-
Recent comments
MPK’s research notebook- Reaction norms for larval viability in Drosophila pseudoobscura November 7, 2011
- Results November 7, 2011
- LRG lab meeting (November 7, 2011) November 7, 2011
- Genotype-by-environment interaction figure November 7, 2011
- Model November 7, 2011
- Woltereck November 7, 2011
- Introduction November 7, 2011
- Questions needing answers November 7, 2011
- Daphnia November 7, 2011
- About November 7, 2011
- My CiteULike
- 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
-
- Unknown Feed
- An error has occurred; the feed is probably down. Try again later.
Category Archives: computing
The Joy of R: A Feline Guide
Just because it’s caturday Images by Mario Pineda-Krch (CC BY-NC-SA 3.0) This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
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
What is R, really?
On CRAN, the official web home of all things R it says, R is a free software environment for statistical computing and graphics. Well, that sounds all hunky dory. But let’s take a close look at what this statement really … Continue reading
Posted in computing, open science, R
7 Comments
Failing grade for Canada’s supercomputer infrastructure
The recent announcement of the collaborative effort between University of Toronto’s SciNet Consortium and IBM to build Canada’s most powerful supercomputer (CBC blurb) came in a time when the Canadian supercomputer infrastructure is in dire straits. In the latest TOP500 … Continue reading
Posted in Canada, computing, Supercomputing, TOP500
1 Comment
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!
Leave a comment
The gitification of my world
A while back I took the leap and changed my source control management system from Subversion to Git. This was not an easy or quick decision. Although I used Subversion for many years I had also grown increasingly unhappy with … Continue reading
Posted in computing, Git, Linus Torvalds, Subversion
2 Comments
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
Leave a comment
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
1 Comment
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
Leave a comment
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
3 Comments
How I skin the cat
Because much of my work involve computationally intensive models I make extensive use of various High Performance Computing (HPC) resources, e.g. high-end work stations and simulation servers, distributed computing infrastructure and cluster based platforms. Some of the HPC resource I … Continue reading
Posted in computer cluster, computing, HPC, Linux
Leave a comment
