Monolithic pipelines are common in bioinformatics and particularly for metabarcoding. My view is that the word pipeline, and the type of software it refers to, may be holding us back and should be rethought. What is a pipeline? Pipelines are connected sets of programs, where information flows through the linked analysis algorithms as water flows…
Tag: Bioinformatics
Software and real carpentry
I like Software Carpentry, a non-profit organization teaching basic computing skills to researchers. But if I had one little criticism it would be that there wasn’t enough carpentry, with tenon saws, and mortising chisels, and rabbet planes. I like actual carpentry, I can’t tell you why, its a bit like asking why somebody likes cheese,…
How can we ensure the persistence of analysis software?
I’ve been thinking about sustainable and accessible archiving of bioinformatics software, I’m pretty scandalized at the current state of affairs, and had a bit of a complain about it before. I thought I’d post some links to other people’s ideas and talk a bit about the situation and action that is needed right now. Casey Bergman…
Reproducible research in phylogenetics
I’ve been reading a lot recently about reproducible research (RR) in bioinformatics on several blogs, and Google+ and Twitter. The idea is that it is important that someone is easily able to reproduce* your results (and even figures) from your publication using your provided code and data. I’ve been thinking that this is a movement…
Calculating intron density
I have a project going at the moment to examine changes in intron diversity, size and location in animal genomes. I am always a bit frustrated with the way introns are treated in many genome characterisation papers- “the genome contained Y introns with mean intron size Xbp” is usually all we get. This sort of…
Bio-Linux in a VirtualBox
For those of you who haven’t come across it before Bio-Linux is an operating system set up for bioinformatics with a huge number of programs pre-installed. It can be obtained (for free) from the NERC Environmental Bioinformatics Centre. I’ve spent quite a while recently messing with installations of software packages and wanted to see how…
Droppable applications from scripts
I’m not a very competent perl programmer. Even writing the word programmer here makes me slightly embarrassed. I do carry out frequent sequence conversions and manipulations with perl scripts I’ve put together though. Sometimes when I need to run a script many times I’ve found the most irritating thing is launching the scripts and pointing…
Annotating trees with Treedyn
In order to really get information out of building phylogenetic trees (especially large ones) some thought has to be given to how to annotate the tips (OTUs).The two programs that seem to do this in a powerful way are ARB and Treedyn. I also want to explore Tree-Q vista, which looks promising, but haven’t really…
EvoPhylo 