GNU Octave for the Life Scientist: An Interview with biochemist and author Heino Prinz

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This time we have for you an interview with Heino Prinz, a biochemist and author of the book Numerical Methods for the Life Scientist: Binding and Enzyme Kinetics Calculated with GNU Octave and MATLAB. Heino tells us about himself, how the book came to be and who will benefit from it. Enjoy the interview and check out the book!

F4S: Hi Heino. Please, tell us a little about yourself.

I have studied Physics in Bonn, did my PhD in Biochemistry at a Max-Planck Institute in Göttingen and got my habilitation (In Germany and Austria you need such a licence to teach) at Innsbruck University in the Pharmacology department. I worked most of the time at the Max-Planck-Institute for molecular physiology in Dortmund. It always was somewhat strange, being a physicist working in biochemistry, chemistry and pharmacology. For a physicist, an equation or a reaction scheme is easy, because it is logical and precise. For a chemist, reaction schemes often seem to be incomprehensible and equations may lead to immediate paralysis when used in lectures. In contrast, chemists can perform complex chemical reactions which are admired (not really conceived) by physicists. I have spent most of my scientific life trying to help life scientists to bridge that gap.

F4S: How did you get involved with open source software?

I am 65 years old, and up to 30 years ago we had to write our own programs for almost every application. It was all public domain, but I used to hate FORTRAN, loved Pascal, and was happy when MATLAB with all its packages became available. Then I realized that most biochemists use other programs like Grafit or Origin. These programs can be run with a few mouse-clicks, but they are limited to a few classical analytical solutions. My colleague Alexander Fieroch introduced me to Linux and the wide world of open software. I therefore decided to translate my MATLAB programs to open GNU Octave versions in order to be able to share them with others.

F4S: Tell us the story behind your book Numerical Methods for the Life Scientist: Binding and Enzyme Kinetics Calculated with GNU Octave and MATLAB.

Textbooks on biochemistry employ a rather limited set of explicit equations for the analysis of enzyme or binding kinetics. They are based on more than 100 years old textbooks (e.g. Michaelis L (1912) Einführung in die Mathematik für Biologen und Chemiker. Springer, Berlin) which require profound mathematical knowledge, because at that time computers were not readily available and mathematicians had to resort to analytical solutions. In contrast, numerical methods are simple to understand. They are instructions to computers and can be applied to any biochemical reaction. Powerful personal computers allow us to calculate these in reasonable times, but we face a didactical obstacle: How can one teach mathematical numerical methods to life scientists?

Such a textbook on numerical methods for life scientists has to be useful. It has to show practical applications which can be run by everyone. Since numerical methods require a computer and software, both have to be easy to use and commonly available. The open source software GNU Octave is rather elegant and runs on almost every computer platform. It is compatible to the popular MATLAB©, so that mathematicians trained in MATLAB can run their programs in GNU Octave with only minor modifications. I have included more than 50 sample programs into the book. The sample programs are free so that they can be adapted to any reaction without an infringement of copyright. Even if you do not want to buy the book, you can download them at http://www.mpi-dortmund.mpg.de/misc/numericalmethods/

The open software GNU Octave therefore was essential for the book. The main reason for writing it is explained in a recent paper (Prinz H., J. Chem. Biol. 5, 1-4, 2012):

When experiments are analyzed with simple functions, one gets simple results. A trap springs when experiments show deviations from the expected simplicity and when the scientists involved are not able to follow up on this. I believe that one reason why most screening campaigns were futile, and why the industry lost billions of dollars, was the inability to calculate experimental dose-response curves. If they would have done it, they would have realized that most of their compounds acted as multiple denaturing agents and therefore were not worth developing into drugs. Proper analysis of experimental data may be tedious, but oversimplification can be costly.

F4S: Who will benefit from reading it?

A physicist who wants to understand biochemical analysis, a pharmacologist who wants to understand dose-response curves, and last but not least a biochemist who wants to fit his or her data to molecular models. Apart from this, it may be fun for Octave users to see how this language can be applied to biochemical problems.


F4S: How will you describe your experience writing the book?

It was fun. Actually writing helped me to organize my ideas.

F4S: Do you have plans for other books?

No, but I would be happy to include more application programs to a new edition.

F4S: Why is free/libre open source scientific software important for your field?

Scientific achievements are based on former scientific results. If one wants to contribute to scientific progress, one therefore has to publish. The same applies to computer programs. Only if these programs are open and transparent, future generations can make use of the techniques developed there.

F4S: Which projects, books, blogs or sites related to open source software for science can you recommend?

The GNU Octave Manual is a useful piece of reference.

F4S: Is there any other topic you would like our readers to know about?

First, I would like to encourage the readers to contribute to open source projects. If you write an Octave program for enzyme kinetics, just send it to me after you have published the results. I promise to make it available at our web page:

I have thought a lot about publishing the book myself on-line and making it available free to everyone. On the other hand, I appreciate the effort of Springer Verlag to bring it into an appealing shape, which is not cheap. Springer Verlag made the book available on-line for all those institutions which have a Springer license. So if you work in one of the big scientific institution, you may download the book for free just by using http://www.springerlink.com/content/p73u1n/#section=935531&page=1

F4S: Where people can contact you?

Email: heino.prinz at mpi-dortmund.mpg.de

F4S: Thank you for taking time to do the interview Heino.

Note: If you liked this interview you can Flattr it at the top of the post!

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