If you have problems setting up a SVN connection using Subclipse, I might have the solution, or if you want to know more about how to set up Eclipse as a LaTeX environment, check out one of my previous posts.

For some reason I do not bother to dive into, openjdk is hard coded into Vuze as its preferred Java implementation on Ubuntu. When I removed openjdk, Vuze would of course not start. It is apparently a bug (or meta bug) but it is quite simple to fix.

Change one line in /usr/bin/azureus by using “sudo gedit /usr/bin/azureus” and change the line JAVA=’/usr/lib/jvm/java-6-openjdk/jre/bin/java -Xmx1024M’ to JAVA=’/etc/alternatives/java -Xmx1024M’

It is imperative to manage the publications your read and the bibliography information for these publications. Searching for something you know you have read somewhere and identifying missing references is really a pain. It is therefore very wise to managing your bibliography using for instance BibTeX, Endnote or similar tools.

As a Latex person I will focus on the tool I use for managing bibliographic information (BibTeX), pdf files, notes and categorization of all this information, Aigaion. Other tools worth checking out are CiteULike and Zotero. I have used CiteULike (a web service) a bit but the lack of quality BibTeX information made med abandon it “long” time ago. Recently I have started using Zotero (a in-browser tool) a bit but primarily for gathering data (it does a very good job). Other people who use it recommends it warmly. However, my recommendation is to share you bibliograhpy with your friends and colleagues using an internet based tool called Aigaion.

I will try to explain why I stared using Aigaion. First, since I am using several computers and both Windows and Linux I wanted a system which was portable. Aigaion allows me to easily export all the information from the system as BibTeX or RIS files. These files can simply be put into a revision control system. Combining the BiBTeX text files with Subversion works like a charm. Second, I wanted to be able to share the publications and the BibTeX information with my colleagues. Aigaion is a web based system which allows several users to share and manage the same information and the same pdf files, and collaborately improve it. This is probably the main reason why I started using it. It is easy to give a colleague access to a publication or I can easily email a publication to someone using a feature I (proudly) contributed myself.

Moreover, being a web system written in PHP it is easy to extend and integrate it. It has a fairly stright forward MVC architecture and it is built on top of a framework called CodeIgniter. I use Aigaion to list my publications in my web site http://oyvindhauge.net (see publications) and our publications at the department in wiki about open source software research http://www.research.idi.ntnu.no/oss (see publications).

So if you are in need of a system for managing your bibliography or if you just need a system to manage your own publications and print them in your own or your department’s web page you would want to chekc out Aigaion. Head over to http://www.aigaion.nl, download it or at least try the demo. It comes highly recommended!

Even though the Norwegian government has established a competency center for open source software, the government has only started using a few open source software applications. One of which is not open source is the application for getting travel refunds. This is clearly an important application but it is unfortunately only a Windows application.

Normally I have used this program on Windows but a few days ago I did not have any PC with Windows so I decided to try Wine. I must say I was impressed. I opened the Synaptic Package Manager in Ubuntu, searched for Wine and installed it. Piece of cake. Then I just downloaded and opened the msi-file for the travel refund application. Wine automatically fired up and installed the application perfectly. Within seconds I was completing my travel form (which is really a pain).

I have not used Wine much besides this travel refund application. However, it worked flawlessly with the Olypus DSS Player, which we use for listening to recordings of interviews, as well. Bottom line, I was impressed by Wine’s simple installation and that it worked flawlessly out-of-the-box. Based on my somewhat limited experience I would warmly recommend it.

My editor or tool package of choice is of course OpenOffice. OpenOffice is very much like MS Office and it contains a text editor, a spreadsheet program and a program for making presentations. These should cover most users needs. I have used both the text editor and the spreadsheets quite a lot and in the latest version of OpenOffice, editing .doc (the MS Word document format) also works like a charm. In previous versions of OpenOffice I have experienced some problems editing the same document with both OpenOffice and MS Word but this seems to be resolved.

Probably the two programs I use the most is my web browser and my email client. Thank you Mozilla for Firefox and Thunderbird. I have been using both for several years and they are in my eyes way better than the alternatives, and they are open source. You should not need any other reasons for using them. Pair Thunderbird with Lightning, the calendar plugin, and you have a very good organizer.

If a calendar isn’t enough to organize your thoughts you might consider, FreeMind. FreeMind is an exelent mind mapping software which I use quite often to brain storm and to structure thoughts.

I will probably come back to other desktop tools when, or if, I write about any Linux distributions. Most such distributions come with a lot of useful tools and applications right out of the box and ready to use.

haugeoy

Rep:

Gamerscore: 12955

Zone: Recreation

haugeoy

Rep:

Gamerscore: 12955

Zone: Recreation

You may want to download the plugin with my modifications but please don’t blame Oliver Baty for the changes I have made and remember that the plugin is provided without any warranties.

Changes to the original plugin (version 1.3 beta)
Unfortunately my webhost does not provide Curl installed so I had to modify the plugin and make it use fopen instead. I replaced some of the code. Edit: the changes were included in this post but the code was removed because it caused some problems with WordPress

There are probably more options for writing your publications and your thesis than there are stars in the sky. I will not go into detail on hardly any of these (see for instance here). Most people choose between an office tool like Mircrosoft Word or OpenOffice, or a typesetting language like LaTeX. Office tools offer easy editing based on WYSIWYG (what you see is what you get) and with reference managers like Endnote they would probably work quite well. That is if you are writing small to moderate sized documents, strictly using document styles, never writing mathematical formulas, and writing alone or with some sort of e-mail document locking.

LaTeX has its shortcomings as well. You have to compile the document, writing tables can sometimes be painful, the treshold for using it is higher and it is sometimes a bit difficult to place tables and figures exactly where you want them to be. However, LaTeX shines when you easily want to create large, good looking documents with plenty of (cross) references. Completely change the style of large documents is done in seconds thanks to the variety of packages and templates available through the Internet. LaTeX is furthermore written in plain text, meaning that you can use your editor of choice. Additionally, you can use Subversion (a revision control system) or similar tools for document version control and backup. This is to me a very important feature as you can easily collaborate with others on the same document, work on it from more than one computer and be certain that everything is safely backed up. Safe and secure backup should be the first commandment of all PhD students and researchers. Take a look at this comparison of Word and LaTeX or use a search engine to find more information about the strengths and weaknesses of the two.

While there are several text editors and editors designed for Latex I started using Eclipse to write LaTeX documents a few years ago while writing documentation for a Java project. It was easy to use the same editor for both tasks. Even though Eclipse is or should I say was an IDE it works quite well as a text editor and it allows me to use the same platform on both Linux and Windows. To simplify the LaTeX editing I use the Texlipse plug-in for Eclipse. This enables auto completion, colored text and visual feedback of compilation errors, see below.

To enable Subversion I use the Subclipse plug-in. This allows easy check out and commit of files from within the Eclipse platform.

Both plug-ins can easily be installed using the “Software update” feature of Eclipse but you do of course need a TeX implementation. This is included in most(?) Linux distributions and on Windows you may download and install MikTeX. What I like the most about MikTeX is that it automatically downloads missing packages.

Fitting different software systems together is not always done without small configuration challenges. As for instance after updating to the newest release of Eclipse (Ganymede) and reinstalling Subclipse I got some error message and I had to set the correct SVN interface. The good thing about many open source products is that they have plenty of users and in this case someone had already found a solution to the problem.

First, the installation process is really simple and really fast. It takes perhaps 30-45 mins on three year old computer. A colleague, sitting next to me, was really impressed by how fast it was. Second, no need to install any drivers. Third, all, or at least most of the software you would need to normal work is already installed. Installing a couple of other products can easily be done through either a simple search in the graphical user interface or through apt get install.

Some new Compiz features were available when installing again from scratch. These make the desktop look quite slick. I really like it. There are probably several other very good Linux distributions out there but after using Ubuntu for the three last years I would really recommend it. Go to http://www.ubuntu.com/ and try it out yourself.