Software
We are developing following software packages to support computational platform for Systems Biology.
- LibSBMLSim: The library for simulating SBML models
- CellDesigner (in collaboration with The Systems Biology Institute (SBI))
- InVivoCrowdingSimulator: A 3D lattice-based simulator for studying the dynamics of particles in the crowded environment.
- ValveConfigurator: A configuration tool for controlling valves attached to microfluidics device.
- iSight Capture plugin for ImageJ 64bit
- High performance sequence analysis library on GPU (comming soon!)
- Accelerated biochemical simulator using GPGPU
- The library for simulating spatial models described in SBML (w/ spatial extension)
- An equation based model builder
News
- 2016-12-14: Matthew Higashionna is invited to give a talk at International Symposium on Micro-Nano Science and Technology 2016 (MNST 2016). His talk title will be "Quantification of the effect of shear stress on the differentiation of SH-SY5Y cells".
- 2016-05-27: Our editorial article entitled: "Quantitative Biology: Dynamics of living systems" by Noriko Hiroi et al. is published in Frontiers in Physiology (Systems Biology).
- 2016-03-01: Our paper entitled: "Detection of Temperature Difference in Neuronal Cells" by Ryuichi Tanimoto et al. is published in Scientific Reports.
- 2016-02-10: A review entitled: "Simulation technology and its application in Systems Biology (in Japanese)" by Akira Funahashi and Noriko Hiroi. is published in Folia Pharmacologica Japonica.
- 2015-06-24: A review entitled: "The principles of whole-cell modeling" by Jonathan R Karr et al. is published in Current Opinion in Microbiology.
- 2015-05-26: A review entitled: "Bioimage Analysis for Quantitative Biology and Its Application to Mammalian Embryogenesis (in Japanese)" by Tetsuya J Kobayashi et al. is published in Medical Imaging Technology.
- 2015-02-13: Our paper entitled: "Acceleration of discrete stochastic biochemical simulation using GPGPU" by Kei Sumiyoshi et al. is published in Frontiers in Physiology (Systems Biology).
- 2015-01-21: Our paper entitled: "High-speed microscopy with an electrically tunable lens to image the dynamics of in vivo molecular complexes" by Yuichiro Nakai et al. is published in Review of Scientific Instruments.
- 2015-01-16: A paper entitled: "A proteomic study of mitotic phase-specific interactors of EB1 reveals a role for SXIP-mediated protein interactions in anaphase onset" is published in Biology Open.
- 2014-07-16: A book chapter entitled: "Modeling and simulation using CellDesigner" is published in Methods in Molecular Biology.
- 2014-04-04: Our paper entitled: "Assessing uncertainty in model parameters based on sparse and noisy experimental data" by Noriko Hiroi et al. is published in Frontiers in Physiology (Systems Biology).
- 2013-08-23: A paper entitled: "Automated tracking of mitotic spindle pole positions shows that LGN is required for spindle rotation but not orientation maintenance" is published in Cell Cycle.
- 2013-07-05: A paper entitled: "The systems biology simulation core algorithm" is published in BMC Systems Biology.
- 2013-07-04: Noriko Hiroi was invited to give a talk at The 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC’13). Her talk title was "In Vivo Oriented Modeling with Consideration of Intracellular Crowding".
- 2013-06-28: Akira Funahashi was invited to give a talk on CellDesigner at The 2nd HD Physiology International Symposium.
- 2013-05-07: Akira Funahashi and Noriko Hiroi were invited to organize a two days workshop on CellDesigner at Monash University, Australia.
- 2013-04-05: Our paper entitled: "LibSBMLSim: a reference implementation of fully functional SBML simulator" by Hiromu Takizawa et al. is published in Bioinformatics.
- 2013-01-28: LibSBMLSim version 1.1.0 released! LibSBMLSim enables you to write your own SBML capable simulator with a few lines of code.
- 2012-12-20: Our paper entitled: "Mathematical Modeling of Sustainable Synaptogenesis by Repetitive Stimuli Suggests Signaling Mechanisms In Vivo" by Noriko Hiroi and Hiromu Takizawa is published in PLoS ONE.
- 2012-12-07: A General Commentary Article entitled: "Meeting Report of the International Workshop on Quantitative Biology 2012: Mesoscopic and microscopic worlds meet." by Viji M. Draviam et al. is published in Frontiers in Physiology (Systems Biology).
- 2012-11-25: We had "5th Annual Meeting of The Japanese Society for Quantitative Biology (Q-BioJP)" at the University of Tokyo.
- 2012-11-22: We had "International Workshop on Quantitative Biology 2012" at the University of Tokyo.
- 2012-07-23: Our paper entitled: "Physiological intracellular crowdedness is defined by the perimeter-to-area ratio of sub-cellular compartments" by Noriko Hiroi is published in Frontiers in Fractal Physiology.
- 2012-06-26: Our paper entitled: "From Microscopy Data to in silico Environments for in vivo Oriented Simulations" by Noriko Hiroi is published in EURASIP Journal on Bioinformatics and Systems Biology.
- 2012-05-10: A paper entitled: "Software support for SBGN maps: SBGN-ML and LibSBGN" by Martijn P. van Iersel et al. is published in Bioinformatics.
- 2012-04-04: LibSBMLSim version 1.0.0 released! LibSBMLSim enables you to write your own SBML capable simulator with a few lines of code.
- 2011-10-21: A paper entitled: "BioPAX support in CellDesigner" by Huaiyu Mi et al. is published in Bioinformatics.
- 2011-09-15: Our paper is taken up on a Japanese news site.
- 2011-03-13: A paper entitled: "Physiological environment induce quick response - slow exhaustion reactions" by Noriko Hiroi is published in Frontiers in Physiology (Systems Biology).
Contact information
Funahashi Lab.
Room 516 and 417, Bld 14,
Department of Biosciences and Informatics,
Keio University,
3-14-1 Hiyoshi
Kouhoku-ku, Yokohama
223-8522 JAPAN
Phone: +81-45-566-1797
Email: info _at_ fun.bio.keio.ac.jp