Monday

Aphaenogaster

Illumina TruSeq RNA Sample Preparation Kit v2 $3,350 for 48 samples, ~$70/sample.

12 hours prep time. Cost calculation:

Item	Cost/sample
DGE	120
Encore Rapid Library	70
BMGC sequencing	202
Bioanalyzer	2.5
TOTAL	394.5

With sequencing cost at $3227/lane, 16 samples per lane

compare to estimates for the Encore Rapid:

Item	Cost/sample
DGE	120
Encore Rapid Library	35
BMGC sequencing	202
KAPPA qPCR	21
TOTAL	378

So comparable of cheaper to use NuGEN. Spoke with Kappa Biosystems rep - after initial runs with qPCR of 4 dilutions/20ul volume/3 replicates could try reducing to 2 dilutions so each kit would work for twice as many samples, further reducing cost.

Guidelines for this available on Kappa FAQ

Lab Notebook

Last week placed first image in a post, but couldn’t get it to appear. Ran into a similar problem with locating my css files when originally setting up jekyll so will document here as this is a major problem with jekyll.

Problem: Need absolute path to get to some resources (css, image files) as otherwise jekyll looks for resources relative to the current page/post.

For css files, I used the second solution proposed by kikito on stackoverflow. Add an optional setting called root on each page with ..\ to go up levels to the root directory of the website. For example, for a post page I need to go up four levels - from date to month to year to categories to main page, so I assign root: "../../../../"

Then inside my head.html file in the _includes folder I include the code to set the page root as specified on stackoverflow.

Medicago

revisions for manuscript to Methods in Ecology and Evolution

Standard errors for repeatability:

http://onlinelibrary.wiley.com/doi/10.1111/j.1469-185X.2010.00141.x/abstract

http://rptr.r-forge.r-project.org/

Reading

Nakagawa, S and H. Schielzeth (2010) Repeatability for Gaussian and non-Gaussian data: a practical guide for biologists. Biological Reviews 85: 935-956.

great review of methods for repeatability calculation