It was and is an step-by-step process in which many ideas and researches ended no where but helped me proceeding. Literature and articles on the internet about Game-design, -play and -development also helped me. Check my book list.
Starting with storytelling I needed to find out how to write a story for a game and what's the difference to writing for film. I had several story ideas and spend much time on writing and developing them further but everything I made up until June 2009 wasn't used ;)
I investigated my favourite games because I wanted to know why they are so much fun. At some point I thought about making a game for children, which should be educational. So I spend three weeks on investigating on-line and off-line games for children. In the end this idea was thrown away because without and psychologists and pedagogues this won't work.
Concerning the technical issues I made a tutorial-game with Unity Gameengine and realized that you get things going pretty quick with this engine. So I will definitely use it to present the graphical appearance of my game concept.
In July 2009 I rediscovered a story idea I totally forgot. Then I knew this is it what my game should be about. So I developed it further and I'm still working on it so It isn't finished ;) but I'm quite confident about that.
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So, how’s your thesis now? I hope you already finish it and successfully defended it. From the looks of it, I think you got everything on your thesis under control. Well, it is really a good idea to plan ahead. That way, you can easily organize all your idea and put them in a place that they belong to avoid mistake that can take too much time to fix.