Author Archives: Dani

Science, Language and Literacy

Posted by 3 de May de 2010

“Argument and debate are common in science, yet they are virtually absent from science education. Recent research shows, however, that opportunities for students to engage in collaborative discourse and argumentation offer a means of enhancing student conceptual understanding and students’ skills and capabilities with scientific reasoning. As one of the hallmarks of the scientist is critical, rational skepticism, the lack of opportunities to develop the ability to reason and argue scientifically would appear to be a significant weakness in contemporary educational practice. In short, knowing what is wrong matters as much as knowing what is right. This paper presents a summary of the main features of this body of research and discusses its implications for the teaching and learning of science.”
Jonathan Osborne

These are words taken from the abstract of one of the articles devoted to Science, Language and Literacy in the special issue of Science Magazine. An unavoidable reading for all those engaged on teaching science, but not just that…

Design and Management of Research Projects 2010

Posted by 19 de April de 2010

Proper project design, management and exploitation are key recipes for success in both science and business. Learning from strategies in the latter environment we can give us new visions on how to propose succesful research projects. This, eventually, will lead to better technology transfer and to a real improve on the society perception of science and on its impact in daily life economy. Within the framework of the MSc on Bioinformatics for Health Sciences we thought, some years ago, that adding a course on project management would be an excellent training for our students, with the perspective to make them aware of the role the society expects researchers to take, beyond the (extremely needed) basic science knowledge.

As the course has a wider scope than just for MSc students, we decided to propose the course as an external activity in which the MSc students are invited to attend.

The new 2010 edition of the course is organized by the GRIB, and it is available for registration and, following the experience of previous years is, doubtless, worth reserving some hours in our busy agenda to attend this extremely interesting and practical course.

Welcome to the new CBBL site

Posted by 17 de March de 2010

The new CBBL site is designed to provide easier acces to information and in a more dynamical way. After having developed group web sites since my PhD time in the Universitat Autònoma de Barcelona, I have gone through the more or less standard process for a (semi-)advanced user: raw HTML pages, small CGI scripting, PHP/MySQL, Plone and…. coming back to a more reasonable approach using the WordPress PHPH/MySQL based system. I am quite happy with this new approach, as it allows concentrating on the content and not on the technicalities. We’ll see how long it takes to get sick of it, a quite common feature of this who writes.

Using the Blog capabilities of the new CBBL site, I’ll try to make a sense of my view of understanding research when other duties allow me to spend some minutes here. As publicly paid staff, researchers are not free to deliver results in the pace and with the global interest we wish, but the ones that the society deserves. In my view, in the same way we are eager to push ourselves to publish more and better every day, such publications should carry information not just important for our ego, but for the society as a whole. That is why we feel sad when a given article, in which we put so much efforts for so long, is after publication forgotten in a obscure library, be analogical or digital. The interest in publishing with high impact should not be seen as an end by itself, but the constant checking of the pace our publications are quoted by others and influence their work is critical.

Research, however, is “just” one of the three legs of our work as teaching staff in public institutions. The other two, teaching and technology transfer, are at least at the same level, in my view. Thus, the CBBL participates with interest in the teaching of several courses and in transferring technology to the commercial world, in order to give back to the society part of the resources we receive.

Last, but not least, researchers are requested to be critical in any part of their work, with themselves and with others. I’ll try not to betray this maxima and be as caustic as politeness allow. Unfortunately, my English is not as good as my native language Catalan and my Spanish, so other non-scientific opinions will be sent to other personal blogs as well, leaving this for issues related to my professional task.

By now, enjoy reading our production and get involved in those areas of the web site that allow such interaction.

As Catalonia is a welcoming country, this blog is also a welcoming blackboard for opinions related to research. Welcome to your home.

“La ciencia que permitió descifrar el genoma” La Gaceta de Tucumán, 04/10/08

Posted by 4 de November de 2008

En los institutos de la UNT comienza el interés por la bioinformática, una disciplina en expansión en Europa y en EEUU

En la voz de Jordi Villá, que acaba de protagonizar una de las tantas historias de reencuentros entre los españoles bajados de los barcos y los que se quedaron en el terruño, hay entusiasmo. “Cuando le dije a mi padre que venía a un curso en Tucumán, él no lo podía creer. Y yo tampoco: yo me había criado en mi pueblo, en Masnou, viendo el libro de Andrés Villá que vosotros tenéis allí en vuestro archivo”, contó Jordi.
Para los más jóvenes: Andrés Villá fue un artista catalán (dibujante y humorista) tucumano por adopción, que a lo largo de 33 años ininterrumpidos acompañó a los lectores de LA GACETA con su “Nota del día”, una viñeta de humor costumbrista.
Una vez en Tucumán, alguien, en el curso, le dijo a Jordi: “no sólo sabemos quién fue Andrés Villá; también podemos contarte que él tuvo dos hijas: una es María Isabel, que trabaja en LA GACETA; la otra se llamaba Nuria, y falleció hace poco tiempo”. De ahí al abrazo con la prima- y un largo café, para ponerse al día sobre la saga familiar – no hubo más que un trecho.
Doctor en Química y experto en bioinformática (dirige una maestría en esa disciplina en la Universidad Pompeu Fabra, de Barcelona), participó con otros colegas en Tucumán en un curso financiado por la Universidad de Andalucía que organizaron el Conicet y la UNT.

-¿Qué es la bioinformática?
– Es un campo de la ciencia en el cual confluyen varias disciplinas tales como: biología, computación, química e ingeniería. Sin ella no habría sido posible la secuenciación del genoma humano. Hay cinco grandes bloques: la bioinformática biomédica; la genómica computacional; la bioinformática estructural (trata de entender las estructuras de las proteínas, sus propiedades); el diseño de fármacos y la biología de sistemas, que es el uso de la informática para estudiar la biología: tomas una célula, y con el ordenador intentas hacer simulaciones, para ver cómo funciona esa célula. Aunque esto es todavía un poco ciencia- ficción.

– ¿Podemos decir que en la bioinformática el ordenador llega adonde no llega el ojo en el laboratorio?
– Podemos. El mundo de la bioinformática está en plena expansión. Hay quienes afirman que en 10 años la biología va a ser computación en un 50 %.

– ¿A qué atribuye que la bioinformática no se haya desarrollado todavía en la Argentina?
– Argentina es muy potente en ciencia; exporta muchos investigadores muy buenos. Es probable que lo que haya ocurrido aquí sea la organización de la Universidad, compartimentada. Quizás falte esa mirada sistémica, interdisciplinar, que exige la bioinformática.

“Simulating life through complex computer networks” El.lipse July 2008

Posted by 9 de September de 2008

An article in the PRBB journal El.lipse on the work done by the CBBL.

Physicists, mathematicians, biochemists, biologists, computer technicians and pharmacists seven men and one woman. This is the profile of the Computional Biochemistry and Biophysics group of the GRIB, directed by Jordi Villà i Freixa since 5 years ago. The group makes simulations of several biochemical processes, and they also develop the computer programs needed for the simulations. These are always created as “Open Source” so they can be used by the rest of the community. The simulations can be at different levels, from individual molecules to groups of cells and tissues. For example, they simulate the interaction between proteins, complementing the experimental studies and based on fundamental principles, in order to predict which ones can interact amongst them and which mutations could prevent or help this interaction. This is the case of their collaboration with Paco Muñoz (UPF), with whom they study the effect of oxidative stress in the activity of certain enzymes and their possible relation to Alzheimer. In the other extreme, the group creates simulations of gene regulation networks during the development of the chicken otic placode and the interaction with morphogens that are differentially expressed within the tissue. This is done with Berta Alsina, also from the UPF.
The group participates in several European projects. On the one hand there is “QosCosGrid”, a project on distributed computing, a way of doing complex calculations from different independent machines connected within a unique network. “This way we don’t depend on a supercomputer, but joining what everyone has at home we can do very complex calculations”,says Villà.
“The problem with distributed computing is that these machines don’t know each other and they have difficulties communicating”, he continues. The aim of “QosCos Grid” is to solve these communication problems.
“BioBridge” is another of the European projects in which they work, a biomedical informatics initiative that aims to create a portal for the integration of genomic and clinical information using systems biology tools. The group uses COPD (Chronic Obstructive Pulmonary Disease) as a working case. The longterm aim is to find biomarkers, molecules that can predict if a person has more or less propensity to suffer COPD. Since this June, the laboratory is also part of the European Network of Excellence “Virtual Physiological Human” (VPH), in which other groups at GRIB, those of Ferran Sanz and Manuel Pastor, also participate. This network will help creating the necessary infrastructure to generate the first virtual human being. For this they must make integrated simulations of what happens within a cell, an organ or the whole organism. “The most important task is to develop standards of how to relate the information from groups working at different levels”, points out Villà. Within VPH, the group is in charge of making a pilot application on drug safety, in close collaboration with “Ramón y Cajal” researcher Gianni de Fabritiis and the other two groups from the GRIB, “Many drugs block specific heart ionic channels as a side effect. What we try to do is to make simulations at multiple scales, to see whether a drug could block these channels at the molecular level, and how would this affect at a supracellular level and at the level of the whole organism”, concludes Villà