Python Unleashed on Systems Biology

Researchers at Cornell University have built an open source software system to model biomolecular reaction networks. SloppyCell is written in Python and uses third-party libraries extensively, but it also does some fun things with on-the-fly code generation and parallel programming.

• Publication year

  2007

• Venue

  Computing in science & engineering (Print)

• Publication date

  2007-04-24

• Fields of study

  Biology, Computer Science

• Identifiers
  DOI 10.1109/MCSE.2007.60arXiv 0704.3259
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Scientific Computing I

  2008cited by this paper
• Universally Sloppy Parameter Sensitivities in Systems Biology Models

  2007cited by this paper
• Sloppy-model universality class and the Vandermonde matrix.

  2006cited by this paper
• The statistical mechanics of complex signaling networks: nerve growth factor signaling

  2004cited by this paper
• Statistical mechanical approaches to models with many poorly known parameters.

  2003cited by this paper
• The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

  2003cited by this paper
• G proteins and phototransduction.

  2002cited by this paper
• Automatic Selection of Methods for Solving Stiff and Nonstiff Systems of Ordinary Differential Equations

  1983cited by this paper
• LSODE and LSODI, two new initial value ordinary differential equation solvers

  1980cited by this paper

• SBcoyote: An Extensible Python-Based Reaction Editor and Viewer

  2023cites this paper
• A non-catalytic herpesviral protein reconfigures ERK-RSK signaling by targeting kinase docking systems in the host

  2022cites this paper
• BMSS2: a unified database-driven modelling tool for systematic model selection and identifiability analysis

  2021cites this paper
• Testing the inferred transcription rates of a dynamic, gene network model in absolute units

  2021cites this paper
• Habitual sleep duration affects recovery from acute sleep deprivation: a modeling study.

  2020cites this paper
• AWARENESS OF THE PROGRAMMING LANGUAGE PYTHON AMONG COMPUTER SCIENCE AND ELECTRONIC ENGINEERING STUDENTS FROM A PERUVIAN UNIVERSITY

  2019cites this paper
• Equifinality, sloppiness, and emergent structures of mechanistic soil biogeochemical models

  2019cites this paper
• SciPy 1.0-Fundamental Algorithms for Scientific Computing in Python

  2019cites this paper
• PP1 and PP2A Use Opposite Phospho-dependencies to Control Distinct Processes at the Kinetochore

  2019cites this paper
• SciPy 1.0: fundamental algorithms for scientific computing in Python

  2019cites this paper
• Implications of alternative routes to APC/C inhibition by the mitotic checkpoint complex

  2018cites this paper
• Zen and the art of parameter estimation in systems biology

  2018cites this paper
• Cells Escape an Operational Mitotic Checkpoint through a Stochastic Process.

  2018cites this paper
• Tellurium: An extensible python-based modeling environment for systems and synthetic biology

  2018cites this paper
• Automated, predictive, and interpretable inference of Caenorhabditis elegans escape dynamics

  2018cites this paper
• The edge of thermodynamics : driven steady states in physics and biology

  2017cites this paper
• ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour

  2017cites this paper
• Software-unterstützte Erzeugung von mathematischen Modellen zur biotechnologischen Prozessführung

  2016cites this paper
• Sloppiness and the Geometry of Parameter Space

  2016influential citation
• Parameter estimation for dynamical systems with discrete events and logical operations

  2016cites this paper
• Tellurium: A Python Based Modeling and Reproducibility Platform for Systems Biology

  2016cites this paper
• Optimization in Biology Parameter Estimation and the Associated Optimization Problem

  2016cites this paper
• Prediction uncertainty and optimal experimental design for learning dynamical systems.

  2015cites this paper
• Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast

  2015cites this paper
• Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves

  2015cites this paper
• Automated adaptive inference of phenomenological dynamical models

  2015cites this paper
• Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution

  2015cites this paper
• A Bibliography of Publications about the Python Scripting and Programming Language

  2015cites this paper
• Estimating Relative Changes of Metabolic Fluxes

  2014cites this paper
• Graphical Modeling Tools for Systems Biology

  2014cites this paper
• Science In High Dimensions: Multiparameter Models And Big Data

  2014cites this paper
• Runtime Compilation of Array-Oriented Python Programs

  2014cites this paper
• Automated adaptive inference of coarse-grained dynamical models in systems biology

  2014cites this paper
• Kinetics of Coinfection with Influenza A Virus and Streptococcus pneumoniae

  2013cites this paper
• A guide to sensitivity analysis of quantitative models of gene expression dynamics.

  2013cites this paper
• Modeling of dynamic systems with Petri nets and fuzzy logic

  2013cites this paper
• Dynamical Models of biological networks

  2012cites this paper
• Hybrid Models and Biological Model Reduction with PyDSTool

  2012cites this paper
• Rapid Development of Interferometric Software Using MIRIAD and Python

  2012cites this paper
• Experiment and mathematical modeling of gene expression dynamics in a cell-free system.

  2012cites this paper
• Supplementary Text S1

  2012cites this paper
• Structural susceptibility and separation of time scales in the van der Pol oscillator.

  2011cites this paper
• Effect of 1918 PB1-F2 Expression on Influenza A Virus Infection Kinetics

  2011cites this paper
• Software Tools for Systems Biology

  2010cites this paper
• A Study Of Small Gene Regulatory Networks: Robustness, Dynamics, And Behavior

  2010cites this paper
• Robustness And Evolvability In Systems Biology And Plectoneme Formation In Dna Supercoiling

  2010cites this paper
• Sloppiness, robustness, and evolvability in systems biology.

  2008cites this paper
• Sloppiness, Modeling, and Evolution in Biochemical Networks

  2007cites this paper
• 2007 Annual Index Computing in Science & Engineering, Vol. 9

  2007cites this paper