Biomolecular Graphics

A recently published article in PLoS Computational Biology is one by Cameron Mura and colleagues that discusses the great potential held by biomolecular graphics. It discusses the terminology, tools and how to go about teaching yourself the basics. While it is very biochemistry-focussed, the highlight of the paper "Box 2: Nine Simple Rules for Biomolecular Graphics" present some very useful hints to guide any scientific illustrator.

Reference:

Mura C, McCrimmon CM, Vertrees J, Sawaya MR. (2010). An Introduction to Biomolecular Graphics. PLoS Computational Biology 6(8): e1000918. doi:10.1371/journal.pcbi.1000918

Speech recognition in Linux

Whenever I'm looking at specimens under the microscope and noticing differences, I find it very difficult to stop what I'm doing, look at a bit of paper, and write it down. I'd much prefer to talk about it while looking at the specimen.

The first solution is to record yourself while talking. Audacity is a free, open-source music editing program that is pretty decent. I don't know how useful hard-core sound engineers would find it, but it's not bad for the application that I'm wanting to use it for, namely, recording my voice while I waffle on about what a specimen looks like. I could then listen to the recording repeatedly and transcribe what I say. More efficiently though, I'd be keen for some sorta sound recognition software a la Dragon NaturallySpeaking. NaturallySpeaking is the biggest-selling voice recognition software, and by all accounts it's pretty good. It does require some coin though, so I'm looking for less expensive, preferably open-source programs.

Unfortunately, it doesn't seem like there's much out there. A wikipedia page is a good entry point to the problem. Apparently one of the biggest issues is the lack of a voice database to test algorithms on. To solve this issue, VoxForge has been set up to encourage people to upload recordings and to work on the problem. The Ubuntu Wiki also has a page giving a bit of a road map of what Ubuntu want to see done. It looks like it might be a good project to start working on.

Phylogenetic trees online

The other day, an article was published in PLoS One describing a newly developed JavaScript library to visualise phylogenetic trees online: jsPhyloSVG. It's pretty nifty, and there's some pretty cool functionality that you can build into the trees. It's all based on the PhyloXML standard for describing phylogenetic trees and networks, but can display trees stored as other formats, in particular the common NEWICK format. The resulting files are viewable in any web browser, though Internet Explorer is dragging the chain a bit and does not yet support the full interactivity that other browsers are capable of.

It would be real cool to be able to export trees made and manipulated in R into PhyloXML format, and subsequent into PhyloSVG. Might be a fun project to work on when I've scraped some other things off my plate...


Reference:

Smits SA, Ouverney CC. (2010). jsPhyloSVG: A Javascript library for visualizing interactive and vector-based phylogenetic trees on the web. PLoS ONE 5(8): e12267. doi:10.1371/journal.pone.0012267

Vanuatu Birds Website

While reading the paper on white-eye blood parasites, I noticed a link to the VanBirds website. It is an incredible website, and an excellent resource for both casual bird watchers and serious ornithologists. It has photos of many of the bird species found in the archipelago. In addition, it has recordings of the calls of many of the species also. Most importantly though, the website collates records of birds throughout the archipelago and displays them on a map as shown by this map of the distribution of the Vanuatu endemic flycatcher, the buff-bellied monarch (Neolalage banksiana, pictured above). It appears to be well-maintained, being last updated on the 25th of May this year.

This website is very impressive and is a highly valuable resource for the ornithology of Vanuatu. It is all the more remarkable, as it appears to be very much a grass-roots type effort and claims to have had no external funding thus far. It would be awesome to see more sites like this spring up for the other Melanesian island groups.

Downloading DNA sequences into R

A while ago, a friend of mine needed to download a number of different DNA sequences from Genbank, the online repository for the vast majority of DNA sequences read from all organisms by labs all over the world. This is not a problem. The "ape" package in R has a nifty function, read.GenBank(), that downloads the sequences identified by the accession numbers given to the function into a DNAbin object. Thus, read.GenBank("AY883003") downloads the sequence AY8833003, the internal transcribed spacer 2 gene for Anthonomus grandis, the cotton boll weevil. read.GenBank() is able to read a vector of accession numbers, making easy to download a lot of sequences if you're willing to give it the time.

All well and good. Unfortunately, the base function returns only the accession number as the name of the sequence. My friend was downloading sequences of many different genes from several different species. Understandably, mere accession numbers are not particularly helpful in this situation, and more information is helpful for processing datasets such as this. Thankfully, a quick hack of the function ensured that species and gene region info could be downloaded with the sequences, solving the problem. It also extended the function's utility significantly and in my opinion is now much more useful for phylogenetics-type work.

The resulting function is read.GB(). It currently reads the "ORGANISM", "DEFINITION", and "ACCESSION" fields of Genbank files which record the information regarding species identity, gene region and accession number respectively. These are stored in the resulting DNAbin object as an attribute, and can be returned in the following manner:

a<-read.GB("AY883003")
attr(a, "species")
attr(a, "gene")
attr(a, "accession_num")

The current default names for the sequences are returned in a standard format: accession number|scientific name.

Full credit goes to Emmanuel Paradis who wrote the original function, and who wrote it in such a way that it was fairly painless to extend it in the manner above.

Tonga Science Network

In a collaboration between the University of Canterbury and the Tongan Ministry of Education, a new website has been launched: the Tonga Science Network. This website aims to promote and help disseminate science that is relevant to Tonga's environment and economy. Researchers are invited to register on the website and contribute content to smooth the flow of knowledge back to those who need to use it. Another cool feature is the "connections" that shows who has worked with who, and encourages the formation of new collaborations.

All in all, it's a neat initiative and hopefully will resolve one of the major issues I see with science in the Pacific, namely that most research is done by foreigners. This in turn means that relatively little of the results (despite the best intentions of most researchers) is returned to interested parties within the country, other than by laborious and ongoing literature searches. As with all community-type initiatives, it will only be as good as those who use it. It's made a good start though, and here's hoping that will continue.

Use these to make your life easier...

I have just started to use the styles function in MS Word, and I'm starting to get rather excited about it... I anticipate that it will make the writing up process just that much easier. Like all things, it takes a little time to learn how to operate, but once you get the hang of it, it's great!

I found this tutorial on Understanding Styles to be immensely useful, and am intending on using this guide to writing books with MS Word further.

Give it a go, you will not be disappointed.