Archive for the ‘Open Science’ category

Generating cool fractals

June 16, 2007

This one is from the Free Software Magazine. Xavier Calbet wrote:

Whether you are a professional or amateur scientist, engineer or mathematician, if you need to make numerical calculations and plots quickly and easily, then PDL (Perl Data Language) is certainly one of the best free software tools to use. PDL has everything that similar high-level, proprietary, numerical calculation languages (like IDL or MATLAB) have. And it certainly comes with all the features you would expect to have in a numerical calculation package.

The full article is available at: Generating cool fractals.




Perspectives on Free and Open Source Software

November 22, 2006

I found this Open Access Book: Perspectives on Free and Open Source Software. I believe that if you are reading this blog, that book will interest you. By the way, kudos to The MIT Press for providing a free version of the book.



Back from the IV World Forum on Free Knowledge

October 23, 2006

Yesterday, I got back from the IV World Forum on Free Knowledge. It was an amazing experience. I had a good time even though I was part of the organizing committee ๐Ÿ˜‰


People were really interested in the democratization of knowledge. Besides my participation as an organizer, I gave a talk on Free Science: Utopia or Reality?, I gave a tutorial on Image Analysis and I chaired a Panel Discussion Session on Intelectual Property in the XXI Century. Some time in the next couple of weeks, I will comment on my experience in the Forum. For now, I just want to comment that Perl was well represented in the Forum with three out of the seven tutorials that were offered โ€œfree of chargeโ€ having something to do with Perl. The three tutorials were:

  • Introduction to Perl with Randal Schwartz
  • Image Analysis with Lino Ramirez, and
  • GUI Development with Perl with Alejandro Garrido



A Beginners Guide to Fuzzy Rules-Based Systems

October 12, 2006

I just finished writing an introductory tutorial on Fuzzy Rules-Based Systems with Perl. I posted it on the Perl Monks’ website. This tutorial is part of a larger tutorial I am giving at the 4th World Forum on Free Knowledge this coming week in Venezuela.



Perl Monks, Granular Computing, and World Forum on Free Knowledge

October 1, 2006

Some days ago, I attained level 3 (Acolyte) in the Perl Monks. It is nice to see how my opinions are getting good reviews ๐Ÿ™‚ . These days, I am working on a Granular Computing tutorial for the Perl Monks community. I plan to divide it into two posts:

  1. General Introduction: from information granules to granular computing; applications: image processing, data mining, signals processing, etc.; common frameworks for Granular Computing: Interval Analysis, Fuzzy Sets, Rough Sets; and finding information granules in a Fuzzy Sets framework.

  2. Plan for a Granular Computing Module: here I present what modules are needed in Perl to write a Granular Computing Module. My idea is that we should create several (small?) modules and combine them to create the Granular Computing module. For instance, we could have a Fuzzy Sets Module (there are already some modules in CPAN related to Fuzzy Sets, so our task would be to chose one and improve it), a Rough Sets Module, an Interval Analysis Module, and a Clustering Module (I already wrote a Fuzzy C-Means script, I certainly would be happy writing all the scripts needed in this area). Our Granular Computing Module would call on these modules and add some additional functionalities. The advantage of doing it this way is that if someone is interested only on an individual module (Fuzzy Sets, Interval Analysis, etc.) that person would not need to use the whole Granular Computing Module. Moreover, I expect it to be easier to maintain smaller modules. The only problem I see with this idea is related to dependences. In any case, I guess that I will be writing a lot of Perl code this coming year ๐Ÿ˜‰

The last point on this post is related to the 4th World Forum on Free Knowledge. This Forum will take place in Maturin, Venezuela from October 17 to October 21, 2006. In the Forum, I will be giving a talk titled: Open Science: Utopia or Reality? In this talk, I describes what is needed to have a truly open science, muse on whether Open Science is attainable, and present some guidelines to help us make it a reality. In the Forum, I will also give a tutorial on Image Analysis using Free and Open Source Software. The tutorial focus on my research in using Granular Computing for image analysis. I will describe my experience with the ITK and the Perl’s AI::FuzzyInference module in my quest for finding a way to help content experts in analyzing images. I will post more on that later.



My first steps with Perl!

September 22, 2006

By the end of OSCON, Alejandro had convinced me that I should try Perl. So I decide to buy a couple of books to get started. If you are curious, I bought Learning Perl (the Llama book) and Mastering Algorithms with Perl. By the end of July, I started learning. Maybe it is just me, but I found Perl to be an easy to learn language (I did a lot of assembly and C programming before). On August, I made a decision: I would code an important portion of my Research work in Perl. That is me, very passionate some times.

To help me with this task, I bought another book (this time it was the Alpaca book –Intermediate Perl) and joined the Perl Monks. After reading a bit of the book (I have not had the time to finish it), I started to port some code that I had in MATLAB to Perl. I decided to start with one of my favorites: a Fuzzy C-Means implementation. You can see it on my Perl Monks’ scratchpad. It works! By the way, if you are a Perl’s expert and have a suggestion or two on how to improve my code, feel free to drop me a line. Remember: I have been programming in Perl for less than two months.



ITK 2.8 was released

July 20, 2006

This month the version 2.8 of ITK (a toolkit for medical image processing, registration, and segmentation) was released. I already tested the new version on my Ubuntu Dapper box and everything works just fine, as expected.

You can download this release from the Download page

or through CVS (see the download page for instructions) by using the tag :


The manifesto of changes in this release can be found in the ITK community Wiki page