Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project
M Hucka, A Finney, BJ Bornstein, SM Keating… - Systems biology, 2004 - IET
Biologists are increasingly recognising that computational modelling is crucial for making
sense of the vast quantities of complex experimental data that are now being collected. The …
sense of the vast quantities of complex experimental data that are now being collected. The …
[HTML][HTML] Space in systems biology of signaling pathways–towards intracellular molecular crowding in silico
K Takahashi, SNV Arjunan, M Tomita - FEBS letters, 2005 - Elsevier
How cells utilize intracellular spatial features to optimize their signaling characteristics is still
not clearly understood. The physical distance between the cell-surface receptor and the …
not clearly understood. The physical distance between the cell-surface receptor and the …
Stochastic simulation of chemical reactions with spatial resolution and single molecule detail
SS Andrews, D Bray - Physical biology, 2004 - iopscience.iop.org
Methods are presented for simulating chemical reaction networks with a spatial resolution
that is accurate to nearly the size scale of individual molecules. Using an intuitive picture of …
that is accurate to nearly the size scale of individual molecules. Using an intuitive picture of …
[PDF][PDF] Whole brain emulation: A roadmap
A Sandberg, N Bostrom - 2008 - ora.ox.ac.uk
Whole Brain Emulation: A Roadmap Page 1 Whole Brain Emulation A Roadmap (2008)
Technical Report #2008-3 Anders Sandberg* Nick Bostrom Future of Humanity Institute …
Technical Report #2008-3 Anders Sandberg* Nick Bostrom Future of Humanity Institute …
Towards a genome-scale kinetic model of cellular metabolism
Background Advances in bioinformatic techniques and analyses have led to the availability
of genome-scale metabolic reconstructions. The size and complexity of such networks often …
of genome-scale metabolic reconstructions. The size and complexity of such networks often …
From genome to crop: integration through simulation modeling
Crop models use mathematical equations to simulate growth, development and yield as a
function of weather, soil conditions and crop management. Such models integrate scientific …
function of weather, soil conditions and crop management. Such models integrate scientific …
A multi-algorithm, multi-timescale method for cell simulation
K Takahashi, K Kaizu, B Hu, M Tomita - Bioinformatics, 2004 - academic.oup.com
Motivation: Many important problems in cell biology require the dense nonlinear interactions
between functional modules to be considered. The importance of computer simulation in …
between functional modules to be considered. The importance of computer simulation in …
Sensitivity analysis of parameters controlling oscillatory signalling in the NF-κB pathway: the roles of IKK and IκBα
AEC Ihekwaba, DS Broomhead, RL Grimley, N Benson… - Systems biology, 2004 - IET
Analysis of cellular signalling interactions is expected to create an enormous informatics
challenge, perhaps even greater than that of analysing the genome. A key step in the …
challenge, perhaps even greater than that of analysing the genome. A key step in the …
Using Petri net tools to study properties and dynamics of biological systems
Abstract Petri Nets (PNs) and their extensions are promising methods for modeling and
simulating biological systems. We surveyed PN formalisms and tools and compared them …
simulating biological systems. We surveyed PN formalisms and tools and compared them …
SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks
SmartCell has been developed to be a general framework for modelling and simulation of
diffusion-reaction networks in a whole-cell context. It supports localisation and diffusion by …
diffusion-reaction networks in a whole-cell context. It supports localisation and diffusion by …