Akira Funahashi

According to our database1, Akira Funahashi authored at least 32 papers between 1997 and 2013.

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Bibliography

2013
The systems biology simulation core algorithm.
BMC Systems Biology, 2013

LibSBMLSim: a reference implementation of fully functional SBML simulator.
Bioinformatics, 2013

In vivo oriented modeling with consideration of intracellular crowding.
Proceedings of the 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2013

2012
From Microscopy Data to in silico Environments for in vivo Oriented Simulations.
EURASIP J. Bioinformatics and Systems Biology, 2012

Software support for SBGN maps: SBGN-ML and LibSBGN.
Bioinformatics, 2012

2011
BioPAX support in CellDesigner.
Bioinformatics, 2011

2010
Automatic Pipeline Construction Focused on Similarity of Rate Law Functions for an FPGA-based Biochemical Simulator.
IPSJ Trans. System LSI Design Methodology, 2010

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.
J. Biomedical Semantics, 2010

A datapath classification method for FPGA-based scientific application accelerator systems.
Proceedings of the International Conference on Field-Programmable Technology, 2010

2009
A Modular Approach to Heterogeneous Biochemical Model Simulation on an FPGA.
Proceedings of the ReConFig'09: 2009 International Conference on Reconfigurable Computing and FPGAs, 2009

Configuring area and performance: Empirical evaluation on an FPGA-based biochemical simulator.
Proceedings of the 19th International Conference on Field Programmable Logic and Applications, 2009

Pipeline Scheduling with Input Port Constraints for an FPGA-Based Biochemical Simulator.
Proceedings of the Reconfigurable Computing: Architectures, 2009

2008
CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks.
Proceedings of the IEEE, 2008

Practical implementation of a network-based stochastic biochemical simulation system on an FPGA.
Proceedings of the FPL 2008, 2008

2007
Integration of CellDesigner and SABIO-RK.
In Silico Biology, 2007

A Framework for Implementing a Network-Based Stochastic Biochemical Simulator on an FPGA.
Proceedings of the 2007 International Conference on Field-Programmable Technology, 2007

FPGA Implementation of a Data-Driven Stochastic Biochemical Simulator with the Next Reaction Method.
Proceedings of the FPL 2007, 2007

A Combining technique of rate law functions for a cost-effective reconfigurable biological simulator.
Proceedings of the FPL 2007, 2007

2006
CellDesigner: a modeling tool for biochemical networks.
Proceedings of the Winter Simulation Conference WSC 2006, 2006

An FPGA Implementation of High Throughput Stochastic Simulator for Large-Scale Biochemical Systems.
Proceedings of the 2006 International Conference on Field Programmable Logic and Applications (FPL), 2006

Performance Evaluation of an Fpga-Based Biochemical Simulator ReCSip.
Proceedings of the 2006 International Conference on Field Programmable Logic and Applications (FPL), 2006

2005
An FPGA-Based, Multi-model Simulation Method for Biochemical Systems.
Proceedings of the 19th International Parallel and Distributed Processing Symposium (IPDPS 2005), 2005

The Design of Scalable Stochastic Biochemical Simulator on FPGA.
Proceedings of the 2005 IEEE International Conference on Field-Programmable Technology, 2005

A Framework for ODE-Based Multimodel Biochemical Simulations on an FPGA.
Proceedings of the 2005 International Conference on Field Programmable Logic and Applications (FPL), 2005

Efficient Scheduling of Rate Law Functions for ODE-Based Multimodel Biochemical Simulation on an FPGA.
Proceedings of the 2005 International Conference on Field Programmable Logic and Applications (FPL), 2005

2002
Routing Algorithms Based on 2D Turn Model for Irregular Networks.
Proceedings of the International Symposium on Parallel Architectures, 2002

2001
Recursive Diagonal Torus: An Interconnection Network for Massively Parallel Computers.
IEEE Trans. Parallel Distrib. Syst., 2001

L-Turn Routing: An Adaptive Routing in Irregular Networks.
Proceedings of the 2001 International Conference on Parallel Processing, 2001

The impact of output selection function on adaptive routing.
Proceedings of the ISCA 16th International Conference Computers and Their Applications, 2001

MMLRU Selection Function: An Output Selection Function on Adaptive Routing.
Proceedings of the ISCA 14th International Conference on Parallel and Distributed Computing Systems, 2001

1999
A Torus Assignment for an Interconnection Network Recursive Diagonal Torus.
Proceedings of the 1999 International Symposium on Parallel Architectures, 1999

1997
Adaptive Routing on the Recursive Diagonal Torus.
Proceedings of the High Performance Computing, International Symposium, 1997


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