Hodgkin-Huxley model in R

One of the great research papers of the 20th century celebrates its 60th anniversary in a few weeks time: A quantitative description of membrane current and its application to conduction and excitation in nerve by Alan Hodgkin and Andrew Huxley. Only a shortly after Andrew Huxley died, 30th May 2012, aged 94.

In 1952 Hodgkin and Huxley published a series of papers, describing the basic processes underlying the nervous mechanisms of control and the communication between nerve cells, for which they received the Nobel prize in physiology and medicine, together with John Eccles in 1963.

Their research was based on electrophysiological experiments carried out in the late 1940s and early 1950 on a giant squid axon to understand how action potentials in neurons are initiated and propagated.

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Dynamical systems in R with simecol

This evening I will talk about Dynamical systems in R with simecol at the LondonR meeting.

Thanks to the work by Thomas Petzoldt, Karsten Rinke, Karline Soetaert and R. Woodrow Setzer it is really straight forward to model and analyse dynamical systems in R with their deSolve and simecol packages.

I will give a brief overview of the functionality using a predator-prey model as an example.

This is of course a repeat of my presentation given at the Köln R user group meeting in March.

For a further example of a dynamical system with simecol see my post about the Hodgkin-Huxley model, which describes the action potential of a giant squid axon.

I shouldn't forget to mention the other talks tonight as well:

• Writing R for Dummies - Andrie De Vries
• News from data.table 1.6, 1.7 and 1.8 - Matthew Dowle
• Converting S Plus Applications into R - Andy Nicholls (postponed to 18 September 2012)
  

For more information about venue and timing see the LondonR web site.

Review: Kölner R Meeting 30 March 2012

The first Kölner R user meeting was great fun. About 20 useRs had turned up to exchange their ideas, questions and experience with R. Three talks about R & Excel, ggplot2 & XeLaTeX and Dynamical systems with R & simecol had kicked off the evening, with Kölsch (beer) losing our tongues further.

Thankfully a lot of people had brought along their laptops, as unfortunately we lacked a cable to connect any of the computers to the installed projector. Never-mind, we cuddled up around the notebooks and switched slides on the speakers sign.

Photos: Günter Faes

Similar to LondonR, it was a very informal event. Maybe slightly forced by myself, as I called everyone by his/her first name, which could be considered rude in Germany. But what I had noticed in London, and the same was true also in Cologne, was that people with a very diverse background and of all ages would meet to discuss matters around R, often not working in the same field. So why worry about hierarchies?

Most attendees were not R experts, but users in its pure sense, trying to solve real life problems, and I suppose that makes those meetings so special. R users are often not programmers by trade, but amateurs, who have a keen interest to extract stories and pictures from their data. And for that reason the discussions are often so engaging. Talking to people using R in social science, psychology, biology, pharma, energy, telcos, finance, insurance or actually statistics opens your mind and eyes. You realise that you are not alone, other people are weird as well. They have similar problems and challenges, but may use a different domain language and look at problems from a different angle. And this can be incredibly refreshing!

Anyhow, we agreed to meet again in about three months time. The pub was a great venue to socialise, yet a bit noisy for the talks. Hopefully we can use a room at the nearby university for the presentations next time. Promises were made already. We shall see. Günter was so kind to set up a mailing list to which you can sign up here. I will continue to use this blog to provide updates on the Cologne R user group in the future and set up a public calendar as well.

Talks

Many thanks to the speakers, who dared to give the first talks and had to improvise on the spot without a projector. Please drop me a line if you would like to speak at one of the next events.

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