2017 Fiscal Year Annual Research Report
The role of the ion channel distribution in dendritic computation of the cerebellar Purkinje cell
| Project/Area Number |
15K06725
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| Research Institution | Okinawa Institute of Science and Technology Graduate University |
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Principal Investigator |
洪 聖昊 沖縄科学技術大学院大学, 計算脳科学ユニット, 研究員 (90600205)
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| Co-Investigator(Kenkyū-buntansha) |
高嶋 聰 沖縄科学技術大学院大学, 計算脳科学ユニット, 研究員 (00374190) [Withdrawn]
Chen Weiliang 沖縄科学技術大学院大学, 計算脳科学ユニット, 研究員 (80596594)
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| Project Period (FY) |
2015-04-01 – 2018-03-31
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| Keywords | Parallel STEPS simulator / Cerebellar Purkinje cell / Large scale simulation / Calcium bursting |
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| Outline of Annual Research Achievements |
We made a substantial progress in developing the STEPS simulator and started developing the simulation of the whole Purkinje neuron. Continuing our effort in FY2016 for designing and implementing a highly scalable, parallel stochastic reaction-diffusion algorithm based on the Operation-Splitting method, in FY2017, we further extend our solution by implementing a parallel electric field (EField) solver using the PETSc library. The integration of TetOpSplit and PETSc EField solvers allows us to simulate complex models on an unprecedented scale. Using this, we finally reconstructed a complete Purkinje cell dendritic mesh of a million tetrahedrons from light microscope imaging data, and simulated our calcium burst model. Our pilot test suggested that the integrated TetOpSplit-PETSc EField solution is capable of dramatically reducing the simulation time compared to the traditional serial solution, even without any load balancing. This was released as STEPS 3.1.0 in June 2017, with subsequent releases of version 3.2.0 and 3.3.0 in October 2017 and April 2018, featuring a more flexible Cython API binding and other performance optimization. While with great success, we discovered in our pilot test that the operator splitting solution and the finite element EField solution demonstrated different scaling properties, which can be further optimized to achieve better speedup. This will be the focus in FY2018.
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Research Products
(8 results)
