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The aim of this tutorial is to provide people working in the biosciences with little to no background in programming an accessible and short tutorial on MATLAB basics for common bioscience workflows. It was developed for some courses here at the EMBL and includes exercises …

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Exercise 1

% there are several ways for creating these arrays
% 1 - squared brackets
A = [1 3 5; 3 6 3; 9 8 5]
% 2 - functions for array creation
A = rand(3)
A = magic(3) 

b = [3; 4: 8] % 3 x 1 - column vector!

A * b(1)
A …

Part i covered the preparations for installing software development and scientific computing tools: Editors, the Terminal, Mac OS X Package Managers and some bash basics. In part ii we will dive into setting up a Python environment and all tools necessary for blogging and scientific computing. Part iii will decribe …

Here at EMBL, many people use a Mac for their work. If you want to use your machine for scientific computing and/or software development, a number of tunings will make your scientific life with the Mac much more enjoyable. This post will demonstrate one way, my way, of setting …

The SimBiology Desktop offers a number of different plot types that can be chosen in a task window. The default plot type in a simulation task, for example, is the Time plot, which plots states against the simulation time:

Three items need to be configured for this plot type:

• tobj …

In the first part I presented a workflow to export a SimBiology model as well as data to the workspace from the SimBiology Desktop, speed up its simulation and prepare it for parallel computation. Here I will set up the actual optimization problem.
The Optimization solvers usually only accept a …

Under some circumstances the parameter estimation tasks built into SimBiology® (sbioparamestim and sbionlinfit) and the SimBiology Desktop (sbionlinfit) are not robust enough for the given data, the model or the initial parameter values.

If the objective function has many local minima - which is nearly always the case for complex systems …