Glasgow/Modeling

Minicap Sensitivity Analysis Program Package

The Multi-Parametric and Initial Concentration Sensitivity analysis (Minicap) package is a Matlab function which executes a chosen Dynamic or Stochastic System Function for a defined number of different variable values across any desired range. The subject of analysis can either be constants in the user's system eg. parameters in a biological system (MPSA) or initial values of the variables in the user's system eg. initial substrate concentrations (ISCSA). The program will output a plot for each variable showing a comparison of acceptable and unacceptable samples across the subject's range with 3 calculated quantitative comparison figures: the Correlation Coefficient, the Area between acceptable and unacceptable curves, and the Standard Deviation of the gradient of the acceptable plot. The comparative and intrinsic sensitivity of each chosen subject is thus highlighted. A plot showing the trend of the Substrate of Interest over time is also displayed.

As well as this report, the Minicap package contains a User Manual in html, a number of example codes and all the novel (i.e. not ode15s) function and text files required to run Minicap.

To see the full PDF report on Minicap [click here].

BioBrick library

[http://compbio.dcs.gla.ac.uk/iGEM2007/BioBricklibrary.zip BioBrickLibrary.zip] An add on Library to Simulink for modelling dynamical biological systems at Brick (Gene) level. Simulink is a program dedicated for dynamical system simulation, however in depth knowledge of dynamics is needed if one is to simulate system mentioned above. The BioBrick® library has all the blocks as well as GUI (Graphical User Interface) needed to do the job without understanding how Simulink works. It uses drag and drop system and shares all constants in Matlab’s .m file, so it is easy to store and update them.

BioBrick® library’s main aim is to tell whether and how different topology will influence the output of the system. If actual rate constants are known it can be used instead or as complimentary to ODE modelling. However it must be noted that ODE rate constants ARE NOT TRANSFERABLE to BioBrick® library.

More information can be found in ElectrEcoBluSimulinkManual document.

Microbial Fuel Cell Evaluation

During the course of the project some introductory work has been done with microbial fuel cells in order to prepare us for the envisaged final stage of the project. We have had three fuel cells at our disposition supplied by the UK's NCBE. The experience we have gained and some of the results have been aggregated in this short work.