TOOLS
TOOLS
CellDesigner™ 4.4 (2014/07)
Garuda 1.1 beta (2015/01)
PhysioDesigner 1.2 (2015/3)
iPathways 1.2 (2011/08)
SERVIES
COVID-19 Taxila Portal (2019)
Influenza research-related tools: (2014)
CTen (Cell type enrichment analysis for microarray data)
CellDesignerTM
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), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW).
Biochemical, Gene Regulatory Networks Modeling with GUI
Visual Representation of Biochemical Semantics
Graphical Notation:
CellDesigner supports graphical notation and listing of the symbols based on proposal by Kitano. Mostly compliant to SBGN Process Description Diagram notation.Linkage to SBW-powered Simulator modules
SBML compliant and easy data exchange with other SBML compliant application.
Check celldesigner.org for detail information.
Garuda-Alliance &
Garuda Platform
Garuda Platform
The Garuda alliance aims to providing platform for systems biology and biomedical research that may leads to development of novel drugs and healthcare approaches.
Garuda is an open, community-driven, common platform that provides a framework to interface,discover, & navigate through different applications, databases and services in bio-medical research.
Garuda provides language independent API to connect software as gadgets, explore them through the gateway and operate them through the dashboard, all the while supported by a global alliance of leaders in computational biology and informatics.
Garuda introduction video prepared for JASIS 2015 exhibition.
Check garuda-alliance.org for detail information.
PhysioDesigner
PhysioDesigner is an open platform for supporting multilevel modeling of physiological systems in the field of integrated life-science and systems biology, including physiology, neuroscience and so forth. Users can combine and build mathematical models of biological and physiological functions on PhysioDesigner. Users can also integrate morphometric data on a model, which is used, for example, to define a domain in which partial differential equations are solved.
The models developed by PhysioDesigner is stored in PHML(Physiological Hierarchy Markup Language) format which is an XML-based specification, to describe wide variety of models of biological and physiological functions with hierarchical structure. PhysioDesigner can import / export models written in CellML format. PhysioDesigner also provides a unique function to create SBML-PHML hybrid models to create multi-level physiological systems.
Check physiodesigner.org.
iPathways
iPathways is an iPad/iPhone application to eExplore biological pathways on your palm!! In comprehending the biological complexity of living systems in disease and healthy states, molecular pathway maps form an integral part of a researcher’s arsenal.
Extended pathway library (over 200 pathways)
Explore pathway channels: Cancer, Signaling, Panther pathways, KEGG metabolic pathways
Check ipathways.org
influenza research-related tools
The following online tool / site were initial Developments by ERATO Kawaoka infection-induced host response project (Kawaoka Lab, IMUT, University of Tokyo), currently hosted by The Systems Biology Institute, Tokyo © 2014
