Science online, safety not defined edition

Tomatoes Are better mass-market tomatoes on the horizon? Photo by rachelandrew.
  • This week at the Molecular Ecologist: Introducing a new repository for useful snippets of code.
  • Yum. Modern genetic methods and old fashioned cross-breeding may yet make supermarket tomatoes tasty.
  • Selection is selection. An evaluation of genetically modified organisms, from an evolutionary biology perspective.
  • God only knows what’ll happen to NSF. The “sequestration” budget cuts are wreaking havoc at NIH.
  • Viral silliness. In which a marine biologist extensively objects to Buzzfeed.
  • With video! NASA’s plan to capture and sample an asteroid.

The Molecular Ecologist: Got code? Share and enjoy!

Fall 2011 Student Hackathon Coding Coding is better when done together. Photo by hackNY.

Over at the Molecular Ecologist, Kim Gilbert announces a new initiative, the Molecular Ecologist code snippet repository. It’ll be a place to put bits of useful code that wouldn’t warrant their own publication as a package or program, but would still be helpful to other biologists:

Do you have a script you regularly run to convert between data formats? A quick and easy way to run a certain analysis? Making a common figure for a given type of data? If you’re willing to share your code, we’ll put it online for public access with credit to your name.

To find out how to submit your snippets, go read the whole thing.◼

Science online, heatmaps and actual heat edition

[DSP] May 18: Heat Wave Photo by jo3design.

The Molecular Ecologist: Making heatmaps in R

Image by Arianne Albert via The Molecular Ecologist.

Over at the Molecular Ecologist, guest contributor Arianne Albert walks through how to make heatmap figures in R.

Heatmaps are incredibly useful for the visual display of microarray data or data from high-trhoughput sequencing studies such as microbiome analysis. Basically, they are false colour images where cells in the matrix with high relative values are coloured differently from those with low relative values. Heatmaps can range from very simple blocks of colour with lists along 2 sides, or they can include information about hierarchical clustering, and/or values of other covariates of interest. Fortunately, R provides lots of options for constructing and annotating heatmaps.

I’ve personally used heatmap graphics for visualizing population structure in a sample, or linkage disequilibrium along a stretch of genetic sequence, but I haven’t done anything very complex. Arianne’s examples use a data set that’s freely available on Dryad, and she includes a lot of step-by-step detail to build up complex figures—if you’re going to be visualizing some microarrary results or metagenomics data any time soon, you should read the whole thing, and probably bookmark it.◼

Science online, sugar-frosted peer review edition

Cereal Photo by Shaun Bascara.

The Molecular Ecologist: Domesticated genes answer the call of the wild

Soay sheep on Hirta, St Kilda, with Cleits Wild Soay sheep, in an assortment of colors. Photo by Commonorgarden.

This week at the Molecular Ecologist, I’m discussing a new study from the blog’s parent publication, Molecular Ecology, which traces the origins of gene variants in a wild population of Soay sheep … back to domestic sheep.

The Soay sheep haven’t been completely isolated from other breeds. In recent centuries, they shared the Saint Kilda islands with humans, who kept domesticated sheep—providing several hundred years of opportunity for what geneticists call “an admixture event,” and everyone else calls “sex,” between the Soay breed and those domesticated sheep.

To learn how the study’s authors pinpointed the origin of the domestic genes variants, and how those variants have fared in the wild sheep, go read the whole thing.◼

Science online, no sharks whatsoever edition

Armadillo Twenty-six percent longer, you say? Photo by Rich Anderson.
  • The Ecological Society of America met in my front yard this week. And there was coverage at Dynamic Ecology and the EEB & Flow, and of course all over Twitter.
  • This week, at Nothing in Biology Makes Sense! I put the “Don’t Sleep with Mean People” spat to rest.
  • And at the Molecular Ecologist: The care and feeding (and protection) of great big genetic datasets.
  • Think I’ll just have the black bean burger. Lab-grown hamburger gets its first taste test.
  • Apart from “because it’d be cool.” Why you should, or shouldn’t, have your genome sequenced.
  • Prepare to start scratching. When you watch this video of a mosquito bite from the inside.
  • In armadillos, naturally. An in-depth study of the structural changes associated with erection of the penis.
  • Establishment matters. What invasive species can teach us about climate-change-induced range shifts.
  • For fish, anyway. Fish raised in stimulating environments are smarter.

The Molecular Ecologist: Storing and protecting your NGS data

Data Barnacles. Photo by UWW ResNet.

This week at The Molecular Ecologist, Mark Christie shares some tips for how to take care of that massive genetic dataset that’s just come off the high-throughput sequencer:

Congratulations! You have recently received a file path to retrieve your hard-earned next-generation sequencing data. You quickly transfer the files to the computing cluster you work on or perhaps, if you only have a few lanes of data, to your own computer. But before you begin messing around with your data, you quickly realize that you should come up with a plan to back up and store unadulterated versions of your files.

For a nice set of recommendations with some step-by-step instructions, go read the whole thing.◼

Science online, cocoa and Congressional whiplash edition

  • Okay, now this is bad. Humans’ supply of chocolate is in trouble because of bug-tending ants.
  • A history of modern lawns, and the alternatives.
  • And with a funding cut. House Republicans unilaterally decide that NASA should ditch its asteroid-capture plans in favor of a moon base.
  • Because mutation happens during mitosis, too. When it comes to genotypes, we each contain multitudes.
  • Not good! The feedback between climate change and wildfires.
  • It’s about deciding. And also not deciding. On starting up a lab.
  • Good news. The next weapon against one group of drug-resistant bacteria might be a fungicide.