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MPK’s research notebook- Reaction norms for larval viability in Drosophila pseudoobscura November 7, 2011
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Category Archives: Gillespie algorithm
Vanilla C code for the Stochastic Simulation Algorithm
The Gillespie stochastic simulation algorithm (SSA) is the gold standard for simulating state-based stochastic models. If you are a R buff, a SSA novice and want to get quickly up and running stochastic models (in particular ecological models) that are not … Continue reading
Paper on the Gillespie Stochastic Simulation Algorithm in press
Just got news that my revisions to the reviewer’s comments on my paper GillespieSSA: Implementing the Gillespie Stochastic Simulation Algorithm in R were accepted. Hence, this paper is not officially in press in the Journal of Statistical Software. Here’s the … Continue reading
Posted in computer simulations, Gillespie algorithm, GillespieSSA, R
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GillespieSSA on CRAN
So it’s official – my R package GillespieSSA has been posted to the official list of packages on CRAN (The Comprehensive R Archive Network). Check it out. Now back to my manuscript. Over the last few days I have been … Continue reading
Posted in Gillespie algorithm, GillespieSSA, manuscript, R
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GillespieSSA 0.2-0 is released
Just finished the new version of the GillespieSSA package. The tar ball of the new version is posted on its web page (here). I also submitted it to CRAN so in (due time) it should appear on the official R … Continue reading
Posted in Gillespie algorithm, GillespieSSA, R
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119 days of number crunching…
Just checked on the 70000+ simulations I submitted to the Cow last night. The purpose of these runs is to explore a given system (the logistic growth model in this case) using different implementations of the stochastic simulation algorithm (aka … Continue reading
A brief history of SSA implementations
Ever since Gillespie blessed the world by giving us the SSA (Stochastic Simulation Algorithm) there has been countless attempts to improve its computational efficiency. A few of these algorithms are exact, just like Gillespie’s SSA, (exact SSAs simulate every reactive … Continue reading
Blazing fast tau-leap methods
Today I added the Decaying-Dimerization reaction set as a template model to GillespieSSA. This model was used by Gillespie in the paper where he introduced the Explicit tau-leap method in 2001. The model consists of three species and four reactions … Continue reading
GillespieSSA poster
Finished my poster for the useR! 2007 meeting. It is also posted on the GillespieSSA web page as part of the package documentation. Now, all I have to do is show it off in Ames next week…, oh, and I … Continue reading
Posted in computer simulations, Gillespie algorithm, GillespieSSA, R
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Adaptive tau-leaping in SSA
Just a brief update on my activities 11 days before the R package GillespieSSA is to be released. I have been hacking away on the code, debugging, and running test simulations like there is no tomorrow. The last SSA implementation … Continue reading
Stochastic simulation in the 1970s
I was re-reading Gillespie’s seminal 1977 paper Exact stochastic simulation of coupled chemical reactions today. Although it’s been around for 30 years now it is even more pertinent today when computer simulations are ubiquitous than in the era when it … Continue reading
Abstract for useR! 2007 poster
Here’s my submitted abstract for the poster I will be presenting at the useR! 2007 meeting in August. GillespieSSA: A stochastic simulation package for R Mario Pineda-Krch Center for Animal Disease Modeling and Surveillance University of California, Davis Abstract Stochastic … Continue reading
Posted in computer simulations, Gillespie algorithm, GillespieSSA, meeting, R
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Are stochastic simulations in continuous time really that hard?
It may be pretty obvious by now that I am a theoretician, I use the language of math to formulate my questions and mathematical analysis and computer simulations to explore the nature of the models I devise. Currently I am … Continue reading
Posted in Ben Bolker, computer simulations, computing, Gillespie algorithm
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