It was only today that I’ve noticed Microsoft Office Live in Available updates (using Microsoft update). Curiosity led me to find out that Office Live is a suite of online word processor, presentation editor, spreadsheet and note-taking software, limited to a 500 MiB diskspace – free, developed by Microsoft. Office Live appears to be built on top of SharePoint.

Main emphasis of their website is on collaboration and access from anywhere to your documents. Although Firefox (together with IE) is listed as a supported browser on XP/Vista/MacOS (Linux is not listed), there is a note that some Office Live features require ActiveX. So Office Live is not really a match for Google Docs in portability (quite expectedly).

An update installs some new menu commands into Office XP/2003/2007, which allow working with Office Live from within your local M$ software.

I wonder if there is already an OO extension which allows working with Google Docs – no more wondering, here it is (thanks Paolo!).

One of my projects – COTRASIF – has grown complex enough to necessitate the use of version control system (VCS).

The most frequently mentioned is definitely SVN (SubVersion).

However, with a characteristic scrupulosity, I decided to run my own comparison of the available tools. I had a look at Darcs, Mercurial, SVN, and Git. Of these, only SVN is not a distributed VCS (but there is SVN addon which adds distributed features to SVN). Unfortunately, I didn’t take any notes during comparison, so there will be no details on how the choice narrowed down to Mercurial vs Git. These dVCSs are quite similar, with the following major differences: Mercurial is better documented and (much?) easier to use than Git; Git is more feature-rich, and Git currently has more add-on modules. Here the differences almost end. I decided that learning curves never were an obstacle, so Git is currently my first distributed VCS of choice (please note: I’ve never before used any version-control systems).

After choosing Git, I had to install Git central repository on a server. (Yes, Git is distributed, but central repository on the always-on server is a convenience worth the trouble; and again, this adds yet another backup copy.)

This is a collection of resources I found useful when setting up my Git repository:

1. Hosting Git repositories, easy and secure way (note: do not create the user manually, installation of gitosis package does that for you automagically).
2. Setting up Git repository on Dreamhost.
3. gitosis: how to add new repository

Some more resources on how to use Git:

1. Git user manual
2. Git guide
3. Git recipes (branching and merging in examples)
4. everyday Git with 20 commands
5. version control with git – tutorial

Update: Git is simple enough to get started in minutes. So far I had only used clone/push/pull/commit/gc commands, but I’m familiar with tag/branch/checkout commands. The drawback of insufficient documentation (as mentioned above) isn’t really a problem now. I’m not using any GUIs for git (as sometimes I’m working on a remote server via ssh), but of the three locally tried GUIs I liked gitk the most; both git-gui and qgit feel less convenient than gitk, but are approximately equal. I wish I had some SVN/Mercurial/Darcs experience to be able to recommend Git – but I don’t have that

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

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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