Published papers

相互結合網RDTは再帰構造をもつTorusの重なりから構成されており, 超並列計算機のプロセッサ間接続を行うために優れた性質を多くもっている.超並列計算機に用いられる相互結合網において, 混雑若しくは故障したノードを回避できるルーチングアルゴリズムは必要不可欠である.既存のベクトルルーチングはシンプルではあるが, 固定ルーチング(deterministic routing)であるためこのようなノードを迂回することはできない.本研究では, Duatoによる必要十分条件を用いることによりRDT(2, 4, 1)/α上でデッドロックフリーなadaptive routing algorithim D-RDTとFD-RDTを提案し, デッドロックフリーであることを証明し, 評価を行った.D-RDTは各ランク内のトーラスではfully adaptive routingを行うが, e-cube routingをベースにしているため使用するランク順が固定される.FD-RDTは自由にランクを使用することが可能なバーチャルチャネルを付加したことにより, D-RDTに比べルーチングの自由度は高い.シミュレーションによる評価の結果, 両アリゴリズムとも既存のdeterministic routingに比べ通過率, レイテンシともに性能向上が見られ, 特にFD-RDTを用いたルーチングでは顕著であった.

Understanding the logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed CellDesigner, a modeling tool of gene-regulatory and biochemical networks. CellDesigner supports users to easily create such networks, using solidly defined and comprehensive graphical representation (SBGN, systems biology graphical notation). CellDesigner is systems biology markup language (SBML) compliant, and has Systems Biology Workbench(SBW)-enabled software so that it can import/export SBML-described documents and integrate with other SBW-enabled simulation/analysis software packages. CellDesigner also supports simulation and parameter search, which is supported by integration with SBML ordinary differential equation (ODE) Solver, enabling us to simulate through our sophisticated graphical user interface. We can also browse and modify existing SBML models with references to existing databases. CellDesigner is implemented in Java; thus, it runs on various platforms such as Windows, Linux, and MacOS X. CellDesigner is freely available from our Web site at http://celldesigner.org/. © 2007 Humana Press Inc.

Non-linear behaviour of biochemical networks, such as intracellular gene, protein or metabolic networks, is commonly represented using graphs of the underlying topology. Nodes represent abundance of molecules and edges interactions between pairs of molecules. These graphs are linear and thus based on an implicit linearization of the kinetic reactions in one or several dynamic modes of the total system. It is common to use data from different sources - experiments conducted under different conditions or even on different species - meaning that the graph will be a superposition of linearizations made in many different modes. The mixing of different modes makes it hard to identify functional modules, that is sub-systems that carry out a specific biological function, since the graph will contain many interactions that do not naturally occur at the same time. The ability to establish a boundary between the sub-system and its environment is critical in the definition of a module, contrary to a motif in which only internal interactions count. Identification of functional modules should therefore be done on graphs depicting the mode in which their function is carried out, i.e. graphs that only contain edges representing interactions active in the specific mode. In general, when an interaction between two molecules is established, one should always state the mode of the system in which it is active. This journal is © The Royal Society of Chemistry.

MathSBML is an open-source, freely downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a tool-neutral, computer-readable format for representing models of biochemical reaction networks, and it is applicable to metabolic networks, cell signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, which is a standard medium for representing and transporting data that is widely supported on the Internet, as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication, and survival. In addition to Math- SBML, a number of other tools that support SBML model examination and manipulation are provided on the http://sbml.org Web site, including libSBML, which is a C/C++ library for reading SBML models; an SBML Toolbox for MATLAB; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica, as well as providing an API for model manipulation and simulation. © 2007 Humana Press Inc.