1. Streamlining the Dissemination of Standardised
Biological Parts -
Programmatic Access to SynBIS Environment
Gan Chong Yee, Prof Richard Kitney
3. SBML Generation
2. Datasheet Generation & Web Services
4. Results A - Datasheet Generation & Web Services
7. References
Figure 2: 2nd page of the generated datasheet of a biological part with an ID of 1; different IDs can be
called by the user to obtain the corresponding datasheets. Original results from SynBIS (right).
5. Results B - SBML Generation & Simulation
The SBML file generated via the
Matlab script, synbis.m was run
on a synthetic biology Computer
Aided Design (CAD) tool. The
results correlate to those
obtained on SynBIS
appropriately.
The web service could be called to generate the datasheet shown on the left side of
Figure 2 via the folowing URL:
http://loaclhost:13614/HelloWorldApplication/rest/myservice/1/file/datasheet
A PDF file of a SynBIS biological part with an ID 1 will be saved on the user’s computer
locally; the file name will be “datasheet.pdf”, as specified by the URL.
Figure 3: Simulation results of the generated
SBML file.
Figure 4: Original results obtained on
SynBIS
As a medium for information exchange, biological part datasheets [2] should
be produced using SynBIS to distribute these data efficiently. Thus, a Java
application and web service was created to automatically generate the
datasheet in human readable format, such as PDF. This is important as:
● accessibility to SynBIS and overall user experience is enhanced, as
characterisation data can be easily obtained via the user’s online
browser (as seen in Results A).
● the datasheet will be automatically updated whenever changes are
made at different points of the characterisation workflow (Figure 1), thus
reducing human error and friction from lab data acquisition to datasheet
generation.
Beyond creating human readable formats, a huge factor in the dissemination
of biological parts lies in its integration with prevalent software tools. By
encouraging its usage in existing modelling tools, the SynBIS data and
results can be constantly refined via direct user feedback.
Thus, an SBML file was also generated, as it functions as a lingua franca for
various synthetic biology modelling tools [3]. The file was created using
Matlab, as it remains as one of the most widely used applications for
commercial and educational purposes [4].
6. Extension to Cell Free Systems
Due to the modular nature of the
datasheet generating software, the
template displays sufficient flexibility to
accommodate new protocol features.
This function is especially crucial in
response to the rapidly changing needs
of synthetic biology, in terms of
characterisation criteria, experimental
protocols and measurement methods
[2].
The figures on the left exhibits a
sample datasheet for another
experimental study carried out Ms.
Deze Kong, a colleague in CSynBI [5].
These results correlate to the cell - free
characterisation of the J23101
biological part, as opposed to the in
vivo studies performed for Box 4.
1. Introduction
Synthetic biology aims to employ engineering methods towards the understanding and
design of biological systems. Such approach necessitates a better understanding of each
fundamental component (biological parts) that make up a larger biological product.
However, the unpredictable nature of biology [1], calls for standardised methods of
characterising biological parts to better predict, measure and reproduce these biological
functions.
Figure 1: Workflow of biological part characterisation done in CSynBI.
Thus, the Centre for Synthetic Biology and Innovation (CSynBI) has employed
standardised experimental protocols, metrics and analyses to characterise these parts via
adequate robotic platforms. The corresponding results and biological part parameters
were then uploaded to SynBIS, a new generation part repository for high quality
characterisation data compatible with DICOM, SBOL and SBML. The publicly accessible
raw data files enable similar experiments to be carried out by other labs to further refine
the characterisation data in SynBIS via collaboration and feedback within the community.
This project aims to optimise the dissemination of SynBIS data (blue arrow) directly to
researchers and designers, to encourage collaboration within the synthetic biology
community towards characterisation efforts.
[1] Csete, M. E., & Doyle, J. C. (2002). Reverse engineering of biological complexity. science,
295(5560), 1664-1669.
[2] Wolf, D.M. & Arkin, A.P. Curr. Opin. Microbiol. 6, 125–134 (2003).
[3] Keating, S. M., & Le Novere, N. (2013). Supporting SBML as a model exchange format in
software applications. In In Silico Systems Biology (pp. 201-225). Humana Press.
[4] Sharma, N., & Gobbert, M. K. (2010). A comparative evaluation of Matlab, Octave, FreeMat,
and Scilab for research and teaching. Department of Mathematics and Statistics.
[5] Kong, Deze (2015). In vitro characterisation of constitutive promoters in E. coli extract
through a combination of modelling and experimental approaches