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Currently, there are job openings for postdoctoral researchers and scientific programmers at RIKEN, Japan. Please contact Koichi Takahashi (ktakahashi at riken.jp) for details.

E-Cell Sprint 2015 at Keio University Hiyoshi Campus

We held E-Cell Sprint 2015 at Keio University Hiyoshi campus (from Aug 29 to Sep 1).

E-Cell sprint is a hackathon for systems biology software projects.

Appearing below is the achievement for each project.

We will hold E-Cell sprint next year. If you are interested in E-Cell sprint, feel free to contact sprint@e-cell.org

E-Cell Sprint 2015

E-Cell Sprint 2015

Suguru Kato Kyoto univ Cellular Potts Modeling
Keigo Nishida Osaka univ Single molecule imaging filter with machine learning
Masaki Watabe Riken cell aggregation modeling and the PALM imaging
Naoki Kumakami, Syoko Jinno, Mao Takiguchi, Yuichiro Tanaka, Maiko Wakita Keio univ porting HuVEC model from Visual Basic to MATLAB
Satya Arjunan Riken Particle simulation model of multiple membrane binding states of PTEN
Kazunari Kaizu Riken ODE model generator gadget for GARUDA
Ryo Niina Kyoto univ particle diffusion simulation on cellular surface
Fudo Fukasawa, Rei Watanabe, Kentaro Nakamura Keio univ reconstruction of deep neural network
Yasuhiro Naito Keio univ Code maintenance of E-Cell 3
Kaito Kikuchi Tokyo univ single cell image analysis
Ryosuke Imai National Institute of Genetics Monte Carlo simulation of nucleosome sliding diffusion based on chromatin domain model
chew wei xiang Riken Volumetric second-order reaction in Spatiocyte for species with radius < voxel radius.
Wataru Takahagi Keio univ “”SimuSEQ””: microarray analysis tool for whole-cell simulation
Kozo Nishida Riken Improving E-Cell4 interoperability with GARUDA
Goki Tanaka Doshisha univ binding simulation of ligand and receptor
Atsuhiro Tomita Tokyo univ simulation of intracellular homeostasis
Yugo Otake Keio univ simulation of pancreatic cancer with cell automata
Hideto Mori, Yasuhide Onuma, Keita Sasaki Keio univ Webbs: Web UI for E-Cell3
Hidetoshi Itaya Keio univ Integration of cognitive computing platform BriCA and the Robot OS software

E-Cell sprint 2014 in Hayama, Kanagawa

We held E-Cell sprint 2014 at International Productivity Center, Hayama, Kanagawa (from Aug 31 to Sep 4).

E-Cell sprint is a hackathon for systems biology software projects.

In this sprint, there were more participants than last year (about forty participants).
Appearing below is the achievement for each project.

 

Screenshot 2014-09-30 20.53.29 sprint-2014 Screenshot 2014-09-30 20.57.13 Screenshot 2014-09-30 20.58.15

E-Cell4 projects

Suguru Kato Kyoto univ Lattice Structure for Ecell4
Kozo Nishida Riken Visualization of E-Cell4 rule-base model
Kazunari Kaizu Riken spatial Gillespie method for E-Cell4
Naoki Nishida Osaka univ Visualizing microbial communities
Yuki Sakamoto Titech Kinetic rate support in ECell4

Spatiocyte projects

Satya Arjunan Riken AVX2 SIMD Implementation of Particle Diffusion
Chin Yin Fai Riken  Simulation of Cell Mechanics Reaction Diffutson Model
Masanori Kawabata, Kazunari Iwamoto Waseda univ, Riken Protein transport, the modeling and visualization

E-Cell3 projects

Yasuhiro Naito Keio univ E-Cell3 IPython
Sayuri Todoroki Keio univ simulation of baby human red blood cell model
Hitomi Sano, Maiko Wakita, Mao Takiguchi Keio univ simulation of heart muscle cell
Hideto Mori Keio univ porting TNNP model from OpenCell to E-Cell
Yuri Yamamoto Keio univ simulation of gut flora

Systems biology projects

Kaito Kikuchi Tokyo univ Creation of a Protein-Protein Interaction Analyzer Garuda Gadget
Soh Ishiguro Keio univ Reconstruction of protein complex network for whole cell simulation of E. coli
Keita Sasaki Keio univ packaging robustness analysis software
Masaki Watabe Riken bioimaging simulation
Nanami Masuyama Keio univ CAI and tAI with G-language

Whole-brain architecture projects

Yuichiro Tanaka Keio univ scripting required element for PS file
Satoshi Tamaki Keio univ Deep layer visualization in Stacked Denosing AutoEncoder
Takeshi ITOH Hokkaido univ Strengthening an Othello AI Using Machine Learning
Taku Tsuzuki Osaka univ Autoencoder with Numpy and the visualization
Keigo Nishida Osaka univ semantic space with word2vec
Hidetoshi Itaya Keio univ A Naive Implementation of Music Classification using a Recursive Neural Network
Naoya Matsumura Hokkaido univ Simulating the dynamics of cell differentiation