Category Archives: howto

Scientific computing doesn't have to hurt

Posted on 24 Sep, 2013 by peterfields

Amy Brown handles communication and scheduling for Software Carpentry. The post title alludes to the goals of Software Carpentry, a volunteer organization whose members teach basic software skills to researchers in science, engineering, and medicine. It’s a great organization, and … Continue reading →

Posted in community, howto, methods, software | 1 Comment

Analytical software management for your Mac? Homebrew to the rescue!

Posted on 9 Sep, 2013 by peterfields

Source: http://www.popsci.com/diy/article/2007-08/ultimate-all-one-beer-brewing-machine Much of the big processing tasks in biological research remain the domain of clusters of computer nodes, whether local or an Amazon EC2 instance, running various flavors of Linux. It is perhaps safe to say that this fact will … Continue reading →

Posted in howto, software | 1 Comment

Using R to run parallel analyses of population genetic data in STRUCTURE: ParallelStructure

Posted on 3 Sep, 2013 by Jeremy Yoder

In this guest post, Francois Besnier explains how to use ParallelStructure, his new R package for running STRUCTURE analyses in parallel computing environments. To start with, thanks to The Molecular Ecologist blog team (Tim and Jeremy) for the invitation to … Continue reading →

Posted in howto, population genetics, R, software, STRUCTURE | 5 Comments

Want to share your code?

Posted on 27 Aug, 2013 by kimgilbert

In this line of work, we have all encountered tasks that are tedious, time consuming, and repetitive.  (Or if not, maybe give it a bit more time.) When confronted with these situations, people tend to fall into one of two … Continue reading →

Posted in bioinformatics, community, genomics, howto, methods, next generation sequencing, phylogenetics, population genetics, quantitative genetics, R, software, theory | 14 Comments

By popular request …

Posted on 20 Aug, 2013 by Jeremy Yoder

The original data set of Joshua tree presence locations, which I used as an example in my post about estimating species distribution models in R, is now available for download from Dryad. Thanks to my coauthors for agreeing to share … Continue reading →

Posted in data archiving, howto, methods | Leave a comment

Making heatmaps with R for microbiome analysis

Posted on 20 Aug, 2013 by Jeremy Yoder

Arianne Albert is the Biostatistician for the Women’s Health Research Institute at the British Columbia Women’s Hospital and Health Centre. She earned a PhD from the University of British Columbia under the tutelage of Dolph Schluter before branching off into … Continue reading →

Posted in howto, microbiology, R, software | Tagged , , | 71 Comments

How to Backup and Store your Next-Generation Sequencing (NGS) data

Posted on 6 Aug, 2013 by Mark Christie

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 … Continue reading →

Posted in bioinformatics, data archiving, genomics, howto | 1 Comment

Species distribution models in R

Posted on 23 Apr, 2013 by Jeremy Yoder

Update, 20 August 2013: Many readers have requested a copy of the Joshua tree data set used as an example in this post, and I’ve finally secured permission from the coauthors of the original study to post it to Dryad. … Continue reading →

Posted in howto, R, software | Tagged , | 27 Comments

Q&A: Julian Catchen helps us dig into STACKS – Part II

Posted on 11 Apr, 2013 by Mark Christie

As promised, below is part II of our interview with Julian Catchen. These questions focus more on the specifics of using stacks (i.e., user-related questions). Please see the first post if you are interested a general overview. Even more information, … Continue reading →

Posted in bioinformatics, genomics, howto, interview, methods | Tagged | Leave a comment

Q&A: Julian Catchen helps us dig into STACKS

Posted on 9 Apr, 2013 by Mark Christie

Julian Catchen is a post-doctoral researcher at the University of Oregon, where he uses computational solutions to facilitate the analysis of next-generation sequencing data. Prior to obtaining his PhD, Julian worked for both Intel and IBM, experiences that no doubt … Continue reading →

Posted in bioinformatics, genomics, howto, interview, methods | Tagged | 2 Comments