Monthly Archives: April 2007

Announcing JoomlaLIMS – formerly MamboLIMS

A couple of years ago, I threw together a basic LIMS for my lab using a CMS called Mambo and a component called FacileForms. I made it publicly available and there was a little interest. Time passed, Mambo forked into the Joomla project, FacileForms went through several upgrades and my LIMS broke and fell into disuse.

Recently I resurrected the project as JoomlaLIMS. It uses the latest Joomla (1.0.12), the latest FacileForms (1.4.7), PHP 5 and MySQL 5. I’ve got it working to the point where I’m comfortable letting it loose in the world. So I give you JoomlaLIMS at Google Groups. You can download the tarball from there, unpack it in your web root, create the appropriate database, tables and user and hopefully, you’ll be ready to go.

If you’re looking for a simple lab LIMS, give it a try and let me know what you think. It works for me but I’m tingling with anticipation of the horrible bugs that others are sure to find.

Removing a MySQL user

Many of us have installed a MySQL database as part of a PHP/MySQL-based web application. Normally this procedure includes adding a specific user and password for the database:

mysql> grant all on mynewdb.* to 'idiot'@'localhost' identified by 'guessme'

What the setup guide never tells you is how to remove that user should you decide to remove the application. You need to see what grants they have, revoke them, then remove the user from the user table:

mysql> show grants for 'idiot'@'localhost';
mysql> revoke all privileges, grant option from 'idiot'@'localhost';
mysql> drop user 'idiot'@'localhost';

Jargon bad, controlled vocabulary good

A post over at Omics! Omics! discusses The gene and the genon concept: a functional and information-theoretic analysis, published in Molecular Systems Biology. This article points out that “gene” is a poorly-defined word and then proposes some new terms: genon (with pre-, proto- and transgenons), P-, R-, s- and c-genes with various combinations thereof and a whole bunch of other jargon. It reminded me of a similar debate that I read recently in Genome Biology on the use of the words “ortholog” and “paralog” – and whether we need additional terms such as “metalog” or “xenolog”.

I find these papers fun but unhelpful and I think they demonstrate another case where a journal article is not an appropriate forum. When articles like these appear out of the blue it’s easy to form the impression, rightly or wrongly, that rather than an honest proposal to improve the situation, it’s an attempt to push a personal agenda. My first thought is always “hey, some crazy people have invented their own language and they want us all to use it!”

We do need to define concepts in biology, but as a community. Can it be so hard for a panel of experts to get together, think about what makes up a complete biological “parts list” and define a controlled vocabulary and an ontology? I know that there are projects like this. Furthermore, can they do it in a visible, public forum where we can all contribute and comment? That way we might end with some useful definitions and tools.

Earthportal.org

I discovered EarthPortal via an intriguing post by John Wilkins. They describe themselves thus:

clipped from www.earthportal.org

The Earth Portal is a comprehensive resource for timely, objective, science-based information about the environment. It is a means for the global scientific community to come together to produce the first free, expert-driven, massively scaleable information resource on the environment, and to engage civil society in a public dialogue on the role of environmental issues in human affairs. It contains no commercial advertising and reaches a large global audience.

  powered by clipmarks blog it

My first impression is very good. Lots of interesting content (all creative commons licensed), good presentation, RSS feeds. If you’re interested in environmental news, go take a look.

How do you feel about English?

influencegraph.pngThrough no more than an accident of birth, I happen to be a native* English speaker. This is fortunate for me as English is the “official” language of science communication (the vast majority of journals are written in English), as well as the major international language in many other human endeavours – including on the internet. The low-quality graphic on the left illustrates what a mongrel the English language is and takes you to an informative Wikipedia page.

My travels on the web and in the world have brought me into contact with people from many countries. We converse in English and I never give that a second thought. So I wonder – if English is not your first language, how do you feel about its dominance in communication? Is it just accepted as fact and taught to you during your science education? Does it ever make you feel a little resentful? Do you wish there were more social networks in your native language? Is there interesting science happening in predominantly non-English speaking regions that we don’t get to hear about?

* I say “native”, but people from my part of the world are blessed with a strong regional dialect (which I’ve long since lost, sadly), derived largely from Frisian and old Norse.

Unexpected shaking

0_50.gif You don’t see this everyday – an earthquake in the UK, large enough to cause damage. The thumbnail will take you to the USGS Earthquake Hazard website, a great source of near-real-time data for your mashups.

I was at the epicentre of a magnitude 5 earthquake in the UK on Boxing Day in 1979. It was strong enough to shake the baubles from the Christmas tree and move furniture but to my lasting regret, I slept through the entire event.

Random WordPress fun

The latest toy from WordPress serves up a random post from your blog. Just add “?random” to the end of your blog URL. I should add that as a sidebar link. Try it out here.

Other new options are a tag cloud widget and drop-down boxes for other widgets. Nice ideas but perhaps rushed to release too early. I found the tag cloud to be big and ugly (with this theme at least) and the category widget drop-down is completely broken. Still, 9/10 for effort.

Update: the drop-down issue seems to be fixed now

Wiley not wily

Take care next time you clip a small section from a journal article to illustrate a blog post. Certain publishers might call in the heavyweight legal division. Or in other cases, perhaps the heavyweight armoured division.

This is being discussed everywhere; links via Pedro, Bill and ‘shelley batts’ or ‘fair use’ and wiley at Techorati. I’m just adding my voice to the indignation.