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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
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Author Archives: Mario Pineda-Krch
Darwin Day 2012: Having a blast with Darwin 2
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.
Posted in Charles Darwin, children, science
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Special section in Science on reproducible research
Recently there was an issue of Science (December 2, 2011, Volume: 334, Issue: 6060) with a special section focusing on data replication and reproducibility in the sciences. It is about time that the big fish put this topic on the … Continue reading
Posted in reproducible research, science
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To Sweave, or not to Sweave, that is the question
I am about to start writing up the manuscript of my recent biomath seminar (Act 3: Pineda-Krch. 2011. Cycles at the edge of existence: Emergence of quasi-cycles in strongly destabilized ecosystems.). While the slides for the talk were put together using … Continue reading
Posted in manuscript, R, Sweave, writing
9 Comments
New paper: Phenotypic plasticity
The proofs are done so I assume this is now officially in press to appear in the Encyclopedia of Theoretical Ecology (eds. Hastings & Gross) by California University Press. The book is slated to appear in May 2012 and at … Continue reading
Posted in manuscript, phenotypic plasticity
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Happy Birthday Origin of Species with a homage to Morse Peckham
152 years ago on the day 1250 copies of the first edition of Charles Darwin’s On the Origin of Species (OOS) went on sale in the United Kingdom. By the end of the day all copies were sold out. All … Continue reading
Posted in Charles Darwin, evolution, Origin of Species
4 Comments
F1000 review: Open science is a research accelerator
As promised previously, today the following post-publication evaluation of Open Science is a research accelerator by Michael Woelfle, Piero Olliaro and Matthew H. Todd appeared in Faculty of 1000 Biology: Pineda-Krch, M. Faculty of 1000 Biology, 14 November 2011 http://f1000.com/13352995 It is commonly taken for granted that difficult … Continue reading
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.
Cycles in finite populations: A reproducible seminar in three acts
For this years Halloween I presented the mathematical biology seminar at the Centre for Mathematical Biology. Here is the title and the abstract… Cycles in finite populations: a reproducible seminar in three acts Many natural populations exhibit cyclic fluctuations. Explaining the underlying … Continue reading
Posted in LaTeX, Open Notebook science, open science, predator-prey model, presentation, programing, R, Sweave
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Open Access(ish) contribution: Cycles in finite populations: a reproducible seminar in three acts
It’s Open Access week and this is what the hoopla is all about “Open Access” to information – the free, immediate, online access to the results of scholarly research, and the right to use and re-use those results as you need … Continue reading
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
Peer reviewed quote of the day
“Just as the corner grocery store lacks variety as compared with a supermarket, so very small populations lack genetic variety (and therefore evolutionary potential) as compared with larger ones.” – Alfred G. Fischer Fischer, A.G. 1960. Latitudinal variation in organic … Continue reading
Posted in manuscript, peer review
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10 years of seminars in mathematical biology as a cloud
Ten years of seminars in mathematical biology later. The cloud was formed from the titles of talks given at the Centre for Mathematical Biology between 2001-2011. This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at … Continue reading
Posted in CMB, Mathematical biology
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From the lowliest of worms
For the Darwin Song Project Mark Erelli composed and performed a piece entitled Kingdom Come. The song is haunting and if you pay close attention to the lyrics you may realize (or not) that it is as if Darwin himself … Continue reading
Posted in Charles Darwin, evolution, fatherhood, Music, natural history
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Darwinian medicine according to a 6 year old
It’s late afternoon and dad is lying sprawled out on the bed with the lights off having a massive migraine. 6 year old enters the dark bedroom with a book under his arm. 6yr old: (holding up the book) Dad, … Continue reading
Posted in children, fatherhood, Origin of Species
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Steve and I
It’s a sad day as guru Steve leaves us. Unbeknownst to Steve, however, Steve and I did designed a unique piece of art together. While he provided the blank slate I made further aesthetic improvements turning an everyday apple into a one of a kind work of … Continue reading
Posted in Uncategorized
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(everybody shout) SHOW ME THE DATA: A presubmission inquiry in one-act
Some Open Access journals require presubmission inquiries. Most of them require you to write a sort of mini-paper of your full paper, you send it to them and then the editor gives you their (virtual) thumbs up or down for … Continue reading
Posted in humour, manuscript, open science, peer review
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The magic of reality is (as of today) real: out with the mumbo-jumbo in with reasoning and logic
Today was the day that the most highly anticipated release of the year was scheduled to take place. No it’s not the new iPhone (I could not care less), or the announcement of this years Nobel laureates in Physics (which I do care about), … Continue reading
Posted in Richard Dawkins, science
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Charles Darwin according to a 6 year old
The following conversation transpired today on the way home from the grocery store. Me: So what can you tell me about Charles Darwin? 6yr old: He was a scientist, he was an entomologist, he was a father of 10, and … Continue reading
Posted in Charles Darwin, children
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The Magic of Reality: Finally a reason to get the iPad
I have never really understood the purpose of the iPad. Anything I would ever want to use the iPad for its little brother the iPod Touch can do equally well + it fits in your pocket. Anything the iPod Touch … Continue reading
Posted in Richard Dawkins, science
3 Comments
Turbo charged Open Science: this sort of thing is my bag, baby
A remarkable commentary appeared today in Nature Chemistry entitled Open Science is a research accelerator. In this commentary Michael Woelfle, Piero Olliaro and Matthew H. Todd describe a case study of an Open Science research project they conducted with the aim devising an alternative … Continue reading
Evolution according to kids
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.
Posted in children, evolution
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Sally Otto awarded a MacArthur Fellowship
Great news in the ether today. Evolutionary geneticist Sally Otto has been awarded the MacArthur Fellowship. Awards get handed out all the time to deserving scientists but this one hits home base. Sally is a friend and a colleague and, to me, it is … Continue reading
Posted in evolution, Sally Otto
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Choosing the tools of Open Notebook Science – redux
After tinkering with and pondering about my Open Notebook Science setup it looks like this time I will have to eat my own words. Specifically my statement “a wiki does not make a good platform for my Open Notebook Science … Continue reading
Posted in Open Notebook science
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Choosing the tools of Open Notebook Science
I will always remember my post Starting an Open Notebook Science project as the day that I almost started with ONS. But, complications arose, ensued, were overcome and here I am ready again to embark on my own ONS experiment. … Continue reading
Posted in Open Notebook science
4 Comments
One step closer to Open Notebook Science
One step closer to Open Notebook Science right here. Now just hacking the tools. 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.
Posted in Open Notebook science
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