Video games for Science! (pt. 2)

For those who want or need to write code and haven’t yet settled on a text editor:

Vim Adventures!

This RPG-style video game teaches you how to use the vim text editor, which is incredibly useful (though has a steep learning curve). Vim comes standard on Unix-like systems (so Linux, Mac), so no additional software needed (unless you’re on Windows).

With this game, you can at least try to enjoy learning how to use vim efficiently, instead of being presented with a dry list of commands and definitions like most vim tutorials. At the very least you can play a game that doesn’t take itself too seriously.

This link is also going permanently on the sidebar under Education.

Interactive introduction to scale

The Scale of the Universe 2

This could be a very useful classroom tool for an introduction to a wide range of science subjects. I’d say it’s probably elementary school level, and would likely be too trivial to use in a high school setting. But it provides a lot of springboards to other topics, so if you have a few different classroom sessions planned around introducing biology, astronomy, and/or physics, this could be a great framing device.

(I’m adding it to the “education” section on the sidebar. Appropriate copyrights and such are on the page; I did not make that animation.)

Ruby

As I mentioned in the “About” page, the picture at the top of this blog is of my dog, Ruby, looking down on the city of Riverside, CA. It just so happens that Ruby is also the name of a programming language. (It’s actually not coincidental.)

I know that diving (or even cautiously stepping) into a new programming language can be daunting. Online tutorials are available for all major languages, but in my experience, these can sometimes be no more helpful than simply picking up a textbook. There are definitely presentation and design requirements in any tutorial that, if unmet, will make learning the material more difficult. Furthermore, workshops and tutorials require that you provide your own computer with some form of software already installed, which can present its own challenges separate from the fact that you’re learning something foreign.

It’s refreshing, then, to see a tutorial as intuitive and approachable as this one: tryruby.org. The nice thing here is that the tutorial is right there with the interactive coding environment: all you need is a browser. It would be great to see something like this for all languages, so that people with no prior background in computer programming can take these first steps on their own time.

I’m not here to plug any one programming language. In fact, I have a corn snake named Perl. I’m also of the opinion that once the basics are learned in any one language, it’s easy (or at least less difficult) to transition to a more appropriate one. All I’m here to say is that a clean tutorial like this could give someone a basic understanding of programming and at least open the door of the path to a marketable skillset. For that reason, I’ve added this tutorial to the list of Education links.

Video games for Science!

Here is a unique video game that dovetails nicely with protein structure prediction. The game is called Foldit, an online multiplayer game that allows users to help predict protein folding.

Players of this game don’t need to have any prior background in biology or protein science. You could go to that website right now, download the game, and start playing. Teams from all over the world compete to predict the folding patterns of proteins based on a few simple rules: keep the protein compact, keep the hydrophobic (“oily”) residues toward the core of the protein, and make sure that residue side chains aren’t bumping into one another. The interface is fairly straightforward as well: click-drag-drop.

In theory, the concept is similar to any ab initio protein structure prediction program. (That is, a program that predicts protein structure based on only the primary sequence, and not taking into account any available similar structures.) In the fully computational approach, the computer will try to produce the best possible folding pattern. Generally, this is the one that minimizes energy and maximizes the stability of the protein, while following a concrete set of rules (like those above). With Foldit, the players are asked to do the same thing, using a similar set of concrete rules.

It would be impossible for any one lab or researcher to manually predict a protein folding pattern in the “drag-and-drop” way of Foldit; there are too many possible confirmations and the time requirement is too high. Foldit’s strength, therefore, is the fact that the same protein is distributed to many teams across the world.

The stated goals of Foldit are twofold. Most importantly, they want to help predict the structures of medically or economically relevant proteins. These structures will in turn inform drug design and possibly novel enzyme design. The production of biofuels, for example, could be made more efficient if better proteins could be designed. Additionally, the researchers are interested in whether or not human pattern-recognition skills can be useful in this regard: Will coupling computational prediction with manual puzzle-solving make structure prediction more efficient? If so, would it be possible to design a program that implements the strategies that the human players have come up with? These are the questions that this project is addressing.

More recent protein structure prediction approaches blur the line between traditional “homology modeling” (use of existing templates) and “ab initio” (purely primary sequence and energy-based) by using solved structures to inform the energy-minimizing scoring functions. A recent paper about Foldit’s success hilites this methodology.

I’ve added the link to Foldit on the side bar under “Education”. Download it and give it a try. This way, you’re playing games for science, instead of watering crops or flinging birds at pigs or whatever.

Squid in Space (pt. 2)

The space shuttle Atlantis returned to Earth yesterday, completing its final flight and wrapping up the US Space Shuttle program. I was able to get down to Florida to watch the launch on July 8th. Like the previous mission, we sent squid up on this one as well. The samples will be examined like last time and will help add to our knowledge about how bacterial-animal relationships are influenced by weightlessness.

I have some opinions on the completion of the US Space Shuttle program, but this is not an opinion blog. I will say this: the Space Shuttle was one of the coolest, most technologically advanced vehicle the nation has ever built. But times change and all good things must end. And, since this is a science blog, I think the science is the important thing here. I look forward to what we can learn from working and living in space, and the experiments we can perform there. It is in our best interests for NASA to gracefully step out of the taxi/delivery business and realign its focus to cutting edge science and research. Now that the International Space Station has been completed, this research can continue in earnest. I am optimistic about the future of human spaceflight.

For educational purposes, there is now a link on the sidebar that points to NASA’s Education Materials that teachers can use in their classrooms. The grades represented here are K through college, so people should be able to find what they’re looking for. If not, the site is fairly easy to navigate.

Protein Structure Prediction II – Folding

(This is a continuation of a presentation I gave for one of my courses. I’m posting it because it’s simple and I need to digest the Indoor Air 2011 conference I just got back from. If you need to, read the Protein Structure Prediction I post for an introduction to the chemistry of proteins.)

Ok so now the important part: why do proteins fold? And more specifically, why should you care? It is certainly simple and useful to deal with the “linear string” concept: this structure can be easily captured in a text file (which we call “FASTA file”) and we can do sequence alignments with it using BLAST. But the cell is not a text editor, and in the cell, proteins exist in 3 dimensions. The 3-dimensional positions of the various side chains, much more than simply their order, are what really dictate protein function.

Proper folding is therefore essential to proper function and misfolding has significant consequences. Proteins are machines within the cell that control all of the things that keep us all alive. (This is in bold because this is why you should care about protein structure.) The complex biological processes that dictate life as we know it (including environment sensing, cell growth and development, and a whole mess of metabolic reactions) all occur in large part because of proteins. More specifically, they occur because these proteins have a certain shape and folding pattern, and any changes in that pattern can be devastating. (Diseases like Alzheimer’s, Scurvy, Cystic fibrosis, and Creutzfeldt-Jakob, among others, are related to improper protein folding.) So it’s a good idea to understand not only how these proteins fold correctly (because for the vast majority of us, they do) but also what their final structure is, how it interacts with other proteins, and why, specifically, that’s important.

Here I’ll introduce arguably the most important website related to this subject: the PDB. The Worldwide Protein Data Bank is a collection of organizations in the United States, Europe, and Japan. It serves as a repository for all experimentally determined protein structures; that is, proteins that have been examined in the lab using X-ray crystallography or NMR, rather than predicted computationally. This is important because it is a single archive that is both freely and publicly accessible, and manually curated. (It also serves as the main place to get benchmark datasets when developing protein prediction programs.) The three international websites simply function as different portals to the same content; the United States site is www.pdb.org. They have a great PDB-101 section that does an excellent job of explaining the concepts of and providing educational resources for structural biology. I’ve included a link to it under “Education” on the right side of the page. I’d suggest taking a look at it.

In the final section next time, I’ll go over the main types of modelling approaches and provide information on commonly used software.

Updates

Two quick updates:

The three squidonauts (Ulises, Kraken and Penny) shot into space last month have been successfully recovered. They are currently undergoing transmission electron microscopy procedures at the University of Florida in Gainesville, FL. Transmission electron microscopy, or TEM, will allow us to generate very high resolution and detailed images of the light sac post-infection. The results of this analysis should be back next month in time for the final shuttle launch ever. We are planning to launch additional squid then as well.

Also, and unrelated: I’m attending the Indoor Air 2011 conference in Austin, TX. The main focus of the conference is trying to understand and improve the air quality of the indoor environment. This includes any and all structures that humans have built and inhabit: homes, offices, airplanes, etc. The majority of the week-long conference is devoted to chemistry and engineering practices. However, there is a two-day symposium starting Wednesday on the Microbiome of the Built Environment, which is far more relevant to my interests and field of study. The built environment represents a relatively new environment in which microbial communities can be found and studied. (“New” in the sense that we’re just beginning to examine the organismal communities located therein; obviously human-inhabited structures have been around for nearly as long as humans themselves have.) Interested? Check out this website for some additional information.

Update: Indoor Air 2011 tweets can be found at #indoorair2011. I’ll do what I can here.