The CBBL has entered in the testing phase of the new Altix UV 1000 at CESCA. Adun’s performance is being benchmarked. tera110_p6_Desembre2010

I learned from Lorena Pantano about the BioGenIn site, a meeting point for bioinformatics students at several levels. Great initiative, worth taking into account if you are a student in the field in Spain. But I better leave the description to them:

We are a national group working to organize Bioinformatics students in Spain with an aim to foster collaborations between students and also create an active network for spreading information about
developments and opportunities in Bioinformatics
We consist of two groups:

And here is the flier you may feel free to distribute: BioGenIn

Excerpt from the upcoming VPH NoE newsletter

A central training activity in WP4 of the VPH NoE is the organization of a series of study groups (SGs) to disseminate the philosophy, the theory and the practical implementations beyond the VPH initiative. After a first SG in Nottingham in July 2009, Barcelona hosted the second of such events in the outstanding premises of the Parc de Recerca Biomèdica de Barcelona (PRBB), a centre that includes several institutions devoted to different aspects of biomedical research, including researchers in two of the general members of the VPH NoE: UPF and IMIM-Hospital del Mar. The SG consisted of five days of highly interactive activities. During the first day, the format of a workshop was used to introduce the participants to the main theme of the SG: multiscale simulations in biomedicine. The approach taken this year was to deal with a generic theme, as it paved the way to discuss basic and applied aspects of the research design from different perspectives: concept of a (multiscale) model, mathematical foundation, physical principles, computational details and, finally, problem-based analysis. To exemplify the meaning of the multiscale approach, three use cases were proposed in the areas of 1) mechanobiology and biomechanics of aneurism evolution, 2) lung mechanics, and 3) drug induced ion-channel blocking in cardiomiocytes and its effect in arrhytmogenesis. The workshop included presentations by Peter Kohl (U Oxford), Kevin Burrage (U Oxford and U Queensland), Alfons Hoekstra (U Amsterdam), Gustavo Deco (UPF), Paul Watton (U Oxford), Blanca Rodríguez (U Oxford) and Bertran Maury (U Paris Sud). After this first day, the participants were distributed in several work groups to discuss possible pipelines for the multiscale description of the suggested questions. For three days, the work groups divided their time between internal discussions and attendance to tutorials on several VPH toolkit related topics. These included tutorials on distributed computing in Europe by Stefan Zasada (UCL), standards for model sharing in systems biology by Jonathan Cooper (U Oxford), an introduction to the VPH toolkit by Keith McCormack (U Sheffield) and Yves Martelli (UPF), and the use of the online research network Activ8 by James Dalton and Albert Mascarell (UPF and O2HLink, inc.). On the last day of the SG, each group gave a short presentation of their conclusions in an informal workshop, sharing the final conclusion that the objective of the SG was achieved: coming back home with more open questions and exciting ideas than clear answers.
The workshop was a success in realizing that good research is often based on simple ideas and hypothesis, even though we often work on complex experimental designs. Clearly, ingenuity and curiosity are pre-requisites for creativity. Computer simulations and, in particular, the work of researchers in the VPH community (understood in a sense that outsources the VPH NoE or the VPH initiative themselves), can not only support other research fields in achieving their goals but also, and this is our central motivation, they can generate scientific results as any other technique may do.

The IUPAC is putting together a definition for hydrogen bond that can include experimental and theoretical results. You can find the IUPAC’s conclusion to this interesting debate here.

In a recent book review in Science of the book “From Populations to Ecosystems” by Michel Loreau, Tadashi Fukami emphasizes the message from the publication: the unfeasibility (and undesirability) to find a unified theory for ecology. Instead, he argues that it is a much better approach to deal with multilayer information, trying to find the links between different levels of organization.
Such problem arises also in other disciplines dealing with multiscale simulations. The unability of finding a unified model for a complete biological problem, for example, from the molecule to the organism, relies not in the difficulty of the mathematical approaches to be merged, but in the obvious difference in scales one faces. Thus, it is well known that it is by no means justified to include short time and small scale details that are not going to affect long time and big scale events, and applied mathematics is able to handle with the different problems by, let’s say, using stochastic to deterministic approaches. A solution in these cases is typically identifying those parameters for the large scale modelling that can be obtained aside from more detailed scale simulations.
Now that it seems that philosophy is menaced by our increasing knowledge of Nature (from the origin of the universe to the birth of conscience in our brain), scientists are falling in the danger to solely look at finding unified visions, while not realizing the power of applying what is already known has on our daily life. Finding a good combination of planning big answers to big questions while touching the ground and integrating what is already around us is the challenge for science in this next years. And multiscale simulations are in their way in many disciplines.

November 20th 2010 is the deadline for applications to the international PhD program of the Adam Mickiewicz University, in Poznan. The program awards ten PhD students to enter in a collaborative PhD between a PI of the polish university and a foreign institution. One of the selected projects is a joint initiative between the lab of Janusz Bujnicki in Poland and the CBBL in Barcelona.

Project 6. New computational methods for simulations of RNA folding and energy profiling.

We are looking for outstanding candidates to fill this postion for such an exciting initiative. Click the link above for details of how to apply.

Diario Médico, a publication for health care professionals in Spain, publishes a note on the 2nd VPH NoE Study group that was held in Barcelona during the week October 4th-8th 2010.

Jordi Villà-Freixa participa al debat sobre la medicina del futur a la Xarxa de Televisions Locals (XTVL), en una taula rodona moderada pel periodista Jordi Sacristán, que va comptar també amb Joan X. Comella, director del Vall d’Hebron Institut de Recerca (VHIR), Albert Jovell, director de la Fundació Josep Laporte, Jordi Villà i Freixa investigador en Biomedicina Informàtica de la UPF, i Karla Islas, periodista de Diario Médico.