Generated by insilicoide. IPSJ Transactions on Advanced Computing Systems Journal. 2:2, pp Yasuyuki Suzuki, Yoshiyuki Asai, Hideki Oka, Er

Size: px

Start display at page:

Download "Generated by insilicoide. IPSJ Transactions on Advanced Computing Systems Journal. 2:2, pp Yasuyuki Suzuki, Yoshiyuki Asai, Hideki Oka, Er"

きのことくやす
5 years ago
Views:

1 Research Activity List Publications in Journals 1. Hidehiko Komine, Yoshiyuki Asai, Takashi Yokoi, and Mutsuko Yoshizawa. (2012) Non-invasive assessment of arterial stiffness using oscillometric blood pressure measurement. Biomedical Engineering Online. 11:6. doi: / x Samik Ghosh, Yukiko Matsuoka, Yoshiyuki Asai, Kun-Yi Hsin and Hiroaki Kitano. (2011) Software for systems biology: from tools to integrated platforms. Nature Reviews Genetics. doi: /nrg Yoshiyuki Asai and Alessandro E.P. Villa. (2011) Integration and transmission of distributed deterministic neural activity in feed-forward networks. Brain Research. doi: /j.brainres Yoshiyuki Asai, Hideki Oka, Takeshi Abe, Masao Okita, Kenichi Hagihara, Taishin Nomura, Hiroaki Kitano. (2011) An Open Platform toward Large-Scale Multilevel Modeling and Simulation of Physiological Systems. 11th Annual International Symposium on Applications and the Internet, SAINT 2011, Conference Proceedings. pp Yoshiyuki Asai and Alessandro E.P. Villa. (2011) Distributed deterministic temporal information propagated by feedforward neural networks. Lecture Notes in Computer Science, pp Yoshiyuki Asai and Alessandro E.P. Villa. (2010) Transmission of distributed deterministic temporal information through a diverging/converging three-layers neural network. Lecture Notes in Computer Science, 6532, pp Yoshiyuki Asai, Yuichi Tasaka, Kunihiko Nomura, Taishin Nomura, Maura Casadio, Pietro Morasso. (2009) Model of Postural Control in Quiet Standing: Robust Compensation of Delay-Induced Instability using Intermittent Activation of Feedback Control. Plos One 4(7): e6169. doi: /journal.pone Eric Heien, Yoshiyuki Asai, Taishin Nomura and Kenichi Hagihara (2009) Optimization Techniques for Parallel Biophysical Simulations 1

2 Generated by insilicoide. IPSJ Transactions on Advanced Computing Systems Journal. 2:2, pp Yasuyuki Suzuki, Yoshiyuki Asai, Hideki Oka, Eric Heien, Takahito Urai, Tatsuhide Okamoto, Yosuke Yumikura, Keisuke Tominaga, Yoshiyuki Kido, Masao Nakanishi, Kenichi Hagihara, Yoshihisa Kurachi, and Taishin Nomura (2009) A Platform for in silico Modeling of Physiological Systems III. 31st Annual International IEEE EMBS Conference Proceedings. pp Yoshiyuki Asai, Yasuyuki Suzuki, Yoshiyuki Kido, Hideki Oka, Eric Heien, Masao Nakanishi, Takahito Urai, Kenichi Hagihara, Yoshihisa Kurachi, Taishin Nomura (2008) Specifications of insilicoml 1.0: A Multilevel Biophysical Model Description Language. Journal Physiological Science. 58:7, pp Yoshiyuki Asai and Alessandro E.P. Villa (2008) Effect of the Background Activity on the Reconstruction of Spike Train by Spike Pattern Detection. Lecture Notes in Computer Science, 5164, II, pp Yoshiyuki Asai, Apratim Guha and Alessandro E.P. Villa (2008) Deterministic neural dynamics transmitted through neural networks. Neural Networks, vol.21:6, pp Yoshiyuki Asai and Alessandro E. P. Villa (2008) Reconstruction of Underlying Nonlinear Deterministic Dynamics Embedded in Noisy Spike Train. Journal of Biological Physics, 34, pp Yasuyuki Suzuki, Yoshiyuki Asai, Toshihiro Kawazu, Masao Nakanishi, Yoshiki Taniguchi, Eric Heien, Kenichi Hagihara, Yoshihisa Kurachi and Taishin Nomura (2008) A Platform for in silico Modeling of Physiological Systems II. CellML Compatibility and Other Extended Capabilities. 30th Annual International IEEE EMBS Conference Proceedings. pp Yoshiyuki Asai, Takashi Yokoi and Alessandro E.P. Villa (2007) Deterministic Nonlinear Spike Train Filtered by Spiking Neuron Model. Lecture Notes in Computer Science 4667, pp

3 16. Alessandro E.P. Villa, Yoshiyuki Asai and Jose P. Segundo (2007) Influence of the temporal distribution of electric pulses on transcallosal single unit responses. BioSystems 89(1-3), pp Yoshiyuki Asai and Alessandro E.P. Villa (2007) Detection of dynamical systems from noisy multivariate time series. Robert C. Dalang, Marco Dozzi, Francesco Russo, (Eds.), Seminar on Stochastic Analysis, Random Fields and Applications V. Progress in Probability, vol.59, pp A Birkhäuser book 18. Yoshiyuki Asai, Takashi Yokoi and Alessandro E.P. Villa (2006) Detection of a Dynamical System Attractor from Spike Train Analysis. Lecture Notes in Computer Science, 4131, pp Yoshiyuki Asai, Tatyana I. Aksenova and Alessandro E.P. Villa (2005) Unsupervised Recognition of Neuronal Discharge Waveforms for Online Real-Time Operation. Lecture Notes in Computer Science, 3704, pp Yoshiyuki Asai, Tatyana I. Aksenova and Alessandro E.P. Villa (2005) On-line real-time oriented application for neuronal spike sorting with unsupervised learning. Lecture Notes in Computer Science, 3696: pp Yoshimi Matsuo, Yoshiyuki Asai, Taishin Nomura, Shunsuke Sato, Satoru Inoue, Isao Mizukura, Toshihiko Yoneda, Akinori Miki, Sauburo Sakoda, Kazuo Abe (2005) Intralimb and interlimb incoordination: Comparative study between patients with parkinsonism and with cerebellar ataxia. Journal of the Japanese Physical Therapy Association, 8 (1), pp Yoshiyuki Asai, Taishin Nomura, Shunsuke Sato, Akira Tamaki, Yoshimi Matsuo, Isao Mizukura, and Kazuo Abe (2003) A coupled oscillator model of disordered interlimb coordination in patients with Parkinson s disease. Biological Cybernetics 88, pp Kazuo Abe, Yoshiyuki Asai, Yoshimi Matsuo, Taishin Nomura, Shunsuke Sato, Satoru Inoue, Isao Mizukura, Saburo Sakoda. (2003) Classifying the dynamics of Parkinson s disease. Brain Research Bulletin 61(2), pp

4 24. Yoshiyuki Asai, Taishin Nomura, Kazuo Abe, Yoshimi Matsuo, and Shunsuke Sato. (2003) Classification of dynamics of a model of motor coordination and comparison with Parkinson s disease data. BioSystems, 71(1-2), pp Yoshimi Matsuo, Yoshiyuki Asai, Taishin Nomura, Shunsuke Sato, Satoru Inoue, Isao Mizukura, Toshihiko Yoneda, Akinori Miki, and Kazuo Abe. (2003) Intralimb incoordination in patients with ataxia. NeuroReport, 14(16), pp Yoshiyuki Asai, Taishin Nomura, Shunsuke Sato (2000) Emergence of oscillations in a model of weakly coupled two Bonhoeffer-van der Pol equations. BioSystems 58, pp Publications in Journals (Japanese) 1. (2010) Physiome.jp 49, pp (2008) 29, pp (2008) 52, 5, pp (Transactions of the Institute of Systems, Control and Information Engineers. 52, 5, pp ) 4. (2008) (The dynamics of lower limb exercise in patients with neurological disease and the plasticity in the cortex). Journal of Rehabilitation Medicine, 45, 1, pp International Conferences 1. Yoshiyuki Asai, Tatsuhide Okamoto, Takeshi Abe, Masao Okita, Kenichi Hagihara, Hideki Oka, Taishin Nomura, Hiroaki Kitano. PhysioDesigner: an open platform for multilevel modeling applicable to computational neurosicence. The 21st annual Conference of the Japanese 4

5 Neural Network Society. December 15-17, 2011, Okinawa, Japan. pp Hideki Oka, Li Li, Tatsuhide Okamoto, Takahito Urai, Takeshi Abe, Yoshiyuki Asai, Taishin Nomura. EEG Analysis in insilicoide / PhysioDesigner. The 21st annual Conference of the Japanese Neural Network Society. December 15-17, 2011, Okinawa, Japan. pp Yoshiyuki Asai, Hideki Oka, Takeshi Abe, Masao Okita, Ken-ichi Hagihara, Taishin Nomura, Hiroaki Kitano. An Open Platform toward Large-scale Multilevel Modeling and Simulation of Physiological Systems. The 11th IEEE/IPSJ International Symposium on Applications and the Internet (SAINT 2011). July 18-21, 2011, Munich, Germany. 4. Yoshiyuki Asai and Alessandro E.P. Villa. Distributed deterministic temporal information propagated by feedforward neural networks. International conference on artificial neural networks. June 14-17, 2011, Helsinki, Finland. 5. Yoshiyuki Asai, Hideki Oka, Taishin Nomura and Hiroaki Kitano. Towards a simulation platform for multi-level neuronal networks. The 3rd International Conference on Cognitive Neurodynamics. June 9-13, 2011, Niseko, Japan. 6. Yoshiyuki Asai and Alessandro E.P. Villa. Spatio-temporal filtering of the distributed temporal information in spike train through a diverging/converging neural network. The 9th International Neural Coding Workshop. pp.1-2, October 29 - November 3, 2010, Limassol, Cyprus. 7. Yoshiyuki Asai and Alessandro E.P. Villa. Transmission of distributed deterministic temporal information through a diverging/converging threelayers neural network. International conference on artificial neural networks. September 15-18, 2010, Thessaloniki, Greece. 8. Eric Heien, Masao Okita, Yoshiyuki Asai, Taishin Nomura, Kenichi Hagihara. insilicosim: an Extendable Engine for Parallel Heterogeneous Biophysical Simulations. The 3rd International Conference on Simulation Tools and Techniques (SIMUTools 2010). March 15-19, 2010, Torremolinos, Malaga, Spain. 5

6 9. Yasuyuki Suzuki, Yoshiyuki Asai, Hideki Oka, Eric Heien, Takahito Urai, Tatsuhide Okamoto, Yosuke Yumikura, Keisuke Tominaga, Yoshiyuki Kido, Masao Nakanishi, Kenichi Hagihara, Yoshihisa Kurachi, and Taishin Nomura. A Platform for in silico Modeling of Physiological Systems III. 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society. September 2-6, 2009, Minneapolis, USA 10. Yoshiyuki Asai, Yasuyuki Suzuki, Yoshiyuki Kido, Hideki Oka, Eric Heien, Takahito Urai, Kenichi Hagihara, Yoshihisa Kurachi and Taishin Nomura. insilicoml and integrated environment. XXXVI International Congress of Physiological Sciences. July 27 - Aug 1, 2009, Kyoto, Japan. 11. Yasuyuki Suzuki, Yoshiyuki Asai, Yosuke Yumikura, Takahito Urai, Tatsuhide Okamoto, Kazuyoshi Kawa, Yoshihisa Kurachi and Taishin Nomura. An integrated development environment for in silico modeling of physiological systems. XXXVI International Congress of Physiological Sciences. July 27 - Aug 1, 2009, Kyoto, Japan. 12. Yoshiyuki Kido, Yoshiyuki Asai, Taishin Nomura, Yoshihisa Kurachi and Hideo Matsuda. Discovery of relation between modeling data using in-silico modeling ontology and meta-ontology. XXXVI International Congress of Physiological Sciences. July 27 - Aug 1, 2009, Kyoto, Japan. 13. Yoshiyuki Kagiyama, Masahiko Nakamoto, Yoshiyuki Asai, Toshiyuki Okada, Masaki Takao, Nobuhiko Sugano, Hideki Yoshikawa, Osamu Oshiro, Yoshinobu Sato and Taishin Nomura. An extension to the insilico ML and insilicoide to support surgical simulation and preoperative planning. XXXVI International Congress of Physiological Sciences. July 27 - Aug 1, 2009, Kyoto, Japan. 14. Yoshiyuki Asai and Alessandro E.P. Villa. Spatio temporal filtering of the distributed spike train with deterministic structure by ensemble of spiking neurons. The 8th International Neural Coding Workshop. pp.81-83, May 8-15, 2009, Tainan, Taiwan. 15. Yoshiyuki Asai, Yuichi Tasak, Kunihiko Nomura and Taishin Nomura. Compensation of delay-induced instability in inverted pendulum con- 6

7 trolled by intermittently switching feedback as a model of human quiet standing. The 8th International Neural Coding Workshop. pp , May 8-15, 2009, Tainan, Taiwan. 16. Yoshiyuki Asai and Alessandro E.P. Villa. Effect of the Background Activity on the Reconstruction of Spike Train by Spike Pattern Detection. International conference on artificial neural networks. September 3-6, 2008, Prague, Czech Republic. 17. Yasuyuki Suzuki, Yoshiyuki Asai, Toshihiro Kawazu, Masao Nakanishi, Yoshiki Taniguchi, Eric Heien, Kenichi Hagihara, Yoshihisa Kurachi, and Taishin Nomura. A Platform for in silico Modeling of Physiological Systems II. CellML Compatibility and Other Extended Capabilities. 30th Annual International IEEE EMBS Conference. August 20-24, 2008, Vancouver, Canada. 18. Taishin Nomura, Yoshiyuki Asai, Kenichi Hagihara, and Yoshihisa Kurachi. An open platform for physiome and systems biology: insilicoml and IDE as a CellML compatible model sharing environment. SIAM Conference on the Life Sciences. August 4-7, 2008, Montreal, Canada. 19. Yoshiyuki Asai, Takashi Yokoi, Alessandro E.P. Villa. Successive filtering of the spike train with deterministic temporal structure by spiking neurons. The 7th International Neural Coding Workshop. November 7-12, 2007, Monetvideo, Uruguay. 20. Yoshiyuki Asai, Takashi Yokoi, Alessandro E.P. Villa. Deterministic nonlinear spike train filtered by spiking neuron model. International conference on artificial neural networks. September 9-13, 2007, Porto, Portugal. 21. Yoshiyuki Asai, Takashi Yokoi, Alessandro E.P. Villa. Reconstruction of dynamical system based on pattern grouping algorithm. International Conference on Artificial Neural Networks. September 10-14, 2006, Athena, Greece. 22. Alessandro E.P. Villa, Yoshiyuki Asai. Multiple spike sorting of neuronal discharge waveforms in unsupervised real-time mode and for offline large recordings. 5th Forum of European Neurocsience. July 7-11, 2006, Vienna, Austria. FENS Forum Abstracts 7

8 23. Alessandro E.P. Villa, Yoshiyuki Asai, Jose P. Segundo. Influence of the temporal distribution of electric pulses on transcallosal single unit responses. The 6th International Neural Coding Workshop 2005, August 23-28, 2005, Marburg, Germany. 24. Yoshiyuki Asai, Tatyana I. Aksenova and Alessandro E.P. Villa. Online real-time oriented application for neuronal spike sorting with unsupervised learning. International Conference on Artificial Neural Networks (ICANN) 2005, September 11-15, 2005, Warsaw, Poland. 25. Yoshiyuki Asai, Tatyana I. Aksenova and Alessandro E.P. Villa. Unsupervised recognition of neuronal discharge waveforms for on-line realtime operation. Brain, Vision and Artificial Intelligence (BV&AI) 2005, October 19-21, 2005, Naples, Italy. 26. Alessandro E.P. Villa, Yoshiyuki Asai. Detection of dynamical systems from noisy multivariate time series. Fifth Seminar on Stochastic Analysis, Random Fields and Applications, May 30-June 3, 2005, Ascona, Switzerland. 27. Alessandro E.P. Villa, Yoshiyuki Asai, I.V. Tetko, B. Pardo, M.R. Velio, B. Schwaller. Cross-channel coupling of neuronal activity in Parvalbumin-deficient mice susceptible to epileptic seizures. 26th International epilepsy congress, August 28-September 1, 2005, Paris, France. 28. Matsuo Yoshimi, Asai Yoshiyuki, Nomura Taishin, Sato Shunsuke, Yoneda Toshihiko, Inoue Satoru, Mizukura Isao, Abe Kazuo. Characteristics of limb coordination in degenerative neurological diseases. Scientific Proceedings of Japanese-Korean Joint Conference on Rehabilitation Medicine, April 23-24, 2004, Kyoto, Japan. p Alessandro E.P. Villa, Jan L. Eriksson, Yoshiyuki Asai, Jose P. Segundo. Influence of the temporal distribution of electric pulses on transcallosal single unit responses. 4th Forum of European Neuroscience. July 10-14, 2004, Lisbon, Portugal. FENS Forum Abstracts, 2, p. A Matsuo Yoshimi, Asai Yoshiyuki, Nomura Taishin, Sato Shunsuke, Yoneda Toshihiko, Inoue Satoru, Miki Akinori, Mizukura Isao, Abe Kazuo Patterns of interlimb coordination on the basis of central pattern generator 8

9 model in patients with Parkinson s disease correlates well with the disease severity. Proceedings of 14th International Congress of the World Confederation for Physical Therapy, June 7-12, 2003, Barcelona, Spain. 31. Yoshiyuki Asai, Taishin Nomura, Kazuo Abe, Yoshimi Matsuo, Isao Mizukura, Shunsuke Sato. A coupled oscillator model of interlimb coordination during pedaling exercise in patients with Parkinson s disease. BIOCOMP2002 Topics in BIOMATHEMATICS and RELATED COMPUTATIONAL PROBLEMS at the Beginning of the Third Millennium, June 3-9, 2002, Vietri sul Mare, Italy. pp Yoshiyuki Asai, Taishin Nomura, Shunsuke Sato. A coupled oscillator model of ordered and disordered inter-limb coordination. The 4th International Workshop on Neuronal Coding 2001, September 10-14, Plymouth, United Kingdom. pp Yoshiyuki Asai, Taishin Nomura, Shunsuke Sato, Akira Tamaki, Yoshimi Matsuo, Isao Mizukura, Kazuo Abe. A coupled oscillator model of interlimb coordinations. ITC-CSCC2001 (International Technical Conference on Circuits/Systems, Computers and Communications 2001), July 10-12, 2001, Tokushima, Japan. vol II, pp Yoshiyuki Asai, Taishin Nomura, Shunsuke Sato. Emergence of inphase and anti-phase oscillations in a two symmetrically coupled Bonhoeffervan der Pol equations. The 3rd International Workshop on Neuronal Coding 99, October 11-15, 1999, Osaka, Japan. pp Domestic Conferences 1.,,,,, (2011) insilicosim GPU. / / SWoPP 2011, Hideki Oka, Li Li, Tatsuhide Okamoto, Takahito Urai, Takeshi Abe, Yoshiyuki Kido, Yoshiyuki Asai, Taishin Nomura (2011) Finite Element Method Analysis in insilicoide. The 50th Annual Conference of Japanese Society for Medical and Biological Engineering. 50,

10 3.,,,,,,,,,, (2010) Development and extension of physiome and systems biology oriented open platform, insilicoplatform. The 49th Annual Conference of Japanese Society for Medical and Biological Engineering. 49, (2010) Development and application of an open platform for multilevel simulations of biophysical functions, The 87th Annual Meeting of the Physiological Society of Japan) 5.,,, (2010). 54, pp , ,,, Eric Heien,,,,, (2009) insilicoml & insilicoide. 24, ,,,,, (2009) insilicoide. 48, ,,,, Eric Heien,,,,, (2008) insilicoml , ,, Eric Heien,,,,,, (2008) insilico IDE. 2008, ,,,, (2008) ISMO: insilico Modeling Ontology. 2008,

11 11.,,, Pietro Morasso G, (2008) (Bounded stability of an inverted pendulum as a model of human quiet standing). 23, ,,, Eric Heien,,, (2008) in silico IDE 47, p ,,,,, (2008) (in silico IDE) CellML 47, p ,, Eric Heien,, (2008) in silico IDE 47, p ,,,, (2008) CoP 47, pp ,,,, (2007) 34, p (2007) , ( p.s ,,, (2006) 36, pp ,,,, (2006) -. 21,

12 20.,,,,,,,, (2006) 27, ,, (2006) 8, ,,,,,, (2006) 61, ( ) 23., Alessandro E.P. Villa (2006). 2006, pp ,,,,,,,,, (2006). 47, ,,,,,,,, (2006) 41, ,,,,,,,, (2005). 60, ( ) 27.,,,,,,,, (2004) Central pattern generator CPG model -. 39, ( ). p ,,,,,,,, (2003) Central pattern generator model 38, ( ). 12

13 29.,,,,,, (2003) 58, ( ). 30.,,,,, (2002). 41, ( )., Vol. 40, Suppl. p ,,,,,,,, (2002) Parkinson pedaling Central Pattern Generator dynamics 37, ( ). 32.,,,,, (2002) 57, ( ). 33.,, (2001) Central Pattern Generator CPG. 40, ( ) Vol. 39, Suppl. p ,,, (2001) 40, ( ), Vol. 39, Suppl. p ,, (2000) CPG 14, ( ) Vol. 38, Suppl. p.20 Books 1. Alessandro E.P. Villa, Yoshiyuki Asai, Javier Iglesias, Olga K. Chibirova, Jrmie Cabessa, Pierre Dutoit and Vladyslav Shaposhnyk. Dynamical Systems and Accurate Temporal Information Transmission in Neural Networks. pp Rubin Wang and Fanji Gu (Eds.) Advances in Cognitive Neurodynamics (II), Part 2, Springer, 2011 ISBN: DOI: /

14 2.,, Samik Ghosh,.. pp ISBN: informatics.html 3... pp ( ), ( ) ISBN: Taishin Nomura, Yoshiyiki Asai. Harnessing Biological Complexity: An Introduction to Computational Physiology. Springer-Verlag. 1st Edition., December 2010, 190 p. ISBN: insilico IDE. pp ,,, (Eds.) ISBN: Other Publications 1. Yoshiyiki Asai (2010) Development and application of an open platform for multilevel simulations of biophysical functions. The Journal of Physiological Sciences. Proceedings of the 87th Annual Meeting of the Physiological Society of Japan, May 19-21, Morioka, Japan. 2. (2010) insilicoml & insilicoide., 62, 1. pp (Open platform insilicoml & insilicoide for Physiome and Systems Biology. Manufacturing & Technology. 62, 1, pp ) 3.,. (2010) Physiome.jp, 49, pp

15 (Development of an open platform for integrative life science at Physiome.jp. Journal of the society of instrument and control engineers, 49, pp ) 4.,,,,,. (2002). (Technical Report of IEICE) CAS , NLP , pp ,, (1999). (Technical Report of IEICE) NC98-142, pp ,, (1998) Z2+Z2. (Technical Report of IEICE) NLP98-16, pp Other Presentations 1. Hiroaki Wagatsuma, Yoshiyuki Asai. Application of brain models written in ISML by DBPF-SimPF linkage. Dynamic Brain Workshop (the 6th DBPF committee). December 17, Okinawa, Japan. 2. Yoshiyuki Asai. Open Platform for Multilevel Modeling of Physiological Systems. OIST Junior Researcher Retreat November 11, Yoshiyuki Asai. Open platform for multilevel and multiscale modeling and simulation -from insilicoide to PhysioDesigner. The 4th Global COE International Symposium on Physiome and Systems Biology for Integrated Life Sciences and Predictive Medicine. Nov Osaka, Japan. p Hideki Oka, Yoshiyuki Asai, Tatsuhide Okamoto. Demonstration of multilevel and multiscale modeling and simulation environment insilicoide/physiodesigner. The 4th Global COE International Symposium on Physiome and Systems Biology for Integrated Life Sciences and Predictive Medicine. Nov Osaka, Japan. 15

16 5. Yoshiyiki Asai, Takeshi Abe. Demonstration of Linkage among PhysioDesigner, ISSim and Garuda Plotter. Garuda Six Workshop. Sept 28-30, Luxembourg. 6. Takeshi Abe, Yoshiyiki Asai. Demonstration of ISSim as a partner of Garuda alliance. Garuda Five Workshop. Sept 1, Heidelberg, Germany. 7.,,,,. insilicoide/physiodesigner , Yoshiyiki Asai. Demonstration of PhysioDesigner as a partner of Garuda alliance. Garuda Four Workshop. February 23, OIST, Okinawa, Japan Brain-IS , 10.. Physiome. 5 DBPF , 11. Yoshiyiki Asai. Possible use case: CellDesigner and insilicoide (PhysioDesigner) Communication for Multilevel Modeling. Garuda Three Workshop. Octorber 9, Informatics Forum, Edinburgh, UK. 12. Yoshiyiki Asai. Physiological simulations using BioModels repository. Garuda Two Workshop. July 4-9, Manchester Interdisciplinary Biocentre, Manchester, UK. 13. Yoshiyiki Asai. Open platform for Physiome. Garuda One Workshop. February 23-25, OIST, Okinawa, Japan. 14. Yoshiyuki Asai. A Multilevel Modeling Open Platform (insilicoml and insilicoide) and its Application to Clinical Database. gcoe 11 Clinical Databases and Physiome Platforms: A Collaborative Approach

17 15.. gcoe insilico ML1.0, insilico IDE, insilico DB Yoshiyuki Asai. insilicoml: An extensible markup language format for describing multi-level biophysical models. CellML SBGN SBO BioPAX MIASE Workshop April 5 - April 9, Waiheke Island, Auckland, New Zealand. 17. Yoshiyuki Asai, Yasuyuki Suzuki, Yoshiyuki Kido, Hideki Oka, Eric Heien, Takahito Urai, Kenichi Hagihara, Yoshihisa Kurachi and Taishin Nomura. Multiscale modeling with insilicoml1.0 and insilicoide. The 3rd International Symposium of MEI Center. November 30 - December 2, San Francisco, CA, USA. 18. Yasuyuki Suzuki, Yoshiyuki Asai, Yosuke Yumikura, Eric Heien, Yoshiyuki Kido, Hideki Oka, Takahito Urai, Kenichi Hagihara, Yoshihisa Kurachi and Taishin Nomura. An Integrated Development Environment for in silico Modeling of Physiological Systems. International Symposium of MEI Center. November 30 - December 2, San Francisco, CA, USA. 19. Yoshiyuki Kido, Yoshiyuki Asai, Taishin Nomura, Yoshihisa Kurachi and Hideo Matsuda. An Architecture of Modeling Data Search using Ontology and Meta-Ontology. International Symposium of MEI Center. November 30 - December 2, San Francisco, CA, USA. 20. Hideki Oka, Yoshiyuki Asai, Yoshiyuki Kido, Yasuyuki Suzuki, Masao Okamoto, Eric Heinen, Takahito Urai, Kenichi Hagiwara, Yoshihisa Kurachi and Taishin Nomura. FEM Simulation Environment for insilicoide. International Symposium of MEI Center. November 30 - December 2, San Francisco, CA, USA. 21. Eric M. Heien, Yoshiyuki Asai, Taishin Nomura and Kenichi Hagihara. Techniques for Automatic Parallelization and Optimization of Biological Simulations from insilicoide. International Symposium of MEI Center. November 30 - December 2, San Francisco, CA, USA. 22. (2008) insilicoml 1.0 Specification. gcoe

18 23. (2008) Yoshiyuki Asai. CellML-Compatible Integrated Development Environment for Multilevel Modeling of Biophysical Functions. The 2nd CellML Workshop. March Auckland, New Zealand. 25., Alessandro E.P. Villa (2008) pp (2003). 4, ( ). Lectures 1. Yoshiyuki Asai. Invited lecture An open platform for development of mathematical models in the integrated life science Dipartimento di Matematica, Universit di Torino. July 25, Yoshiyuki Asai. CellDesigner & PhysioDesigner Tutorial PhysioDesigner (Basic usage, Modelng with Morphology and SBML/ISML Hybrid Modeling) Yoshiyuki Asai. Lecture Open Platform for Physiome. insilicoml and insilicoide Winter School on Computational Modeling in Biology. Data and model sharing by SBML and insilicoml. Devember 14-18, OIST, Okinawa, Japan. 4. Yoshiyuki Asai. Lecture Neuronal Dynamics in silico Medicine Spring School 2009 Course on Computational Biology and Biomedical Engineering March 8-11, Cosmosquare, Osaka, Japan. Patents

研究成果報告書(基金分)

研究成果報告書(基金分) 様式 C-19 F-19 Z-19( 共通 ) 1. 研究開始当初の背景生命現象のシステム論的理解の深化, 予測生理学あるいは予測医学への応用を目的としたシステムバイオロジーやシステムフィジオロジー的アプローチの進展に伴い, 多階層多スケールな生理現象のモデリング, ならびにシミュレーションを実行するための基盤技術の重要性が増加している. このような基盤技術には, ウェットドライをまたぐグループ間共同開発,