Biology Reference
In-Depth Information
either edit or use information that has already been added for biological constructs. This
information can subsequently be used by the SynBioSS Desktop Simulator (SynBioSS DS)
to simulate the behavior of synthetic systems of interest . A more detailed description of
SynBioSS Wiki can be found at http://synbioss.sourceforge.net/wp-content/uploads/
supplement.pdf .
SynBioSS Designer constitutes the second component of SynBioSS, and is the means for
automatically producing a reaction network that captures the interplay between different
molecular components of a biosystem, or among different biosystems. 54,55 These molecular
components include promoters, operators, repressors, and effector molecules. SynBioSS
Designer carries information about these molecular components and is linked to the
database of BioBrick Standard Biological Parts. In short,
are open source
molecular biology elements (promoter components, genes, terminators, proteins, etc.) that
have been functionally well-characterized and can be used to design and build synthetic
biological constructs. 62,63 Once the user has defined the molecular elements from the
BioBricks database to use in building their system of interest, SynBioSS Designer
implements the available information to produce a reaction network describing the
molecular interactions associated with these elements.
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BioBricks
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With SynBioSS Wiki and Designer, synthetic biologists can now efficiently develop a model
describing a synthetic construct by just inputting to SynBioSS Designer the desired
molecular parts participating in this construct
s output is then
a reaction cascade describing the behavior of the synthetic system. The output can be saved
in a Systems Biology Markup Language (SBML) format, making the simulation of the
network accessible using a software package. Users can then simply load the model into the
SynBioSS DS to calculate the evolution of the system
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s function. SynBioSS Designer
'
s behavior as outlined below. Thus,
this software suite greatly simplifies modeling synthetic biological systems.
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131
Even though the SynBioSS Designer package has rendered the development of synthetic
biology models quite trivial, it currently still has the following limitations: 55
1. Numerous molecular parts are not well-defined, and therefore there are no kinetic para-
meters associated with them. In this case, SynBioSS Designer uses default values increas-
ing the assumptions underlying the model which, in turn, decreases its accuracy.
2. The SynBioSS Designer modeling approach is focused on biology
s central dogma
neglecting other mechanisms, such as antisense regulation, transcriptional inhibition,
and RNA silencing, that may be important for the simulated phenotype. The results
could therefore be inaccurate in cases where these mechanisms significantly influence the
behavior of the system.
3. The desired molecular parts required for constructing the synthetic system may not be
available in the BioBricks database. In this case, SynBioSS Designer cannot produce a
reaction network, as it currently only retrieves information from this database.
(More details about the SynBioSS Designer can be found in reference. 55 )
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As mentioned previously, the third component of SynBioSS, SynBioSS DS, simulates the
behavior of the biological systems of interest. Unlike other software packages, SynBioSS
DS accounts for the stochasticity which is omnipresent in gene expression. 64 66 It
possesses a windows graphical user interface (GUI) where the user can provide all of the
biochemical reactions and the conditions describing the synthetic system of interest.
The conditions of the system include the cell volume, time interval between the saved
points, the mean cell division time, and other fundamental information associated
with the model. The algorithm behind the GUI then implements a fusion of a
stochastic-discrete and stochastic-continuous approach 67 to calculate the evolution of
each species participating in the synthetic system. Subsequently, the results are stored in
an. nc or .xls format so that the user can process them.
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