Transforming Living Cells into Computers
By Sara Elizabeth Cody
Whether it’s artificial skin that mimics squid camouflage or an artificial leaf that produces solar energy, a common trend in engineering is to take a page out of biology to inspire design and function. However, an interdisciplinary team of BU researchers have flipped this idea, instead using computer engineering to inspire biology in a study recently published in Science.
“When you think about it, cells are kind of computers themselves. They have to communicate with other cells and make decisions based on their environment,” says Associate Professor Douglas Densmore (ECE, BME), who oversaw the BU research team. “By turning them into circuits, we’ve figured out a way to make cells that respond the way we want them to respond. What we are looking at with this study is how to describe those circuits using a programming language and to transform that programming language into DNA that carries out that function.”
Using a programming language commonly used to design computer chips, ECE graduate student Prashant Vaidyanathan created design software that encodes logical operations and bio-sensors right into the DNA of Escherichia coli bacteria. Sensors can detect environmental conditions while logic gates allow the circuits to make decisions based on this information. These engineered cells can then act as mini processing elements enabling the large scale production of bio-materials or helping detect hazardous conditions in the environment. Former postdoctoral researcher Bryan Der facilitated the partnership between BU and the Massachusetts Institute of Technology to pursue this research study.
“Here at BU we used our strength in computer-aided design for biology to actually design the software and MIT produced the DNA and embedded it into the bacterial DNA,” says Densmore. “Our collaboration is a result of sharing the same vision of standardizing synthetic biology to make it more accessible and efficient.”
Historically, building logic circuits in cells was both time-consuming and unreliable, so fast, correct results are a game changer for research scientists, who get new DNA sequences to test as soon as they hit the “run” button. This novel approach of using a common programming language opens up the technology to anyone, giving them the ability to program a sequence and generate a strand of DNA immediately.
“It used to be that only people with knowledge of computers could build a website, but then resources like WordPress came along that gave people a simple interface to build professional-looking websites. The code was hidden in the back end, but it was still there, powering the site,” says Densmore. “That’s exactly what we are doing here with our software. The genetic code is still there, it is just hidden in the back end and what people see is this simplified tool that is easy, effective and produces immediate results that can be tested.”
According to Densmore, this study is an important first step that lays the foundation for future research on transforming cells into circuits, and the potential for impact is global, with applications in healthcare, ecology, agriculture and beyond. Possible applications include bacteria that can be swallowed to aid in digestion of lactose to bacteria that can live on plant roots and produce insecticide if they sense the plant is under attack.
“The possibilities are endless, and I am excited about it because this is the crucial first step to reach that point where we can do those amazing things,” says Densmore. “We aren’t at that level yet, but this is a stake in the ground that shows us we can do this.”
The BU/MIT collaboration will continue underneath the Living Computing Project which was recently awarded a $10M grant from the National Science Foundation. Future studies will look to improve upon the circuits that were tested, add other computer elements like memory to the circuits and expand into other organisms such as yeast, which will pave the way for implanting the technology into more complex organisms like plant and animal cells.
MOC successfully rallies academia, government and industry in developing new cloud.
By Rebecca Jahnke (COM ’17)
The Massachusetts Open Cloud (MOC) project – led by ECE Professor Orran Krieger – just announced a set of core industry partners, spanning key hardware, software and services industry sectors. The MOC is an ambitious project that aims to create a public cloud, based on a revolutionary model for a multi-provider Open Cloud eXchange (OCX).
In existing public clouds one provider operates the entire cloud. In contrast, the OCX model underlying the MOC allows for multiple entities to provide computing resources and services in a level playing field. Having multiple providers – all with their own specialties – participating in the same cloud will enable a broader range of users and applications to be supported.
The core corporate partners of the MOC – Brocade, Cisco, Intel, Lenovo, Red Hat and Two Sigma – have made financial commitments as well as in-kind commitments, ranging from computer infrastructure in support of MOC deployment and operation, to engineering expertise to support the development of OCX functionality. The companies have also pledged executive sponsors to keep company and project goals aligned and to support MOC’s development. These new partnerships underscore the strong and growing industry support for the project, which has already secured in excess of $14 million of funding – more than quadruple the $3 million in seed funding that the MOC received from the Mass Tech Collaborative in 2014.
Incubated at and seed-funded by the Hariri Institute for Computing at BU (as part of the Cloud Computing Initiative led by its Director, Orran Krieger), this complex project has benefitted from strong BU institutional and administrative support, including the offices of the Provost, Corporate Relations, General Council, and IS&T Research Computing. Anchored at BU, the project is a collaboration that also involves Harvard University, MIT, UMass, and Northeastern University, as well as the Massachusetts Green High-Performance Computing Center (MGHPCC). The project leverages and builds on current and prior research by a number of ECE and CS faculty members at BU including Jonathan Appavoo, Azer Bestavros, Ran Canetti, Ayse Coskun, and Orran Krieger.
Wireless Sensors Developed by Interdisciplinary Engineering Team to be Launched into Space
By Rich Barlow Video by Joe Chan for BU Today
On March 10, 1989, a solar eruption blasted plasma toward Earth. Canadian utility Hydro-Quebec noticed a hop-skip-and-jump in the voltage on its grid two days later. On March 13, with plasma sweeping Earth’s magnetic field and causing electric currents in the outer atmosphere, the grid shut down, plunging the province into darkness for nine hours.
Such bolts from the blue (or black) of space rarely wreak such havoc. But less severe irritants—interrupted radio transmissions, disrupted GPS devices, even rusting of pipelines—can result when electric currents course through the magnetic field, says Joshua Semeter, who’d like to know more about this phenomenon (largely because the magnetic field may be an essential ingredient for life on Earth). So would the federal government, which is why NASA has agreed to launch a network of wireless sensors named ANDESITE, developed by Semeter’s College of Engineering students to study changes in Earth’s magnetic field caused by space weather.
It is the final frontier, finally crossed: the first space launch for eight-year-old BU Student-satellite for Applications and Training, overseen by Semeter (ENG’92,’97), an ENG professor of electrical and computer engineering. Colloquially known as BUSAT, the program engages students in designing and operating small satellites. Earlier this year, the BUSAT group was one of the teams from a half dozen universities that beat out nine competitors to continue receiving support from the Air Force, which has contributed more than $500,000 to BUSAT projects. (BU also provided funding.) NASA will set a date for the launch late this year, Semeter says, assuming the agency’s review shows that ANDESITE’s ejecting sensors “won’t blow up their vehicle.”
ANDESITE sensors are DVD-sized boxes packed with electronics boards, and eight of them will hitch a ride on a NASA spacecraft that will spit them out roughly 280 miles above the Earth. Each sensor, traveling at a speed of approximately six miles per second, will complete an orbit of the Earth in roughly 90 minutes. The sensors will measure variations in electrical currents flowing in and out of the upper atmosphere along Earth’s magnetic field. “From this we will learn about how turbulence forms in space plasmas and what the eventual effects of this will be” on things like radio signals, allowing for better modeling of those effects, Semeter says.
ANDESITE’s success has already led to one terrestrial development, he adds. ENG has hired Brian Walsh (GRS’09,’12) as an associate professor of mechanical engineering. Walsh researches small satellites and space technology.
“This whole idea of taking any kind of spacecraft and spitting out small sub-payloads is really experimental,” says Semeter.
“This whole idea of taking any kind of spacecraft and spitting out small sub-payloads is really experimental,” says Semeter, although ANDESITE employs “technology that’s very well established here on Earth. They use it for self-driving cars and finding cabs in a city; Uber uses this kind of thing. This is wireless mesh network technology.…Our innovation was, why can’t we use that in space? What science could you do?”
In July, government representatives visited the students’ lab at the Engineering Product Innovation Center for a demonstration of how the sensors would deploy during an upcoming zero-gravity test flight, a nausea-inducing trial that previous BUSAT students have experienced firsthand. The students rigged a contraption to gently fire sensors into a mesh net, a form of soccer-meets-space.
“Looks like a good setup,” Zane Singleton of the Defense Department’s Space Test Program and tech company MEI Technologies said at the demonstration.
Earlier in the history of miniaturized satellites, “NASA didn’t give a rat’s ass” about them, Semeter says, with one official harrumphing, “Why would somebody who drives a Ferrari care about Matchboxes?” Then the National Science Foundation convinced NASA that solid science research could be done by mini-satellites. Today, ANDESITE is but one government effort to study space weather. Last February, a National Oceanic and Atmospheric Administration satellite was launched to record data about solar wind.
Cody Nabong (ENG’15), ANDESITE’s project manager, joined BUSAT on a buddy’s recommendation after being stymied in his search for an internship. (A picture of his friend on a zero-gravity flight was a grabber.) “I’ve been interested in aerospace since I came here, so it wasn’t a hard decision,” says Nabong, who appreciates the hands-on practice of the classroom concepts he’s studied that the team has provided. “The computer program that you use to make your 3-D models—I got a lot of practice with that. And then I learned a bunch about communications stuff that I wouldn’t have been exposed to if I had just had courses.…The biggest thing I’ve learned is how you meet requirements for an engineering project,” he says, referring to the government competitions and reviews the ANDESITE project has hurdled.
If the foregoing sounds uber-Star Trek-y, BUSAT’s members include some liberal arts disciplines majors who came for graduate engineering study through BU’s LEAP (Late Entry Accelerated Program) initiative. One BUSAT alumnus was a building contractor from San Francisco, who was “perfectly suited for this job,” says Semeter. “He’s used to going to the project site, telling people what to do. That’s all we needed. And he was technically competent.”
By Bhumika Salwan (Questrom ’16)
ECE Associate Professor Ayse Coskun and Assistant Professor Manuel Egele were awarded $189,000 for their research in data analytics with Sandia National Laboratories for improving energy efficiency and security of high performance computing (HPC) systems. Sandia Labs is one of the nation’s premier science and engineering laboratories for national security, with strategic areas in nuclear weapons, defense systems and assessments, energy and climate, and international, homeland, and nuclear security.
Professor Ayse Coskun’s research group at Boston University is widely-cited, with expertise in the topics of energy-efficient computing, computer system modeling and simulation, design of intelligent scheduling and power management techniques, and green computing in data centers and HPC systems. Professor Manuel Egele is an expert on systems and software security whose research has been published at top-tier peer reviewed conferences including NDSS and CCS.
Their project aims to identify which data collected out of HPC systems would be useful for identifying performance characteristics, inefficiencies, and malicious behavior. It will then design methods to leverage these data to design runtime strategies to improve efficiency and security. Professors Coskun and Egele’s research teams will first collect data on real HPC clusters at Sandia Labs and at the Massachusetts Green High Performance Computing Center (MGHPCC). They will then analyze that data to determine the most relevant, minimum set of metrics that are good indicators of energy and normal system behavior, and construct models that can predict performance variations and anomalous behavior resulting from security breaches or fraudulent activities.
The knowledge gained through this project will aid users and admins in answering questions such as the following: How much resources (e.g., how many cores or what size of memory) do I need for my application? Why does the performance of my application wildly vary across different runs? What information can we provide to system administrators to enable more efficient problem diagnosis? Can we determine whether software applications are behaving “normally”?
By Paloma Parikh (COM’15)
Three ECE undergraduate students won grants from two programs affiliated with Boston University’s Undergraduate Research Opportunities Program. Annie Lane (ENG’16) and Maya Saint Germain (ENG’16) are recipients of the Clare Boothe Luce Award; and Dean Shi, (ENG’16) won the Hariri Award.
Annie Lane won the Clare Boothe Luce Award for her research project, “Data Center Power Regulation Modeling,” which she is working on with mentor Assistant Professor Ayse Coskun (ECE). The goal of the project is to minimize electricity costs for data centers. To do so, Lane is developing a power control policy based on a mathematical model. Additionally, she will evaluate alternative research models in the hopes of finding the most effective process. Lane believes the practicality of her project caught the attention of the judges. In an email correspondence, Lane mentioned that the project has potential for real-life application, “BU has partnered with other universities, the state, and companies to build and manage the Massachusetts Green High Power Computing Center (MGHPCC) in Holyoke, MA. The research results will help increase energy savings at MGHPCC.”
Maya Saint Germain, with mentor Professor and Associate Chair for Graduate Studies Hamid Nawab (ECE), won the Clare Boothe Luce Award to fund a project entitled “Human-in-Circuit Signal Processing.” Saint Germain explains Human-in-Circuit Signal Processing as, “a subfield of signal processing in which the signal that is being processed is produced by a human, and – after processing – will be perceived by a human.” Her goal is to improve how the signal is processed. Saint Germain feels proud that she won the award, “It means that my research is important and relevant.”
Dean Shi won the Hariri Award for his project, “Power Optimization and Development of Power Policies on Mobile Devices,” which he is working on with mentor Assistant Professor Ayse Coskun (ECE). Shi is working to lengthen battery life for cell phones. To do so, he is researching how cell phones use battery power through different functions, such as applications. With this understanding, he will be able to optimize power usage and make cell phone batteries last longer. Shi recalls, “All of my friends are always complaining, ‘Oh I just charged my phone this morning but it’s already at 10% battery.’” This award will help Shi achieve his goal of lengthening cell phone battery life.
The Undergraduate Research Opportunities Program (UROP) is a supportive resource for faculty-mentor research. It provides grants to students through various organizations such as the Clare Boothe Luce Program and the Rafik B. Hariri Institute for Computing and Computational Science & Engineering. The Clare Boothe Luce Program aims to support women in science, mathematics, and engineering. Recipients of the undergraduate research awards receive funding to conduct a research project with a faculty mentor. The Hariri Institute promotes innovation in the sciences of computing and engineering. With the Hariri award, they provide grants for collaborative research and training initiatives.