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COSBI Celebrates 5 Years of Success
November 30, 2010 12:01 AM PT

On Feb. 2, 2005, Microsoft announced the European Science Initiative, designed to accelerate fundamental innovation in science and computing through the pursuit of novel avenues of research by Microsoft and key research bodies across Europe.

A key part of the initiative was investment by Microsoft Research in a network of centers of excellence, hosted by key European research institutions and groups that had created a hub of knowledge in a particular research area. The first of those centers, announced the same day, was established in Italy as the Microsoft Research-University of Trento Centre for Computational and Systems Biology (COSBI).

COSBI logo

COSBI was inaugurated with fanfare on Dec. 7, 2005, an event that featured illustrious participants including Rick Rashid, senior vice president of Microsoft Research, and Andrew Herbert, then-managing director of Microsoft Research Cambridge and now chairman of Microsoft Research for the Europe, Middle East, and Africa (EMEA) region.

It has been an eventful five years, to say the least. Over that time, COSBI has provided biological researchers with a set of software tools to understand complex dynamic systems and has developed a programming language tailored to the needs of biologists. The facility has entered a partnership with Nobel Prize winner Renato Dulbecco. COSBI researchers have won several significant awards, and the lab captured the first international competition on Formal Methods in Molecular Biology.

“I am very proud of the achievements made by COSBI in these five years,” says Davide Bassi, professor of Experimental Physics and rector of the University of Trento, “in terms of both research results and strategic networking and collaborations.

“The competencies and research results gained by COSBI in these five years will be exploited with scientific and industrial partners, concurring to innovate and increase the competitiveness of local and national development. Both the public and the private sector can benefit from these results and be involved in the ultimate challenge of innovation.”

Since its inception, COSBI also has hosted significant conferences, such as Converging Sciences 2006, Computational Methods in Systems Biology 2006, and Biology Without Borders 2007.

Add another. From Nov. 30-Dec. 3, in Povo, Italy, just north of Trento, COSBI will celebrate its fifth anniversary by presenting the conference Merging Knowledge: From Programming Languages to Personalized Healthcare. During the event, to be held in the Terzo Padiglione FBK building on the University of Trento campus, a procession of renowned scientific speakers will discuss the relevance of computer science to the study of biology.

Front of commemorative medal
On its fifth anniversary, COSBI received a medal (front above; rear below) from Giorgio Napolitano, president of the Italian Republic, in recognition of its contribution and commitment to enhancing research in Italy.

Beyond its scientific content, though, the gathering also will provide an opportunity to celebrate the success COSBI has enjoyed over its first half-decade. Corrado Priami, president and chief executive officer of the facility, says that, under the circumstances, a gala occasion is warranted.

“In these five years,” Priami says, “we managed the initial challenge of a system-level understanding of interactions between various molecular machineries of organisms.”

That was the plan. From the outset, the center was focused on a pair of goals: enhancing biology and enhancing computer science. The former was a desire to increase understanding of fundamental biological processes at the system level by using programming-language theory to design new conceptual tools.

Biological systems, notes the COSBI website, are the most parallel systems ever studied, and computer science increasingly is seeking to employ parallelism in computer processors. COSBI’s second objective is to use increased understanding about how living systems handle information to design new computational paradigms, programming languages, and software-development environments. This approach of an additional foundation for systems biology rooted in computer science is called algorithmic systems biology.

Reverse of the commemorative medalThis direction has borne fruit in a number of areas. COSBI Lab, for example, is a collection of software tools to help scientists pursuing systems-level research to understand complex dynamic systems as biological or ecological networks of interaction. Its goal is to support the scientific methods underlying algorithmic systems biology by focusing on the in-silico study of the dynamics of biological systems.

COSBI Lab gives researchers an integrated method to write a model and simulate it to see if the simulation behaves as expected. They then can perform further analysis and experiments on the results.

Another COSBI contribution is BlenX, a programming model that enables the compositional and molecular description of biological systems by keeping the inherent complexity and concurrency of natural systems under control. BlenX models—programs—embed the components of the system and the rules driving their interactions. The programs are executed automatically to provide a description of the dynamics of the modeled biological system.

To estimate the vulnerability of biological communities and ecosystems, a BlenX-based ecosystem model for food-web analysis uses data collected from Alaska’s Prince William Sound. The COSBI approach defined interactions and simulated the behavior of the entire network, and researchers were able to identify “dynamic key species” and compare the results to those from structural analysis, thereby providing new keystone species to conservation biologists. This work has the potential to predict and quantify the global effects on local environments of factors such as environmental damage, global warming, and excessive fishing.

Another validation of the COSBI efforts came in 2008, when the center was selected by an international scientific committee as a computational-biology partner for an initiative started by Italian virologist Dulbecco, winner of the 1975 Nobel Prize in Physiology or Medicine. He is supporting research in bio-medicine in northern Italy’s Lombardy region, and COSBI is pursuing new, biology-inspired modeling languages and tools to represent and analyze the properties and behavior of complex systems consisting of huge numbers of competing, cooperating, and communicating components.

This is not the only Nobel-related interaction the lab has enjoyed. On Nov. 4, 2008, Sydney Brenner, co-winner of the 2002 Nobel Prize in Physiology or Medicine, delivered a keynote lecture at COSBI, underscoring the increasing prestige and influence of the facility.

And then there are the awards garnered by COSBI over its five-year history:

  • In September, Marco Scotti, COSBI researcher, received the Young Researcher Special Prize 2010 in the field of ecological sciences during the 20th national congress of the Società Italiana di Ecologica, held at the University of La Sapienza in Rome. The award, presented annually to the author of the best article in ecological sciences, was given for Scotti’s paper Using trophic hierarchy to understand food web structure.
  • In February 2009, a team of 11 COSBI researchers, working with three colleagues from France and one from Germany, won first prize in the first international formal biological modeling competition during the 27th Formal Methods in Molecular Biology conference, held at the Leibniz-Zentrum für Informatik, at Germany’s Schloss Dagstuhl. The COSBI team, led by Attila Csikász-Nagy and represented during the event by Alessandro Romanel, won for COSBI Lab, evaluated as the most promising technique for modeling and analysis of biological systems.
  • In May 2008, Matteo Cavaliere, a COSBI researcher, received the Exceptional Doctorate Award for the technical/scientific area from Spain’s University of Seville. The award is given each year to the university’s 30 best Ph.D. theses. Cavaliere won the honor after completing his European Ph.D. in Computer Science, Logic, and Artificial Intelligence.
  • In November 2007, COSBI Ph.D. student Judit Zámborszky captured the Pro Scientia Gold Medal for outstanding scientific performances at the Hungarian Academy of Sciences. The Hungarian minister of Education and the president of the Hungarian Academy of Sciences present the biannual honor to the nation’s top 45 young scientists. Zámborszky, who had won first prize in the National Conference of Scientific Students, received the award in biological sciences. She was advised by Csikász-Nagy, who also received a medal during the ceremony.
  • In October 2007, Paola Lecca, COSBI researcher, won a best-paper grant from the Societá Italiana di Neuroscienze. Her paper, Molecular Mechanism of Glutamate-Triggered Brain Glucose Metabolism: A Parametric Model from FDG PET-Scans, was presented during the second International Symposium on Brain, Vision and Artificial Intelligence, held in Naples from Oct. 10 to 12, 2007.
  • In 2009, a COSBI research group received the Young Investigator Grant from the Human Frontier Science Program, in support of novel, innovative, interdisciplinary basic research focused on the complex mechanisms of living organisms. The team, collaborating with experimentalist researchers from the University of Tokyo and the University of Cambridge, won for its investigation of the regulatory network that controls polarized cell growth.

The latter effort impressed Tony Hoare, principal researcher at Microsoft Research Cambridge and winner of the A.M. Turing Award in 1980.

“It was a delight to exchange newly emerging ideas with so many of your researchers,” Hoare told COSBI management. “You have reinforced my hopes that algorithmic modeling techniques developed to help understand computational phenomena will be adopted and instrumented in tools that contribute to biological understanding.”

Having established a tradition of achievement, COSBI welcomes those attending the Merging Knowledge conference. The event website describes the vision for the gathering:

“We envision a unique, multidisciplinary environment which stimulates discussion and encourages collaboration on challenges such as the intersection of life sciences and computer science by considering the road from programming languages to personalized healthcare.”

Speakers will discuss programming languages, simulation, verification, and computational thinking—the underpinnings of algorithmic systems biology. To highlight the lab’s key findings, the conference will feature the defense of three Ph.D. theses conducted at COSBI and will include a public session of the facility’s advisory board review. In addition to systems biology, other topics to be addressed include nutrigenomics, which merges personalized medicine with personalized diet.

Among the lecturers to speak during the Merging Knowledge event are Hoare; Leroy Hood, president of the Institute for Systems Biology; James Kaput, a director within the U.S. Food and Drug Administration; and Jeannette M. Wing, President’s Professor of Computer Science and department head of the School of Computer Science at Carnegie Mellon University.

COSBI staff
In preparation for COSBI's fifth anniversary, staff members gathered for a team photo to mark the occasion.

COSBI speakers will include Csikász-Nagy, Lorenzo Dematté, and Priami. They will be joined by Herbert; Hoare; Luca Cardelli, principal researcher at Microsoft Research Cambridge; Fabrizio Gagliardi, director of External Research EMEA; and Daron Green, general manager of the External Research division of Microsoft Research.

Also among the speakers for the conference are Frédéric Chyzak, Jean-Jacques Lévy, and Enrico Tassi of the Microsoft Research-INRIA Joint Centre, based near Paris, and Adrian Cristal, Oscar Palomar, and Osman Unsal of the BSC-Microsoft Research Centre, headquartered in Barcelona, Spain.

The INRIA and BSC speakers, along with Green, will appear during a Joint Workshop of Microsoft Research Institutes during the afternoon session on Dec. 3.

Part symposium, part celebration, the Merging Knowledge conference will point to what seems sure to be continued COSBI progress.

“In the next five years,” Priami says, “we will exploit further our understanding to enlarge the interaction domain with diseases, drugs, nutrients, and environment.

“There is great excitement and potential for the use of computer-science solutions to enhance biology-related disciplines, both in the scientific community and in the industrial community.”