Autarchy of the Private Cave

Source: George from vbulletin team.

Two most common reasons (and fixes) for the MySQL server has gone away (error 2006) are:

1. Server timed out and closed the connection. How to fix: check that wait_timeout variable in your mysqld’s my.cnf configuration file is large enough. On Debian: sudo nano /etc/mysql/my.cnf, set wait_timeout = 600 seconds (you can tweak/decrease this value when error 2006 is gone), then sudo /etc/init.d/mysql restart. I didn’t check, but the maximal value for wait_timeout might be around 28800 seconds (8 hours).
2. Server dropped an incorrect or too large packet. If mysqld gets a packet that is too large or incorrect, it assumes that something has gone wrong with the client and closes the connection. You can increase the maximal packet size limit by increasing the value of max_allowed_packet in my.cnf file. On Debian: sudo nano /etc/mysql/my.cnf, set max_allowed_packet = 64M (you can tweak/decrease this value when error 2006 is gone), then sudo /etc/init.d/mysql restart.

If you get MySQL server has gone away (error 2006) when using MySQL ODBC driver – give this hint a try.

If you were a frequent user of GNF SymAtlas, then you’d better bookmark BioGPS – Your Gene Portal System. BioGPS is basically the same gene expression atlas, but with a completely different interface, and more flexible ideology (e.g. expression atlas is now just a “plugin”, and more of those can be plugged in).

There are also some easter-egg-like features: try hovering the BioGPS logo in the top left corner several times…

Joel Spolsky has an interesting (and useful) post on evidence-based scheduling, as he calls that approach. The post discusses an approach to estimate project volume and key dates (such as milestones and release) based on prior performance of each of the project developers. As Joel argues, this approach provides several benefits, and – among others – allows releasing the software product on the date planned.

I would recommend learning more about “evidence-based scheduling” to anybody who is somehow involved into software development.

Also, for me personally it was useful to read the preceding article by Joel (called painless software schedules), which summarizes some basic ideas you should keep in mind while trying to develop some piece of software (mostly from the manager’s viewpoint). If you are going to read that “obsolete” article – better do so before reading evidence-based scheduling.

This in itself wouldn’t be so exciting, if it were not for the new webcode! If you do visit Ensembl now, you will be definitely surprised with the page loading speed – it is amazingly faster than it used to be! Also, as you dig deeper and deeper, you’ll see that there are a lot more other differences – starting with the new design, and not forgetting the changed page organization logic.

To cut the long story short, here’s the list of changes in the new Ensembl 51 webcode release. Other changes to Ensembl in release 51 are also available.

One of the new features which caught my attention is the ability to add custom tracks in Ensembl (which is a long-available feature in UCSC Genome Browser). Interestingly, you do not even have to be logged in to use this feature. We shall be considering providing the TFBS custom track for several species, as predicted de-novo by our evolutionary conserved tfbs search tool (binding site finder), but this is a long shot, given the already published COTRASIF development roadmap.

There is one more great news which is kinda insufficiently highlighted: the brand-new Ensembl Genome Browser website, which (as planned, it hasn’t yet started operations) will provide access not only to vertebrates, but also to other taxonomy groups. The full list is:

• Metazoa
• Protists
• Bacteria
• Plants
• Fungi

Excellent play of Hugh Laurie (Doctor House), terminology-enriched plots, and the style of “medical detective story” – all add up to an excellent viewing pleasure.

If you enjoyed Jeeves and Wooster – be sure to check House M.D.. It is completely different, but Hugh Laurie really excels in both.

Highly recommended!

There are several ways to do that, I’ll describe the one which worked for me. Please note, that printing from CLI has an advantage of being able to print out something at work from the comfort of your home and ssh (provided that the printer is on and is loaded with paper).

To extract a single page (or a range of pages), I used pdftops:
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For some period of time, I had to switch to my Windows installation when writing articles with references, because I keep my references database there and there is an extremely convenient add-on for MS Office to insert citations and format bibliography on the fly.

However, it is quite inconvenient to make/run programs/scripts under Linux, and then switch to Windows to describe the obtained results in the article-like form. Thus, I briefly investigated available citation managers for Linux.
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