Tuesday, 3 August 2010

Another dissertation

So I'm almost at the end of my second MSc and hard at work with the writing of my dissertation. This time it is a MSc in Bioinformatics and Computational Systems Biology. So still very computery, but with a lot of Biology. Specifically molecular and synthetic biology.

I have decided to start writing this just to take a break from the dissertation every now and then. It has been difficult to get my thoughts organised and I hope thinking about something else every now and then will help.

Like last year I decided to use LaTeX. Unlike last year, I don't have to write a 10 to 15 thousand word document, but rather a 16 page write up of my research in the style of the Bioinformatics Journal. For this purpose I had to download a template provided by the Bioinformatics Journal.

I have selected applications again that will run on both Linux and Windows because my computer at uni runs Windows and all my computers at home run Linux. Off course the main requirement is that the software has to be open source.

Firstly there is Mendeley for managing references. It is quite good and I have been using it all year. It has a plug-in for OpenOffice and it works well with LaTeX too. Mendeley also keeps itself synchronised with a web account so when I work on a different computer I can synchronise that too with my references.

Then off course there is Texmaker that I used last year. I managed to set it up to run my own make script from one of the customizable menu items.

I managed to create a nice E-R diagram with DBDesigner4 for the mySQL database that I had to design and the rest of my graphics I have been making with Inkscape. As usual it is a bit of a faff to the graphics in the right place, but I found some nice tips here http://andrewjpage.com/index.php?/archives/48-Figure-spanning-2-columns-in-Latex.html.

I have had quite a bit of success this year running Windows applications on Linux using Wine. My favourite photo manipulation program is still Irfanview. It is not open source and you should really register it (which I have done). For £6 it is more than worth it though. I really don't mind supporting software like this little gem.

PDF-XChange Viewer is another application that I have really become attached too. I run it on both Windows and Linux. On Linux it runs quite successfully with Wine. It allows one to mark-up PDF documents, so unlike last year I don't have two files full of printed papers.

I also started using Dropbox this year. And boy, has that made my life easier! I now know my stuff is backed up and it is usually in at least three places, my PC at uni, my PC at home and my laptop. I only need to log on to the Internet and my computer is synchronised with the Dropbox website. If off course I am on somebody else's computer or a computer in one of the clusters at uni I only need to log onto the Dropbox website and download the document I need. Amazing.

Well, I should probably get back to the dissertation - or to bed, if I can convince myself to fall asleep ...