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All Projects → darrenjw → smfsb

darrenjw / smfsb

Licence: GPL-3.0 License
Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology

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systems-biologyinferencemcmcsbmlgillespie-algorithm

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SMfSB 3e

SMfSB3e

Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology

This page contains links, code snippets, software and other information relating to the third edition of the book, Stochastic Modelling for Systems Biology, published by Chapman & Hall/CRC, November 2018.

The book has ISBN-10 113854928-2 and ISBN-13 978-113854928-9. It can be ordered from CRC Press, Amazon.com, Amazon.co.uk and similar book sellers.

New in the third edition

  • New chapter on spatially extended systems, covering the spatial Gillespie algorithm for reaction diffusion master equation (RDME) models in 1- and 2-d, the next subvolume method, spatial CLE, scaling issues, etc.
  • Significantly expanded chapter on inference for stochastic kinetic models from data, covering approximate methods of inference (ABC), including ABC-SMC. The material relating to particle MCMC has also been improved and extended.
  • Updated R package, including code relating to all of the new material
  • New R package for parsing SBML models into simulatable stochastic Petri net models
  • New software library, written in Scala, replicating most of the functionality of the R packages in a fast, compiled, strongly typed, functional language

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