Cloud-based resource to support microbiology data sharing

Cloud Infrastructure for Microbial 

Bioinformatics

The third week of July 2016 saw the launch of the UK's Cloud Infrastructure for Microbial Bioinformatics (CLIMB)— probably the largest dedicated cloud microbial bioinformatics resource in the world. Cloud Infrastructure for Microbial Bioinformatics (CLIMB) is a collaboration between academic and computing staff at the Universities of Bath, Birmingham, Cardiff, Swansea and Warwick.

The impressive scale of the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) computational infrastructure matches its ambitions as a national resource for the UK's medical microbiology community and our international partners. However, size isn't everything—Cloud Infrastructure for Microbial Bioinformatics (CLIMB) also represents a user-friendly, one-stop shop for sharing software and data between medical microbiologists in the academic and clinical arenas. 

An exciting feature of Cloud Infrastructure for Microbial Bioinformatics (CLIMB) is our use of "cloud computing". This means that rather than dozens, or even hundreds, of research groups across the country having to set up and maintain their own servers, users can access shared pre-configured computational resources on demand. Key to this set-up is the concept of virtualization, which allows users to work in simulated computer environment populated by virtual machines (VMs), which sit on top of the physical hardware, but look to the user just like conventional servers. Perhaps a useful analogy is with the digitization of images or text, which allows an object to be stored and reproduced indefinitely without loss of quality. 

Virtualization is widely used to consolidate many VMs on to a single physical machine, ensuring efficient use of hardware.  However, this approach has several other important advantages. As with other digital objects, virtual machines can be stored and shared with ease. Thus, you can launch a VM, install programs and pipelines tailored to microbial bioinformatics and then take a snapshot or image of the customized virtual server. These snapshots can then be stored, copied and shared with others in the research community, freeing downstream users of the hassle of installing complex programs and their often-troublesome dependencies. 

Beyond-Pokemon-Go-Interact-With-Real-Objects

An example here is CLIMB's use of the Genomics Virtual Laboratory (GVL), which comes pre-installed on one of our standard VM offerings. GVL, which was developed in Australia, provides access via the web and command line to a virtual desktop, a personal Galaxy server, together with fully featured environments for the programming language R and the iPython Notepad. Crucially, GVL also provides access to Torsten Seemann's groundbreaking Nullarbor pipeline, which incorporates a range of microbial bioinformatics analyses, while presenting results as a simplified web report . 

However, it is important to stress that the advantages of virtualization go beyond mere efficiency. The creation of multiple standardized VMs with pre-configured software and settings will facilitate training in microbial bioinformatics. Furthermore, the ability to encapsulate a complex server environment into a publishable digital object will allow the entire community to explore and exploit published pipelines and guarantee that complex bioinformatics analyses can be replicated, enhancing the reproducibility of science. 

All this would mean nothing if the system were a private playground for the CLIMB investigators. Instead, CLIMB has been set up as a national facility, with access provided free-of-charge to academic medical microbiologists and microbial bioinformaticians within the UK. But we see CLIMB as more than an academic facility: instead, we hope it will act as a bridge between academics and public health professionals, facilitating sharing of skills, knowledge and approaches between the two communities, as well as exchange of software and data.  We are pleased to note that the system has already seen early exploratory use by Public Health Wales, Public Health England and the Animal and Plant Health Agency. We anticipate that our virtualization approach will facilitate the development of standard operating procedures in clinical and public health microbiology, suitable for national or international accreditation.

Beyond 'Pokémon Go': Future Games

Beyond 'Pokémon Go': Interact with Real Objects

The augmented-reality game "Pokémon Go" may be the hottest thing in mobile gaming right now, but new advances in computer science could give players an even more realistic experience in the future, according to a new study. In fact, researchers say a new imaging technique could help make imaginary characters, such as Pokémon, appear to convincingly interact with real objects.

A new imaging technique called Interactive Dynamic Video can take pictures of real objects and quickly create video simulations that people, or 3D models, can virtually interact with, the researchers said. In addition to fueling game development, these advances could help simulate how real bridges and buildings might respond to potentially disastrous situations, the researchers added.

The smartphone game "Pokemon Go" superimposes images onto the real world to create a mixed reality. The popularity of this game follows a decades-long trend of computer-generated imagery weaving its way into movies and TV shows. However, while 3D models that can move amid real surroundings on video screens are now commonplace, it remains a challenge getting computer-generated images to look as if they are interacting with real objects. Building 3D models of real items is expensive, and can be nearly impossible for many objects, the researchers said.

Now, Interactive Dynamic Video could bridge that gap, the researchers said.

"When I came up with and tested the technique, I was surprised that it worked quite so well," said study lead author Abe Davis, a computer scientist at the Computer Science and Artificial Intelligence Laboratory at the Massachusetts Institute of Technology.

Analyzing movement

Using cameras, this new technique analyzes tiny, almost imperceptible vibrations of an object. For instance, when it comes to curtains, "it turns out they are almost always moving, just from natural air currents in an indoor room," Davis told Live Science.

The distinct ways or "modes" in which an object vibrates help computers model how it might physically behave if an outside force were to interact with it. "Most objects can vibrate and move a certain amount without a permanent change to their shape," Davis said. "To give you an example, I can tap on a branch of a tree, and it might shake, but that's different from bending it until it snaps. We observe these kinds of motions, the kind that an object bounces back from to return to a resting state."

In experiments, Davis used this new technique on images of a variety of items, including a bridge, jungle gym and ukulele. With a few clicks of his mouse, Davis showed that he could push and pull these images in different directions. He even showed that he could make it look as if he could telekinetically control the leaves of a bush.

Even 5 seconds of video of a vibrating object is enough to create a realistic simulation of it, according to the researchers said. The amount of time needed depends on the size and directions of the vibrations, the scientists said.

"In some cases, natural motions will not be enough, or maybe natural motions will only involve certain ways an object can move," Davis said. "Fortunately, if you just whack on an object, that kind of sudden force tends to activate a whole bunch of ways an object can move all at once."

New tools

Davis and his colleagues said this new technique has many potential uses in entertainment and engineering.

For example, Interactive Dynamic Video could help virtual characters, such as those in "Pokemon Go," interact with their surroundings in specific, realistic ways, such as bouncing off the leaves of a nearby bush. It could also help filmmakers create computer-generated characters that realistically interact with their environments. And this could be done in much less time and at a fraction of the cost that it would take using current methods that require green screens and detailed models of virtual objects, Davis said.

"Computer graphics allow us to use 3D models to interactive simulations, but the techniques can be complicated," Doug James, a professor of computer science at Stanford University in California, who did not take part in this research, said in a statement. "Davis and his colleagues have provided a simple and clever way to extract a useful dynamics model from very tiny vibrations in video, and shown how to use it to animate an image."

Major structures such as buildings and bridges also vibrate. Engineers can use Interactive Dynamic Video to simulate how such structures might respond to strong winds or an earthquake, the researchers said.

"Cameras can not only just capture the appearance of an object, but also their physical behavior," Davis said.

But, the new technique does have limitations. For example, it cannot handle objects that appear to change their shape too much, such as a person walking down the street, Davis said. Additionally, in their experiments, the researchers used a stationary camera mounted on a tripod; there are many technical hurdles to overcome before this method can be applied using a smartphone camera that might be held in a shaky hand, they said.

"Also, sometimes it takes a while to process a video to generate a simulation, so there are a lot of challenges to address before this can work on the fly in an app like 'Pokémon Go,'" Davis said. "Still, what we showed with our work is that this approach is viable."

Davis will publish this work later in August as part of his doctoral dissertation.