Monthly Archives: December 2012

Anaerobic Stress in Seeds – A Chemical Similarity Network Story

December 31, 2012
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Anaerobic Stress in Seeds – A Chemical Similarity Network Story

The chemical similarity network or CSN is a great tool for organizing biological data based on known biochemistry or chemical structural similarity. Here is an example CSN for visualizing metabolomic  changes (measured via GC/TOF) due to anaerobic stress in germinating seeds. In this network edges are formed for chemical similarity scores > 75. Node color describes

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Getting Genetics Done 2012 In Review

December 31, 2012
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Here are links to all of this year's posts (excluding seminar/webinar announcements), with the most visited posts in bold italic. As always, you can follow me on Twitter for more frequent updates. Happy new year!New Year's Resolution: Learn How to Code...

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The forward (explicit) Euler method

December 31, 2012
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The forward (explicit) Euler method

The forward (explicit) Euler method is a first-order numerical procedure for solving ODEs with a given initial value. The forward Euler method is said to be the simplest and most obvious numerical ODEs integrator. In fact, the simulation using the forward Euler only … Continue reading →

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Nested loops with mapply

December 31, 2012
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Nested loops with mapply

So as I sink deeper into the second level of R enlightenment, one thing troubled me. “lapply” is fine for looping over a single vector of elements, but it doesn’t do a nested loop structure. These tend to be pretty ubiquitous for me. I’m forever doing the same thing to a set of two or three

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Top Posts of 2012

December 31, 2012
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Top Posts of 2012

This has been a great year for my blog. I've seen tremendous growth in my subscribers. I look forward to engaging with and learning from my followers in 2013 and I plan to offer valuable content in return. If you're interested in following along, you can quickly subscribe via RSS or e-mail. I use Google I encourage you...

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How odd was the UEFA draw?

December 31, 2012
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I've been away for some time without closely following the media, and without significant internet access. When such a period is over it takes some time to regain momentum. Thus my short exit poll series will be continued in 2013. For now I'm still sor...

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STL random_sample

December 31, 2012
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An earlier post looked at random shuffle for permutations. The STL also supports creation of random samples. Alas, it seems that this functionality has not been promoted to the C++ standard yet — so we will have to do with what is an extensions ...

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Software engineer’s guide to getting started with data science

December 30, 2012
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Software engineer’s guide to getting started with data science

Many of my software engineer friends ask me about learning data science. There are many articles on this subject from renowned data scientists (Dataspora, Gigaom, Quora, Hilary Mason). This post captures my journey (a software engin...

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Modeling in R with Log Likelihood Function

December 30, 2012
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Modeling in R with Log Likelihood Function

Similar to NLMIXED procedure in SAS, optim() in R provides the functionality to estimate a model by specifying the log likelihood function explicitly. Below is a demo showing how to estimate a Poisson model by optim() and its comparison with glm() result.

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Tips for R Package Creation

December 30, 2012
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Tips for R Package Creation

I’m being tortured by the mistakes of my past self. I think I’ve made most every mistake possible in creating a package and I want to go back in time and tell year ago me all I know now. But … Continue reading →

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