Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration

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Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration is …
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scholarly articleQ13442814

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P356DOI10.1089/153623103322637670
P8608Fatcat IDrelease_n72kaisq25g35psxqb3zmzyeqy
P698PubMed publication ID14683609
P5875ResearchGate publication ID8952012

P50authorHerbert M. SauroQ42624413
Michael HuckaQ56427730
Hamid BolouriQ89555884
Hiroaki KitanoQ3915986
John DoyleQ6230055
P2093author name stringAndrew Finney
Cameron Wellock
P2860cites workThe systems biology markup language (SBML): a medium for representation and exchange of biochemical network modelsQ28212902
P433issue4
P921main subjectsystems biologyQ815297
P304page(s)355-372
P577publication date2003-01-01
P1433published inOMICS A Journal of Integrative BiologyQ15753054
P1476titleNext generation simulation tools: the Systems Biology Workbench and BioSPICE integration
P478volume7

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cites work (P2860)
Q45945650A Predictive Model for Selective Targeting of the Warburg Effect through GAPDH Inhibition with a Natural Product.
Q41043010A Quantitative Systems Pharmacology Platform to Investigate the Impact of Alirocumab and Cholesterol-Lowering Therapies on Lipid Profiles and Plaque Characteristics
Q64228220A Survey of Software Tool Utilization and Capabilities for Quantitative Systems Pharmacology: What We Have and What We Need
Q27324767A computational model predicting disruption of blood vessel development
Q52713114A domino effect in drug action: from metabolic assault towards parasite differentiation.
Q48500935A grid layout algorithm for automatic drawing of biochemical networks
Q41896416A metabolic model of human erythrocytes: practical application of the E-Cell Simulation Environment.
Q36600060A model qualification method for mechanistic physiological QSP models to support model-informed drug development
Q33434485A modeling-derived hypothesis on chronicity in respiratory diseases: desensitized pathogen recognition secondary to hyperactive IRAK/TRAF6 signaling
Q42968339A novel strategy for mechanism based computational drug discovery
Q88950474A portable structural analysis library for reaction networks
Q37600716A system biology approach to identify regulatory pathways underlying the neuroendocrine control of female puberty in rats and nonhuman primates
Q30436382A systems analysis of importin-{alpha}-{beta} mediated nuclear protein import
Q24809632A two-way interface between limited Systems Biology Markup Language and R
Q33754388An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences.
Q51901985Automated learning of generative models for subcellular location: building blocks for systems biology.
Q64281567Best Practices to Maximize the Use and Reuse of Quantitative and Systems Pharmacology Models: Recommendations From the United Kingdom Quantitative and Systems Pharmacology Network
Q28652344BioModels: Content, Features, Functionality, and Use
Q33285434BioPP: a tool for web-publication of biological networks
Q30239072Bioactive Nutrients and Nutrigenomics in Age-Related Diseases
Q24598185Bioinformatics and systems biology of the lipidome
Q33736281CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models
Q42588973Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns
Q34495098Cell-signalling dynamics in time and space
Q55007219Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches.
Q33402444Computational modeling of the hematopoietic erythroid-myeloid switch reveals insights into cooperativity, priming, and irreversibility
Q24534940Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway
Q38013124Computational tools for metabolic engineering.
Q28748354Consistent design schematics for biological systems: standardization of representation in biological engineering
Q46908229Control and regulation of gene expression: quantitative analysis of the expression of phosphoglycerate kinase in bloodstream form Trypanosoma brucei
Q30500495CytoModeler: a tool for bridging large-scale network analysis and dynamic quantitative modeling
Q24648654Design and implementation of three incoherent feed-forward motif based biological concentration sensors
Q37443420Designing and encoding models for synthetic biology
Q33197917Developing complex signaling models using GENESIS/Kinetikit
Q36966455Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference
Q45991316Enzyme kinetics and computational modeling for systems biology.
Q38867546Experimental and in silico analyses of glycolytic flux control in bloodstream form Trypanosoma brucei
Q33800030FASIMU: flexible software for flux-balance computation series in large metabolic networks
Q34506734Fan-out in gene regulatory networks.
Q45715391Fluorescence resonance energy transfer based quantitative analysis of feedforward and feedback loops in epidermal growth factor receptor signaling and the sensitivity to molecular targeting drugs
Q34520533Genetic circuit design automation
Q36322160Improved understanding of gene expression regulation using systems biology
Q34652065Improving collaboration by standardization efforts in systems biology.
Q28757241Increased glycolytic flux as an outcome of whole-genome duplication in yeast
Q30480219Integrated network reconstruction, visualization and analysis using YANAsquare.
Q33881486Kinetic modeling of biological systems
Q43150299Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets
Q33806474MEMOSys: Bioinformatics platform for genome-scale metabolic models
Q28082151Mathematical and computational modeling in biology at multiple scales
Q37403978Mathematical modeling and synthetic biology.
Q36012417Mathematical modeling as a tool for investigating cell cycle control networks
Q34594733Measuring retroactivity from noise in gene regulatory networks
Q35188924Mentoring interdisciplinary undergraduate students via a team effort
Q33280162Modeling biochemical transformation processes and information processing with Narrator
Q34014546Modeling biology spanning different scales: an open challenge.
Q42253923Modeling molecular regulatory networks with JigCell and PET.
Q35179460Models in biology: 'accurate descriptions of our pathetic thinking'.
Q35680769Molecular interaction maps--a diagrammatic graphical language for bioregulatory networks
Q30639272On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data.
Q33557078Onset dynamics of type A botulinum neurotoxin-induced paralysis
Q34922805PROMOT: modular modeling for systems biology
Q28728627PathCase-SB: integrating data sources and providing tools for systems biology research
Q37043499Pathway analysis tools and toxicogenomics reference databases for risk assessment
Q38199642Plant systems biology: insights, advances and challenges.
Q37641112Point process models for localization and interdependence of punctate cellular structures
Q61982458PyCoTools: a Python toolbox for COPASI
Q37200950Quantitative Systems Pharmacology: A Framework for Context
Q38680217Quantitative computational models of molecular self-assembly in systems biology
Q34056400Quantitative in vivo fluorescence cross-correlation analyses highlight the importance of competitive effects in the regulation of protein-protein interactions
Q31066861Resources for integrative systems biology: from data through databases to networks and dynamic system models
Q30424527Robustness portraits of diverse biological networks conserved despite order-of-magnitude parameter uncertainty
Q21563497Rule-based cell systems model of aging using feedback loop motifs mediated by stress responses
Q34274480RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry
Q34310662SBML2TikZ: supporting the SBML render extension in LaTeX.
Q30830288SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML)
Q27499005SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks
Q34350920Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity
Q37952114Software for systems biology: from tools to integrated platforms
Q33369508Standards and ontologies in computational systems biology
Q38056560Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks
Q34571547Systems biology: the next frontier for bioinformatics
Q27987775The BioPAX community standard for pathway data sharing
Q29617466The Systems Biology Graphical Notation
Q33347636The Systems Biology Research Tool: evolvable open-source software
Q30443799The adapter importin-alpha provides flexible control of nuclear import at the expense of efficiency
Q39763725The scaffold protein Shoc2/SUR-8 accelerates the interaction of Ras and Raf.
Q58558223Thermodynamic constraints on the regulation of metabolic fluxes
Q30491644TinkerCell: modular CAD tool for synthetic biology
Q83956232Tools for kinetic modeling of biochemical networks
Q34672597Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains.
Q33257709Transcriptional dynamics of the embryonic stem cell switch
Q24814326Transition to quorum sensing in an Agrobacterium population: A stochastic model
Q41788959Virtual Systems Pharmacology (ViSP) software for simulation from mechanistic systems-level models
Q33535721Visualization of omics data for systems biology
Q26796849Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future
Q37089705Web-based applications for building, managing and analysing kinetic models of biological systems

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