Christoph Champ

27April2012

Random CLI tips and tricks

Posted by Christoph under: Code.

This is just a random collection of #Linux #CLI commands:

See also:

• My GitHub page
• commandlinefu.com
• @climagic

21April2012

Gist

Posted by Christoph under: Code.

Testing my new Gist plugin:

See: My GitHub page.

20April2012

Better Colour Scales

Posted by Christoph under: HOWTOS.

I have been using a certain technique to bring out the differences in my data when plotting them for a long time and thought it would be useful for others if I explained the technique:

In all the colour scales, average values are represented as a light grey, while larger and smaller values are shown in progressively higher intensity colours the farther they are from average. For most scales, the values that are more than plus or minus three standard deviations from average are shown as very dark (almost black) lines.

Here is an example colour scale (as used on the GenomeAtlas, where I used to work):

#colour, #color, #plotting

20April2012

axel

Posted by Christoph under: Linux.

In this article, I discuss axel; a command line tool similar to wget. The difference is that it is both an accelerator and it splits the file into multiple pieces.

Axel accomplishes its speed performance by opening more than one connection at a time, effectively multiplying allowable bandwidth.

20April2012

agrep

Posted by Christoph under: Linux.

In this article, I discuss agrep (approximate grep); a “fuzzy string searching” program or command line tool for use with the Linux operating system.

agrep selects the best-suited algorithm for the current query from a variety of the known fastest (built-in) string searching algorithms, including a bitap algorithm based on Levenshtein distances.

agrep is also the search engine in the indexer program GLIMPSE. It is free for private and non-commercial use only, and belongs to the University of Arizona.

23January2009

Bioinformatics wiki

Posted by Christoph under: Bioinformatics.

I have put together a collection of articles relating to Bioinformatics on my wiki. These articles cover techniques, tools, tutorials, etc. relating to many different areas of Bioinformatics.

See: Category:Bioinformatics.