Posts about technology and arts.

Bioinformatics tools: Stacks

It is the first post about bioinformatics tools, but I will try to post more about other tools such as MrBayes, Structure, maybe some next generation sequencing tools too, and Bioperl, Biojava, and so on.

As I am more a computer geek, rather than a bioinformatics one, I will focus on requirements for running these tools on clusters and the requirements to install them on your machine. The instructions require that you have an intermediary knowledge on *nix OS and sometimes a bit of programming experience.</em>

I will be using tutorials available on the Internet and hosting my code in GitHub/kinow. Hammer time!

Running word-count example on a Hadoop commodity-hardware cluster and on a Hadoop local installation

Last weekend I spent some hours assembling old computer parts to create my commodity hardware cluster for running Hadoop. I already had a local installation in my notebook, so I thought it would be cool to run the word-count example in both scenarios to see what would be the results.

But first, let's review the hardware configurations:

Integrating Nutch 2.x, MySQL and Solr

Right now we are working on a new project using Apache Nutch 2.x, Apache Hadoop, Apache Solr 4 and a lot of other cool tools/modules/API’s/etc. After following the instructions found on, I’ve successfully connected Apache Nutch, MySQL and Apache Solr.

Invoking Testopia XML-RPC or JSON methods using Java

Most TestLink [1] users are aware that there is an external API, maybe for the external API token being displayed in the user profile section. Today after a meeting with Peter Florijn [2], I realized that the same may not be true for Testopia [3] users.

I am quite new to Testopia, and there are many features that I haven’t used yet. But if I understand it correctly, the database is interfaced by several Perl scripts that are, by its turns, exposed as Web Service (most of them). The web services are available via a JSON and a XML-RPC API (what is very useful, TestLink supports supports only XML-RPC).

The communication between different programming languages and the external API’s is accomplished by a client API. In TestLink you have testlink-java-api [4] and testlink-api-java-client [5].

Testopia has a Java client too, available in Testopia source repository [6] and can be used to integrate your existing Java code with Testopia.

How I started in Open Source

I was studying at Mackenzie Presbyterian University when I met Professor Rogerio Brito. Most of my friends were terrified of him. Maybe because of the class name “Structured Programming I”. Or maybe because of what Brito taught us at class.

My degree was in computing, Bachelor in System Information. Although it is related to Computer Science, we don’t have the same classes. In Computer Science you have more math, statistics and even physics, while in System Information you have administration, strategic planning, law and others related to business.

Although Structured Programming had a list of topics, Brito didn’t limit himself to those. Eventually he would try to teach us about algorithms, software complexity, the importance of writing academic papers and explain about Open Source software.

I remember one day we were dismissed before 10PM. I used to run for the bus stop for not being too late at home and cause it could be dangerous lingering on the streets of Consolacao neighborhood by myself, waiting for the bus. But that day I stumbled with Brito near the Professor’s Room.