Does Nobel Prize == quality teacher?

In a speech to the NAACP, John McCain wrote:

First, how many Nobel Prize winners would want to teach in America’s public schools. I don’t think he realizes that this would be a serious pay cut for most Nobel Laureates.

Second, there is much more to be an effective teacher than simply having “knowledge, wisdom, and experience.” Nobel laureates are usually good for ribald seminars but I’m not certain I’d want them teaching my kids. And I don’t even have kids

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Implementing a simple web-log based recommender system

I’ve now implemented such a system as an extension to Catalyst, the open source Perl web framework. The system isn’t yet ready for general distribution, but I’d like to share my approach.

First, I’ve gathered ten years of web access logs from WormBase, a generic model organism database where I work as the project manager.

Next, I correlated IP addresses with requests and tried to trace browsing patterns from one object to the next. This isn’t an exact science since we haven’t historically tried to uniquely identify users.

Data is loaded into a simple MySQL schema with object and object2related tables. Expediently simple.

Recommender systems for biological databases

Recommender systems [Wikipedia] seek to provide users with information related to what they are currently browsing. These are now ubiquitous in e-commerce sites such as Amazon, where each page contains a list of items viewed or purchased by other users.

I’ve long felt that a recommender system could revolutionize the browsing and mining of biological data. The idea would be to provide users with a list of related objects based on browsing history of cadres. See this post for some preliminary implementation notes.

I am worried that a recommender system won’t be received with open arms. Given that my current implementation is based on web log analysis it presents serious privacy issues. It’s conceivable that it’s use could inadvertently reveal the identity of uncloned and unpublished loci.

GUI prototyping add-on

Check out the GUI prototyping add-on Pencil Project for Firefox.

Bizarro Perl problem

I just came across a fairly strange Perl issue:

Consider:

protein => {
title => '%s release [%s]‘,
qq{formatdb_cmd => ‘-p T -t ‘%s’ -i %s’},
filename => ‘protein.fa’,
},


Yes, there’s a typo, with the qq enclosing an entire hash entry. This doesn’t raise an error, but obviously obscures the hash entry!

Bioinformatics is dead! Long live bioinformatics!

A few years ago, my boss Lincoln Stein prognosticated the end of bioinformatics.

According to Google Trends he just might be onto something. Searches for bioinformatics have dropped in half in the past four years. C’est incroyable! Not surprisingly, the top-ten sites for searches for bioinformatics are all in India.

Gory details available by searching Google Trends for bioinformatics.

Interesting parallels in the trends between bioinformatics, molecular biology, proteomics, and C. elegans:

Installing Trac

We’re already using 37 signals Basecamp for project management. It works well for collaborative work and management of distributed teams but is tedious when used as a feature tracker.

Today we discussed the need for a bug/issue tracker. In the past, we’ve considered RT since it integrates with our existing email flow. But frankly, RT is a PITA to configure.

I know that some people are hot and heavy on Mantis. I’m not. For one, I don’t like it’s name or it’s logo.

Here’s how I installed Trac:


// install Python
cd ~/src
wget http://python.org/ftp/python/2.5.2/Python-2.5.2.tgz
cd ../build
tar xzf ../src/Python*
cd Python*
./configure; make ; sudo make install