I came by another interesting video at ted. The speaker talks about how there are no “one best product”, people rather prefer different things. However, people are generally unable to put what they like into words. Though the speaker talks about pasta sauce, his points are easily relevant to research and product development. The bottom line is that you should not look for one perfect product, you should rather find several good products which sever groups of your customers.

The topic is interesting and the speaker gives a very good presentation. So if you are interested in either incentives/motivations or giving presentations you should have a look at it.

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.

To include images in a LaTeX document is it very nice to have resizable figures which look good. To be able to resize an image it is recommendable to use vector graphics. Vector graphics consist of geometrical objects which can easily be resized while maitaining crisp images. Bitmap images on the other hand will often become unclear when resized. To make vector graphics figures I use Inkscape. It is simple and really easy to use.

To create graphs and plots I would use OpenOffice (Calc) and export the figures as pdf with lossless compression of images. The resulting pdf file can be imported directly when using LaTeX. I don’t really make that many graphs so I have not exported that many figures like this and there may be other, easier was to do it. However, this works quite nicely for me. It is of course possible to edit the pdf file in for instance Inkscape or some other image editor like gimp. Gimp is an open source equivalent of Photoshop. Some say it is better while others prefer Photoshop. I have not used either of them that much to have a clear meaning. Nevertheless, gimp should cover most of your needs.

When making plots and graphs gnuplot is a much used option. I must admit that I have not personally used it a lot but I know that other researchers swear to it. Like Inkscape, gnuplot is able to save scalable vector graphics. This is as mentioned a big advantage when resizing images. Everyone who has tried to export a graph or a plot as an image from Excel and resized this shold know what I am talking about.

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.

First, download and install Eclipse. Second, install Texlipse by following these instructions. Then follow the four steps below.

One, create a new project.

Two, select a Latex project.

Three, give the project a name.

Four, select the output and source folders. I always use src and out and so does the template.

Five, extract the files from the template into the project’s folder under the your workspace. Finally, refresh  the content of your project.

The project is now ready to be modified all you want. Good luck with your thesis

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.

I will provide information about the tools and links to Wikipedia and other resources for more information. Links to the tools themselves and in some cases also to other tools which I do not use will also be provided. While writing I will strive to keep it short and simple and provide as many useful tips as possible for other PhD students and researchers who want to start using OSS products in their research.

What is Open Source Software?

For those of you who do not know what OSS is, I will provide a short explanation. Open Source Software and its closely related sibling, Free Software, provide the user with certain freedoms. There are mainly ideological differences between the two terms and I do not differentiate between them unless necessary. Free Software mentions four freedoms: The freedom to run, study, redistribute and improve a software program. A requisite for these freedoms is the source code of the software program. The open source definition mentions ten criteria, similar to the four freedoms, a software license has to comply to be considered as open source.

Software programs are written or developed in a language which can be understood by humans. This is called a programming language and it is the source code of the program. This source code is then normally translate or compiled into binary code which can be understood and run by a computer. Normally when buying a license to a software product, for instance a game or MS Windows, you are normally only paying for the right to run the program. You are commonly not given the right to study, redistribute and improve the program and you are not given the source code.

The advantage of OSS is that you are given the right to study, improve and redistribute the software which means that you can further extend any piece of OSS if you have the skills to do so. This gives a lot of flexibility and this flexibility is great! Both for people who like to work with programming but also for normal software users because they can chose where they get their support. Furthermore, OSS come without licensing fees. This does not necessarily mean that using OSS is for free and it does not mean that companies cannot make money on OSS. However, you as a user do at least not have to pay any license fees. All the programs I will discuss in this series can be downloaded, used, improved and redistributed without paying anything to anyone, unless you want to of course.