1. Dash (Zeal) and Julia

   Mo 21 Oktober 2013

   Dash is a brilliant Documentation App for Mac OS X, Julia is a promising new language for technical computing. What's better than getting the Julia documentation, which up to now has mostly lived on the web, into Dash, so that those long train rides through the countryside can be spent …

2. MATLAB in the Biosciences - a Tutorial

   Fr 11 Oktober 2013

   Download as pdf or epub

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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 …

3. MATLAB in the Biosciences - Solutions

   Do 10 Oktober 2013

   Download as pdf

   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 …

4. Julia for MATLAB users III

   Do 19 September 2013

   Previous articles explored julia and its plotting facilities in the Winston package. The workflow used there, (i) data import, (ii) plotting and (iii) graphics export, will be used in this article as well, however, this time using Dataframes and Gadfly in julia and dataset arrays in MATLAB.

   Dataset arrays are …

5. Julia for MATLAB users II

   So 25 August 2013

   In the last posts I installed julia, some graphics packages and some dependencies on a Mac and compared one way of plotting in julia - using Winston and plotting several datasets into one plot - with the typical approach in MATLAB. This post will show how to plot each individual dataset into …

6. Julia for MATLAB users I

   Do 22 August 2013

   A number of excellent free open-source alternatives to MATLAB have arrived in the last couple of years that have managed to bite away parts of MATLAB's market share. Most notable are R, which is now the dominant language for statistical computing and bioinformatics and Python (with numpy, scipy etc.) which …

7. Installing julia for data visualization stuff

   Di 20 August 2013

   Julia is a relatively novel language intended for technical computing, basically a direct contender of MATLAB/Octave, Python/scipy/numpy or R. The crucial difference between Julia and the other languages is its powerful JIT compiler, which is responsible for some impressive benchmark results. I'm exploring Julia as a replacement …

8. Setting up a Mac for Scientific Computing and Software Development II

   Mi 10 Juli 2013

   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 …

9. Setting up a Mac for Scientific Computing and Software Development I

   Di 09 Juli 2013

   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 …

10. Creating “real” subplots in SimBiology using the Plot Type Library

    Mi 27 Februar 2013

    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 …

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