Neural Ensemble

The Neuralensemble project brings together several efforts to make simulations of neurons easier. Currently, I spend most of my time working with the tools they created. Since a few days I have an account on their TRAC server, so I thought this is a good time to blog about it.

The project which got me into neuralensemble is PyNN , which provides a unified front end to several widely used neural simulators, e.g. NEURON, NEST and PCSIM. PyNN greatly facilitates setting up neural networks, because it provides an abstraction from simulator-specific languages. As the name suggests, it's written in Python, and lets you specify the network in Python, too.

For experiment design and analysis of simulated data there is Neurotools. It's written for PyNN (in Python), but can also be used independently from it. One of the most promising design goals is its ability to control large experiment sets, e.g. to systematically investigate the impact of certain parameters on network function. I'm sure every scientist who does computational modeling has written code to deal with this tasks at least once. Having a common API for this is a great thing.

Neuralensemble is a dynamic community which is still very open to all sorts of contributions. So if you're into modeling of neural networks, you should definitely give it a shot!

Python IDE revisited

Today Komodo edit got released under various open source licenses. Since I'm still looking for a decent Python IDE I could not wait to try it.

My very first impression is a very good one! It looks like Eclipse, but I can live with that... especially because it lets me use Emacs keybindings. Killer feature :). Beyond that, code completion seems to do a good job in Komodo Edit, something I never got around to set up in emacs.

Of course, I still need to check out things like code navigation, refactoring and other IDE goodies... soon to be reported here!

Two machines, one keyboard

Daily computer work can be quite annoying when you have to work on two machines simultaneously. If those two machines are connected through the network, synergy was my method of choice to solve this problem. It's like having a dual-screen setup, your mouse can move between both screens. The difference is that each monitor is a separate machine. Keystrokes from one machine go the window that has focus, irrespective to which the keyboard is hooked up. I liked that tool a lot, but in practice I found it too cumbersome in the long run.

Now I came across this blog post, which advertises Mango Lassi as a better synergy. It even has packages for OpenSuse, via the Buildservice. Sounds promising, have to check it out when I find time.

Yet another python primer

Another python tutorial, this time specially for life science researchers. Published back in November last year, but it took me until today to run across it. It seems to be focused towards bioinformatics, at least from what I can tell by quickly going through it. Might be useful for students entering the field, not knowing which lagnuage to learn.

Citation: Bassi S (2007) A Primer on Python for Life Science Researchers. PLoS Comput Biol 3(11): e199

Python + Emacs, cont.

I came across this blog post which states some very interesting additional resources for python development in emacs. Very cool!

The quest for a Python IDE - Back to good old emacs

Since I started using Python last year, I've been looking for a nice IDE that supports that language. When I was programming in Java, Netbeans made programming REAL fun. I was really missing such a powerful tool for Python.
Not that I haven't tried a few. First, there is jpydbg for netbeans. Or at least it seems to be, since I never managed to start a project with it. It has been written for jedit, and it does not really integrate into netbeans' look and feel, let alone it's usabilit concept.
Then there was Eric. It made a good impression, but unfortunately, it stopped working on my machine for some obscure error relating to QT4 libs not being found. This ain't Eric's fault, other Qt4 also won't work under my account.... I have no clue which config file causes confusion here. But still, I can't use it.
So I went on to Eclipse. As an e- netbeans user, I was quite reluctant to take that step, somehow it felt to me like switching from Linux to Windows again ;)... Nevertheless, I've been using it for about half a year now, but still haven't got comfortable with it. I'm sure it offers every tool a programmer might probably want at some point in his life, but I just haven't managed finding out how to open the toolbox... I couldn't even manage to update an SVN repo from the IDE! Don't get me wrong, I'm sure there is an easy way how to do this, but I just couldn't figure it out. And I don't want to spend my time digging through docs and forums and mailing lists when I really want to spend it programming. Especially if the solution to my problem is only an "svn update" away... on the command line.
And this was the point when I remembered my good old friend emacs. Long time back, when desktop envirenments under Unix still needed their diapers changed regularly, I used emacs for all programming related tasks. And how I liked it. And of course, today it comes with a python mode, with syntax highlighting and all bells and whistles. Who needs more?
Well, actually I need more... :) I want version control, refactoring tools, auto completion and quick navigation through large source trees. And naturally, emacs seems to offer it all. There's psvn.el for SVN. Navigation has always been the domain of Speedbar (M-x speedbar). For refactoring, there seems to be BicycleRepairMan. Haven't used it yet, but voices all over the web praise it. And finally, for auto-completion Pymacs claims to do the job. This will be the next thing to try for me.
So for now, I'm happy again with emacs!

Parallel computing made easy

Yo, back I am.... Just discovered how easy parallel computing is nowadays. Excuses for lazy programmers get sparse! :)

I stumbled upon Ipython 1, an ingenious solution to do parallel computing with python. The developers have set up a nice tutorial which got me started in no time. Check it out!

Further, I found a nice tutorial on the MPI Api. Very well written, with clear and concise language.

So, armed with those, I'm looking forward to make our shiny new 8-core Xeon crunch numbers in parallel. :)