Category: System Biology & Modeling

UBViz 0.9R04- Explore Metabolic Pathways in 3D

UBViz 0.9R04

:: DESCRIPTION

UBViz is a software tool designed to make biochemical pathways easier to understand for biologists. Users can visualize and interact with a biochemical pathway from KEGG’s website in 3-D space, and browse all related web pages within one window.

With UBViz’ built-in network functionalities, pathway data are obtained directly from KEGG’s website and automatically processed. As a result, users are guaranteed to view the newest version of the biochemical pathways. UBViz uses the popular XML format as its input, with very little modification UBViz can be easily adapted to view any database which stores pathway information in XML.

::DEVELOPER

Complex Computation Laboratory ,Iowa State University

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /Mac OsX

:: DOWNLOAD

Registration First ; UBViz

:: MORE INFORMATION

Citation

UBViz: a software tool for exploring metabolic pathways in 3-D space
Song Li and Hui-Hsien Chou
BioTechniques Vol. 38, No. 4: pp 540-542 (Apr 2005)

MOMA – Minimal Perturbation Analysis

MOMA

:: DESCRIPTION

MOMA (Minimization of Metabolic Adjustment) generates predictions of flux distribution for perturbed metabolic networks.

::DEVELOPER

Daniel Segre’

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

MOMA ; BioSpice MOMA

:: MORE INFORMATION

Citation:

Analysis of optimality in natural and perturbed metabolic networks
by Daniel Segre’ , Dennis Vitkup and George M. Church, Proc. Natl. Acad. Sci. USA (2002), 99(23), 15112-15117

Bio-SPICE Dashboard 7.0 – Viological Simulation Program for Intra- & Inter-Cellular Evaluation

Bio-SPICE Dashboard 7.0

:: DESCRIPTION

Bio-SPICE, an open source framework and software toolset for Systems Biology, is intended to assist biological researchers in the modeling and simulation of spatio-temporal processes in living cells. In addition, our goal is to develop and serve a user community committed to using, extending, and exploiting these tools to further our knowledge of biological processes.

Bio-SPICE is intended for modeling and simulation of spatio-temporal processes in living cells.

The core of the Bio-SPICE application is called the Dashboard. The Bio-SPICE Dashboard has an Update Center and allows for different tool functionality to be downloaded, data to be specified, and both to be integrated into tool chains and work flows for modeling, analysis, and simulation.

::DEVELOPER

Biospice Project Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

Bio-SPICE Dashboard ; Tutorial ; plugin modules

:: MORE INFORMATION

Bio-SPICE is now released under the open-source Bio-SPICE BSD License.

Pointillist 2.1.2 – MATLAB Codes of Iterative Framework for Biological Modeling

Pointillist 2.1.2

:: DESCRIPTION

Pointillist is a set of MATLAB codes for inferring the set of elements affected by a perturbation of a biological system, based on multiple types of evidence. The integration methods in Pointillist are general-purpose and may be applied to integrate data from any existing and future technologies without requiring training datasets.

::DEVELOPER

Computational Biology, Institute for Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Pointillist ; maunal ;  Java version

:: MORE INFORMATION

Citation:

Hwang D, Rust AG, Ramsey S, Smith JJ, Leslie DM, Weston AD, de Atauri P, Aitchison JD, Hood L, Siegel AF, Bolouri H. “A data integration methodology for systems biology.” Proc Natl Acad Sci U S A 2005; 102(48) 17296-17301.

ISBJava 2.4.4 – Java library for Research in Computational Biology

ISBJava 2.4.4

:: DESCRIPTION

The ISBJava project is a library (collection) of classes written in the Java programming language, that are intended to be used for research in computational biology.

::DEVELOPER

Stephen Ramsey in the laboratory of Hamid Bolouri at ISB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

ISBJava ; manual

:: MORE INFORMATION

The license agreement is the GNU Lesser General Public License (LGPL), which is a standard “free software” and “open source” license.

Please e-mail comments or corrections regarding this document to:  isbjava at systemsbiology.org

Cellware 3.0.1 – Modeling & Simulation Tool for Modeling Cellular Transactions

Cellware 3.0.1

:: DESCRIPTION

Cellware is a new modeling and simulation tool for modeling cellular transactions.Cellware has been designed to model whole cell biochemical reactions. Besides the capabilities of simulating biochemical pathways that consist of gene regulation networks and metabolic pathways, Cellware also includes analysis tools like parameter estimation and graph layout algorithms.

Cellware has not only been designed to conduct modeling and simulation of gene regulatory and metabolic pathways but also offer an integrated environment for diverse mathematical representations, parameter estimation and optimization. In addition, a user-friendly graphical display and capability to run large and complex models would be provided by default. A very special feature of Cellware is that it would be the first grid based modeling and simulation tool in the field of Systems Biology

::DEVELOPER

Systems Biology Group ,Bioinformatics Institute, Singapore

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

Cellware ; manual

:: MORE INFORMATION

Citation:

Tan Chee Meng, Sandeep Somani, Li Ye, Anand Sairam, Zhu Hao, Arun Krishnan, Kishore Sakharkar, Pawan Dhar “Cellware: The Grid-Enabled Tool for Cell Modeling And Simulation”, Bioinformatics 2004

SSC 0.6 – Stochastic Simulation Compiler

SSC 0.6

:: DESCRIPTION

SSC (Stochastic Simulation Compiler) is a tool for creating exact stochastic simulations of biochemical reaction networks. The models are written in a succinct, intuitive format, where reactions are specified with patterns. Patterns mention only the part of the compound relevant to a given reaction, and correspond to an intuitive view of biochemical reactions. This enables complex biochemical signaling networks to be specified without the knowledge of any formal programming languages.

::DEVELOPER

Lis, Mieszko; Artyomov, Maxim N.; Chakraborty, Arup K.; Devadas, Srinivas @ MIT

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

SSC

:: MORE INFORMATION

Citation:

Lis, Mieszko et al. “Efficient stochastic simulation of reaction–diffusion processes via direct compilation.” Bioinformatics 25.17 (2009): 2289 -2291.

E-Cell 3D demo – 3D Cell Simulation

E-Cell 3D demo

:: DESCRIPTION

E-Cell 3D introduces a whole new dimension for the understanding of dynamic behaviors of complex cellular systems, with dazzling visualization using cutting-edge 3D graphics. This visualization approach allows the user to capture the entire system at a glance, and aids the heuristics of system biologists in the process of modeling.

E-Cell 3D accelerates the understanding of the whole cell with sophisticated 3D graphics.With E-Cell 3D, scientists can easily capture the dynamism in the cellular system, including the molecular concentrations of each of the components, flux and enzymatic activities, and compounds that are controlling the system that change their coordinates. Central process in systems biology is the modeling process, and this type of visualization aids the heuristics of experienced research scientists while modeling.

::DEVELOPER

Dr. Kazuharu Arakawa and Mr. Nozomu Yachie, working under the direction of Dr. Masaru Tomita, Institute for Advanced Biosciences, Keio University

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

E-Cell 3D

:: MORE INFORMATION

This demo is a fully functional E-Cell 3D software equipped with the circadian oscillation model of Drosophila by Ueda et al. (2001, Journal of Theoretical Biology), but currently the model cannot be changed.

BioSPI – SIMULATION OF BIOCHEMICAL PROCESSES

BioSPI

:: DESCRIPTION

BioSPI is a computer application we have developed for simulating the behavior of biochemical systems specified in the pi calculus. It is based on the Logix system, which implements Flat Concurrent Prolog (FCP). The use of FCP allows both mobility and synchronized communication, two of the major features of the pi-calculus.  To the best of our knowledge this is the only implementation of the full synchronous calculus, including mixed choice.

::DEVELOPER

BioSPI Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Sun Solaris/ Linux/SGI

:: DOWNLOAD

BioSPI

:: MORE INFORMATION

In order to obtain the PSI system, please write BioSPI Team, and specify your name, affiliation, and preferred platform.

CHARON 1.0 – Language for Modular Specification of Interacting Hybrid System

CHARON 1.0

:: DESCRIPTION

CHARON is a language for modular specification of interacting hybrid systems based on the notions of agent and mode. For hierarchical description of the system architecture, CHARON provides the operations of instantiation, hiding, and parallel composition on agents, which can be used to build a complex agent from other agents. The discrete and continuous behaviors of an agent are described using modes. For hierarchical description of the behavior of an agent, CHARON supports the operations of instantiation and nesting of modes. Furthermore, features such as weak preemption, history retention, and externally defined Java functions, facilitate the description of complex discrete behavior. Continuous behavior can be specified using differential as well as algebraic constraints, and invariants restricting the flow spaces, all of which can be declared at various levels of the hierarchy. The modular structure of the language is not merely syntactic, but also reflected in the semantics so that it can be exploited during analysis.

::DEVELOPER

Biocomputation Group at the University of Pennsylvania

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

CHARON ; manual

:: MORE INFORMATION

If you have questions. Please contact the friendly folks at the CHARON help desk (charon-help@cis.upenn.edu).