IBM, Scientists Seek Public’s Help With Millions Of Virtual Experiments Mapping The Human Microbiome

Have you ever wished you were a scientist? Have you ever imagined yourself making a contribution to the scientific, technological and medical innovations that are taking place as the world settles into the 21st century amid all of its potential? Well you may think it’s too late to go back for your doctorate, but there is something you can do to help change the world in a big way—at any age—and maybe help yourself and your health along the way.

This week, the biggest study of the human microbiome in history has commenced in a project run by IBM with the Broad Institute of MIT and HarvardMassachusetts General HospitalUniversity of California, San Diego and the Flatiron Institute, and you too can be a part of it.

It’s called The Microbiome Immunity Project, and it aims to understand how trillions of bacteria in and on our bodies impact diseases like Type 1 Diabetes, Crohn’s disease and ulcerative colitis – illnesses that are being diagnosed with increasing frequency.

Did you know that each of us has as many as 30 trillion bacteria living in and on our bodies? These bacteria, which live in our digestive systems, are part of a system called the human microbiome. Most of these bacteria are harmless or even beneficial. But some have been implicated in diseases such as Type 1 diabetes,ulcerative colitis and Crohn’s. And as scientists gain a better understanding of the role of human microbiome in the development of disease, they will be able to find and create better diagnoses and treatments.

“But to better understand the roles played by the various bacteria in the human microbiome, scientists need to study the proteins produced by these bacteria, which are encoded in their genomes,” said Dr. Rob Knight, a professor at the UC San Diego and founder of the American Gut Project, wherein scientists work with non-scientists in an effort to understand the life inside the gut (how many and which species live in our guts) and to figure out what characterizes healthy and sick guts. “The first step is to determine the physical structures (shapes) of the protein molecules coded by each bacteria’s genes. This is important because the physical structure of a protein determines its function. Once the protein functions are determined, scientists can explore how the bacterial proteins react with each other and determine which proteins play a role in any number of diseases. From these insights, scientists would be able to develop drugs to control those particular proteins and help treat diseases that originate in or are influenced by the human microbiome.”

Knight said the implications of The Microbiome Immunity Project are massive, especially to older Americans. The project will look at the entire human body, starting with the gut, which alone has trillions of bacteria, and has been linked to more and more diseases and health risks in recent years. “Many disorders implicating the gut microbiome first appear, or increase in severity, later in life,” he said adding that the following are among the diseases recently linked to the gut microbiome by both association studies in humans and causation studies in mice (i.e. studies where changing the microbiome changes the outcome in a model of disease): obesity, asthma, rheumatoid arthritis, major depressive disorder, inflammatory bowel disease, type 1 and type 2 diabetes, Parkinson’s disease and autism.

And scientists are fully aware of the enormity of their task. That’s where IBM and its World Community Grid comes in.

In order to take on this monumental task and complete it in years instead of decades, scientists need massive supercomputing power to complete simulations and virtual experiments on behalf of scientists. So, they’re enlisting the public’s help to power IBM’s World Community Grid, a massive supercomputer that runs on crowdsourced computing power from desktops that are not being used. Anyone with a computer and internet connection can get involved and contribute. By simply downloading a secure software to your desktop, the Grid is able to identify spare processing power and run experiments in the background.

The data from these experiments will then be used by scientists from the Broad Institute of MIT and Harvard, Massachusetts General Hospital, UC San Diego and the Flatiron Institute, to discover new strategies for preventing and treating these diseases.

“The reason why it takes so much computation is that calculating protein structures is extremely time-consuming and has not previously been done on this scale because there are so many distinct proteins and distinct protein families in the microbiome,” Knight said. “In the past, researchers interested in individual proteins have solved the structures of those proteins either using computational techniques or in the laboratory. In this project, we are trying to do it for all proteins in the microbiome at once, which will provide a far more comprehensive view.”

Juan Hindo, IBM Corporate Citizenship Program manager and leader of World Community Grid explains the process: “The first step to understanding the role of the bacteria within the microbiome is to determine the structure of the protein molecule coded by each gene of the bacteria. The structure of a protein molecule determines its function. But the scale of this research is enormous. The microbiome is comprised of about 3 million unique bacterial genes. By comparison, the human body has about 20,000 genes. To study the proteins corresponding to each of these genes would be a monumental task that is nearly impossible in a laboratory setting.”

Instead, researchers have developed modeling tools which can predict the structure of a protein, Hindo said. “But such computational research techniques require more computing power than scientists typically have access to. Most of these proteins have therefore not been explored. By harnessing the unused computing power of volunteers' devices and crowdsourcing the problem, millions of calculations, that would've taken decades, can be done in just a few years,” Hindo said.

But what exactly is the World Community Grid? IBM Corporate Citizenship, the company’s corporate social responsibility division, created World Community Grid in 2004.  “Think of World Community Grid as a sophisticated way of recycling—in this case, taking unused power of our people's computers when they are turned on but not otherwise in active use, and putting it to work,” Hindo said.

“In the old days, scientists would perform experiments in petri dishes and test tubes. Now, they often rely on computers to simulate those experiments to see what would happen if different compounds are created and how they might react to microscopic chemical and biological substances or materials,” Hindo explained. “Mathematical computations are often now performed in place of physical experiments, at least initially, because they can perform a lot of experiments very quickly, and you don't have to wait for something to show up in a petri dish. These days, thanks to experiments conducted by computer simulations, actual and physical experiments occur in a lab only when they look like they have a high probability of showing us something important.”

But there is a catch. A kind of citizen science project, The Microbiome Immunity Project needs the help of the general public to succeed. The primary goal of the project is to generate a set of predicted protein structures of the entire human microbiome–containing some 3 million unique genes–to help scientists determine the role played by these bacteria. The results of the project will then be shared with scientists around the world to further facilitate research on diseases implicated with the microbiome.

“This is the largest computing effort directed at the human microbiome,” Knight said. “The amount of computation is massive because protein 3D structures are difficult to compute.”

Performing these simulated experiments on a large scale requires a lot of number crunching, a massive amount of computer power and a great deal of money, Hindo said. Instead of scientists renting supercomputers to provide the enormous amount of needed computing power, IBM’s World Community Grid taps into the spare computing power of volunteers' computers and Android devices all over the world.

Hindo said volunteers with The Microbiome Immunity Project will download a tiny software program that detects when their device is idle, such as when people step away from their desks, or if the device is charging. The software program then activates the computer to perform calculations for  the scientists' virtual experiments.

“Volunteers simply use their computer as they normally would. The software determines the amount of unused computing power and runs in the background, using up only whatever computing resources are not being used by the volunteer. It is set to give priority to everything else and only uses resources that would've gone to waste otherwise. This non-intrusive design makes sure that it doesn't slow down or get in the way of what you’re doing on your device,” Hindo said.

In addition, the program only runs when the volunteer’s device is charging, thus it doesn’t use up their battery. For Android devices, a calculation is downloaded and a result is uploaded only when the volunteer’s phone or tablet is connected to Wifi, so it doesn't use up data from the volunteer’s data plan.

“This process happens quickly and behind the scenes, and does not affect the computer's normal operation,” Hindo said. “When the calculation is complete, the software returns the result back to World Community Grid, which IBM combines with the results from all other volunteers and sends to the scientists for their analysis. The researchers then analyze the data for insights and findings.”

With the help of volunteers, research that would've taken decades is done in just a few years. “For The Microbiome Immunity Project, the calculations volunteers are running predict the function of bacteria—specifically by predicting the structure of their associated proteins—within the human microbiome. All they need to do to participate is join World Community Grid and install the software on their device – the work doesn't rely on any sample of or info about their own microbiome.”

Hindo said potential volunteers need not worry about the security of their personal information. “The software that volunteers download cannot access your personal files on that device. It simply detects the amount of computing power being used by your device to determine if there's any available to run a calculation,” he said. “Security is our top priority and experts are constantly testing the system for vulnerabilities to the latest threats to ensure the software is up to date. The security is built into the little software program that people download. The programming behind it has been developed and well tested successfully against security risks for nearly 20 years. World Community Grid uses technology developed by The University of California and Berkeley and National Science Foundation-funded project.”

To date, more than 738,000 volunteers and the employees of 440 organizations from 80 countries have donated more than one million years of computing time from more than three million computers and Android devices. Volunteer participation in World Community Grid has helped researchers identify potential treatments for childhood cancer, more efficient solar cells, and more efficient water filtration and has helped  scientists perform research related to 29 humanitarian areas overall such as cancer, Zika, HIV/AIDS, tropical neglected diseases and more.

“It’s important to remember that what counts as supercomputing is a moving target. What your readers hold in their hands in the form of a smartphone would have been the fastest supercomputer on earth in the 1980s,” Knight said. “So advances in computation have enabled all kinds of technologies ranging from CT scans to speech recognition. The World Community Grid has thus far focused mainly on infectious disease and diseases that first manifest in childhood such as muscular dystrophy. However, several projects on cancer and AIDS have provided the basic biological information about protein structure that will ultimately help identify new drugs that help people with these diseases live longer, healthier lives.”

Knight said that while the field of computational research isn't new, such research techniques have become increasingly more accurate such as predicting the outcomes of lab experiments. “The 2013 Nobel Prize in Chemistry was awarded to computer scientists who pioneered the field, recognizing the essential role computational techniques play in modern day research,” he said. “But these tools are resource intensive – often requiring more computing power than scientists typically have access to. Even if a researcher has access to a supercomputer at their facility, access is usually limited and shared with several other research groups. Scientists therefore scope their computational projects down to match available resources.”

But the vast amount of computing power provided by World Community Grid volunteers allows scientists to tackle research at an unprecedented scale and pace. Much of the research supported by World Community Grid simply wouldn't have been attempted without it. In turn, this has led to several important scientific advances listed here:

    • A global team led by researchers at Tsinghua University in Beijing were able to model water flow through nanotubes at an unprecedented level of detail, leading to a breakthrough discovery of how nanotechnology could be used to improve access to clean water for the 1 billion people around the world who lack it.
    • In just a couple of years, researchers at the Chiba Cancer Center in Japan used World Community Grid to screen millions of chemical compounds as potential candidates for neuroblastoma, a common and dangerous form of childhood cancer. The compounds predicted to be most effective were then tested in the lab, leading to a groundbreaking discovery of seven promising drug candidates to treat neuroblastoma. Following the success of that project, the team has grown, incorporating collaborators across Japan, Hong Kong and the United States and has come back to World Community Grid for another project to search for treatment options for a wider range of pediatric cancers.
    • Researchers at Harvard University conducted what is believed to be the most extensive investigation of quantum chemistry every performed. They leveraged World Community Grid to screen millions of compounds for their effectiveness as potential solar cell materials. They discovered more than 35,000 with the potential to double the carbon-based solar cell average efficiency.

For this initiative, Hindo said IBM identifies scientists who need computer power to perform research, and then helps design virtual experiments with them. “IBM then keeps the technical and administrative aspects of the project going, making sure that IBM's computer servers are sending computational assignments to volunteers, collecting the results, then sending them to the scientists for their analysis, all while keeping the information safe.”

Anyone can support the Microbiome Immunity Project by joining World Community Grid and installing the free software application on their computer.

Progress will periodically be updated on the project web site, and the screen saver associated with the project shows how your own processing is proceeding. Major outcomes will be published in the scientific literature.

Robin Seaton Jefferson lives just outside of St. Louis with her husband of 23 years and two daughters. Find her on Twitter and Facebook @SeatonJefferson or contact her at rsjreporter@charter.net.

Related Posts