Category Archives: Computational

Lab Website Organization

This website is set up to have primarily dynamic content. There are a few static pages, but most of the content is in the form of “posts” that are organized into “categories”. Lab-members aim to post updates at least once a semester on what they’re up to. We’ve also started a biweekly undergrad journal club under the “What we’re reading” category. There are also posts on funded projects, general cool science, and protocols that we’ve found handy.

Software Carpentry Workshop

Maren, Roxanne, & Ellie attended the hpcc swc bootcamp. Thanks instructors!

Maren’s notes from the bootcamp are posted here.

From the organizers:
We hope you enjoyed the Software Carpentry bootcamp this week and picked up a few new skills to speed up your research workflow.
If you’re still unsure how to integrate any of these tools or skills into your workflow, we’d be happy to meet with you to discuss your specific needs and help you get started. (Note: The longer you wait to integrate these skills into your workflow, the less likely you are to do it, so it’s best to start now.)
Respond to this email if you’d like to schedule consultation with us. As always, the only cost is your time and effort.
MSU’s ICER department also offers weekly office hours and can provide similar consultation on a weekly basis.
We’d also like you point out that Software Carpentry has free online materials (video lectures and notes) for all of the material we covered in the workshop (and much more).
Finally, if you’d like to get involved with Software Carpentry (or know someone that might want to), take a look at SWC’s Get Involved page. We’re always looking for more helpers and instructors at bootcamps, new places to run bootcamps, and new contributors to help us improve our teaching material.
MSU Software Carpentry team

Making ape work on Mac OSX 10.8

ape 3.0.7 on Mac OSX 10.8 has some problems reading fasta files! read.dna doesn’t see “G” (???) and line endings are messed up.

From the internet (

Feb 6, 2013

“Hi Rupert, The Mac version of ape on CRAN is not correct and has a few bugs particularly in read.dna(). Another problem is that “G” is not read (but “g” is). This does not affect the Windows version nor the sources. A solution for Mac users is re-install from the sources. Another one is to use the code of read.dna() from a previous release of ape.   I’m waiting for other tests and feed-back before releasing ape 3.0-8 (within one or two weeks).

Best, Emmanuel”

 Solution: install from source:

1. Install Xcode (from Mac App store, running OSX 10.8.2)

2. In Xcode, under “Preferences”, “Downloads”, select “Command Line Tools” install button

3. Still need gfortran, go to and download (for Mountain Lion only).

In Terminal, cd to the Download folder:

gunzip gfortran-mlion.tar.gz

sudo tar -xvf gfortran-mlion.tar -C /.

4. In R Installer, select CRAN (sources) and install ape 3.0.8

5. It works!