Toluu : What You're Doing Is Rather Desperate

What You're Doing Is Rather Desperate

Notes from the life of a bioinformatics researcher

The three phases of MySQL usageOctober 17

As Mike keeps reminding me, getting your data into database tables is A Good Thing. Like many people, my database of choice is MySQL - largely because it was the first one that I tried and it works for me.

However, I’m far from being an expert MySQL user. In fact, I’ve identified 3 stages in my use of MySQL over the years; see if you recognise yourself in any of them.

The single table database

Early in your MySQL career, you discover either “LOAD DATA INFILE” or the command-line tool “mysqlimport”. You realise that this is a quick and easy way to get all of those delimited text files straight into a database. Off you go, merrily importing everything on your hard drive into tables.
At some stage, you begin to wonder whether listing the same identifier (gene name, PDB ID, species…) many times in multiple columns is sensible. This eureka moment leads you to…

…Discovery of the join

At some stage, you get your head around joining tables. At first, you can’t quite see the point - isn’t it easier to devise a query on a single table? Maybe so, but it’s inefficient and severely limits the combinations of data that your query can return. It’s a slow realisation but pretty soon, you’re chopping up your data into multiple tables and joining all over the place. Including example

Giant panda genome: mapped or sequenced?October 17

I’m with Ogden Nash who said:

I love the baby giant panda,
I’d welcome one to my veranda

This week, I learned via Keith that Chinese scientists announced the completion of the giant panda genome. An impressive achievement, given that the project was announced in March this year, but what exactly has been completed? Has the genome been sequenced - that is, there are strings of A, C, G and T covering most chromosomes, or mapped - that is, the approximate chromosomal location of most genes determined? The media seem unsure.

The Australian: Scientists in China have mapped the genome of the giant panda…
Window of China (the official source, it seems): Chinese scientists have completed sequencing the genome of giant pandas…
The China Post: The Chinese-led genome-mapping effort…
Melbourne Herald Sun: Genome sequencing confirms pandas are bears…but then “endangered giant pandas have had their

Open Access DayOctober 13

It’s Open Access Day. Mission: to broaden awareness and understanding of Open Access. Their approach: “synchro-blogging” - an attempt to get as many folks as possible to blog on the given topic at the same time.

So, to answer their questions:

Why does Open Access matter to you?

OA is important for many reasons: go and read this by Jonathan Eisen instead of my rambling. One that stands out for me: it signals a fundamental change in the way that information is conveyed from writers to readers and an admission that the traditional publishing process is obsolete in the internet age. We live in a world where people expect instant, relevant information in the top 20 hits from a Google search and that expectation is transferring to science too. I don’t care how prestigious you think your journal is, or whether you see yourself as some kind of “guardian of knowledge”. I want information, I want it now and if you can’t deliver, I’m going somewhere else (*).

How did you first become aware of it?

I honestly don’t remember, but it was some years ago. I suspect it was around the time that journals such as Nucleic Acids Research and Bioinformatics introduced an OA option for authors. I also remember quite vividly the appearance of BMC on the

It would be too easy to rant and rave about thisSeptember 27

Zotero is a marvellous, active open-source project, providing a Firefox extension that captures and formats bibliographic information from web pages.

Thomson Reuters describe themselves as “the world’s leading source of intelligent information for businesses and professionals.” Whatever. They specialise in closed-source, proprietary solutions which to my simple mind is at odds with a role as an information source.

Via FriendFeed from Rafael Sidi’s blog, I learn that Thomson Reuters are suing George Mason University, developers of Zotero, for “violating its license agreement and destroying the EndNote customer base”.

Here’s my simple, black-and-white view of the world. The greatest achievement of the internet is the potential to set information free. There are free-thinking, forward-looking organisations like GMU who see this potential and act upon it. There are also organisations who see only threats to their corporate interests. Publishing corporations no longer control the flow of information to consumers and some of the

Genomic analysis of Pseudoalteromonas tunicataSeptember 25

Some years ago, I provided advice and a little analysis for a group at UNSW studying marine bacteria. It’s nice to see that they remembered me:

Thomas, T., Evans, F.F., Schleheck, D., Mai-Prochnow, A., Burke, C., Penesyan, A., Dalisay, D.S., Stelzer-Braid, S., Saunders, N., Johnson, J., Ferriera, S., Kjelleberg, S. and Egan, S. (2008).
Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment.
PLoS ONE 3:e3252.

If correlating genomic features with microbial physiology is your thing, go and check it out. The article is open access, for your pleasure - as are five of my last six efforts, I just noticed.

Posted in bioinformatics, genomics, publications, research diary Tagged: plos one, pseudoalteromonas tunicata