Center for Biomedical Computing Annual Report 2009
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Center for Biomedical Computing Annual Report 2009 Being awarded a Norwegian Center of Excellence obviously results, but there will also be additionalfocus on strategy related provides unique opportunities for any research group. After al- to research plans for the final five-year period of CBC. Most of most three years in operation, CBC is very satisfied to see that the research carried out in 2009 was, in fact, shaped in 2005 as these opportunities have led to substantial growth in research part of developing the proposal for a Center of Excellence and quantity and quality since the start-up. For example, the number renewal of research projects at Simula. Successful research is of peer-reviewed papers in archival journals and conference pro- about balancing the need for renewal, the need to concentrate ceedingshas more than doubledin 2009as comparedto previous resources over long periods of time to achieve results of lasting years. impact, and a short-term demand of steady output of papers and However, even more important than modern metrics of re- candidates. The managementof CBC, in close collaboration with search productivity is the increased intensity in the center: there the management of Simula, strives to reach an optimal balance is an overflow of creativity and novel research directions, earlier between these competing requirements in today’sresearch world, recruitments prosper, ambitions are bolder, all current activities a goal which has been largely successful. are highly promising, challenging future goals seem closer, col- The CBC research projects remained scientifically unaltered laborations are improved, better outlet channels for results are through2009. As a follow-upto the scientific evaluationof Sim- found, and external invitations and recruitments indicate that ula, the BasicResearch unit performedareorganizationwhere the CBC people are highly visible in their specialities. Unfortunately, threedepartmentswerereplacedby10researchgroups,effective wehaveusedourbudgetstotheverylimit,so2009and2010are from January 1, 2010. Four of these constitute the former Sci- years with minor opportunitiesto employ more talentedpeopleto entific Computing department - the core of CBC. Simula’s strong further accelerate these positive trends. focus on research leadership at all levels, and the eagerness to When working on the CBC proposal in 2005, identification revise and improve the organizational model when needed, is a of a new and exciting multi-disciplinary application area was re- great benefit for a Center of Excellence that is expected to im- quired, and our choice was biomedical flows and structures. En- plement an effective management of research, education, and tering a new research field that entails significant recruitment outreach activities. of new staff is always challenging. We are therefore extremely An immediately important and useful result of fundamental pleasedwith the position we have attainedin this new field, both research is the training of candidates for industry and academia. internally at Simula and within the collaborating groups, in only The year of 2009 was a successful year for CBC in this respect. a few years. Output volume is increasing in general, and more Monica Hanslien, Mary MacLachlan, and Emil Løvgren moved papers, based on mathematical modeling and computations, find on to challenging research and consulting positions in industry their way to pure medical journals. It is striking to note the same and academia, after finishing their postdoctoral engagements at trend in our Computational Geosciences group, which now ad- CBC. Two other central CBC researchers, Svein Linge and Mar- dresses geoscientific journals and conferences, and experiences ius Lysaker, managed to get permanent positions as associate increasinglyenthusiasticsupportfrom theirclose industry partner professors, both at Telemark University College. Five Ph.D. stu- Statoil. dents in CBC defended their theses this year, while nine Master CBC is advantageously hosted by Simula Research Labora- of Science candidates were produced by the center’s staff. All of tory. The continued governmental funding of Simula is tightly CBC’s Ph.D. and Master candidateshave quickly found promising connected to successful evaluation of the institution every five career tracks in academia or industry. years. Acomprehensive scientificevaluationofSimulatook place Kirsten ten Tusscher recently accepted an offer as an as- in the first half of 2009 by an international committee of experts sociate professor at the University of Utrecht. CBC is proud of covering the three principal research areas of Simula. The com- having hosted her group, and not particularly surprised that that mittee was appointed by the Research Council of Norway. The such an internationally profiled scientist would be recruited as resulting evaluation report was very positive overall. In particu- permanent faculty at a highly renowned university. Dr. ten Tuss- lar, the Scientific ComputingDepartment,being the core and vast cher also received the Simula Research Award for 2009, in com- partofCBC,wasregardedas"excellentin everyaspect". Besides petition with the 100 researchers at our host institution. When being impressed by the effective organizationof the research and highly talented and productive researchers move to pursue addi- thevolumeandqualityof theresultsobtained,thecommitteehad tional career opportunities, it is a loss for a center such as CBC. also highly useful comments on future improvements and poten- However, we must ourselves that it is the very nature of such tial upcoming challenges. There is no doubt that the increased centers to host and train great talents for a shorter period and ambitions, efforts, and collaborations that naturally arise from make them qualified for other opportunities. Fortunately, we will running a Center of Excellence constitute a main reason for the collaborate closely with ten Tusscher, Linge, and Lysaker – all of top marks given by the committee. More information about this them are employed in part-time positions at CBC, and continue thorough evaluation of a large part of CBC is found in a separate with their current research projects at their new institutions. section of this report. We are also very proud to report that the CBC-funded post- The year of 2009 has been characterized by a steady focus doc Murat Tutkun received a position as an adjunct professor on established research projects and collaborations. Implement- at Ecole Centrale de Lille in France. This is one of the most ing a strong, long-term research focus is believed to be a key famous French engineering schools, belonging to the Grandes factor for successfully harvesting investments in basic research. Ecoles group. Dr. Tutkun works in the CBC-FFI collaboration 2010 will continue in this philosophy, which has yielded fruitful project with analysis of very detailed simulations of turbulent 2 flow. His science has received significant recognition, which is Understanding heart function and heart disease are both fo- clearly manifested by the fact that an elite engineering school in cal research points at CBC. The other featured research article France has hired him as a full professor. in this annual report explains how a complicated mathematical Much attention and many resources at CBC have been put model of coupled, highly nonlinear ordinary and partial differen- into the development ofa software framework,named FEniCS, for tial equationscan describe the interaction betweenthe electrical solving partial differential equations. This software framework activity in the heart and the mechanicaldeformationsof the heart is completely novel in that it combines four key features that wall. Computer simulations based on this model contribute both are normally viewed as contradictory: generality in the range of to increased fundamental understanding of physical processes in applications supported, simplicity in usage, efficiency of compu- theheartandimprovementsinspecifictreatmentsofheartfailure. tations, and reliability of computed results. Several institutions world wide contributeto FEniCS, but CBC is, at present, the driv- Examining the original CBC proposal, it is evident that none ing force in the development, testing, and distribution of this is of the planned activities and milestones have faced significant software. FEniCS is a long-term effort, and will likely achieve obstacles or delays. Some of the research activities which ap- substantial impact in the scientific community. Already before peared most challenging at the time of the proposal writing, such the first official release, planned for 2010, FEniCS is quite popu- as biomedical flow applications or fluid-structure interaction, are lar, andhasgainedusers frommorethan70countries. Aseparate now far ahead of original plans. In general, we believe, CBC has featured article in this report details what FEniCS is specifically, far exceeded our most optimistic expectations for performance and why it has such a great potential in science. as anticipated at the time of final proposal submission in 2006. 17 generations of a branching lung geometry. 3 WORDS FROM THE DIRECTOR 2 RUNNING THE CENTER 5 Organizational Changes 5 People, Recruitment and Gender Diversity 6 Gender Diversity 6 Integration of Foreign Researchers and Students 6 Evaluation 6 SCIENTIFIC ACTIVITIES 9 Computational Middleware 9 Robust Flow Solvers 10 Biomedical Flows and Structures 11 CBC at NTNU 12 CBC at FFI/UCy 13 Cardiac Computations 15 Inverse Problems 15 Computational Biology