physiodesigner.org

PhysioDesigner

A modeling tool for multilevel physiological systems. An open platform for multilevel modeling. The models developed by PhysioDesigner are stored in PHML (Physiological Hierarchy Markup Language) format, which is an XML-based specification, to describe a wide variety of models of biological and physiological functions with a hierarchical structure. PHML fully inherits the specifications from. Format and export models to CellML (some model expressions in PHML cannot be exported to CellML). Simulator, whic...

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The Systems Biology Institute

Hiroaki Kitano

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The Systems Biology Institute

Hiroaki Kitano

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Mi●●to , Tokyo, 108-0071

JP

81.3●●●●2181

ad●●●@sbi.jp

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The Systems Biology Institute

Hiroaki Kitano

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PhysioDesigner | physiodesigner.org Reviews

<META> DESCRIPTION

A modeling tool for multilevel physiological systems. An open platform for multilevel modeling. The models developed by PhysioDesigner are stored in PHML (Physiological Hierarchy Markup Language) format, which is an XML-based specification, to describe a wide variety of models of biological and physiological functions with a hierarchical structure. PHML fully inherits the specifications from. Format and export models to CellML (some model expressions in PHML cannot be exported to CellML). Simulator, whic...

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1 physiodesigner

2 welcome

3 screen shots

4 download

5 simulation

6 documents

7 manuals

8 tutorial movie

9 publications

10 specifications

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PhysioDesigner | physiodesigner.org Reviews

https://physiodesigner.org

A modeling tool for multilevel physiological systems. An open platform for multilevel modeling. The models developed by PhysioDesigner are stored in PHML (Physiological Hierarchy Markup Language) format, which is an XML-based specification, to describe a wide variety of models of biological and physiological functions with a hierarchical structure. PHML fully inherits the specifications from. Format and export models to CellML (some model expressions in PHML cannot be exported to CellML). Simulator, whic...

INTERNAL PAGES

physiodesigner.org

1

About us

http://www.physiodesigner.org/about_us/index.html

A modeling tool for multilevel physiological systems. Dr Yoshiyuki ASAI (OIST). Mr Takeshi ABE (OIST). Ms Li LI (Intasect). Mr Zhihui LUAN (Intasect). Mr Yoshinori TAJIMA (CRC). Mr Shoya OHTSU (Osaka Univ.). Mr Takeshi ABE (OIST). Mr Ken Kuwae (OIST). Dr Masao OKITA (Osaka. Dr Yoshiyuki ASAI (OIST). Prof Hiroaki KITANO (SBI, OIST, Sony CSL). Prof Yoshihisa KURACHI (Osaka Univ.). Prof Taishin NOMURA (Osaka Univ.). Prof Ken-ichi HAGIHARA (Osaka. Prof Yoko YAMAGUCHI (RIKEN). Prof Hiroaki WAGATSUMA (Kyutech).

2

Download

http://www.physiodesigner.org/download/index.html

A modeling tool for multilevel physiological systems. 30 June, 2016. Once you mount the disk image file you download, you will find a directory named "PhysioDesigner1.5". Please move the directory any place you want to put. That's all for installation. Note 2) If launch process fails, please try to remove $Users/.physiodesigner directory where some configuration related to PhysioDesigner are stored. By removing this file, configurations are reset to the default. Allow applications downloaded from Anywhere.

3

Flint

http://www.physiodesigner.org/simulation/flint/index.html

A modeling tool for multilevel physiological systems. Flint is a simulator of bio-physiological models written in PHML and SBML. It parses those languages, compiles internally and execute simulations. Flint can also interpret PHML-SBML hybridized multilevel models, which can be created on PhysioDesigner. Flint uses. The simulation results are written in CSV or ISD format which is a binary format to describe time series. ISD format specification can be found. There is a cloud based flint service called.

4

Documents

http://www.physiodesigner.org/documents/index.html

A modeling tool for multilevel physiological systems. Enter the name for this tabbed section: PhysioDesigner. Explain how to install PhysioDesigner and Flint. Showing a simple start with loading a model and run a simulation. Brief explanation of how to use PhysioCanvas. Create a simple model. Showing how to create a simple model (BVP model, as an example) on PhysioDesigner. Create a SBML-PHML hybrid model. The way to create a multilevel model using a SBML-PHML hybridized technique is illustrated. There a...

5

PhysioDesigner

http://www.physiodesigner.org/index.html

A modeling tool for multilevel physiological systems. An open platform for multilevel modeling. The models developed by PhysioDesigner are stored in PHML (Physiological Hierarchy Markup Language) format, which is an XML-based specification, to describe a wide variety of models of biological and physiological functions with a hierarchical structure. PHML fully inherits the specifications from. Format and export models to CellML (some model expressions in PHML cannot be exported to CellML). Simulator, whic...

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ios.unit.oist.jp

News

http://ios.unit.oist.jp/news/index.php

Integrated Open Systems Unit. Open Energy Systems Introduction. 10/04/15 12:28 Filed in: Research. Movies to introduce Open Energy Systems are released. There are two versions, short. PhysioDesigner 1.2 / Flint 1.2 were released. 31/03/15 17:51 Filed in: Software. PhysioDesigner 1.2 and Flint 1.2 have been released on 31 March 2015. Please visit our website. 17/02/15 12:12 Filed in: Event. The 2nd International Symposium on Open Energy Systems was held on February 17th. The article can be found here.

physiome.jp

Flint

http://www.physiome.jp/tools/flint/index.html

Flint / Flint K3. Flint is a simulator which can perform simulations of PHML models and SBML models. It parses those languages, compiles internally and execute simulations. Flint can also interpret PHML-SBML hybridized multilevel models, which can be created on PhysioDesigner. A cloud-based simulation service based on Flint is called Flint K3, which has been developed so that users can process simulation jobs in a high performance computing environment without the cost of high performance hardware.

physiome.jp

ImageViewer

http://www.physiome.jp/tools/imageviewer/index.html

ImageViewer is one of applications bundled in PhysioDesigner. It is possible to. Visualises image data in the format of. MAT (Matlab binary),. Wavefront OBJ, VTK, STL. Extract pixels over threshold, smoothing, deresolution,. Select voxels in RAW and VOL format images, and to export the selected voxels into a file. Mutually convert among VTK, VRML, OBJ and STL. Put dipoles on an image object data. Put markers such as cone, sphere, cuboid, on image data. Convert from VTK,. Please visit PhysioDesigner's site.

sbi.jp

The Systems Biology Institute: Systems Biology Tutorial JA

http://sbi.jp/tutorial

21271;野宏明, Dr.北野のゼロから始めるシステムバイオロジー, 羊土社 2015. 2014年7月号 Vol32 No.11). SBGN (Systems Biology Graphical Notation) : http:/ sbgn.org. サンプルファイル CellDesignerがインストールされたフォルダの samples で、MAPK.xmlを開いてください。関連ドキュメント CellDesignerがインストールされたフォルダの documents にある StartupGuide43.pdf. CellDesignerの[Detabase]メニューから、[Import Models from BioModels.net.] メニューを開く。ダイアログボックスのリストから、BIOMD0000000019 の Schoberl2002EGR MAPKを選択し、Import ボタンをクリックする。レイアウトしなおしたモデルファイル Schoebel2002 cd14.xml. CellDesigner Ver4.3) このモデルには式パラメータは入っていません。

sbi.jp

The Systems Bioilogy Institute: Links

http://sbi.jp/news.htm

Skip to: page content. Links on this page. Drug Safety Datawarehouse Symposium. In Nihonbashi, Tokyo on Jan 21, 2016. (2016/1/22). Garuda, a multi-purpose research platform from SBI, reaches new heights through InfiniCloud, a scalable High Performance Computing Cloud platform for Data-Intensive Workflows. Npj Systems Biology and Application. The first issue is now online! Sept 2 -4, 2015, Makuhari, Japan. Garuda Platform for Open Innovations in Systems Medicine. Keynote by Hiroaki Kitano. SBI to work wit...

sbi.jp

The Systems Bioilogy Institute: Links

http://sbi.jp/software.htm

Skip to: page content. Links on this page. Garuda 1.1 beta (public preview). CellDesigner™ 4.4. CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation. System proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML. Biochemical, Gene Regulatory Networks Modeling with GUI. Visual Representation of Biochemical Semantics. Linkage to SBW-powered Simulator modules.

sbi.jp

The Systems Biology Institute

http://sbi.jp/indexJ.html

2015/9/2-4@幕張メッセ) にGaruda Platform を出展. 新オープンアクセスジャーナル npj Systems Biology and Applications. 2014年9月15日(月)、特定非営利活動法人システムバイオロジー研究機構は、ネイチャーパブリッシンググループ NPG と新たに提携し、質の高い研究成果の出版に特化したオープンアクセスジャーナル. Npj Systems Biology and Applications. NatureJapanJobs 特集記事現代投資理論を生物システムに応用した理論を構築 (2010/09). NIHS Toxicology Platform (2008- ). US FDAとの共同研究 (2012 - ). JST-BBSRC Strategic International Cooperative Program. From text to pathways: text mining techniques for reconstructing signalling pathways (2009- 2012). 2001年4...

sbi.jp

The Systems Bioilogy Institute: Links

http://sbi.jp/links.htm

Skip to: page content. Links on this page. NIHS Toxicology Platform (2008- ). Open Source Drug Discovery(OSDD). TB Project (2009- ). Parkinson's Disease project with LCSB. Other joint researches / funded researches with corporates. JST ERATO-SORST Kitano Symbiotic Systems Project. GNP (Genome Network Project). Development of a Vertically Integrated Information Platfom for the Analysis of Intercellular Molecular Interaction Networks (in Japanese). JST-BBSRC Strategic International Cooperative Program.

celldesigner.org

CellDesigner.org

http://www.celldesigner.org/news.html

The Systems Biology Institute. Kitano Symbiotic Systems Project. Is available. (2011/06/22). Plugin is now available (2011/11/8). Supports Reduced Notation, Simulation Parameter Polymorphism, SBMLsim solver. Tool: iPathways 1.2. You can access the colleection of the pathway models from your iPod/iPad! SBSI CellDesigner plugin. (2011/01/19). Merge Models and Payao Uploader. (2010/10/10). CellDesigner Plugins for Pathway Databases. New Model using CellDesigner. Is now available (2010/06/28). Wu G et al.

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physiodesigner.org

PhysioDesigner

A modeling tool for multilevel physiological systems. An open platform for multilevel modeling. The models developed by PhysioDesigner are stored in PHML (Physiological Hierarchy Markup Language) format, which is an XML-based specification, to describe a wide variety of models of biological and physiological functions with a hierarchical structure. PHML fully inherits the specifications from. Format and export models to CellML (some model expressions in PHML cannot be exported to CellML). Simulator, whic...

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