What You’re Doing Is Rather Desperate

Another year, another ISMB/ECCB meeting and – another great blogging effort.

It’s all at the FriendFeed group: ISMB/ECCB Stockholm 2009, with outgoing links to individual blogs too.

Thanks and congratulations to all involved for a great effort. Looking forward to the official write-up.

Here’s a problem. You’d like to construct a complex query at NCBI Entrez using various fields. Example:

“9606″[Taxonomy ID]

to limit your search to Homo sapiens. Except – you don’t know which fields are available for the database that you want to query.
Read the rest…

It’s apparent that my activity at this blog has been on a downward-slope for some time. I currently post about once a month and when I do, it’s more likely to be a rant about some social network/web2.0 application than about bioinformatics.

So the question is what to do about it.
Update: thanks for the many, rapid and helpful responses. The unanimous view was – stay here, keep blogging. So that’s what it will be!
Read the rest…

*Cough*. Quiet, isn’t it? I’ll tell you what’s been happening soon.

In the meantime, BioSysBio 2009 is underway. Lots of interesting coverage:

• the FriendFeed room
• the Twitter search (#biosysbio)
• the industrious Ally

Are you looking for a postdoctoral position in structural bioinformatics? Preferably at a highly-regarded university, on an attractive campus in a lovely city with a great climate? Did I mention great colleagues?

I highly recommend my old job – details here.

In a nutshell: we went to ISMB 2008, had a great time and live-blogged the meeting using this FriendFeed room. The nice people at ISCB were so impressed that they asked us to write up a report.

So here it is. FriendFeed life scientists might recognise some (or all) of the author names.

Saunders, N., Beltrão, P., Jensen, LJ, Jurczak, D., Krause, R., Kuhn, M. and Wu, S. (2009).
Microblogging the ISMB: A New Approach to Conference Reporting.
PLoS Comput Biol 5(1): e1000263
doi:10.1371/journal.pcbi.1000263

This is a highlight of my career to date. Thanks are due: to the authors (especially Roland who got it all started); to everyone who contributed at the ISMB 2008 room; and to BJ Morrison and Phil Bourne for their support in making this happen.

The terms “big science” and “big data” have recently become quite prominent on the Web. For commentary, I point you to the man with the tag.

There are those who believe that big data means fundamental change in how science is done. We’ll take all this data, make it machine-readable, put it in the cloud and – poof! – science will emerge. Almost as if it were self-aware. At the other extreme are those who see no fundamental difference in how we go about our business – there’ll just be “more” of it.

One analysis, of course, is that they’re both right and they’re both wrong.
Read the rest…

Over the last 3 years, I’ve stored many small snippets of information in a set of Google Notebooks. Sample topics: notes for blog posts, programming skills that I’d like to learn and preliminary (or half-baked) ideas for research or software projects. I’ve learned that:

• Whilst Google Notebook is great for scraping information from web pages, it leaves a lot to be desired in terms of editing and presentation
• Ideas left in private notebooks quickly become dead ideas

Yes you can publicise, tag and collaborate at a Google Notebook, but this doesn’t fit with my workflow – or that of many others, I suspect. So, I’ve taken as much of the material as I want to make public and dumped it on a wiki at Wikidot.com. By the way, if you’re looking for a free hosted wiki with plenty of features, you could do a lot worse.

If anything there interests you enough to add material, let me know and I’ll invite you as an editor (you’ll need to create a wikidot account if you don’t have one).

I’ve signed the contract and told the boss. So, for those of you who expressed interest, here are the details of my latest career move.
Read the rest…

Here’s a common problem solved: how to generate a pretty picture of your database schema. A Google search throws up all manner of home-brewed solutions using graphviz, perl scripts and so on. Or you can make life easier and simply install SQLFairy.

Under Ubuntu: as simple as “sudo apt-get install sqlfairy”.

Next, dump your database tables, e.g. for MySQL:

mysqldump -u username -p -d mydatabase > mydatabase.sql

Finally, for a PNG image of your schema:

sqlt-graph -f MySQL -o mydatabase.png -t png mydatabase.sql

Too easy. Example shown is the BioSQL schema.

update: if your schema lacks explicit foreign keys, try the –natural-join options (man sqlt-graph, man sqlt-diagram)