Supercomputer

Computer Science Internship Involves Work With Supercomputer

Thomas Corcoran, a senior computer science major at Hood College, is completing a yearlong internship with the Blue Waters Student Internship Program (BWSIP) as well as the National Cancer Institute at Fort Detrick.

Corcoran, along with approximately 30 other student interns, traveled to the University of Illinois at Urbana, Champaign (UIUC) in June, where they spent two weeks training at the National Center for Supercomputing Applications (NCSA). There, Corcoran learned the principles of parallel programming, scientific computing and management of big data.

“UIUC is also home to the Blue Waters supercomputer, for which the internship is named,” Corcoran explained. “We toured the supercomputer, which was astonishingly cool.”

The interns were allotted time on the machine to conduct their private research. The nature of Corcoran’s research was to apply machine-learning techniques to the detection of important features like cancer in biomedical images.

His work caught the interest of the National Cancer Institute at Fort Detrick, where he worked full time over the summer and continues to work part time along with his continued internship at UIUC.

In addition to learning and being able to apply his studies at Fort Detrick, Corcoran was able to work with Yanling Liu, Ph.D., of NCI, tackling the scourge of cancer, which Corcoran said was an “illuminating and rewarding experience.”

Corcoran credits his mentor, Xinlian Liu, Ph.D., associate professor of computer science at Hood and chair of the computer science department, and George Dimitoglou, associate professor of computer science at Hood, with helping him obtain the internship. Both professors played a role in Corcoran’s application process and taught him about conducting independent research.

“My experience with [the NCI and UIUC] has been fantastic,” Corcoran said. “The instruction I was given [at UIUC] was in-depth, challenging and has been proven to be highly useful. I am incredibly grateful to them and their support, trust and encouragement.”

In June 2017, at the end of his studies, Corcoran will be publishing a paper, which will be a culmination of his work at the Blue Waters internship program.

To learn more about the Blue Waters internship program visit https://bluewaters.ncsa.illinois.edu/internships.

Pictured above: the Blue Waters supercomputer

Miranda Darby

Bioinformatics Program Director Named

The Hood College bioinformatics master’s program is pleased to introduce a new program director who has more than a decade of experience in conducting research, teaching and directing educational programs.

Miranda Darby, Ph.D., is an expert in molecular biology and computing. She comes to Hood after working since September 2012 as a postdoctoral fellow in the Stanley Division of Developmental Neurovirology in the Johns Hopkins School of Medicine, where she developed and implemented bioinformatics tools to study the genome. Prior to that, she completed thesis research at the Johns Hopkins School of Medicine, examining the mechanisms that regulate gene transcription.

“I am excited to establish the new bioinformatics program at Hood because I want to inspire Hood students to flourish in this rapidly evolving field,” Darby said. “I arrived at the beautiful campus and met smart, curious, passionate faculty members who are dedicated to providing the best opportunities for their students to thrive. I am eager to work with my new colleagues and to find opportunities for those who are interested in contributing their expertise to the bioinformatics program.”

Bioinformatics is the interface between computer science and biology. It is the application of the principals of computer science to the collection, classification, storage and analysis of biological and biochemical data. The recent boom in bioinformatics centers on the analysis and interpretation of molecular genetics and genomics data that is generated by next-generation, whole genome sequencing.

With the demand for knowledge and expertise in the field by regional employers including the National Cancer Institute, the U.S. Army Medical Research Institute for Infectious Diseases, the Frederick Cancer Research Center at Fort Detrick and others, students can find themselves with multiple job opportunities after finishing the program. Darby is focused on helping her students achieve success in the industry and in their lives.

“I knew I belonged at Hood when I read Hood’s mission statement, which describes my own goals: ‘to empower students to use their hearts, minds and hands to meet … challenges and lead purposeful lives …’”

Also, having completed her undergraduate studies at Carleton College in Minnesota, she understands the value of the liberal arts education that Hood provides.

“I think that a liberal arts education is the best possible foundation for future study in the sciences because liberal arts students are exposed to a wide variety of ideas concerning a full range of topics,” Darby said. “This prepares students to think outside of the confines of a specialized field and gives them a fresh perspective on the range of possibilities available to them.”

Alex Jarnot
Reem Zeitoon
Reem Zeitoon
Rob Sargsyan
Rob Sargsyan 2

Several Hood College students presented their research in chemistry and biology at the UMBC Undergraduate Research Symposium in October.

These students included Alex Jarnot, Reem Zeitoon, Rob Sargsyan, Elizabeth Slick, Kaitlin Recabo, Angela Mansfield, Sarah Meyer, Kenny Garced-Valle and Zachary Peck. The research projects were all funded by NASA, the National Science Foundation (NSF) or Hood’s Summer Research Institute (SRI). The SRI projects were funded by the Hodson Trust.

Jarnot’s research involved trying to understand the atmosphere inside of Crystal Cave in Sequoia National Park in California. His work was through his internship with NASA’s Student Airborne Research Program and funded by NASA and the National Suborbital Education and Research Center (NSERC).

“We sampled the air inside the cave and found that the concentrations of several trace gases in the air were extremely low compared to the outside air,” he said. “I am working to try to determine what could be causing this decrease in trace gas concentration.”

His presentation included a poster on his research from the summer that displayed the data that was examined and some possible causes of the low concentrations.

Zietoon spent her SRI-funded summer trying to express and purify a protein called Myxoma virus leukemia associated protein so later they would be able to study its structure. This specific protein contains a zinc-finger motif, which involves a zinc ion complexed with several parts of the protein. These motifs are usually involved in binding DNA or RNA in the cell. She worked with her mentor, Dana Lawrence, Ph.D., associate professor of chemistry.

Lawrence also worked with Sargsyan during his SRI project, which studied the solubility of a zinc-finger antiviral protein cloned with and without solubility tags. This particular protein has antiviral activity and therefore provides the host organism with resistance to viral infection. According to Sargsyan, the experiment was intended to find a method that would extract and isolate the protein. Sargsyan presented the data and results, then how they relate to a bigger picture.

As an SRI project, Slick and Recabo worked with Susan Ensel, Ph.D., Whitaker professor of chemistry, to find inhibitors for the botulinum neurotoxin, the toxin responsible for botulism and the most toxic naturally occurring substance known to humankind. Slick and Recabo synthesized and isolated several compounds that were designed as inhibitors of the neurotoxin. During the UMBC symposium, the senior chemistry and biochemistry majors presented their research on six such inhibitors that will contribute to the body of knowledge necessary to ultimately develop a drug to combat botulism.

Mansfield and Meyer won first place for their poster presentation on expanding student access to instrumentation through incorporation of portable infrared spectroscopy into the curriculum. Their research used a hands-on approach to scientific education and research and discussed how to make equipment more accessible to more students. This work is funded by a NSF Improving Undergraduate STEM Education grant and was conducted with Kevin Bennett, Ph.D., professor of chemistry, and Christopher Stromberg, Ph.D., associate professor of chemistry.

Oney P. Smith, Ph.D., professor of biology, mentored Garced-Valle and Peck on separate SRI projects.

Garced-Valle investigated the gene expression of heat shock protein 70 (HSP70) found in the sea anemone, Aiptasia pallida, when they experience environmental stress, specifically elevated temperatures. Hood maintains these animals under laboratory conditions. The research found that there was a 60-fold increase in the HSP70 gene expression when the anemone was subjected to the higher temperature.

“Overall, the knowledge I gained was very beneficial to future lab experiences, including my current independent study,” Graced-Valle said. “In addition, the experience has made me more interested in laboratory-type jobs.”

Peck worked this summer to isolate, clone and sequence a DNA fragment found in red-eye fruit flies to help identify its location in the Drosophila genome. His work included computer-assisted searching of the database for the fly genome, which indicates the 1,800 base pair fragment is a part of the DNA found on several fly chromosomes. The information found will be used in an introductory cell biology and genetics course at Hood to improve a lab activity on Drosophila genetics.

“This past summer taught me what it was like to perform research and work in a lab environment, as well as how to present my findings,” Peck said. “It was an experience like none other and one that I will most definitely want to repeat.”

Simulation Editor

CS Internship Leads to Learning New Software and Computer Languages

John Pigott, a senior computer science and mathematics major, interned over the summer at the Advanced Biomedical Computing Center (ABCC), which is part of the National Cancer Institute at Fort Detrick.

He got a hands-on feel for working in an office environment with professionals, where he learned multiple computer languages that he later used to create a simple simulation of a blood vessel.

“It was a great experience for me because it allowed me to learn and work with the Unity3D Game Engine,” Pigott said. “This is a piece of software I had learned about and was interested in learning, but had never had the opportunity.”

The Unity3D Game Engine is a cross-platform game engine that is typically used to develop video games for websites, consoles or mobile devices.

In addition to the Unity3D Game Engine, Pigott had the chance to work with Blender and MeshLab softwares, which were required in able for him to complete his project.

Both Blender and MeshLab are computer softwares that allow users to develop 3D models, and both are commonly used for video game purposes.

“The computer science knowledge that I gained at Hood was most helpful during my internship,” stated Pigott. “One particular example coming in handy was the technique of Karnaugh maps, which I learned in my digital logic class where we learned how to simplify circuits to save space on a circuit board.”

Karnaugh maps provide a pictorial method of grouping expressions with common factors, which eliminates unwanted variables.

While he was learning the languages at the ABCC, the theories and principles he had learned at Hood allowed him to understand the languages necessary for the completion of his project.

At the end of his internship and project, Pigott completed a 30-minute presentation to some of the doctors at the ABCC explaining his project, the challenges he faced, the technologies he used, how the project was beneficial and what he was learning.

Photo: Pigott’s blood vessel simulation running in the Unity3D Game Engine editor.

Paige Rawl

Paige Rawl Visits for the First-Year Read

Paige Rawl, an author who has documented her struggle to find acceptance after being born HIV positive, visited Hood College in October as part of the school’s First Year Read program.

Rawl is co-author of “Positive: A Memoir,” this year’s First-Year Read, a required reading chosen for first-year students. Sophomore Abbey McAlister nominated “Positive” for the First-Year Read last year, so she had the pleasure of introducing Rawl to Hood. McAlister said she believed the book would be beneficial for first-year students because it had helped her in times of transition.

The book follows Rawl’s struggle with bullies in middle school because of her HIV status. The bullying got so bad she left for homeschooling, a hard decision for the extroverted teen. When leaving, her principal said, “I wish you could go to this school, but I can’t protect you.”

During that time, she realized her passion for educating people on HIV and AIDS and advocating against bullying in schools. Not long after, she transferred to a high school with a zero-tolerance bullying policy. She spent her first year keeping her HIV secret. However, after developing strong relationships with students and staff, she talked to the principal and began sharing her story with her school.

She went on to Ball State University but took some time off after “Positive” was published to promote the book. She originally intended to study molecular biology for HIV research, but she plans to switch to business and entrepreneurship to help her build her foundation, Paige Power. The foundation will allow her to educate low-income schools on HIV and anti-bullying advocacy.

At Hood, Rawl began her discussion by explaining the basics of HIV and AIDS. She explained how every strand is different, how one can contract the disease, and how she copes with having the disease.

She shared statistics about bullying, including that 64 percent of bullying incidents go without being reported, and she spoke about students getting bullied even at home through cyber bullying.

She gave students a piece of advice surrounding bullying: “Think about what you say before you say it, think about what you do before you do it.”

She also urged parents to be involved and take their children’s reports of bullying seriously.

After reading from her book, Rawl took questions from the audience and held a book signing.

Video Interview with Paige Rawl