Fixing it was rather easy. Have a look at the solution provided by M.Srinivasaverman (thanks man!).

I am an engineer, I am partly writing about software reuse, and I think it is rather practical to be able to benefit from the good work of others. Therefore, I decided to have a look at some of the WordPress themes. I liked the one you see now (pyrmont-v2) and decided to try it out, at least for some time. It was perhaps not a very original choice but it was among the first ones I found and I did not want to spend hours looking… Hope you like it too!

I just have to say I am really happy with how easy it is to search for and install a new theme. Good work WordPress guys and girls!

It is time for the SourceForge community choice awards. I have of course nominated Aigaion, my favourite web bibliography tool. Some time ago I wrote about it here.

The nominations close May 29th so you should be quick to nominate your favourite. Voting starts June 22nd and I do of course think you should vote for Aigaion.

While I do not think these products will dissappear it would be sad if they lost some of its support in the software industry. Oracle on their hand has also supported several open source initiatives but you never know the consequences of a merger between two large companies.  In particular, I wonder what this will mean for all the open source projects Sun has supported. It could be very positive if Oracle continue and increase their support to open source.The new Oracle+Sun would be a serious player in the software industry and in particular in the open source world. I beleive that the open source community depend on having the support from the industry, and in particular the large flagship companies like IBM, Sun, Oracle and so on. However, you must break some eggs to make an omelet and merging two large software companies is one big omelet (something which we already see speculations about). I just don’t hope the broken eggs will be open source ones. I wish the two good luck and hope that they will continue supporting open source even stronger.

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!

Personally, I think this is great news. By providing their works at no cost (preferably also with the freedoms attached), artists and software developers are able to attract people who are willing to pay for their services. I believe this is the future for an increasingly larger share of the software industry. Attract customers with free, both as in free beer and free speech, commodity and charge for value-adding development and services.

I have personally seen the same with other books as Producing OSS by Karl Fogel, Thinking in Java by Bruce Eckel, several books by Eric Raymond, and the O’Rilley’s Open Books project. Even though they are available for free I have ended up buying several of these books (which I recommend). Bruce Eckel claimed that the feedback he got from his online readers enabled him to write an even better book. This is very much the same as with a lot of the high quality open source software out there. Open it up to contributions from others.

Having material freely available on the Internet enables artists to reach out to new potential fans. I would never have found nor bough anything from stand up artists like for instance Carlos Mencia, Steven Lynch, and Jeff Dunham if it wasn’t for the Internet and youtube. I have also found music and movies in the same way. So keep up this free trend. I believe it will pay off for everyone in the end, well except perhaps for distributors of movies, music and so on.

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.

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.

First things first, I have to make a layout because this one is kind a dull.