Radio interview at “Fábrica de la Ciencia”

May 25, 2015 at 11:54

A few weeks ago I was interviewed at Gavà radio station in the radio program directed by Jorge Onsulve called “La Fábrica de la Ciencia“. The interview was about protein simulations in supercomputing environments. You can listen to the program via podcast (sorry, only in Spanish):

A stage in Japan

July 30, 2013 at 13:19

doraemon

While I’m compressing all the data I’ve been working on over the last months (more than 250GB!), I’m thinking of how fast time goes by. It was still spring and everything was ready: my flight was departing soon and I was leaving Barcelona for the next three months. Destination? Ōsaka, Japan.

I had an amazing experience living and working in Japan and I’ve been writing about some of my adventures during this time in this blog (sorry, it’s only in Spanish). During my time in the hosting research center, I’ve met extraordinary people at Mizuguchi Laboratory: open-minded, brilliant scientists and, not less important, excellent people always kind and open to help me. Let me thank you again if you’re reading this post. You made me feel like at home.

But I also had the opportunity to meet other people apart from the office. Kaori and Snoo, from Bar Kitty. What started as “let’s teach some Spanish for fun” became “you guys are awesome”. In a few days we’re going together in a crazy road trip…I can’t wait for it! Edu (The Parallel Dimension), David (@CreativoenJapon, Un Creativo en Japón), Flapy (@Flapy, Un Español en Japón) and Víctor (Nihon Travel), it was a pleasure to share a couple (or more!) beers with you. I hope to meet you again in the future, but I’m not sure exactly where and how 🙂

I’m very sorry for having been complaining all the time about the weather: Kansai summer was really hot and humid, but oh, irony! I’ve finally got used to. Dealing with ATM’s and furikomi was complicated too…but I’ve improved my japanese language skills (when you’re starting from scratch it isn’t difficult at all 😛 ), worked hard and now I feel less gaijin than before.

This city will always be a part of me.

じゃね、大阪!

5th CAPRI Evaluation Meeting

April 16, 2013 at 17:06

Random Protein

The CAPRI evaluation meeting is the most important date in my research group’s agenda. Tomorrow, the 5th CAPRI evaluation meeting starts in Utrecht. The 4th evaluation meeting was celebrated in Barcelona and organized by my group, but I hadn’t started my PhD at that moment, so this is my very first “CAPRI”. I am presenting a poster and I am very excited about personally meeting all the good scientists who wrote the best articles in the protein-protein docking field.

You can follow the live feed from twitter hashtag #CAPRI2013Utrecht.

By the way, I’m participating in the e-ScienceTalk (www.e-sciencetalk.org) initiative, so I’ll post about the 5th CAPRI evaluation meeting in the GridCast blog.

After three very intensive days in Utrecht, I will visit Amsterdam for a couple of days. It is going to be my third time in Amsterdam, but the first one I can visit the Rijksmuseum.

Distributing N points on a sphere

February 25, 2013 at 22:55

In one of my PhD projects, I had the need to distribute n points on a sphere of radius r. I found a very interesting post in stackoverflow about how to solve the problem and I tested a few of the solutions they proposed by myself. In my opinion, one of the most elegant solutions consists in using a spiral function to distribute the points uniformly. Below you can find a little snippet in Python which uses the spiral method to calculate a list of n points (thanks to my colleague Iain for sharing his source code with me):

This function is based on the original work “Minimal Discrete Energy on the Sphere” which you can find online here.

An this is how a sphere of radius 10 with 300 points looks.

Points on a sphere using the spiral method

Points on a sphere using the spiral method

Japan, there I go!

October 24, 2012 at 18:32

Next Friday I’m flying to Japan. I’m going to spend a couple of weeks visiting the Kansai region (Kyoto, Osaka, Kobe and Nara), Tokyo and Hiroshima. I’m really excited about this trip because this time I can articulate a few phrases and even read in hiragana (wow!) and I’ll give a talk at Mizuguchi Laboratory. If I get the grant I’ve applied for, next year I’ll spend three months at Kenji’s lab, living in Osaka 🙂

Some pictures I took during my first trip to Japan in 2010: Japan-Flickr set.

Glowwom Swarm Optimization C++ implementation

October 24, 2012 at 17:58

As a part of my PhD thesis, I developed together with my friend trikitrok a C++ implementation of the GSO (Glowworm Swarm Optimization) algorithm. This algorithm is based on the ability of a given glowworm to attract its neighbors depending on its emitting light. At the same time, emitting light is dynamic and depends on the number of neighbors of the given glowworm. This metaphor has been demonstrated to capture really well local optima in multi-modal functions. You can find more information at the Wikipedia article.

Here I show how the agents (glowworms) have found the different local maximum points after 500 iterations of the algorithm (this plot reproduces one of the test functions used in the original paper by K.N. Krishnanand and D. Ghose, 2005). Left image is the original function bounded to -6, 6 and right image represent agents positions (crosses) after 500 iterations.

Agents position after 500 iterations

The repository is public and is currently hosted by Bitbucket at glowworm++.

FEBS-IUBMB 2012

September 9, 2012 at 11:07
Ada Yonath

Ada Yonath

Today, the 22nd IUBMB and 37th FEBS congresses have finished. They were celebrated at the same time this year in Sevilla, Spain, and the theme was “From Single Molecules to Systems Biology”. I enjoyed many of the talks, but my favourite was the one given by Ada Yonath, Life: expectancies & origins. It was the second time I listened to Ada and I’d like to say that I really appreciate how Ada makes an one-hour talk as shorter as a ten-minutes one. Ada Yonath was awarded in 2009 with the Nobel Price in chemistry for her work on the ribosome structure.

You can see one of the videos she reproduced during her talk here: antibiotics targeting ribosome.

Subunit of the ribosome

The congress was held at the Seville Conference and Exhibition Centre, a nice venue, but a little far away from downtown. The organization was good in average, but it was a real pain to get my money back from the boursarie I won and during the weekend, the Renfe circular line was stopping around twenty minutes in one of the stations…

Anyway, I had the opportunity to present one of the projects I’m working on during my PhD. You can take a look at the poster I presented here.