What You’re Doing Is Rather Desperate

It’s Christmas Eve tomorrow and so I declare the year over. My Christmas gift to you is a summary of activity in 2009 at the FriendFeed Life Scientists group. It’s crafted using R + Ruby, with raw data and some code snippets available. If you want to see the most popular items from the group this year, head down to the bottom of this post.

(Note: this post is a work in progress)
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)

Alan says:

I’m liking TwitterFriends

I agree. Finally, social network visualisation that tells you something useful; e.g. well-connected people = useful to know. All without asking for your password too.
TwitterFriends.

Would it tell us anything useful? Does it tell us anything useful about the current state of journal RSS feeds, or suggest areas for improvement?

Let’s find out. It’s as simple as locating the feed URL from your journal subscriptions, pasting it into Wordle and eyeballing the results. Here’s what came back for the 25 journals in my current subscription list.
Read the rest…

Everyone seems to be having fun with Wordle. Except for me, until I realised that all my machines were cursed with something named “icedtea-gcjwebplugin”, as opposed to the Sun java plugin. Problem solved. So there it is. But for the prominent “bioinformatics”, you’d never guess I was a biologist, would you. I do believe that this is telling me something.