en News - BIOINFORMATICS BARCELONA News Tue, 20 Jun 2017 11:37:06 +0000 Tue, 20 Jun 2017 11:37:06 +0000 Houdini 2 (http://houdini.antaviana.cat/) http://www.bioinformaticsbarcelona.eu/news Researchers describe the complete epigenomes of the most frequent tumours

A team of researchers led by the lecturer Manel Esteller, ICREA researcher in the Bellvitge Biomedical Research Institute (IDIBELL) and the Faculty of Medicine and Health Sciences of the University of Barcelona, have characterized the complete epigenomes of the most common tumours, among which are the ones from colon cancer, lung cancer and breast cancer. The new study -an important step forward in the study of the origins and progress of these tumours published in the journal Oncogene- counts with the participation of Professor Modesto Orozco, from the Department of Biochemistry and Molecular Biomedicine of the Faculty of Biology of the UB, and member of IRB Barcelona and the Association Bioinformatics Barcelona (BIB), among other authors.

"This analysis has enabled us getting a first unbiased view of the tumour cells methylomes in solid tumours" says Manel Esteller, head of the Cancer Epigenetics and Biology Program (PEBC) in IDIBELL. "Not only proved that lots of anti-cancer genes' activity has stopped specifically in cancer-affected organs, but we have also shown that there are other alterations in distant chromosomal areas, since in three-dimensional world of cells these sequences are in close relative positions".

]]>
Tue, 20 Jun 2017 11:37:06 +0000 http://www.bioinformaticsbarcelona.eu/news//news/67/researchers-describe-the-complete-epigenomes-of-the-most-frequent-tumours http://www.bioinformaticsbarcelona.eu/news/67 0
Scientists reveal for the first time the details of protein association at the atomic level

Scientists from the Computational Biophysics group of GRIB (IMIM-UPF) jointly with Freie Universität Berlin (FU Berlin), for the first time, simulated the association and dissociation of protein molecules in atomic detail. The results were published in the scientific journal Nature Chemistry and were validated with experimental data.

Almost everything that happens in our body is driven by proteins that find and bind each other - to transmit information or build up living matter. Proteins and other molecules move around in our cells, and they can associate to and dissociate from each other. Our muscles, for example, consist of proteins that have associated to each other so as to form long fibers. If we move our muscles, the muscle fibers must slide relative to another, and they do so by continuously forming protein-protein contacts between each other. One fiber pulls the other to exert the muscular force, and then the protein-protein pairs dissociate again, in order to prepare for the next step.

A computational and temporarily costly process

As yet, nobody has been able to observe how proteins associate in atomic detail. The problem is that proteins are extremely small, about a billionth of a meter, and their structures fluctuate a lot, making this process invisible to microscopes or other experimental techniques.

The groups of Frank Noé, at FU Berlin, and Gianni de Fabritiis, ICREA research professor at UPF, have now collaborated to produce what is the first atomic-detail computer simulation of the process of protein-protein association and dissociation. The main challenge was that atomic-detail molecular dynamics are incredible expensive to simulate. The interactions of about 100,000 atoms need to be computed, and the force felt by every atom is evaluated. Then, the simulation moves every atom by a small distance in the direction of the force while it advances the simulated time by a femtosecond - a tiny fraction of a second. Each such step is computationally expensive, but a billion times a billion of such steps need to be performed in order to simulate the time of one hour that is the typical time the proteins stay bound before they dissociate again.

The simulation in molecular dynamics of protein association was thought to be impossible to perform at the computational level due to the amount of time needed to take samples of the biochemical process: even using a supercomputer, it is estimated that the process would have required 10,000 years to complete. "It is the type of high-risk project that is very difficult to get funding for, because when we started, no-one would believe that it's even possible", says Noé.

Key to the success of the Berlin-Barcelona team was the combination of several new technologies that enabled a "divide and conquer" approach to the problem. GPUGRID, a distributed network developed by De Fabritiis' group was employed to collect compute time on graphic processing units (GPUs) from Nvidia by volunteers around the globe. Thousands of short simulations were conducted that way, coordinated by a novel machine learning algorithm in such way that the overall protein association process could be simulated within one year instead of having to wait 10,000 years. Markov modeling, a method pioneered by Noé and colleagues, was used to combine the many short simulations to an overall dynamical model that describes protein association and dissociation in full detail.

"This was clearly a risky but important proof of principle and we are happy that we managed to show that the simulations are able to capture associations between proteins", says De Fabritiis, head of the Computational Biophysics group at the Research Programme on Biomedical Informatics (GRIB), a joint program of Pompeu Fabra University (UPF) and the Hospital del Mar Medical Research Institute (IMIM).

Nuria Plattner, the lead author of the study, explains the implication of the results: "Our simulations revealed many previously unknown details on how proteins find and bind each other. But the most valuable result of our study is the demonstration that studying protein-protein association in atomic detail is possible." This achievement opens the door to understanding the details of viral infections, the inner workings of the immune system, and many other problems with biomedical or biotechnological relevance.

The project was supported by the European Research Council (ERC), the German Research Foundation (DFG), the Spanish Research Council (CSIC) and the Einstein Foundation Berlin

Reference work: Nuria Plattner, Stefan Doerr, Gianni De Fabritiis, Frank Noé. Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling. Nature Chemistry, Junio 2017. DOI: 10.1038/NCHEM.2785

]]>
Thu, 08 Jun 2017 12:22:57 +0000 http://www.bioinformaticsbarcelona.eu/news//news/63/scientists-reveal-for-the-first-time-the-details-of-protein-association-at-the-atomic-level http://www.bioinformaticsbarcelona.eu/news/63 0
VET in bioinformatics, a good way to attract young talent

Vocational Education and Training (commonly known as VET) in bioinformatics is sure to be a way for many young people to enter the job market and a good gateway to companies in the healthcare and life sciences sector looking to add junior technicians to their teams, not just PhDs.

Our sector is growing in Catalonia, as are the companies that are moving past the start-up phase to become professional organisations with multidisciplinary teams.

At Mind the Byte, established in 2011, we are a team of 10 professionals, mainly biotechnologists and bioinformatics engineers. This year, we have begun working with two VET centres: Escola Gimbernat in Sant Cugat del Vallès, where we are teaching classes as a training company, and Institut Provençana in Barcelona, which offers Dual Vocational Education and Training. Through this programme, we have had the opportunity to work with a second-year student doing work experience in our company as part of their training.

The VET in bioinformatics in Catalonia was created through an initiative of the Bioinformatics Barcelona Association (BIB) and the Government of Catalonia Department of Education.

We are particularly interested in Dual Vocational Education and Training, as it combines in-company work experience with academic training. This is so important for our educational model! With this system, everyone wins: contact with companies allows training centres to offer programmes that are more in line with reality, companies cover their needs and students have the opportunity to gain quality practical experience that will make it easier for them to enter the job market.

The Dual VET programme is an educational model that gives future professionals better skills and boosts the competitiveness of Catalan companies. Nevertheless, we've read that the II Foro de la Alianza para la FP Dual was held recently by the Bertelsmann Foundation, in Spain, and one of their conclusions was that many of the spots available in companies go unclaimed due to a lack of candidates, which is surprising given the high unemployment rate among young people in the country.

]]>
Mon, 29 May 2017 11:24:04 +0000 http://www.bioinformaticsbarcelona.eu/news//news/61/vet-in-bioinformatics-a-good-way-to-attract-young-talent http://www.bioinformaticsbarcelona.eu/news/61 0
Computational research details the activation mechanism of a protein involved in many diseases
  • p38α is a protein involved in chronic inflammatory diseases and cancer, among other pathological conditions.
  • Published in the journal eLife, the study provides a deeper understanding of the structure of this protein, thereby paving the way for the development of more effective inhibitors.
  • These findings are the result of combining fundamental biological data using computational techniques.

The protein p38α is a member of a family of molecules that transmit outside signals throughout the cell, thus allowing for an appropriate cell response, such as proliferation, differentiation, senescence, or death. Moreover, the participation of p38α in pathological conditions, like chronic inflammatory diseases and cancer, makes it a promising pharmacological target. In this regard, a complete picture of the activation mechanism of this protein is essential in order to design specific inhibitors that do not affect other processes.

The journal eLife has published a study on p38α by Antonija Kuzmanic, an EU Marie Curie COFUND fellow who is undertaking postdoctoral training simultaneously in two IRB Barcelona labs - the Molecular Modelling and Bioinformatics Laboratory and the Signalling and Cell Cycle Laboratory. Collaborative research between the lab headed by Modesto Orozco and that led by Angel R. Nebreda, the latter an international authority on p38α, has provided an integrative picture of the p38α activation mechanism and new insights into the molecular effects of various molecules that regulate the enzymatic activity of the protein.

Using computational techniques, researchers have deciphered the key elements of the complex molecular mechanism underlying p38α activity. This study describes the protein activation mechanism in unprecedented detail and reconciles the apparent contradictory results reported in previous structural studies. "Considering the importance of p38α for pathological processes, we hope the knowledge obtained in this study will help to target the protein with more specificity," stresses Antonija Kuzmanic, first author of the study.

Identifying new inhibitors

p38α has already been targeted for inflammatory diseases and some types of cancer; however, none of the drugs have yet made it to the market. "Our study reveals novel conformations of the protein, which could be used as a starting point in virtual screening studies aimed at uncovering new inhibitors," explains Kuzmanic. And she adds, "We were also able to highlight important electrostatic interactions, which may allow us to explore alternative activation pathways with increased specificity".

A computational biology approach

"We used only computational techniques. Mainly, we employed numerous molecular dynamics simulations combined with an advanced sampling technique called metadynamics," explains Kuzmanic. This combination has an advantage over standard molecular dynamics simulations, as it allows researchers to observe large conformational changes in a reasonable amount of computational time. She goes on to say, "we are able to add statistical significance to the conformations we observed in our simulations".

This study has received funding from the Seventh Framework Programme, the Engineering and Physical Sciences Research Council, the European Research Council, Horizon 2020, and the MINECO (Spanish Ministry of Economy, Industry and Competitiveness). 

 

Reference article:

Antonija Kuzmanic, Ludovico Sutto, Giorgio Saladino, Angel R. Nebreda, Francesco L. Gervasio and Modesto Orozco. Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations. eLife (2017) DOI: 10.7554/eLife.22175

]]>
Thu, 04 May 2017 12:45:59 +0000 http://www.bioinformaticsbarcelona.eu/news//news/59/computational-research-details-the-activation-mechanism-of-a-protein-involved-in-many-diseases http://www.bioinformaticsbarcelona.eu/news/59 0
Made of Genes brings personal genomics to national-scale through its participation in Dubai Future Accelerators Made of Genes, a personal genomics start-up based in Barcelona (Spain) whose beginnings lie in ESADE Business School (both BIB members), has been selected to join the 2nd edition of the Dubai Future Accelerators program, an initiative of the Dubai Future Foundation.

This unique program connects the world's most innovative companies with the government of Dubai to create breakthrough solutions to global challenges. The Dubai Future Accelerators program partners with ground-breaking companies from around the world and gives them the opportunity to find and test new solutions to real-life challenges using the city of Dubai as a living test bed.

The first program, which ended in December 2016, resulted in US $33M in commercial partnerships, MoU's and pilot projects in just three months. Three members of Made of Genes will join the regional carrier Etisalat Digital to work to improve the chronic disease management of UAE patients.

More information at the oficial press release URL.

]]>
Tue, 04 Apr 2017 10:53:28 +0000 http://www.bioinformaticsbarcelona.eu/news//news/57/made-of-genes-brings-personal-genomics-to-national-scale-through-its-participation-in-dubai-future-accelerators http://www.bioinformaticsbarcelona.eu/news/57 0
Alfonso Valencia is appointed as Director of the Life Sciences Department within BSC

The Biologist Alfonso Valencia has been appointed at the Barcelona Supercomputing Center - Centro Nacional de Supercomputación (BSC-CNS) as Director of the Life Sciences Department, with the support of the ICREA program.

Alfonso Valencia is Director of the National Institute of Bioinformatics (Salud Carlos III Institute platform (INB-ISCIII) and node of ELIXIR the European Infrastructure of Bioinformatics), Founder and President of the International Society for Computational Biology and Co-Executive Director of the main journal in the field (Bioinformatics of Oxford University Press).

The incorporation of Valencia to BSC, which participates in the Bioinformatics Barcelona (BIB) Association, confirms the centre's commitment to personalized medicine as an area of future development for supercomputing. In the opinion of the new head of the Life Sciences Department, "the BSC offers a privileged environment to create an analysis platform of genomes of biomedical interest, capable of coordinating the efforts of internal and external BSC groups, making it competitive at an international level. Facing the enormous biomedical challenges of the future will only be possible with the coordination of the incredible scientific and technical resources of the BSC, in the rich scientific environment of Barcelona, and in combination with both National (INB-ISCIII) and European scientific infrastructures (ELIXIR)".

Alfonso Valencia's research is centred in the area of Bioinformatics and Computational Biology. The computational methods for the genome analysis are particularly application to Precision Medicine. He has also worked in the development of computational methods for the prediction of protein structures and functions, the analysis biological networks and for modelling of molecular systems. These methods are based in the development of open and collaborative structures and are immersed in large international collaborative projects.

Alfonso Valencia is also a Member of the Scientific Advisory Committee of the Swiss Institute of Bioinformatics, EBI chemical and protein domain databases, IRB, UPF_DCEX, Greek ELIXIR-Node, amongst others; Associate Editor of eLIFE, PeerJ, FEBS Letters, and co-leader of the new journal f1000 "Bioinformatics, Biomedical Informatics & Computational Biology". In addition to being a member of the European Molecular Biology Organisation (EMBO) and Founder of the BioCreative challenge in text mining.

During the last ten years, Valencia has performed his research in the National Oncology Research Center, CNIO, where he was also the Vice-Director of Basic Research and Director of the Structural Biology and BioComputing Program.

 

]]>
Fri, 17 Mar 2017 11:07:03 +0000 http://www.bioinformaticsbarcelona.eu/news//news/55/alfonso-valencia-is-appointed-as-director-of-the-life-sciences-department-within-bsc http://www.bioinformaticsbarcelona.eu/news/55 0
Genetic signature of natural selection in first Americans

When 18,000 years ago humans entered America through the Bering Strait they found a totally different climate and food. A recent study published in the journal Proceedings of the National Academy of Sciences USA (PNAS) shows that this migration left traces in the genome of Native Americans, descendants of those early settlers. These are genetic variants that facilitate the digestion of fats, which is distinctive feature of adaptation to Arctic climate and diets rich in proteins.

David Comas, a scientist at the Institute of Evolutionary Biology of Barcelona (IBE, CSIC-UPF) and director of the Department of Experimental and Health Sciences at the Pompeu Fabra University (UPF), who has participated in the research, states: "The environmental and dietary pressures that found the first settlers of America marked them genetically."

In fact, this is what in evolutionary biology is known as the founder effect. Namely, from the small group of people who crossed the Strait for the first time, only those who had these mutations survived. "As a result, all the populations that emerged from those early settlers carry the same genetic variants," explains Comas.

The paradox is that Inuit who live in the Arctic Circle still benefit from this biological adaptation, but the Amazonian Indians, who live in a tropical climate, also conserve them. According to Comas, "the fact that current populations contain adaptations of the past is not necessarily negative but can lead to metabolic dysfunctions."

These mutations had already been seen in the Inuit, but now have also been found with high frequencies in many of the 53 current and prehistoric populations that have been studied, including Amazonian tribes and native peoples of North America. Being present in almost all, the scientists believe that the adaptation happened in an ancestral population, before crossing the Strait, and then it was selected due to the environmental conditions.

Understanding how natural selection has shaped our current physiology in response to changes in climate, diet and past diseases allows us to understand the current genetic makeup of humans in relation to the susceptibility of different diseases.

Reference Article: Amorim, C.E.;  Nunes, K.; Meyer, D.; Comas, D.; Bortolini, M.C.; Salzano, F.M.; Hünemeier, T. 2107. Genetic signature of natural selection in first Americans. Proc Natl Acad Sci U S A. pii: 201620541. doi: 10.1073/pnas.1620541114.

]]>
Wed, 08 Mar 2017 11:52:12 +0000 http://www.bioinformaticsbarcelona.eu/news//news/53/genetic-signature-of-natural-selection-in-first-americans http://www.bioinformaticsbarcelona.eu/news/53 0
New role of cholesterol in regulating brain proteins discovered

A study led by researchers of GRIB (IMIM-UPF) and the Institute of Medical Physics and Biophysics at the Faculty of Medicine in Charité Hospital, Berlin, published in the journal Nature Communications, demonstrates that the cholesterol present in cell membranes can interfere with the function of an important brain membrane protein, through a previously unknown mode of interaction. Specifically, cholesterol is capable of regulating the activity of the adenosine receptor, by invading it and accessing the active site. This will allow new ways of interacting with these proteins to be devised that in the future could lead to drugs for treating diseases like Alzheimer's.

The adenosine receptor belongs to the GPCR family (G Protein-Coupled Receptors), a large group of proteins located in cell membranes, which are key in the transmission of signals and communication between cells. GPCRs are therefore involved in the majority of important physiological processes, including the interpretation of sensory stimuli such as vision, smell, and taste, the regulation of the immune and inflammatory system, and behaviour modulation.

Explanatory video in which you can see how cholesterol leaves the neuronal membrane and get within the adenosine receptor:

"Cholesterol is an essential component of neuronal membranes, where GPCRs reside along with other proteins. Interestingly, the levels of cholesterol in the membrane are altered in diseases such as Alzheimer's, where GPCRs like the adenosine receptor play a key role", explains Jana Selent, head of the GPCR Drug Discovery research group of GRIB  (IMIM-UPF). "This study has shown that cholesterol can exert direct action on this important family of proteins in neuronal membranes, the GPCRs, and establishes the basis for a hitherto unknown interaction pathway between the cell membrane and proteins", adds the researcher.

Up to now, it was thought that membrane cholesterol could regulate the activity of these proteins through two mechanisms: either by altering the physical properties of the membrane, or by binding to the surface of the protein. In both cases, it was thought that cholesterol could only exercise its modulatory action from outside the protein.

However, by using latest-generation molecular simulations the researchers were able to detect the fact that cholesterol can leave the neuronal membrane and get within the adenosine receptor, in particular accessing the receptor's active site. With this information, and in collaboration with Dr. Mairena Martin and Dr. José L. Albasanz from the University of Castilla-La Mancha, we designed an experimental protocol using cell assays to demonstrate that cholesterol is able to modulate the activity of this receptor by accessing its interior.

"Cholesterol levels in cell membranes could have a more direct effect than previously thought on the behaviour of key proteins in central nervous system diseases. In particular, high levels of membrane cholesterol like those present in Alzheimer's patients probably block the adenosine receptor, which could in turn be related to certain symptoms observed in this disease", explains Ramón Guixà González, a postdoctoral researcher at the Institute of Medical Physics and Biophysics at the Faculty of Medicine in Charité Hospital in Berlin and first author of the article. "Although other studies are needed to prove this relationship, this work provides key knowledge that could be used in the future in the development of new molecules that, like cholesterol, have the ability to get inside the receptor and modulate its activity", says the researcher.

The results from this study represent a paradigm shift in the relationship between membrane cholesterol and GPCRs in the central nervous system, and open up new avenues of research in fields where the cholesterol-GPCR relationship is essential. It also appears that the cholesterol access pathway into the receptor is an evolutionary footprint. It is therefore necessary to discover whether the molecular mechanism described in this paper is present in other GPCRs and therefore potentially involved in a wide range of central nervous system diseases.

About the GRIB

The Research Programme on Biomedical Informatics (GRIB) is a joint research programme of the Hospital del Mar Medical Research Institute (IMIM) and the Department of Experimental and Health Sciences of the Universitat Pompeu Fabra both of them partners of the Bioinformatics Barcelona Association.

Reference article

Guixà-González R, Albasanz JL, Rodríguez-Epigares I, Pastor M, Sanz F, Martí-Solano M, Manna M, Martínez-Seara H, Hildebrand PW, Martí M, Selent J. Membrane cholesterol access into a G-protein-coupled receptor. NatureCommunications, 8: 14505, 2017. DOI: 10.1038/ncomms14505.

]]>
Mon, 27 Feb 2017 13:25:45 +0000 http://www.bioinformaticsbarcelona.eu/news//news/51/new-role-of-cholesterol-in-regulating-brain-proteins-discovered http://www.bioinformaticsbarcelona.eu/news/51 0
A new study reveals the level of physical activity and sport per European country

Sweden, Finland and Denmark are the European countries that do more sport on a regular basis, according to a study published in the Open Access Library Journal, by the experts Antonio Monleón-Getino, Marta Cubedo, Martín Ríos, from the Faculty of Biology of the University of Barcelona, and Daniel Ríos, professor at the Sales Upper Secondary School in Viladecans (Barcelona). According to the conclusions, people in Portugal, Italy, Spain and especially Greece, are listed below the European average regarding the indicators on population and sport.

Sedentarism and lack of physical activity is having more and more incidences in the public health of western countries. According to the World Health Organization (WHO) , which has been reminding about the value of physical activity to promote health and prevent some pathologies, the lack of physical activity is the fourth risk factor in global mortality, and the main cause of more than 21% breast and colon cancers, the 27% of diabetes cases and around the 30% of the coronary heart diseases.

The new study published in Open Access Library covers general aspects of the physical activity and does not focus on any sport in particular. It is based on the multivariate analysis of data from around 27.000 people from 27 European countries according to the information published by the Eurobarometer of the European Commission on the practice of sport stated by people over 15. For each analysed country, the experts analyse the practice of physical exercise and sport of their inhabitants, who are listed in four categories: the ones who never play sport, barely play, occasionally play, and regularly play sport.



Physical activity in Europe: a new inequality map?

"Once we analysed the regularity with which people do sport in 27 countries of the European Union, we saw that Nordic countries, Sweden, Finland and Denmark, play sport more regularly" says Daniel Ríos, lecturer of secondary education at the Sales High School.

After Sweden, Finland and Denmark, the countries with best indicators of physical activity are Slovenia, the Netherlands, Belgium, Luxembourg, Germany, the United Kingdom and France. The lower levels in physical activity were recorded in Bulgaria and Greece.

"As a conclusion -says Daniel Ríos- we think educational and economical levels of these countries are highly related to the practice of physical activity and sport of the people". This scientific study describes how the regular practice of sport and exercise is related to adults involved in educational activities, and with a high level of satisfaction with their economic status and career profile.

In the case of Spain, "the level of sport practice is co-related with the socioeconomic status, as it was seen in the Survey of Sporting Habits in Spain 2015. The survey, carried out in the National Statistics Plan 2013-2016 by the Ministry of Education, Culture and Sport; the Senior Council for Sports and the National Institute of Statistics, aimed to bring the main indicators of sporting habits and practices of people from all the country" says Antonio Monleón-Getino, from the Department of Genetics, Microbiology and Statistics of the University of Barcelona, and member of the Research Group on Biostatistics and Bioinformatics (GRBIO), team integrated in the platform Bioinformatics Barcelona (BIB).

A multivariate statistical technique with great analytical power

The study uses a multidimensional scaling method (MDS) to represent the series of variables or the 27 European studied countries and a country with an average value (which would be the average of the countries that make the European Union up).

According to professor Daniel Ríos, "the MDS method tries to show in a Euclidean space, with few dimensions, the proximities or distances between a set of objects, countries in this case. This technique combines a great capacity to reduce data with high a high graphic potential and represent them in a space with few dimensions (two or three)".

"The MDS is very interesting because it complements other multivariate techniques (factor analysis, cluster, etc.) and allows resolving complex multivariate data collections where the relation between variables is defined with statistical proximity or distance. In this article, as a methodological novelty, the Bhattacharyya distance is applied to calculate the distance between countries" said the authors.

According to the experts, the new study wants to promote future researches based on the application of multivariate methods on the management and interpretation of statistical information.


Original article

D. Ríos, T. Monleón-Getino, M. Cubedo, M. Ríos. «A Graphical Classification of European Countries According to Physical Activity Level of Its Citizens». Open Access Library Journal, December, 2016.

]]>
Thu, 16 Feb 2017 14:08:04 +0000 http://www.bioinformaticsbarcelona.eu/news//news/49/a-new-study-reveals-the-level-of-physical-activity-and-sport-per-european-country http://www.bioinformaticsbarcelona.eu/news/49 0
CompBioMed, a centre of excellence in computational biomedicine, is born

Predictive models of diseases are gaining importance in medicine thanks to their usefulness when customizing treatments. Hence, computational methods based on human biology have become a key factor for the development of customized medicine. This scenario has led to the birth of CompBioMed project, a centre of excellence in biomedical computing that promotes the uptake and exploitation of high performance computing (HPC) in the field of biomedicine. Basic, clinical and industrial researchers will be able to participate as users in the new project, which, for the moment, will work in three different areas: cardiovascular, molecular and neuromusculoskeletal. University College of London is leading the initiative, which promotes interdisciplinary business opportunities by getting its industrial partners to participate, as well as support and facilitate modelling and simulation activities and provide education to a diverse set of communities.

Among the 14 centres participating in the project is the Computational Biophysics research group, led by the ICREA researcher Gianni de Fabritiis, at the Research Programme on Biomedical Informatics (GRIB), a joint programme between Universitat Pompeu Fabra (UPF) and Hospital del Mar Medical Research Institute (IMIM). This group will play a substantial role in work package 2 of CompBioMed: Molecularly-based Medicine Exemplar Research, and also in work package 6: Empowering Biomedical Applications

The Barcelona Supercomputing Center, (BSC-CNS) is another CompBioMed partner. The researcher Mariano Vázquez, team leader of the CASE Department, is the CompBioMed application manager, responsible for coordinating the research work of the Centre of Excellence. CompBioMed will develop parallel software (including Alya, the BSC's multiphysics simulation code) that will be installed in European supercomputing centres (BSC-CNS, SurfSARA in the Netherlands and EPCC in Scotland) for use by biomedical researchers.

CompBioMed is part of one of the new centres of excellence funded by the Horizon 2020 programme and has funding of more than 4.9 million euros. In addition to University College of London and Pompeu Fabra University, the universities of Amsterdam, Edinburgh, Oxford, Geneva and Sheffield, as well as the Barcelona Supercomputing Centre (Spain); the SURFsara organization (Netherlands); consultant CBK Sci Con (United Kingdom); companies LIFETEC Group (Holland), Bull Sas (France), Janssen Pharmaceutica (Belgium), and Acellera (Spain) and Evotec Ag (Germany), will be the project partners.

]]>
Wed, 15 Feb 2017 12:39:34 +0000 http://www.bioinformaticsbarcelona.eu/news//news/47/compbiomed-a-centre-of-excellence-in-computational-biomedicine-is-born http://www.bioinformaticsbarcelona.eu/news/47 0