A. Finney

Publications27
h-index13
Citations4,338
Highly Influential Citations348
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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
TLDR
We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. Expand
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Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.
TLDR
In this paper, we describe the Systems Biology Workbench (SBW), a software framework that allows heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' capabilities via a fast binary encoded-message system. Expand
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SBMLToolbox: an SBML toolbox for MATLAB users
TLDR
We present SBMLToolbox, a toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model. Expand
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Controlled vocabularies and semantics in systems biology
TLDR
The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Expand
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Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
TLDR
The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange. Expand
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The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology
TLDR
In this paper, we describe the ERATO Systems Biology Workbench (SBW), a software framework that allows heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' data and algorithmic capabilities. Expand
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MathSBML: a package for manipulating SBML-based biological models
TLDR
MathSBML is a Mathematica package designed for manipulating Systems Biology Markup Language (SBML) models. Expand
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CellML2SBML: conversion of CellML into SBML
TLDR
CellML2SBML is implemented as a suite of XSLT stylesheets that convert models expressed in CellML into SBML without significant loss of information. Expand
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The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks
TLDR
The SBML ODE Solver Library (SOSlib) is a programming library for symbolic and numerical analysis of chemical reaction network models encoded in the Systems Biology Markup Language (SBML). Expand
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Programmer's Manual
TLDR
All contents of this document are furnished for informational use only and are subject to change without notice and do not represent a commitment on the part of Dialogic Inc. and its affiliates or subsidiaries ("Dialogic"). Expand
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