September 19, 2008 – 21:54
At last, since it’s been like ages, I decided to put out a new version of DataMatrix. For those who haven’t seen my previous post, DataMatrix is a Pythonic implementation of R’s data.frame. It enables you to manipulate a text file by columns or rows, to your liking, using a dictionary-like syntax.
In this new version there have been a few improvements and correction to a couple bugs (for example saveMatrix did not really save) and the start (only a stub at the moment) of an append function to add more columns (I’ll also think about a function to add rows).
DataMatrix is licensed under the GNU GPL, version 2 only. You can download the installer (Windows) or the source distribution (Linux and other *nixes). The only requirement is Python 2.5 or later installed on your system.
The README currently is a stub, but you can browse the pydoc generated documentation, which details how to instantiate and use DataMatrix objects (or you can turn to my older post).
Also, since git is the new “cool feature of the day”, DataMatrix is is hosted on github’s repository, and you can grab the source with
git clone git://github.com/cswegger/datamatrix.git
Comments and suggestions are welcome. I’ll be putting a static page on DataMatrix tomorrow, if time permits.
For a long time I have tried to handle text files in Python in the same way that R’s data.frame does - that is, direct access to columns and rows of a loaded text file. As I don’t like R at all, I struggled to find a Pythonic equivalent, and since I found none, I decided to eat my own food and write an implementation, which is what you’ll find below.
Read More »
I wanted to write this earier, but I couldn’t: I’m now in a hotel in Maastricht, Netherlands, and waiting to get back tomorrow. I’ve been attending the 4th NuGO hands-on advanced microarray data analysis course and I even wanted to blog about it… but the hotel’s connection did not resolve any non-European web page until late today.
Read More »
I’ve been wondering about why FOSS is often compared to the academic world, but at least in my limited experience, I see little people that grasp its concept in the world of research. On a quick look, developing FOSS in a research environment would be very good: not only you’d get publicly available results when you publish, but at the same time you can make sure that in an extreme case your application will be carried on by someone else should you not be able to continue development.
At least in the life sciences, it’s hard to see such a mentality. I can understand the publish or perish frenzy, but at the same time, don’t we all remember about published and unmantained software? For me, such an idea would be optimal. Once the paper is out, you can release your software (GPL would be best) and make sure someone will improve or mantain in. Of course you won’t be able to publish for each upgrade you do, but I would generally think of that as a bad policy, one made just to increase the publication count.
Does something like that happen with FOSS in other research areas?
