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MPK’s research notebook- Reaction norms for larval viability in Drosophila pseudoobscura November 7, 2011
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- Model November 7, 2011
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- Introduction November 7, 2011
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- About November 7, 2011
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- Density Dependence Slows Invader Spread in Fragmented Landscapes Jonathan Levine
- Names are key to the big new biology
- Community ecology: stasis, evolution or revolution?
- Assessing rapid evolution in a changing environment
- Adaptation genomics: the next generation
- A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus
- Low-altitude airbursts and the impact threat D Crawford
- Aging in a Long-Lived Clonal Tree Sarah Otto
- Using Environmental Correlations to Identify Loci Underlying Local Adaptation Jonathan Pritchard
- Mathematics Is Biology's Next Microscope, Only Better; Biology Is Mathematics' Next Physics, Only Better Joel Cohen
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Category Archives: computer simulations
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
GillespieSSA 0.5-4 is released
I just uploaded GillespieSSA 0.5-4 to CRAN. It should be just a matter of days before it has propagated itself across all mirrors. This release consists of minor revisions with no (intended) changes in functionality. The main change (and it is … Continue reading
Posted in computer simulations, GillespieSSA, Git, Linus Torvalds, R
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High-performance computing in R at useR! 2008
The useR! 2008 meeting is about to commence. Although I am not able to go this year I will be keeping a close eye on the talks and slides that (I assume) will be posted. Last years useR! meeting (which … Continue reading
Posted in computer cluster, computer simulations, computing, R, useR!
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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 0.5-1 is released
I just uploaded GillespieSSA 0.5-1 to CRAN. Now it’s just a matter of days before it has propagated itself across all CRAN mirrors. This version consists primarily of revisions I made in response to the reviewer comments on the paper … Continue reading
Posted in computer simulations, GillespieSSA, programing, R
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Painful week at WestGrid
WestGrid (Western Canada Research Grid) is a interconnected network of really juiced up computers, e.g. clusters, super computers, and high performance work stations, from 14 different partner institutions across four provinces in Western Canada. I tend to use some of … Continue reading
Posted in computer cluster, computer simulations, computing, HPC
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GillespieSSA 0.3-1 released
I recently rolled up the new version of the GillespieSSA package, version 0.3-1. 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 … Continue reading
Posted in computer simulations, 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
Cow chewing on GillespieSSA
Sorry blog for the long silence. Lately I have been juggling several time critical projects and there hardly seems to be time for such mundane activities such as sleeping, eating, never mind shaving (someone pointed out that I am starting … Continue reading
Posted in computer simulations, computing, GillespieSSA, R
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Looking for a few good beta testers
Sitting in a dreary hotel room in San Jose with Interstate 101 on my left and a burger joint/truck stop on my right (see previous post Report from the meeting of the Ecological Society of America in San Jose for … Continue reading
Posted in computer simulations, GillespieSSA, R
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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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The perils of numerical simulations
Sorry blog for the lack of posts lately. As the devoted reader may have realized it is less than a week left before I am supposed to finish (i.e. release) the GillespieSSA R package. Within this time period I am … Continue reading
Posted in computer simulations, computing, GillespieSSA
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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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Computational and Mathematical Epidemiology galore
If theoretical biology rings your bell, particularly mathematical epidemiology, ecology and game theory then the the DIMACS 2002-2009 Special Focus on Computational and Mathematical Epidemiology should be right down your ally. This program consists of regular meetings in the form … Continue reading
Posted in computer simulations, epidemiology, meeting
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Show me the code
An email came this morning to one of the mailing lists I subscribe to. It goes like so, Dear Colleagues, This to inform you that we must retract Hall, B.G. and S. Salipante. 2007. Measures of clade confidence do not … Continue reading
Posted in academia, computer simulations, PLoS, Sally Otto
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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
3 Comments
Unconventional laptop cooling
After noticing that my laptop seemed to be getting very warm while running simulations I started tracking its CPU temperature. There is a little nifty free program, MobileMeter, that allows one to keep track of the temperature of various hardware … Continue reading
Posted in computer simulations, computing
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