The following is a brain dump of some of the things I've been thinking about lately.
One of the biggest changes over the past several years in biology has been the incredible deluge of information. In response to this there's been a rise in bioinformatics to cope with all this. While this has led to some major successes, where it's failed is in its ability to impart a greater understanding of the subject at hand. Biologists still learn primarily from reading papers, the same way we always have. There are massive databases full of wonderful information but most of it is encoded with minimal or no context so you're always forced to go back to the papers to understand what the database is actually telling you. In that sense, these databases are fantastic at indexing information, but very poor at organizing it in such a way as to teach people about the topic at hand. We're still forced to slog through papers for just about everything.
What's striking about this is that the most informative bits in any biological paper I've ever read are encapsulated in the figures. The images themselves, provided you have sufficient background knowledge, show the basic data and give you the most understanding for the smallest investment of time. You can skim an article's abstract, it's figures and figure legends and gain a fair understanding of the topic before deciding whether or not to go further.
Now, there's a contradiction of sorts here. Many of these figures are generated via computers, usually an excel-made graph. The rest are actual photographs of things, such as blots, gels, or stained tissues, eventually inserted and processed via the computer. The contradiction is that the computer is used intensively to organize this data for publication, but we have a hard time extracting the essence of that visualization for indexing in "big picture" sorts of ways. That almost always has to be done by hand (and brain) by the biologist. This, of course, is suboptimal when you have thousands of individual genes.
The fundamental reason for all of this is that biological information depends wholly on context. For example, you can sequence the whole genome, but it's totally unclear what genes will be expressed at any given time unless you have much more information about the cell type, developmental stage, pathologies, and so forth. As far as I can see, all our bioinformatics tools have failed completely at providing any sort of context for their information. A common thing to see is so-called
"wiring diagrams" that display molecular interactions. These diagrams are full of nodes and edges and it looks almost impossible to understand such things. While there is a great deal of complexity, contextual information provides us with a framework to understand what's actually working. Looking at these diagrams, there's no sense of this though, it looks instead like complexity overrun.
So that presents us with the challenge for the future. What's required of bioinformatics is to not only index the raw data, but also the context, and then present the data to us in a context-dependent manner. I am convinced that the key to presenting data this way is to come up with novel visualization methods because it's the visualizations in the papers that we use today to get the most out of our time. I believe that this problem is tractable and that there is a solution. More than likely we'll need several solutions, and I look forward to seeing them develop.
The dpkg maintenance team just changed the priority of the good old
dselect from Important to Optional. Simultaneously, overrides were
changed by FTP masters.
As a consequence, dselect will no longer be installed by default when
installing a "standard" Debian system.
Thanks to the dpkg maintainers for the first move (Required->Important), as well as Joey Hess who suggested to downgrade from Important to Optional.
Old timers, this is time for a little tear in memory of dselect..:-)...as well as a thought to people who wrote and maintained it (it is still in the archive and part of dpkg source package but noone really maintains it, now).
Time to hunt a few more "Important" packages that should be downgraded.
Working!
Long time ago I used 
In an old 
As one of the females in #d-o might I add that this is not at all a sexist channel. Sure, like all friggen channels on IRC, and not to speak of the internet in general, there will be jokes, about men, women, monkeys, MacGyver and politicians. If you walk into a channel as a stranger and immediately draw conclusions because one
Recently I bought a new desktop PC and rotated my existing machines around, leaving me with one spare. Last night I donated that PC to a local friend, (co-incidentally the same woman who had been out cat-sitter when I went to stay at Megan's parents for Christmas).
I said "Its got Debian on it, that funny operating system that you used when you were looking after our kitten, remember?".
She said "Linux ssems to be getting popular these days I might as well try it out".
But seriously she used it. It had GNOME, it had firefox, she seemed happy. It isn't rocket science these days to point a technicalish user at a Debian Desktop and expect them to know what to do with it. The only minor complication was the lack of flash/java since it was etch/amd64 - but thats probably a plus with the amount of flash adverts!
In other news I made a new release of