology and delivered a
number of successes [Carlson, 2007]. However, in most cases, the
development of biotechnology applications has been the product of
a manually-driven, trial-and-error-based approach.
In order to achieve efficient and reliable biological system fabrica-
tion, synthetic biology promotes the application of engineering
*To whom correspondence should be addressed.
principles such as abstraction, standardization, and characterization
to biology [Endy, 2005]. These concepts have proven to be crucial
in other engineering disciplines in order to mature from ‘dedicated
craftsmanship’ to successful industrial solutions. Arguably, to date
in synthetic biology, the best example of such an approach is the
Registry of Standard Biological Parts (SBPs) [Peccoud et al.
2008]. The Registry (http://www.partsregistry.org) provides a col-
lection of standard DNA parts (BioBricks) [Knight, 2005] that
have been designed to facilitate DNA assembly. Through the
iGEM (International Genetically
http://www.igem.org) competition, the use of the Registry has
clearly demonstrated the power of standardization in biology to
stimulate innovation and creativity [Goodman, 2008].
A critical lesson learnt from other engineering disciplines is that
mathematical modeling can dramatically increase the speed of the
design process as well as reducing the cost of development. A
‘Holy Grail’ in biological modeling would be to design reliable
and robust biological systems in silico prior to fabrication, just as
aeronautic engineers design planes using their computer aided
design (CAD) tools.
CAD tools are already being developed in order to ease the process
of designing synthetic biological systems [Goler et al., 2008].
However, they currently lack access to modular and reusable ma-
thematical models. Accurate models of SBPs are required for the
prediction of system function, but it is also crucial that mecha-
nisms to easily compose part models into complete systems are
available. Therefore, in parallel to increasing the number of parts
available and characterizing them experimentally, a logical exten-
sion to the Registry would be to build a repository of modular
models of SBPs to complement the physical part Registry [Rouilly
et al., 2007].
Here we describe the development of an online repository of Stan-
dard Virtual Biological Parts (SVPs) – mathematical model com-
ponents describing the function of SBPs which can be downloaded,
extended and recombined to aid the design, in silico, of synthetic
Repositories of models are already available, such as the BioMod-
els database [LeNovere et al., 2006]. However, the curated models
in this database are monolithic and do not allow further composi-
tion without some modification. Previous work has already ex-
© The Author (2010). Published by Oxford University Press. All rights reserved. For Permissions, please email: firstname.lastname@example.org
Associate Editor: Prof. Alfonso Valencia
Bioinformatics Advance Access published February 16, 2010
by guest on September 13, 2015
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