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BMCBI
2004
323views more  BMCBI 2004»
13 years 9 months ago
Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks
Background: Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true ...
David Adalsteinsson, David McMillen, Timothy C. El...
JCC
2011
87views more  JCC 2011»
13 years 4 months ago
NUPACK: Analysis and design of nucleic acid systems
: The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables...
Joseph N. Zadeh, Conrad Steenberg, Justin S. Bois,...
BIOINFORMATICS
2011
13 years 1 months ago
ProDy: Protein Dynamics Inferred from Theory and Experiments
Summary: We developed a Python package, ProDy, for structurebased analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heteroge...
Ahmet Bakan, Lidio M. Meireles, Ivet Bahar
ISMM
2009
Springer
14 years 4 months ago
Spatially-Variant Anisotropic Morphological Filters Driven by Gradient Fields
Abstract. This paper deals with the theory and applications of spatially-variant mathematical morphology. We formalize the definition of spatially variant dilation/erosion and ope...
Rafael Verdú Monedero, Jesús Angulo,...
FASE
2010
Springer
14 years 4 months ago
Proving Consistency and Completeness of Model Classes Using Theory Interpretation
Abstract. Abstraction is essential in the formal specification of programs. A common way of writing abstract specifications is to specify implementations in terms of basic mathem...
Ádám Darvas, Peter Müller