Software

Stochastic simulation of a synthetic gene circuit with quorum sensing and feedback

Efficient stochastic simulation of gene synthetic circuits using langevin, an OpenFPM client in C++. The code can be dowloaded here

Information about OpenFPM installation can be found in its webpage http://openfpm.mpi-cbg.de/.
More information about the software is available in:

Engineered control of genetic variability reveals interplay between quorum sensing, feedback regulation and biochemical noise
Yadira Boada, Alejandro Vignoni, and Jesus Pico
ACS Synthetic Biology, 2017, 6(10) pp.1903-1912.
DOI: 10.1021/acssynbio.7b00087

In order to ensure financial support for our project and allow further development of this software, please cite above publications in all your documents and manuscripts that made use of this software. Thanks a lot!

sPMODE_SynBio Toolbox: a MATLAB tool for Wet-lab friendly Tuning of Synthetic Biological Circuits

A MATLAB implementation of the spMODE_SynBio for tuning synthetic biology circuits, together with the Incoherent feed-forward loop example, can be dowloaded here. The original spMODE code was written by Gilberto Reynoso-Meza, and modified by Yadira Boada and Alejandro Vignoni for the following article:

Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case
Yadira Boada, Gilberto Reynoso-Meza, Jesús Picó, and Alejandro Vignoni.
BMC Systems Biology, 2016, 10, 27
DOI: 10.1186/s12918-016-0269-0

In order to ensure financial support for our project and allow further development of this software, please cite above publications in all your documents and manuscripts that made use of this software. Thanks a lot!

PFA Toolbox: a MATLAB tool for Metabolic Flux Analysis 

The PFA Toolbox for MATLAB provides a set of MATLAB functions to apply Interval MFA and Possibilistic MFA in a simple and flexible way. These MFA-wise methods are particularly well suited to deal with scenarios of high uncertainty and scarce measurements, which are common in research laboratories and industry. The PFA Toolbox includes a Graphical User Interface (GUI) to represent the flux measurements in possibilistic terms

You can get the toolbox at: https://github.com/kikollan/PFA-Toolbox/

The toolbox uses YALMIP as optimizer. This can be freely obtained at http://users.isy.liu.se/johanl/yalmip/ .

More information about the toolbox is available in:

PFA toolbox: a MATLAB tool for Metabolic Flux Analysis
Y. Morales, G. Bosque, J. Vehí, J. Picó and F. Llaneras..
BMC Systems Biology, 2016, 10, 46
DOI: 10.1186/s12918-016-0284-1

In order to ensure financial support for our project and allow further development of this software, please cite above publications in all your documents and manuscripts that made use of this software. Thanks a lot!

 

DISCLAIMER

IN NO EVENT SHALL THE SB2CL GROUP BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE SB2CL GROUP HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. THE SB2CL GROUP SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE SB2CL GROUP HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.