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Computational approaches to the modelling of topological and dynamical aspects of biochemical networks

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Dynamic photosynthesis under a fluctuating environment: a modelling-based analysis

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An Extendable System for Conceptual Modeling and Simulation of Signal Transduction Pathways

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BioModels Database: A Public Repository for Sharing Models of Biological Processes

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SBML ODE Solver Library: a command-line tool and library for numerical analysis of reaction networks

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Systems Biology of the β-Cell – Revisited

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Computational Methods for Modelling and Analysing Biological Networks

Larjo, A. (2015) · Tampere University Institutional Repository (Tampere University)

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Using Neuroconstruct to Develop and Modify Biologically Detailed 3D Neuronal Network Models in Health and Disease

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Du monomère à la cellule: Modèles de la dynamique de l'actine

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Computational Approaches for Multiscale Modeling

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Virtual experiments for reusable models

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PathCase-SB

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An Integrative Model for Representation of Signaling Pathways on the Basis of Device Ontology

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Multilevel modeling platform and its application for modeling in neuroscience

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Collaboration visualization on large dataset for protein-protein interaction network

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Mechanistic modelling of cancer: some reflections from software engineering and philosophy of science

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Assembly of Logic-Based Diagrams of Biological Pathways

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Pathway Pioneer: A Web-Based Graphical Tool for the Organization and Flux Analysis of Metabolic Networks

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Mathematical Modeling of Metal Ion Homeostasis and Signaling Systems

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Autocatalytic closure and the evolution of cellular information processing networks

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AVRA: a Architecture for VR-based Applications

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Model Composition for Biological Mathematical Systems

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Toward provably correct models of ventricular cell function

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NOVEL MODELING FORMALISMS AND SIMULATION TOOLS IN COMPUTATIONAL BIOSYSTEMS

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A method of biological pathway similarity search using high performance computing

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Advanced computing for systems

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Extending inner-ear anatomical concepts in the Foundational Model of Anatomy (FMA) ontology

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Multilevel modeling of physiological systems on PhysioDesigner

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Онтологии в биоинформатике и системной биологии

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Management of Signaling Pathway Information: Introduction to the SigPath Project

Chan, E., & Campagne, F. (2007)

Modeling Tools for Cancer Systems Biology

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Database Systems in Biology

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The development of data standards and a database to aid proteomic research.

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Identifying and modeling perturbed networks in cancer through statistical and constraint-based analysis

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The System for Population Kinetics

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Standards and Tools for Model Exchange and Analysis in Systems Biology

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Dynamic Partitioning of Stochastic Networks of Molecular Interactions

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Medicine in New Era with Artificial Intelligence and Systems Biology

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Comparing Classical Pathways and Modern Networks: Towards the Development of an Edge OntologyPreprint

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Virtual Experimentation Using DVASim

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