Thinking outside the 2D Box

It is no secret that Johns Hopkins is ranked #1 on the list of universities that spend the most money on research (and if you don't believe me, check out this press release). While part of the research budget is going to the Applied Physics Laboratory, which supports thousands of full time researchers, staff, and maintenance members, a good chunk goes to the famous medical school as well. And let's not forget our fellow brilliant students, who are making huge leaps forward in the myriad fields studied at Johns Hopkins. 

One of these labs in particular is challenging the way scientists study cancer and the way it spreads throughout a body. The Wirtz Lab in the Physical Sciences-Oncology Center has been focusing on studying the spread of cancerous cells, but in three dimensions.

If this doesn't sound revolutionary, consider the fact that most labs study cancerous cells that are contained to a Petri dish, a two dimensional surface on which cancer cells have a known motility (movement). But in 2010 Stephanie Fraley, a then-doctoral student in the Wirtz Lab, thought outside convention and wondered what would happen if a cancer cell was introduced to a cylindrical arrangement of a gel based on collagen I, the most common type of connective tissue in the human body. The results were enough to knock Denis Wirtz, the lab's director, off his feet and onto the 3D path.

While cells in a 2D environment would move slowly, adhering firmly to stiff surfaces within the Petri dish, the 3D cells appeared to move as though propelled by springs, and actively sought out softer parts of the gel-collagen. For decades scientists wondered why cancer cells remained around stiff, mutated flesh in the lab, but actively metastasized within a human body. The discovery of the Wirtz lab resolves this paradox. 

This discovery also raises questions about the efficacy of pharmaceuticals in the fight against cancer, and how tumors can be studied in 3D at all. The former has implications for drugs and chemotherapy; what if there is a drug that would be successful in the human body, but because it was tested in 2D (where cancer cells behave in a drastically different manner), it failed? Should all drugs be retested? How can we use current technology to study tumors in 3D? We need to design a new lens for SEMs to reach this information. Who will design that, and is there funding for it?

Like all good research, this discovery simply raises more questions to pursue. Wirtz, who received his training in physics, not biology, is adamant that the discoveries of his labs will pave the way for new, groundbreaking studies. This would not have been possible if not for the hard work of all who participate in supporting his research, not only financially. Donald E. Ingber of Harvard and Kenneth Yamada, NIH investigator and second most cited researcher in biology according to Google Scholar, both think 3D cancer research is the "missing link" between the 2D lab and a live human or animal model. 

Armed with this research, Wirtz intends to finally beat cancer once and for all, and he is only one of hundreds of hard working researchers at Hopkins. Truly, we earned the status as #1. Let's go Blue Jays! 

Building Virtual JHU

So, how do we make all those buildings you see in Virtual JHU? Here's a quick run-down:

The primary 3D modeling program we use is Google Sketchup. Sketchup is convenient for a couple reasons. For one thing, there's a basic version that you can download for free. (Right now we're using the Pro version, which you have to pay for.) Unlike other 3D modeling programs, learning Sketchup is pretty easy, and it is remarkably powerful given how easy it is to use. The other thing that's nice about Sketchup is that it integrates very well with Google Earth, which is what we're using to present Virtual JHU. If you're interested in 3D modeling at all, I highly recommend getting started with Sketchup. Google has also come out with a tool called Building Maker, which is the quickest way to make buildings for Google Earth.

The first step for modeling any building for Virtual JHU is getting the floor plans. We are deeply indebted to the Office of Facilities Management for providing floor plans to us for Virtual JHU. Once we have the CAD drawings for each floor, we import them into separate Sketchup files. (The ability to import .dwg files is only offered in Sketchup Pro now.) We then pull up the walls outlined in the 2D floor plans to create a basic model of the floor, finishing by adding a floor slab underneath.

Once we have made models for each individual floor we stack them on top of each other in a single Sketchup file. Then we make a roof for the model based on photographs, first-hand observations, and (sometimes) measurements. At that point we've built a model that looks roughly like the real building (except very plain).

The next step is to begin photo-texturing the model. When we started modeling the buildings currently in Virtual JHU we took photos of each individual feature of the building (windows, doors, brick, etc.), used Photoshop to crop them, and then positioned them on the model in Sketchup, tiling materials like brick and marble siding as necessary.

This process resulted in models that were high in detail, but also in file size and are a drag on users' graphics cards. That's one of the reasons we have to continue to work on increasing the performance of Virtual JHU.

To help with performance, one of our programmers wrote a script that removed interior geometry from the Sketchup models, enabling us to present exterior-only versions for all the buildings (until you "open up" a building to see its individual floors). The script caused some issues with some of the models, damaging their materials. (You can notice some pretty significant issues with some of the buildings.)

To solve this problem, now once we have a building stacked we create a shell made of simple planes, on which to apply the textures. This reduces the geometry in the exterior-only versions of the models without having to use the "gutting" script. We have also been trying to use lower-resolution imagery that isn't quite as detailed.

So there you go, that's how we make our models in a nutshell. I'll leave other parts of Virtual JHU to another post. If you have any comments or suggestions, we'd love to hear them.

Virtual JHU 2.0 Released!

Today we released version 2.0 of Virtual JHU, which contains a lot of new features. Keep reading for more information.

We are happy to announce the release of Virtual JHU 2.0. We have made a lot of changes and added many new features for this release. The most obvious change is the new website design, for which we can thank STS’s team of web designers: Allison Tse, Lia Cefalu, Steve Han, and Lavanya Sivakumar.

Depending on the speed of your internet connection and your computer's graphics card, you may experience performance difficulties. We are working to decrease the amount of time it takes to load Virtual JHU and hope you will be a little patient. One thing to note is that once you have loaded Virtual JHU, it will load quicker within the same browser session.

Here is the full list of new features:

1. Google Earth Browser Plugin

For the first version of Virtual JHU, the models were contained in a Google Earth file (kmz) that users downloaded and then opened in Google Earth. Version 2.0 utilizes the Google Earth browser plugin to display the Virtual JHU models inside the user’s browser window.

2. Realistic Terrain

If you have ever visited the Homewood Campus, you know that the terrain there is unique, to say the least. Virtual JHU now includes a realistic representation of the terrain and accurately places buildings in the terrain.


3. New Models – Including Interiors!

Almost all of the Homewood Campus buildings have been remodeled for version 2.0. Why? Because we wanted to include the interiors of the buildings as well as the exteriors. Now you can look inside a building and see its individual rooms. This is great for locating classrooms, offices, and many other relevant places on campus.

4. New Levels of Data

As mentioned, you can now view individual rooms by clicking on their icon inside the Earth viewer. When you do this, you will get information associated with that room: if it’s an office, you will see a description of the office, a link to its website, and maybe a video talking about what goes on there. Classrooms contain a list of classes that meet there, and dining locations around campus are tagged, showing hours, payment options (Dining Dollars, J Cash, etc.), and more. In the coming months we will be adding more kinds of data as well as extending our coverage of tagged data. If you would like input in what data is included in Virtual JHU, email us. We need your help!