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CBC Annual Report 2015

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CBC Annual Report 2015 Center for Biomedical Computing Annual Report 2015 Last year’s annual report emphasized that CBC is approach- work. In addition to CBC researchers being core member of the ing the end of its funding period, and this fact is of no less impor- FEniCS development community, we continue to fund key tech- tance this year. The focus has remained on reaching milestones nical personnel responsible for software maintenance and less and deliverables laid out in the CBC research plan, and on posi- research-oriented development tasks. As pointed out in several tioning the research team for securing continued funding. Both previous annual reports, this kind of work is essential for bring- focus areas have seen considerable success through 2015. Sev- ing advanced software tools out to a larger community, and it is eral new research projects have been granted from the Research normally very difficult to fund with smaller and more short-term Council of Norway and various international funding agencies, research grants. The substantial long-term funding of a Centerof which serve to reduce the negative impact of the Centre of Ex- Excellence has therefore been essential in providing these ser- cellence grant ending in 2017. However, none of the granted vices to the FEniCS community, and this contribution may end projects have the broad, long-term scope of the CBC, and the up as one of the most important long-term results of the CBC loss of a large and stable funding source will impact the research funding. In May 2016, CBC will host the annual FEniCS work- environment. The group therefore continues to seek new oppor- shop, again manifesting its role as a key partner in the FEniCS tunitiesforcontinuedfundingof thekey activities, and we expect consortium. this situtation to be the normal in years to come. With respect Since the very beginning, CBC has had the aim of both pro- to completing the planned research for CBC milestones, a sub- viding generally applicable computational software tools, and stantial number of the original milestones have been reached at address specific biomedical applications. This split focus has this point, and we are making goodprogresstowardsreaching the continued through 2015, and the continuation and expansion of major software releases and milestones scheduled for the end of our biomedical research is an important part of the Centre’s exit the CBC funding period. strategy. The integration of advanced ICT tools in health care A particularly welcome eventforCBCin 2015wasthe award is a strategic focus area for both National and European author- of the Wilkinson Prize for Numerical Software to Patrick Farrell, ities and funding agencies. Moving towards a stronger focus on Simon Funke, David Ham, and Marie Rognes, for the develop- biomedical applications, and expanding our target areas beyond ment of dolfin-adjoint. The Wilkinson Prize is awarded every the current focus on biofluids and cardiovascular research, are fourth year at the International Congress on Industrial and Ap- important steps for increasing the potentialfor continued funding plied Mathematics, and is one of the most prestigious awards in and for high impact research. Over the last year, computational the fields of numerical mathematics and computationalsoftware. neuroscience has grown from a niche activity on cerebrospinal The dolfin-adjoint software automatically derives and solves ad- fluid flow to become a major application area for CBC research. joint and tangent linear equations from high-level mathematical Many of the tools and techniques developed for cardiovascular specifications of finite element discretizations of partial differen- research can be adapted for use in neuroscience, and the field tial equations. Adjoint mathematical problems have a wide range has a large potentialfor high-impact research. We are pleasedto of applicability in engineering, in particular for optimization and see a number of small-scale research collaborations in this area, sensitivityanalysis,andwhilederivingtheadjointofalinear equa- as well as funding initiatives on various scales. tion is relatively straightforward, performing the same task for a In conclusion, we are pleased with the current state of CBC non-linear or time dependent problem may be extremely difficult. and of computational science in general at our host institution. This task is automated by dolfin-adjoint, and thereby making the The long-term, stable funding combined with the visibility of the powerful analysis based on adjoints available to a much wider Center of Excellence brand has helped us create a vibrant re- group of researchers and engineers. search environment that attracts excellent research talent. At Although dolfin-adjoint has been the most celebrated soft- the time of writing CBC has just entered its last year of funding wareprojectthrough2015,workhascontinuedsteadilyonadding and CoE status, but the future still looks bright for the research featuresand improving other partsof the FEniCS software frame- environment that has been created. 2 WORDS FROM THE DIRECTORS 2 RUNNING THE CENTER 4 Project overview 4 The Scientific Advisory Board (SAB) 4 People, Recruitment and Gender Diversity 4 Gender diversity 5 SCIENTIFIC ACTIVITIES 6 Computational Middleware 6 Robust Solvers 7 Biomedical Flows and Structures 8 CBC at NTNU 9 Cardiac Computations 10 FEATURED RESEARCH 2015: 11 Generalized geometry handling using Multimesh 11 EDUCATION AND OUTREACH 13 The Simula School of Research and Innovation 13 University Teaching 13 APPENDIX 14 Staff 14 Accounting and Budget 18 Publications 20 Conferences, Workshops and Seminars 28 Other Activities 30 Refereeing Activities 30 Prizes and Recognition 30 Committee Work 30 Organization of Minisymposia and Workshops at Conferences 30 Editorial Boards 31 Invited talks 31 Collaboration partners 33 List of International Guests in 2015 36 3 Project overview The SAB convened at CBC in February 2015, and was pre- sented with research, education and innovation activities within All research activities in CBC are organized in large projects with the scope of the Center’s activity. The generalfeedback from the an appointed project leader and a well-defined project plan. board was that they were pleased with the obtained results and 1) Computational Middleware. This project is devoted to devel- supported the overall choice of research topics and strategy. On oping generic high-performance software componentsforbuilding a more detailed level, the SAB made numerous useful comments the simulation programs needed in the Center. The results also and suggestions, in particular for increased collaboration with serve the global computational science community with a new medical industry. Although most of these collaboration leads are generation of widely applicable computational software. At the of a long-term nature, they may be extremely valuable for in- core of the developmentis the finite elementsoftwaresuite FEn- creasing visibility and relevance of CBC research, and potentially iCS. for securing valuable funding. Several of the SAB’s recommen- dations regarding sustainability and funding opportunities have 2) Robust Solvers. The Robust Solvers project focuses on ef- already been addressed and acted upon, as they will have impact ficient and stable numerical methods with error and uncertainty on our exit strategy. estimation, as well as implementation of such methods for prob- lems arising in the two application projects Cardiac Computations (CC) and Biomedical Flows and Structures (BFS). People, Recruitment and 3) Cardiac Computations. This project performs research on med- Gender Diversity ical problems involving models of heart electrophysiology and Recruitmentto the Center. We recruitedseveral newpeopleto mechanics. The current activity is closely aligned with the goals the Center’s activity during 2015, both through the RCN funded ofthe Center for CardiologicalInnovation(CCI), whichisaCenter part of the Center and through research collaboration and exter- for Research Based Innovation funded by the Research Council nallyfundedactivities. All in all we recruited9 new people to the of Norway. Center: 1 postdoctoral fellow, 6 PhDs, and 2 Research trainees. The Cardiac Computations staff was expanded with a Re- 4) Biomedical Flows and Structures. Research in the Biomedi- search Trainee (Kariline Horgmo Jæger), funded by our host in- cal Flows and Structures project centers around biomedical flow stitution. Dr. Benjamin Ragan-Kelley (funded through the Moore and tissue interaction problems of high clinical importance. In Foundation) joined the Computational Middleware project to con- a short to medium time frame, the applications to be targeted tinue hiswork on IPythonand Jupyter. The BiomedicalFlows and are aneurysm formation and rupture in the Circle of Willis, the Structures project has been strengthened with 3 PhD students: relation between Chiari I malformation and cyst formation in the Giulia Pizzichelli (IIT), Karl Erik Holter (SUURPh), Lars Magnus spinal cord, modeling of large cardiovascular networks, and fluid- Valnes (UiO), and one Research Trainee (Aslak Bergersen). In structure interactions in cardiovascular biomechanical systems. addition the PhD student Jacob Sturdy (NTNU) has joined the The research on the lattertwo topics is headedby our partnersat CBC@NTNU node. Finally, the Robust Solvers project strength- the Biomechanics Division at the Department of Structural Engi- ened its work on high performance computing by collaboration neering at the Norwegian University
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  • CV & Publication List
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