Every new semester has its quickoff overhead. Besides trying to get back on track after travelling, and having meeting after meeting, now I am sitting at the inagural act of the Institute for Advanced Computing Applications and Technologies at the University of Illinois at Urbana-Champaign. A list and description of the three kicking off projects of the center is also available. These three themes are:

• Next-Generation Acceleration Systems for Advanced Science and Engineering Applications
• Multiscale Simulation in Science and Engineering
• Synergistic Research on Parallel Programming for Petascale Applications

Remember everything. is the tagline of Evernote Corporation. Evernote concept is simple, your notes with you everywhere and always accessible. They version may seem a bit more accurate:

Evernote allows you to easily capture information in any environment using whatever device or platform you find most convenient, and makes this information accessible and searchable at any time, from anywhere.

I was a bit skeptical at the beginning. I have tried several times to use the Google notebook, and I never felt they got it quite right. I had to force myself into it. So far Evernote is looking promissing. Evernote, besides the web app interface to your notes provide desktop apps (for Mac and Windows), cellphone apps, clippers, and more. Definetely worthed to take for a spin.

One of the benefits of working with people smarter than you is the chance to never stop learning. My office mate, Bernie Ács, is an extraordinary source of experience and wisdom on production systems. Just right after coming back from vacation, he started unfolding a virtualized solution for high availability and load balancing of services. It is not me the one who should disclose the solution, but I just want to mention a piece of the puzzle that I found very interesting: ldirectord. In the words of the ldirectord developers:

ldirectord is a daemon to monitor and administer real servers in a LVS cluster of load balanced virtual servers. [...]  A LVS cluster consists or one or more virtual services each of which may have zero or more real servers. The IP address of a virtual service is what end-users connect to and is typically advertised over DNS. When a connection is made to a virtual service, it is allocated a real server, and all packets for this connection are forwarded to this real server. A more detailed overview of LVS can be found here.

What does this mean? Let me sketch a simple example. Imaging you have a web server that hosts your new cool site providing content to the web. To get to your site people navigate to a particular server name that, via DNS, gets resolved into the particular IP address where a service runs providing your cool content over HTTP. So far so good. But what happens when a lot of people starts coming to visit your cool and now more and more popular site? Maybe somebody mentioned your site at Slashdot…

The answer: Your server starts getting slow to a crawl, or it even goes down because it cannot serve content to all the incoming requests, and people do not want to wait for your cool content any longer and they eventually end moving on and, eventually, forget your site.

To avoid getting to that extreme, ldirectord comes into the picture. The idea is simple, make people hit a high available virtual server whose only purpose in life is to forward incoming requests to a farm of real servers, each of which providing your cool content—yes, you can see them as clones of your original server. Moreover, if you can be a bit cleaver about how you d

Long time delayed, I finally got a copy of The Emperor’s New Mind by Roger Penrose. The book was originally published in 1989. Yes, I never read it from cover to back, and finally yesterday I run out of self imposed excuses and got me a copy. I guess that it was the result of listening to the Teaching Company lecture series The Phylosophy of Mind by John Searl, also falling on the same alley. Recreative reading, may be, but I am still fascinated to keep running into belivers and detractors of strong and soft AI almost 20 years after Penrose’s book was published.

Yes, I disappeared from my blog during GECCO 2008. Yes, I started blogging about the International Workshop on Learning Classifier System 2008 held on Sunday 13 at GECCO 2008. The workshop was terrific. Lots of new ideas were presented, but more importantly, lots of new ideas end sparking in participants head. As usual, the big workshop family went to dinner together where we all end having a blast. Some good traditions do not change, fortunately. 

Then, GECCO started. Monday, Tuesday, and Wednesday have been the most unusual GECCO days in my 10 years of attendance. Yes, I presented our paper and attended some interesting talks, but what made it different was that I spend a lot of time on hallways talking to people. There was an unusual concentrations of very interesting people to talk to, not to mention friends I have not seen in a long time. So, overall was really fun, and now I am trying to catch up with the papers published on the proceedings…

The 11th edition of the International Workshop on Learning Classifier System 2008 is hot. So far a lot of idea exchange and interesting discussions. So far Gilles Enee, myself, Natalio Krasnogor, Albert Oriols, Thyago Duque covering map problems, encoding language and model building, TSP and metaheuristics, learning association rules, and multi class labeling. Had to rush back to the next one

Yup, I am just packing on the run. Should get to Atlanta late afternoon or early evening. Wish me luck :D  A bit of information about the city provided by Wikipedia

Atlanta (pronounced /ətˈlæntə/ or /ætˈlæntə/) is the capital and the most populous city in the state of Georgia, and the core city of the ninth most populous metropolitan area in the United States at 5,278,904. It is the county seat of Fulton County, although a small portion of the city extends into DeKalb County. As of July 2007, the city of Atlanta had a population of 519,145^[4], and a combined statistical area population of 5,626,400^[5]. Residents of the city are known as Atlantans.^[6]

For more information see the GECCO 2008 website.

Preparing for the upcoming Meandre release, as part of the larger SEASR on, I have been exploring a bit the inner machinery of WordPress to create a simple plugin for the SEASR site that could render Meandre component and flow descriptions straight out of their RDF desciptors. Actually, it turned out to be a breeze. After being a heavy user of WordPress in several project for few years now, its extensibility keeps sparking new possibilities in my mind every time I look into any of its facets. Anyway, I am rambling. Back to the point. To hit the ground running, I started by creating a simple generic plugin that would replace a tag with parameters for something else.

I looked into several freely available plugins, the one that got me going was a very simple one, the SlideShare plugin by Joost de Valk. The plugin transforms a formated tag into code that embed a flash player for SlideShare presentation. Below, I reproduce the skeleton of a plugin that will replace the tags in your post/pages/comments for whatever you like. A tag takes the form [tag-mnemonic param1 param2] and the plugin replaces it by just a HTML list of the two parameters.

 <?php
/*
Plugin Name: Simple Plugin
Plugin URI: http://host.org/
Description: Replaces a tag for a list.
Version: 0.1
Author: Xavier Llor&amp;amp;amp;amp;amp;amp;amp;amp;agrave;
Author URI: http://www.xavierllora.net

Based on SlideShare plugin (http://wordpress.org/extend/plugins/slideshare/)

Installation: copy simple-plugin.php to the wp-content/plugins directory of
your Wordpress installation, then activate the plugin. Use the following syntax
for your tag

[tag-mnemonic Param1 Param2]

When the plugin is active, the tag will be replaced by a simple HTML list
containing the parameter values.

*/

define("SP_REGEXP", "/\[tag-mnemonic ([[:print:]]+) ([[:print:]]+)\]/");
define("SP_TARGET", "<ul><li>###Param1###</li><li>###Param2###</li></ul>" );

function sp_plugin_callback($match)
{
	$output = SP_TARGET;
	$output = str_replace("###Param1###", $match[1], $output);
	$output = str_replace("###Param2###", $match[2], $output);
	return ($output);
}

function sp_plugin($content)
{
	return (preg_replace_callback(SP_REGEXP, 'sp_plugin_callback', $content));
}

add_filter('the_content', 'sp_plugin');
add_filter('comment_text', 'sp_plugin');

?>

That means that if you write the tag [tag-mnemonic http://foo.org http://example.org], the plugin will reformat the tag and inject the following html code

<ul>
<li>http://foo.org</li>
<li>http://exampl.org</li>
</ul>

where the tag originally was. And that’s it!

One more thing. The only thing you may want to be aware is the filtering chain. The add_filter has a third numeric parameter. When you have multiple plugins that rely on filters to do their job, sometimes you may need to force a certain order of execution to avoid stepping on each others toes. If that is your case, you better check the add_filter documentation. It may save you some time, trust me

PS: Joost had some comments on improving this simple plugin. Check the comments below

Did you ever run into the situation that your analysis/simulation data is too large to fit it in memory? Does the flat file format you use for storing your data sets become to big that renders it slow to a crawl? If you answered yes, you may want to give a spin to the HDF5 library. HDF5 file are not replacement for relational data bases. They are catered for storing complex data objects and a wide variety of metadata. It is also optimize for efficiency of storage and retrieval. The underlying library is written in C.

If you are a Python user, PyTables provides a very efficient wrapper for HDF5 files. It gives you access to all the HDF5 api, plus it is nicely integrated with NumPy and provides natural naming conventions. In another words, you can quickly store and retrieve your arrays/matrix to HDF5 files, giving you a very interesting persistence layer.  For instance you can do a simple table scan by:

import tables;
 
h5f = tables.openFile("test.h5f","r")
for r in h5f.root.Table :
    pass
h5f.close()

The code above opens an H5DF file called “test.h5f” which contains a table at the root named “Table”–see the natural notation here. Then it just scans the table using the common Python syntax. You can also do grouped reads, read all into memory, filtered wheres, and the like.

Definitely worth to give it a spin if you have to much data for your available memory or flat file format. Also, I am wondering how fast this may fly on a SSD…

Yes, I am back. Almost 28 hours later than expected, but I am back to Urbana. The trip started with a very tiny little delay of 8 hours in Barcelona. Yes, COA121 was the flight to Newark. Yes, COA121 was the first leg toward Urbana. Yes, the plane had technical problems on the way to Barcelona and had to land at the Azores islands to get it “fixed”. Yes, we did not dare to ask. Yes, we were tired of waiting for a plane that seemed never to come; but you should have seen the faces of the passengers deplaning at Barcelona, exhausted is not a word descriptive enough. Yes, we all filled a complaint form asking for money back according to the European Union bill of right for air passengers. Yes, we know that it was a bit of wishful thinking and the lack of anything better to do while waiting.

I was surprise how civilized was everybody. Nobody shouted. Everybody was polite and ordered. It was also surprising how little the company told the ground personal. The poor guys did and outstanding job to keep everybody relaxed and informed, given the circumstances. Having almost zero information—yes even with almost zero information there were two competing versions of what was going on—they manage to finally do the job. The poor guys also had a never-ending day. I bet they spend more than 14h there. But of course, if you get delayed 8 hours you arrive to Newark at 10pm and, hence, you leave the airport at 11pm. Yes, you leave the airport because there are no more flights that late at night. So they give you an hotel and meal voucher, and they book you for the next flight to O’Hare. I was “lucky” that the next available flight was at 1:50pm. Some folks had only 3 hours sleep at the hotel before leaving back to the airport to catch 5am flights.

And a new day starts. And you get to the airport refreshed and optimistic. And you board the plane on time. And you are happy that you will be able to finally leave on time. And it is summer. And O’Hare has slowed down because of the weather—some storm going one. And you sit for another hour on a plane waiting for the O’Hare to bless your departure. And you got there late; luckily you call the day before the rental car company. And you do not see your luggage. And when you walk toward Continental’s lost luggage office to complain, you find your luggage between the lost luggage of the earlier flight you could not get in. And you go to the rental. And finally you find yourself in a traffic jam driving back to Urbana, one day later than planned, a bit exhausted, and having missed some things at work, but having meet a lot of new people you would never have talked to.

A while a go I wrote about tools for managing your LaTeX bibliography. Despite the fact that the tools I described help managing your LaTeX bibliography collection, it still did not help much with managing the tons of PDFs files you end pilling up when doing research on a particular topic. BibDesk has now the ability to attach files to entries, Zotero with its ability to store snapshots is still the closest thing I have found so far.

However, a friend just pointed me to Papers, a Mac tool—yes it is just available for Mac—for managing your digital library of papers. Very much like iTunes, it allows to streamline your search, reading, organizing, and writing—there is a very interesting webcast by the creators of the software. If you have a Mac, it is worthwhile to give it a spin.

If you are looking for a list of the related blogging done during ICEIS 2008 just follow this link. During Sunday morning I run into Angel A. Juan, an assistant professor at Open University of Catalonia (UOC), interested on analyzing online teaching efforts and how tools to assist professors monitoring students performance on online media. I visited him yesterday at his office and we got and interesting exchange of ideas. Most of them revolved around the work we have conducted under the DISCUS project, and how similar is our efforts on marketing focus groups and their online teaching environment. His group, Distributed, Parallel and Collaborative Systems, was also interested on the work done under the SEASR project, mostly focusing on the Meadre infrastructure for data-intensive flow computing we are getting close to release.