Akito Tabira (@mythosil)

I'm working on communication and learning platforms for medical professionals as an engineering manager.

In my previous job I was developing the systems of payment, e-commerce, genomics and etc.

I've been working on a simulator for biochemical reactions since when I was a graduate student. The mathematical models of the reactions are expressed as ODEs in SBML, and our simulator libSBMLSim can solve them.
I'm a member of National Resource for Network Biology (NRNB) organization. We do mentoring for Google Summer of Code. If you're interested in participating in GSoC, see this page and contact us.

Products

libSBMLSim: A library for simulating SBML models.
sss4j: Secret sharing scheme library for Java.
regzar: Remote control for REGZA TV.
Rich Brackets Plugin for Insomnia

Skills

Java, Spring Boot
Node.js, Koa.js
PHP, Laravel
Vue.js
React
Numerical simulation
Genome analysis

Presentations

秘密分散法の数理(in Japanese)

Publications

Hiromu Takizawa, Kazushige Nakamura, Akito Tabira, Yoichi Chikahara, Tatsuhiro Matsui, Noriko Hiroi, Akira Funahashi, LibSBMLSim: a reference implementation of fully functional SBML simulator, Bioinformatics, Volume 29, Issue 11, 1 June 2013, Pages 1474–1476, https://doi.org/10.1093/bioinformatics/btt157
N. Hiroi et al., "In vivo oriented modeling with consideration of intracellular crowding," 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Osaka, 2013, pp. 2716-2719. doi: 10.1109/EMBC.2013.6610101
Keller, R., Dörr, A., Tabira, A. et al. The systems biology simulation core algorithm. BMC Syst Biol 7, 55 (2013) doi:10.1186/1752-0509-7-55
Hiroi, N., Klann, M., Iba, K. et al. From microscopy data to in silico environments for in vivo-oriented simulations. J Bioinform Sys Biology 2012, 7 (2012) doi:10.1186/1687-4153-2012-7
Hiroi N, Okuhara T, Kubojima T, Iba K, Tabira A, Yamashita S, Okada Y, Kobayashi TJ and Funahashi A (2012) Physiological intracellular crowdedness is defined by the perimeter-to-area ratio of sub-cellular compartments. Front. Physio. 3:293. doi: 10.3389/fphys.2012.00293
Hiroi N, Lu J, Iba K, Tabira A, Yamashita S, Okada Y, Flamm C, Oka K, Köhler G and Funahashi A (2011) Physiological environment induces quick response – slow exhaustion reactions. Front. Physio. 2:50. doi: 10.3389/fphys.2011.00050