Monthly Archives: March 2011

New publication: analysis of large protein assemblies in macrophage cytoplasm

First for 2011:

Proteomic and electron microscopy survey of large assemblies in macrophage cytoplasm.
Maco, B., Ross I.L., Landsberg, M., Mouradov, D., Saunders, N.F.W., Hankamer, B. and Kobe, B. (2011)
Molecular & Cellular Proteomics, in press, doi:10.1074/mcp.M111.008763

This is an in-press article which is freely-available just now (although strangely, the supplemental data are not). I’m pleased to note that we also made the raw data available in Proteome Commons. In fact, it was a condition of publication.

Lots of hard work went into this one. My contribution was quite minor: some bioinformatic analysis and hacking away at PyMsXML to make it work with newer versions of vendor formats. I’d like to thank Brad Chapman with respect to PyMsXML, who provided invaluable advice via BioStar.

Ruby Version Manager: the absolute basics

Confession: I’m still using Ruby version 1.8.7, from the Ubuntu 10.10 repository. Why? I have a lot of working code, I don’t know how well it works using Ruby 1.9 and I’m worried that migration will break things and make me miserable.

Various people have pointed me to RVM – Ruby Version Manager. As the name suggests, it allows you to manage multiple Ruby versions on your machine. Today, I needed to test an application written for Ruby 1.9.2, so I used RVM for the first time. Here are the absolute basics, for anyone who just wants to test some code using Ruby 1.9, without messing up their existing system:

# install rvm
bash < <( curl http://rvm.beginrescueend.com/releases/rvm-install-head )
# add it to your .bashrc
echo '[[ -s "$HOME/.rvm/scripts/rvm" ]] && source "$HOME/.rvm/scripts/rvm"' >> ~/.bashrc
# add tab completion to your .bashrc
echo '[[ -r $rvm_path/scripts/completion ]] && . $rvm_path/scripts/completion' >> ~/.bashrc
# source the script; check installation
source ~/.rvm/scripts/rvm
rvm -v
# returns (e.g.) rvm 1.2.8 by Wayne E. Seguin (wayneeseguin@gmail.com) [http://rvm.beginrescueend.com/]
# install ruby 1.9.2
rvm install 1.9.2
# use ruby 1.9.2
rvm use 1.9.2
ruby -v
# returns (e.g.) ruby 1.9.2p180 (2011-02-18 revision 30909) [i686-linux]
# do stuff as normal (install gems etc.)
# when you're done, switch back to system ruby
rvm system
ruby -v
# returns (e.g.) ruby 1.8.7 (2010-06-23 patchlevel 299) [i686-linux]

That’s it. The key thing is that RVM sets up Ruby in $HOME/.rvm so for example, when using version 1.9.2 under RVM, gem install GEMNAME will install to $HOME/.rvm/gems/ruby-1.9.2-p180/gems/. Your system files are untouched.

The RStudio IDE: first impressions are positive

Integrated development environments (IDEs) are software development tools, providing an interface that enables you to write, debug, run and view the output of your code.

Whether you need an IDE or find them useful depends very much on your own preferences and style of working. In my own case for example, I’ve tried both Eclipse and NetBeans, but I find them bloated and rather “overkill”. On the other hand, my LaTeX productivity shot up when I started to use Kile.

Most of my coding involves either Ruby or R, written using Emacs. For Ruby (including Rails), I use a bundled set of plugins named my_emacs_for_rails, which includes the Emacs Code Browser (ECB). For R, I occasionally use Emacs Speaks Statistics (ESS), but I’m just as likely to run code from a terminal or use the R console.

RStudio, released yesterday, is a new open-source IDE for R. It’s getting a lot of attention at R-bloggers and it’s easy to see why: this is open-source software development done right.
Read the rest…