NZ's hottest researchers from 2010-2012.

In response to the recently released "The Hottest Research of 2011" report from ScienceWatch (where several of my former colleagues at the Wellcome Trust Sanger Institute feature) I thought I'd take a look at NZ's hottest research and researchers.

Re-blogging: Rfam 11.0 is out!

The really BIG news for this release is the Xfam-Biomart. Which finally allows researchers to easily fetch all the sequences in Rfam from their favourite organism. For example, lets pretend I was really interested in Helicobacter pylori 35A. I go to the NCBI Taxonomy, look the species up there and record the taxid (585535). Back at the Biomart I enter the taxid beside "NCBI Taxonomy ID:", hit "Next", then select a number of handy looking features, hit "Results" and suddenly I have ALL the sequences from Helicobacter pylori 35A. This is an extraordinarily useful feature that has, until now, been missing from the Xfam arsenal. I'll be making heavy use of it in future.

See the Xfam blog for more details.

LaTeX fun with periodic tables

For a while now I've wanted to generate a simple periodic table of elements in LaTeX. I've googled around a bit without too much joy. So I've made a simple one myself.

Here is the code:

\documentclass[a4paper,12pt]{article}
\pagestyle{empty}

\usepackage{rotating}

\linespread{1.2}

\begin{document}

\begin{sidewaystable}

 {

  \renewcommand{\arraystretch}{1.5}

  \bfseries

\centering

\begin{tabular}{|c|c|c|c|c|c|c|c|c|c|c|c|c|c|c|c|c|c|}

\cline{1-1} \cline{18-18}

H &       \multicolumn{16}{|c|}{}                                                  & He \\

\cline{1-2} \cline{13-18}

Li & Be & \multicolumn{10}{|c|}{}                         & Bo & C  & N  & O  & Fl & Ne \\

\cline{1-2} \cline{13-18}

Na & Mg & \multicolumn{10}{|c|}{}                         & Al & Si & P  & S  & Cl & Ar \\

\hline

K  & Ca & Sc & Ti & V  & Cr & Mn & Fe & Co & Ni & Cu & Zn & Ga & Ge & As & Se & Br & Kr \\

\hline

Rb & Sr & Y  & Zr & Nb & Mo & Tc & Ru & Rh & Pd & Ag & Cd & In & Sn & Sb & Te & I  & Xe \\

\hline

Cs & Ba & *  & Hf & Ta & W  & Re & Os & Ir & Pt & Au & Hg & Tl & Pb & Bi & Po & At & Rn \\

\hline

Fr & Ra & ** & Rf & Db & Sg & Bh & Hs & Mt & Ds & Rg & Cn & Uut & Uuq & Uup & Uuh & Uus & Uuo \\

\hline

\end{tabular}

}

\end{sidewaystable}

\end{document}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

And here is the resulting table:

Two Lecturer positions in Bioinformatics/Genomics : Auckland / Palmerston North, New Zealand

Lecturer positions in NZ are as rare as Moa teeth. If you are interested read more at UniJobs, NewScientist and NatureJobs.

PhD position in the evolution and bioinformatics of RNA in New Zealand

Anthony Poole and I are seeking a talented PhD candidate to explore the evolution and bioinformatics of RNA. Tell your friends!

Closing Date: 30 March 2012
For more, see the information sheet. 

RNA Biology provides incentives to review

The full text of the email from Renee Schroeder and Eva Riedmann from RNA Biology is below. The gist of it is that researchers get free subscriptions and discounts on publication costs in exchange for reviewing. This is a clever move by them (in my completely biased opinion). The journal, Nucleic Acids Research, is the only other journal I know of that offers incentives for reviews. They offer a few pounds towards books or CDs from their preferred suppliers in exchange for reviewing. This is nice, but frankly the selection from those sources is very limited. I'd much rather have full access to the journals I review for (actually, I'd rather everyone had full access, that's another battle). All too often I've wanted to look at the published version of a manuscript that I've reviewed and not had access to it. This is ridiculous.



Dear Research Community –

We are writing to you now because you have either served as a reviewer or have submitted a manuscript to the journal RNA Biology in the past.

RNA Biology will be instituting a reviewer incentive program offering free subscriptions and discounts on publication costs in exchange for timely reviews. To guarantee the success of this program we need to update our database and are requesting a few moments of your time.

Please login to the RNA Biology submission and peer-review website here:

http://rnabiol.msubmit.net/

and click on the link “Modify Profile/Password.”

If you could please ensure that your institutional affiliation, address, and email address are up to date AND please select up to five ‘Areas of Expertise’, we would greatly appreciate this. (For your convenience, we have listed the areas of expertise below.)

This will ensure that we are able to notify you of new developments with the journal. Additionally, this information will help ensure that we have a robust database from which to quickly identify appropriate peer-reviewers.

If you have any questions or concern please contact us at rna@landesbioscience.com

Thank you very much for your help.

Sincerely,

Renee Schroeder
Editor-in-Chief
University of Vienna

Eva Riedmann, Ph.D.
Acquisitions Editor
Landes Bioscience

Areas of Expertise

Apatamers
biogenesis
bioinformatics
cancer
cell biology
chromatin
developmental biology
epigenetics
mechanism of translation
methods
miRNA
mRNA transport/localization
natural antisense
neurobiology/neurological disease
prokaryotes
protein-RNA interactions
regulation of stability/degradation
regulation of translation
ribonucleases
ribosome
riboswitches
ribozymes
RNA binding proteins
RNA damage/repair
RNA in disease
RNA stability/degradation
RNA viruses
RNomics
siRNA
small and large non-coding RNAs
splicing/pre-mRNA processing
therapeutics
transcriptome
TRNA

Fetching sequences from EMBL/ENA using wget/curl

Every time I want to download several EMBL files (eg. all the bacterial genomes) I spend at least an hour trying to find the right URL syntax. This post is a public note to self that will help me next time and perhaps help others who are also receiving a few lines of HTML when all they want is a verdammt plain-text EMBL formatted file.

There is actual documentation on the right syntax here, which again takes a while to find, searching for wget, curl, EMBL and various related combinations doesn't get you there quickly. However, the main issue I have is, if I go to the recommended sequence record eg. here, none of the links work with a simple "wget URL" or "curl -G URL".

So, if I want to fetch the Roseobacter denitrificans genome sequence with EMBL accession CP000362. I use:
wget http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/CP000362
or if you're into curl:
curl -G http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/CP000362 > CP000362.embl

Simple!