Team:Edinburgh/newinformatics(introduction)

Personal note

Working in a wet lab is absolutely the same as programming in Java. You make an assumption, you then build a small model, then you implement it and then you see the result. Depending on the results which might be right or not the ones you expected, you adjust your model and/or implementation and get another set of results. But there is really huge difference between biology wet lab and computer programming. In computer programming you get your results usually immediately but in a wet lab... you have to wait starting from 1 hour and ending by +infinity : )) Wet lab is definetely not for the real informatician guys.

JD

This section of our team WIKI will present thoughts, ideas and results of our team work conecerning informatics side of the project. Usually informaticians are mainly meant to be "modelling guys" or guys "who should know how to do wiki". In our team things happened bit other way and all the moddelling job was captured by engineers and due to lack of knowledge and mostly patience (see personal note above) our informaticians absolutely declined to work in a lab. There were also set of other reasons why this happens and this section of Edinburgh iGEM Team 2009 WIKI will be about those reasons.

iGEM competition is definetely scientific biological comptetition. However, such highly specialised technical competitions are the greatest possible way to influence public perception about scientific ethical issues/problems/discoveries/needs. Like in every community there needs to be a very strong core and if you have one you can build strong community around such a core and this community depending on its strength will be able to influence and help unrelated communities and communities from realted fields.

iGEM development and huge increase in number of teams in last years shows that iGEM already has strong core and I am sure that in next few years iGEM competition from highly specialized biological competition will turn out into each year cultural event like TED, for example. Fact that iGEM will turn from event for restricted group of people into widely acceptable and useful event for me is absolutely obvious. And that is the place where we - informaticians come out : )

Conventionaly, informatician is meant to be a geeky programming guy. That's not true. Conventionaly, informatician is meant to love black screen with lines of white code and hate all those "GUI guys". That's true, but not always. There exists also another type of informaticians who are able to "trade data". They sell scientific and mostly boring for non-specialized person data and get public's understanding of things happening from inside science as a payment. Look at the NASA web-site! Organisation which applies probably the most cuting edge technologies and scientific discoveries has the web-site which I would easily consider as an amazing web-site of spaceships related MMORPG game. What they do? They trade their data.

iGEM competition and its underlying idea is even more fascinating then space discoveries, at least for me. You can't go to the moon by yourself in the nearest future but you can do your own synthethic biology discoveries already in the high school. iGEM can directly impact public perception about science. But in order for those things to happen team websites from scientific WIKIs should start moving towards interactive pieces of art which take its visitors to the amazing and colourful world of synthethic biology. You definetely should visit this link: http://labs.blitzagency.com/?p=388. How about in iGEM 2010 we will see some teams' lab modeled exactly in a such way? What if it will be even more interactive and based on smart engine and WIKI user will be able to perform his own virtual experiments and help the team in solving their project problems? Believe me it only sounds as a pure science fiction but it is achievable by group of 5-8 people in 12-18 weeks. Moreover, tt shouldn't be one year project or one team's project - whole iGEM community might join implementing this idea and we will get virtual lab where iGEMers and public will be able to model and discuss experiments.

In this section I will tell a bit about our thoughts concerning idea of iGEM infromatician team members starting to take the role of data traders on the same level of gravity as a role of modellers. Maybe after some time when teams of future iGEMers' generations will be gathered there will be demand in people who are able to transfrom scientific data into data which is interesting, understandable and what is the most important into the data which will push people to get more knowledge about things happening in the world of science. From our side we hope we made the very small but important step in this direction. Presented map (huge thanks goes to oz_sprog) applied to the real data and our thoughts about DEMOCS Card Game we hope those are the steps in the right direction.

All thoughts presented in this section are personal thoughts and does not pretend to have any scientifical foundation. Those are just observations and personal experiences presented here.

Web market right now is very hot. It is very bad for startups who try to get into this market because level of competition is unbelievably high but it is great for people who just want to use the cuting edge technologies. Core concept in the data trading idea is data representation. Ten thousands lines of numbers concerning landmines victims is hardly readable even for interested person and absolutely unreadable for the person who is not interested in this data. But if you transform those 10 thousands numbers into interactive map data readability will greatly increase and this data transformation will allow inhabitant to leave a small point in his mind, that even in my country we have something happening about landmines. This small point might never come out but might accidentally mentioned to one of the friends during conversation and so on and in fact bring public understanding of the landmine problem to some new level.

There are lots of web-based technologies. Current web trend tries to make the whole user life absolutely autonomic from their standalone operating systems and software. Personally, I don't like this trend, but in terms of data trading it gives us a huge advantage - whatever you can do as a standalone application there is a huge chance you will be able to do it as an online driven application. In the table below is outlined set of technologies and concepts which are in my opinion very useful and easy to use for data trading.

Technology	Description
Adobe Flash	Flash looks like the most appropriate development tool for data trading. Its main issue is the definete need of high drawing skills ability. From the very beginning it was meant to be as a graphic tool for creating lightweighted animations (this is personal opinion). But with the development of ActionScript pure informaticians with strong programming knowledge got access to the world of fancy graphic. With no doubts Flash is the core development tool for purposes of data trading.
Papervision (Official website demos)	Papervision is Great! Papervision is Sweat! Papervision is absolutely amazing tool for helping pure programming guys to create fancy looking graphical solutions. Papervisins is a framework, more precisely, set of ActionScript classes which allow you through using pure ActionScript to create 3D animation which will be perfectly showed and interprete by any Flash Player starting from 9th version. Such industry giants as Audi and BMW are using Papervision for building their highly interactive web-sites. Papervision is very popular in small circles of advanced flash programmers but is very quickly becoming standard tool in the bag of every Flash developer. It has huge amount of tutorials of all levels, it is very logical and easy understandable tool, especially if you have object oriented programming background. Globe tutorial presented in the next section is based on PaperVision.
Tweener	This is another set of classes for flash which is usually tightly used with Papervision3D. This set of classes allow in one line of code create any type of object motion inside 3D space you can only imagine. Unbelivable, but motions inside 3D space can be categorised and be very standart. I doubt that you will find any way of moving object in 3D space that won't be captured by Tweener.
Adobe Photoshop	One of the biggest titans of graphical design. I always use it when I need to make small website or any type of graphics. All current wiki was fully done in photoshop with minimal usage of third party products.
Adobe After Effects	Have you seen our team introductory movie in Team Members page? This was done using After Effect and bit of Photoshop.
Java	Brain of the whole data trading. If you want to interact with data - Adobe Flash is your choice, but if you want data to produce another data - Java. I prefer Java to another programming languages because of the community. Java users tend to be much more frindly then C++ ones, for example. Also Java is very suitable for Web Programming. But anyway each language is more or less task specific, so definitely you should think about Python/PHP/Prolog/Haskell/C++ as alternatives depending on your task.
Imagination	Tool you can't buy because you already have it. Moreover, you have thousand of examples in the web which you can use, combine, upgrade, redevelop and whatever else you need.
Drawing skills	When I was in a high school I was sure that I will never need drawing skills or any music related skills. How wrong I was! I had an amazing change to get perfect Eastern European art education during my school but I was too self-confident that I won't need it ever in my life. Right now this is one of the most desirable skills I would like to get.

This is the minimal set of tools needed for interactive websites creation. In world of web-programming minimal usually equals to everything you need. I can't be sure, but I doubt that titans of data trading, such as guys from NASA, AUDI/BMW use more then 2-3 additional special tools.

Creating interactive things is easy. And I really think that iGEM community should start thinking about moving in this direction because it will bring iGEM idea to the new frontiers.

Edinburgh University iGEM Team 2009