Autarchy of the Private Cave

The title of this post is my current – “forthcome”, as in “done” – field of interest.

First article on topic: Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data.

Another one, on combining different high-throughput data sources to get higher-quality results: Uncovering signal transduction networks from high-throughput data by integer linear programming.

I’m especially interested in time-series network reconstruction algorithms. If you have a good advice to share with a newcomer to the networks field – don’t hesitate

With this post, I’m finally announcing the opening of the (mostly) functional COTRASIF web-tool, created for the genome-wide identification of promoter regulatory sequences (transcription factor binding sits, TFBS). You can learn more from the About and Help pages. For an example of use, see the Supplement page (article is currently being prepared; as soon as it’s ready, I’ll make it available).

If you are interested – have a look at the News page, where there is information on joining COTRASIF Google group. For non-public enquiries, please use my contact page.

Note: the problem of identifying eukaryotic transcription factor binding sites stays acute for many years in a row – see e.g. the most recent Eukaryotic transcription factor binding sites – modelling and integrative search methods.

Note, that under Gnome I only had to use a single system-wide utility to bind volume buttons to volume control. Under KDE things were a tad tougher.

First, you may want to look for kmilo (if you don’t have it yet). It has several plugins e.g. for ThinkPad and Vaio laptops, as well as “generic” plugin. I didn’t try this solution, though.

If you need more than kmilo can offer: keyTouch could help. keyTouch should be good also for non-laptop multimedia keyboards. However, this also wasn’t the solution I used.

If you want to know how to map your special keys to functions yourself – then read on.
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Some things to be aware of when enhancing Drupal site with FLV video playing/conversion features.

• Setup wizard for the free JW FLV Media Player (and the JW FLV Media Player itself)
• Flash Video in Drupal 5: A complete multimedia tutorial to the flashvideo module
• actual flashvideo module page on drupal.org

If you had some programming experience – read it here. Otherwise ignore, it’s targeted for a narrow group.

I’m providing regularly updated compiled linux and freebsd ffmpeg binaries, and also described how to use ffmpeg on shared hostings if not all the required libraries (like libmp3lame) are present. However, the solution recommended might not “fit all”, so here is another one – simpler and even more portable/universal than setting LD_LIBRARY_PATH.
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NicEdit – lightweight inline configurable rich-text editor for the web. Can fit where both FCKEditor and TinyMCE are too clunky and monstrous.