Team:Calgary/Second Life/Blog

Every Tuesday (started at the end of June), our second life team uses our Synthetic BLOGology blog to update both the public and the rest of the team of their progress in Second Life on the LINDSAY Sim. For more details regarding Synthetic BLOGology, please click HERE.

-June
-July
-August
-September

These updates have been posted with the newest ones at the top.

Dear Mandy,

Due to finals early this week and you having left for Hawaii, second life team members have been sparse. I wanted to stay in touch and keep you up to date somehow.

As you are aware, since scripting and equipment in the lab has been completed, last week we began the base of the Biobrick spiral where some of the fundamentals of molecular biology, including the central dogma will be located. You will be happy to know I have completed the DNA replication animation that avatars will be able to click on in order to learn what is required to happen for successful replication as well as a initiation point/button to begin the activity as well as reset it. All that is left is make it user friendly since everything that can be touched will perform some action and these actions just need to be explained and secured so that order is important. This may also be done with the help of a notecard that has been made. The only reason this went so slowly is the fact that I am attempting to complete wiki notebook updates in parallel and believe me, it has been a painful experience decrypting the notes that I have. Now, transcription and translation will have to be added and will most likely be tackled by either you or myself in the near future. I have started the initial framework for transcription, but most likely will not be able to complete it before this week is finished.



As I understand it, the biobrick simulator is basically completed and now the levels have to be organized and the textures for the buttons of the biobrick simulator interface. Thank you for completing the buttons Patrick required for the HUD he has made. They look great and I’m sure he really appreciates it.



I see the area avatars first enter the island has been expanded by you and Stefan and now includes a map (including teleportation areas) and directive tubing into synthetic kingdom. To ignore the big red X’s and arrows would have to be intentional and pathway stones litter the landscape throughout. Stefan has been working on his eukaryotic cell and finishing up his disease hunting bacteria within it. Also, I would like to thank you for allocating an area for previous iGEM projects and I see that the logo now decorates the outer walls of the virtual lab. A section of the island will now be filled with worthy iGEM projects, which may be done in the fall with enough linden dollars.



Hoping you are able to locate a bobtail squid,

Katie

Hello again! This week has been another busy week for us Second Lifers. We are wrapping up a lot of our work for the summer. Patrick's update about the biobricker from last week was awesome, and this week I'll be describing what we've been up to in the Synthetic Kingdom and the Labs.



In the Synthetic Kingdom (where we show potential applications of synthetic biology), we are completing the pathway through the levels, and the descriptions and instructions for the stations. We will also be completing descriptions of free moving bacteria that can be interacted with, which visitors can try to look for them while following the path, creating a dynamic environment that still provides guidance for users. This area will also be expanded to include descriptions of past iGEM projects in an "iGEM Hall of Fame". The pathway through the kingdom is complete, as well as the individual stationed activities and the drop in point. Now we are just building on it to make it clear what sort of things we want users to learn as they travel through the kingdom.



All of the lab scripts are complete, and all of the lab activity parts have been duplicated and modified for the second lab. We are still working on the instructions and descriptions for each of these activities. Now that the lab missions are fully functional, we've also created prizes to be given for successful completion of the lab , as an incentive. As the lab missions get successively more difficult, the awesomeness of the prizes increases. :)

Since the lab component is mainly complete, we have begun working on base of the biobricker helix, where we will be putting up exhibits and other objects that will explain some basics: what are genes, how gene expression can be modified, replication, transcription, translation, and some important parts of iGEM (the registry, how biobricking works, etc.).

We're getting nearer to the end of summer, so now we're trying to complete as much as we can in hopes of having most (if not all) of the island ready for people to explore.

Hello again,

This will be a shorter update than the last few weeks, mostly because the SL team is hard at work. Our iGEM season ends alarmingly soon, on the 21st of August, so we're in crunch mode now to get the sim polished and ready for public consumption.

I will tell you what I've been up to toward the end of last week and the beginning of this one: the Biobrick builder (aka the Biobricker). This is one of the most important features of the Biobrick Simulator in SL, because it turns the very static devices seen in the video last week into plastic and redesignable systems. The interface for the Biobricker is finished, which enables the user to piece various promoters, coding sequences, terminators, and other Biobrick parts together. You can build a device of any length, insert and delete parts anywhere in the Biobrick too. The system isn't only critical for the final package, it will be very useful for testing the other new features that are yet to come. Clicking around the interface already feels nice and responsive, and very powerful!

The system is designed to be expandable, so while the initial selection of parts will be small it will be easy for myself or another intrepid SL coder to add additional elements. Did I mention that all of the components we're designing this summer will be made available for all to use in Second Life? We saw no point in restricting the use of the work we've done this summer, and I'd love to see what people can come up with.

The interface was finished up last week, but I have just finished the Linden Scripting Language code (that's Second Life's built in scripting language) to accomplish the construction of these Biobricks in world today. The Biobricker needs so pass a few more trace-throughs and a lot of testing before I certify this part of the project complete though.

A simplified view of what's going on behind the scenes, is that after using the Biobricker's interface to design the device you want, the interface object directs the assembly of a number of Biobrick objects in the real world. It creates each Biobrick part, gives it a name and position within the completed device, and orders all the DNA to link together into the final device. Guaranteeing that each part gets the information it needs is harder than it sounds though, especially given the nature of communications in Second Life! It's impossible to guarantee messages will arrive in the order they were sent, or that they will even arrive at all, so the construction system has a lot of fail-safes to ensure that your device comes out right every time.

That's all for this week, stay tuned!

NOW WITH WORKING SOUND!

Hello, my name is Patrick King, and I am one of four students at iGEM Calgary working on a very unique subproject this year: creating an educational environment for synthetic biology in Second Life.

Second Life is an online, virtual world, where every object, costume, creature, and patch of land is designed by the world's inhabitants. It is a 3D chat engine, a videogame platform, a virtual reality, and an online classroom all rolled into one. It's a fascinating place, an internet search or two will reveal the variety of creations and experiences to be had there. Access to Second Life is free, create a free account at their website, download the client, and you're ready to go.

iGEM is the International Genetically Engineered Machines competition. It is an annual contest of scientific skill between teams of undergraduates at universities around the world, to engineer the most useful and most interesting organisms around. I can't sum up all of iGEM in this space, but for the unfamiliar, the official introduction is a great place to start.

So what does iGEM have to do with Second Life? Well, the problem with doing an iGEM project at university is this: sooner or later all of the students graduate. Even those who decide to participate in an iGEM team several years in a row (those poor souls!) have to get on with their lives sooner or later. The result is that a huge amount of time is spent educating the new year of students, and this problem can be especially acute for teams of entirely undergraduates like ours. Many of our students are in their first or second year, many have never been in a molecular biology lab before, and they've got to learn all the ropes if they want to have a hope of competing at iGEM level.

Ultimately, all this time spent training the next generation will pay off (we hope!) with a generation of new scientists, the synthetic biologists. But for right now, we really just need to get all the cloning and biobrick assembly and system tests and a dozen other kinds of work done by the end of summer.


An educational area in Second Life offered by Nature Publishing Group

Enter Second Life. SL has gained a lot of attention for its potential as an educational platform. The most often touted feature is that SL can offer a classroom-like environment for people at any distance from one another. While the iGEM Calgary island will make an excellent hangout for idle igemmers the world over, our focus is less on creating a classroom, and more on presenting concepts directly. We want to make it easier for new students to grasp the basics of synthetic biology by making it accessible and interactive. This is where SL's object creation and scripting facilities come into play: we can create anything we want, from molecules to cells to lab equipment, and then make it behave like the real thing.

For example, take one of the Second Life subprojects: the Biobrick Simulator (provisional title). The goal of the simulator is to represent a number of commonly used biobrick types by simulating the actions of single molecules. In Second Life, you won't read about RNA polymerase in your textbook, or hear about it in lecture, or click buttons on a flash animation. You will grab an RNAP molecule floating in front of you, and bring it to the promoter region on the DNA also floating before you, and watch it create an mRNA and pop off at the terminator. Unless you drag the RNAP to some DNA that doesn't happen to be a promoter, or move it perhaps to a promoter with a repressor complex attached. Then it won't do anything at all. Simple!

The Biobrick Simulator is my pet project, I will be posting more about it in the future. I plan to have examples for the visitor drawn from the real world, including classical systems like the Lac operon and the Tetracycline resistance operon, and synthetic systems like the repressilator, and the bistable switch (and many, many other systems). The main event will be the ability to assemble your own genetic circuit from scratch, and see how it works!

You've already heard from Mandy a little about the virtual lab that is also under construction, next week we'll give an introduction to the third and final subproject: the Synthetic Domain (name also tentative!). It seems quite unlikely that SL will replace traditional instruction, but the power of learning by doing is enormous. Putting some smart students together in a lab with a few biological reagents is the basis of the iGEM competition, after all.

My number one goal for this project is for it to be useful to others, especially early university or high school students just beginning with iGEM, but also biology students in general, and the public. For it to be useful, it must be used; feedback on the accuracy of our work is essential! I hope that Lindsay Island will be open to the public near the end of the summer, but the real test will not come until iGEM 2010, when we will meet our first batch of fresh students.