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Tweaking Ubuntu fo the Lenovo Flexpad

I don't like to get new equipment if I have old equipment that still works fine. My Asus A2500S laptop is now more than 10 years old, and although it has received a few small repairs and a memory upgrade over the years, it still works fine. Its Pentium 4 Mobile processor may be a power hog, but it's not slow. Its main bottleneck is memory. The full Ubuntu is getting a bit too heavy for the old guy, but Xubuntu still runs like a charm. On the other hand, at over 5 kg (including power-supply) the thing is HEAVY.

Fixing video drivers in Linux

One of the drawbacks of a monolithic kernel is that you're often stuck with outdated drivers that don't work for your hardware. Even if a fix is available upstream, there's no easy way to update just a single driver. Luckily, LinuxTV now at least offers a script to automatically recompile the entire Video4Linux subsystem against your current kernel version, and replace the default modules with the latest versions: http://git.linuxtv.org/media_build.git

Useful tricks with spatial data

For my research on Avian Influenza in waterbirds, I recently needed data on lakes and marsh-areas in Europe. I ended up compiling a spatial dataset from a number of different sources, including the EU Corine Land Cover database (CLC2000v13), the lake depth dataset compiled by Ekaterina Kourzeneva for the FLake model and data from the Finnish national lake register.

On Filesystems

Filesystem types and (lack of) compatibility

Fun With Shapefiles

Shapefiles are a format developed by ESRI (the makers of ArcGIS) to store and share geospatial data. Many interesting datasets are freely available in shapefile format. Shapefiles can be viewed with a number of freely available applications, such as ArcGIS Explorer (which requires the .NET framework or Silverlight) or ArcReader (which is multi-platform but closed-source).

Faxing in Ubuntu

It seems hard to believe, but fax-machines have been around for over a century, and the current digital fax technology stems from the 1980s. Back in the days, for most people faxing a document was the only fast alternative to sending it by normal (as in non-electronic) mail. These days, as multi-function printers and copiers with scanning-capability are becoming more widespread, fax-machines are slowly obsoleted by the ability to easily scan documents as PDF and send them over e-mail. Nonetheless, every now and then someone asks me if I can send or receive something by fax.

Useful graphics software

Here is a list of some graphics software I find useful:

Raster graphics

The GIMP A cross-platform photo and image editor
Phatch A cross-platform photo batch processor
IrfanView An excellent image viewer and batch processor for Windows (which runs fine under Wine as well)

Vector graphics

Inkscape A cross-platform vector graphics editor, which is easy to use

Scientific Software Favourites

Here's a little list of software I regularly use for science-related work.

Zotero

PDL, The Perl Data Language

PDL is an extension of Perl for numeric/scientific data processing. It was originally developed by astrophysicists as a free alternative to packages like IDL and Matlab. It's quite fast and memory-efficient, and very powerful. I've found it to be most useful in cases where you have to mix data-processing with the strengths of Perl (anything involving list & hash-operations, regular expressions and/or text-parsing or output). Its main drawback however is that it has a rather steep learning-curve, because the documentation is quite fragmented and not always clear.

Data Clustering

I've written a fast perl/PDL implementation of UPGMA data clustering for very large datasets. The problem is that existing clustering packages have difficulty handling datasets with more than a few thousand data points. Especially the distance matrices tend to become a problem. For example, clustering the outcome of a 300x300 grid-based simulation (90,000 data points) would require a (non-sparse) distance matrix of 8.1 billion entries. This would use over 30 Gb of memory when stored as 4-byte floating point values.

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