photo Christopher Mendez and Alannah Oleson
Christopher Mendez and Alannah Oleson received NSF Graduate Research Fellowships this year.

Two students of computer science in the College of Engineering at Oregon State University received National Science Foundation (NSF) Graduate Research Fellowships that will provide three years of research funding while they attend graduate school. This prestigious award recognizes and supports outstanding early career graduate students in science, technology, engineering and mathematics disciplines.

Christopher Mendez, a graduate student, and Alannah Oleson, an undergraduate, received the awards for research in the field of human-computer interaction (HCI). There were a total of eight students across the U.S. to receive the award for HCI research.

This prestigious award recognizes and supports outstanding early career graduate students in science, technology, engineering and mathematics (STEM) disciplines. A total of 2,000 fellowships are awarded per year across all STEM fields.

Both Mendez and Oleson are advised by Distinguished Professor Margaret Burnett who co-founded the area of end-user software engineering, which aims to improve software for computer users who are not trained in programming. Her current research investigates gender-neutral software, uncovering gender inclusiveness issues in software from spreadsheets to programming environments.

Mendez and Oleson are extending Burnett’s research into different areas: Mendez is investigating how technology can empower people of low socioeconomic status; and Oleson is researching how best to teach inclusive software design methods and principles to university-level computer science students.

Mendez is continuing his research with Burnett at Oregon State, and Oleson will be starting graduate school next fall at the University of Washington.

photo of Oregon State team
Oregon State took first place at the regional DOE Cyber Defense Competition 2018. Pictured are (left to right) Zach Rogers, Khuong Luu, Hadi Rahal-Arabi, Yeongjin Jang, Devon Streit (DOE), Zander Work, Cody Holliday, and Aidan Grimshaw

A team of six computer science students at Oregon State University competed for the first time and won the regional Department of Energy Cyber Defense Competition held at Pacific Northwest Laboratory in Richland, Washington.

The competition simulates a real-world situation in which the teams defend a corporate network infrastructure from professional hackers. Each team built a mock infrastructure including a web server, a file server, a database server, email, and other network operations. During the competition, a group of users utilized the services while the hackers launched attacks. The defending teams had to monitor and respond to the cyberattacks throughout the day and were scored on how well they defended their infrastructure and how well they documented what they had done.

The Oregon State team placed first among six teams from the western U.S. at the regional competition, and placed fourth nationally among 29 teams.

“The competition was a lot of work, but it was also a lot of fun,” said Zander Work, a freshman in computer science who led the team. “The team put in many long nights leading up to the competition to finish hardening our defenses, and it paid off.”

Zander and the other five students who competed — Aidan Grimshaw, Cody Holliday, Khuong Luu, Hadi Rahal-Arabi and Zach Rogers — are all members of the OSU Security Club.

“Although it was a very first time the students participated in such a competition, they did a great job,” said Yeongjin Jang, assistant professor of computer science in the College of Engineering who advised the team. “I was very happy to see the students working hard for an entire month of preparation, not hesitating to tackle difficult tasks, and working well as a team at the competition venue.”

Kenneth Squire did not know what to expect when attending his first academic conference — SPIE Photonics West 2018, a conference about light-based science and technology. So, he was pretty surprised to take home two awards.

“It’s really exciting to get that recognition and to know that I am capable of doing research and presenting my findings at that level,” said Squire, a graduate student in electrical and computer engineering in the College of Engineering at Oregon State University.

Squire’s research advances techniques to detect antigens such as biotoxins that can infect food or biomarkers for disease. His research is under the direction of Alan Wang, associate professor of electrical and computer engineering who heads the Engineering Photonics Research Laboratory in the School of Electrical Engineering and Computer Science.

The paper for which Squire received the Prizmatix Young Investigator Award was “Ultra-sensitive fluorescent imaging-biosensing using biological photonic crystals.”

In this research, Squire, along with Dr. Xianming Kong and other collaborators, were able to enhance the optical signals for florescence imaging using diatoms, which are single-celled algae.

“The hope is that this can be used for cellphone based biosensors,” Squire said. Sensitivity is the challenge for developing sensors that can be used outside of pristine laboratory conditions.

“Using these diatoms, we were able to enhance the sensitivity. So, even though your equipment isn’t quite as good, and even though you don’t have the perfect conditions, you can still get detection levels that are practical,” Squire said.

They have applied for a patent on the technology and are currently working on an application to detect a biomarker for cardiovascular disease.

Squire’s second award at the conference was runner up for Best Student Presentation for his paper entitled, “Facile detection of toxic ingredients in seafood using biologically enabled photonic crystal materials.“

This research utilized the fossilized remains of diatoms, called diatomaceous earth, which is sometimes used for filters. The device that Squire, Kong and collaborators developed was able to separate the target from other material in the sample, and enhance the optical signals for better detection of biotoxins that can infect food.

The study demonstrated successful detection of Sudan I, an illegal carcinogenic dye, in various chili products, and histamine, a naturally occurring toxin, in seafood that was intentionally contaminated and in decomposing tuna.

The device, called a thin layer chromatography plate, separates the target molecule from the rest of the sample matrix and enhances the performance of the detection.  The detection method that was employed uses scattered light from a laser which creates a unique fingerprint for different molecules (surface-enhanced Raman scattering).

“The Photonics West conference was a great opportunity to present our work.  Leading up to the conference, many of our group members were instrumental in the preparation and polishing of the presentations that led to these awards and I am very grateful to them for their help and support,” Squire said.

Abstracts

Ultra-sensitive fluorescent imaging-biosensing using biological photonic crystals

Kenneth Squire, Xianming Kong, Paul LeDuff, Gregory Rorrer, Alan X. Wang

Optical biosensing is a growing area of research known for its low limits of detection.  Among optical sensing techniques, fluorescence detection is among the most established and prevalent.  Fluorescence imaging is an optical biosensing modality that exploits the sensitivity of fluorescence in an easy-to-use process. Fluorescence imaging allows a user to place a sample on a sensor and use an imager, such as a camera, to collect the results.  The image can then be processed to determine the presence of the analyte.  Fluorescence imaging is appealing because it can be performed with as little as a light source, a camera and a data processor thus being ideal for nontrained personnel without any expensive equipment.  Fluorescence imaging sensors generally employ an immunoassay procedure to selectively trap analytes such as antigens or antibodies.  When the analyte is present, the sensor fluoresces thus transducing the chemical reaction into an optical signal capable of imaging.  Enhancement of this fluorescence leads to an enhancement in the detection capabilities of the sensor.  Diatoms are unicellular algae with a biosilica shell called a frustule.  The frustule is porous with periodic nanopores making them biological photonic crystals.  Additionally, the porous nature of the frustule allows for large surface area capable of multiple analyte binding sites.  In this paper, we fabricate a diatom based ultra-sensitive fluorescence imaging biosensor capable of detecting the antibody mouse immunoglobulin down to a concentration of 1 nM.  The measured signal has an enhancement of 6× when compared to sensors fabricated without diatoms.

 

Facile detection of toxic ingredients in seafood using biologically enabled photonic crystal materials

Xianming Kong, Kenneth Squire, and Alan X. Wang

Surface-enhanced Raman scattering (SERS) spectroscopy has attracted considerable attention recently as a powerful detection platform in biosensing because of the wealth of inherent information ascertained about the chemical and molecular composition of a sample. However, real-world samples are often composed of many components, which renders the detection of constitutes of mixed samples very challenging for SERS sensing. Accordingly, separation techniques are needed before SERS measurements. Thin layer chromatography (TLC) is a simple, fast and cost-effective technique for analyte separation and can a play pivotal role for on-site sensing. However, combining TLC with SERS is only successful to detect a limited number of analytes that have large Raman scattering cross sections. As a kind of biogenic amine, histamine (2-(4-imidazolyl)-ethylamine) has a relationship with many health problems resulting from seafood consumption occurring worldwide. Diatomaceous earth consists of fossilized remains of diatoms, a type of hard-shelled algae. As a kind of natural photonic biosilica from geological deposits, it has a variety of unique properties including highly porous structure, excellent adsorption capacity, and low cost. In addition, the two dimensional periodic pores on diatomite earth with hierarchical nanoscale photonic crystal features can enhance the localized optical field. Herein, we fabricate TLC plates from diatomite as the stationary phase combining with SERS to separate and detect histamine from seafood samples. We have proved that the diatomite on the TLC plate not only functions as stationary phase, but also provides additional Raman enhancement, in which the detection limit of 2 ppm was achieved for pyrene in mixture.

Alannah Oleson

Alannah Oleson was selected as a finalist for the Computing Research Association’s (CRA) Outstanding Undergraduate Researcher Award. The award recognizes undergraduates who have made significant contributions to research.

For the past three years Oleson has been working with Margaret Burnett, Distinguished Professor of computer science in the College of Engineering, who studies human computer interaction. Oleson has worked on two different areas of research with Burnett: end-user programming and gender-inclusive software.

Oleson’s involvement has been extensive, including helping to plan and program the studies, debug procedures, collect and analyze data, and write up the results. She is co-author on six research papers and is one of the primary co-authors of a document describing the foundations of GenderMag, which is a software inspection process for programmers to uncover gender inclusiveness issues in software.

In the nomination letter for the CRA award Burnett wrote of Oleson: “In my 25 years as a faculty member, she is one of the very best undergraduate students I have seen.”

Last year, Oleson was one of 10 women to win the Adobe Research Women-in-Technology Scholarship.

Alannah Oleson
Alannah Oleson’s award led to a summer internship with Adobe in San Jose.

Alannah Oleson, undergraduate student in computer science at Oregon State University, was one of a handful of students from all over the world to win the Adobe Research Women-in-Technology Scholarship. The scholarship acknowledges women who are improving technology and have demonstrated outreach for their community.

Oleson is helping to improve technology in the area of human-computer interaction (HCI) with Margaret Burnett, distinguished professor of computer science. Oleson is working on the GenderMag project which helps programmers to design gender inclusive software.

Her outreach to the community included mentoring two high school students through Saturday Academy, which is a program designed to help students from under-represented communities gain experience in STEM fields. She taught them how to program and what it is like to work on a research project. A couple of years after the summer-long program, Oleson saw one of her students at Oregon State going through engineering orientation. Oleson felt proud to see him choose to major in computer science after participating in the Saturday Academy program.

“To see him go from whatever he had overcome to being a computer scientist and feeling like I played a part in that was really cool,” Oleson said.

Scholarship winners are awarded $10,000 and a one-year creative cloud subscription; are assigned an Adobe research mentor; and are given an opportunity to interview for an Adobe internship. Oleson succeeded in receiving an Adobe internship and worked in San Jose, CA for 10 weeks on a research team this summer.

“All I had known was living in Roseburg, so the experience of being in the middle of the tech world was fantastic. It made me feel more confident in my career,” she said.

After the internship, Adobe decided to sponsor Oleson’s senior capstone project. In the future, Oleson hopes to pursue a Ph.D. in human-computer interaction and eventually work in industry research.

Story by Raiza de Vera

Image of coal mining waste.
Distribution of coal mining waste along streams and water bodies. Created by Taylor Alexander Brown, Heidi Ann Clayton, and Xiaomei Wang for their project called Coal and Open-pit surface mining impacts on American Lands (COAL).

Three Oregon State University students working with the Jet Propulsion Laboratory received the Extreme Science and Engineering Discovery Environment (XSEDE) Startup Allocation based on their senior design capstone project.

Taylor Alexander Brown (computer science), Heidi Ann Clayton (computer science),  and Xiaomei Wang (finance), also won the CH2M Multidisciplinary Collaboration Award at the 2017 Undergraduate Engineering Expo at Oregon State for their project called Coal and Open-pit surface mining impacts on American Lands (COAL).

The team created a system to process remote-sensing data to identify land surface types, coal mining operations, and the environmental impacts on water resources to help NASA’s Jet Propulsion Laboratory study the effects of coal mining on the environment.

The XSEDE award will allow the team to continue development on the project including the use of XSEDE resources for benchmarking, evaluation and experimentation. Funded by the National Science Foundation, XSEDE is a collection of integrated advanced digital resources and services.

“The availability and opportunity to use computational infrastructure of this caliber will further enable the development of a science gateway to continue foundational COAL research,” said Lewis John McGibbney, data scientist at the Jet Propulsion Laboratory, and the client for the project.

“I am extremely proud of the team’s achievements and know that such endeavors set a high standard for each and every one of them as they progress further through their journey in higher education and beyond.”

2017 Rohde & Schwarz Engineering Competition team photo.
Braxton Cuneo, Erich Kramer, Andy Tolvstad, Karen Harper, and Aaron Schraner (left to right) advanced to the world final of the 2017 Rohde & Schwarz Engineering Competition.

Five students in the School of Electrical Engineering and Computer Science will be heading to Germany this summer to compete in the 2017 Rohde & Schwarz Engineering Competition. Their performance in the U.S. preliminary round earned them a spot at the world league competition.

Aaron Schraner, an electrical and computer engineering student, was motivated to compete since he participated last year on a team from the Oregon Institute of Technology that won the 2016 regional competition. Based on his experience there, he recruited Karen Harper for additional electrical engineering knowledge. All the other team members are in computer science:  Braxton Cuneo, Erich Kramer, and Andy Tolvstad.

Their task was to make improvements to software for a digital-signal processing application that could ultimately make video streaming better. Specifically, they were asked to speed up the processing of the software-based DVB-T2-Coder, based on the open source GNU Radio project, while maintaining accuracy.

“Signal processing is traditionally very, very computationally intensive, so any optimizations you can get out of something like that are going to be very beneficial to your workflow,” Andrew Tolvstad said.

“There was one loop we optimized that was run about 1.2 million times,” Karen Harper agreed.

“Just by changing a data type that was 32-bits wide to one that was 64-bits wide, we took another 5 to 10 percent off the total amount of time it took to run the program,” Aaron Schraner said.

During the competition, students made improvements to the code that was then automatically compiled and tested for performance once they submitted it via Git. Rohde & Schwarz continuously published a leader board of the top performing teams so the teams could watch their ranking move up or down.

The team members are excited to have an all-expenses paid trip to Germany, and are squeezing the trip into very busy lives of classes and internships. They also have a chance to win $3,000 for the top prize, $1,500 for second place, and $750 for third place.

But the money was not the only objective.

“It’s been a lot of fun,” Tolvstad said. “Just the thrill of trying to take something and make it the best it can possibly be by just rearranging its parts.”

This final will be held in Munich, Germany at the Rohde & Schwarz headquarters. Rohde & Schwarz is a privately held company with over 10,000 employees worldwide, including a design center in Beaverton.

Kedi Yan (electrical & computer engineering) and Nick Wong (computer science) work on their self-playing guitar. More photos in the OSU EECS Flickr album.

“Gadgets and Gizmos” was the theme for the first HWeekend of 2017 on January 20-22, jointly sponsored by the College of Business and the College of Engineering.

In just one weekend, forty-seven students from business and engineering designed, built, and pitched their idea for a marketable product including temperature based alarm clock, a computer controlled potato launcher, a 3-D printed longboard fender, and a self-playing guitar.

It was the seventh iteration of the popular event that provides students from different disciplines an opportunity to work together in teams. Students came from a variety majors including business, bioengineering, civil engineering, chemical engineering, computer science, electrical and computer engineering, environmental engineering, and mechanical engineering.

“This event is really cool, because I get to do things that I normally don’t get to do in my major,” said Alec Westbrook, a chemical engineering student who worked on the 3D printed longboard fender project. “I mean, how often can a guy that is mixing chemicals all day work with his hands and create something new?”

Photo of potato launch team.
The potato launch team tests out their device. More photos in the OSU EECS Flickr album.

This event allowed students to make use of the new Buxton Hall Makerspace and Mastery Challenge lounge, which gave students access to 3-D printing, soldering irons, a drill press, laser cutting, and UV ink logo printing.

Mentors for this HWeekend included six industry members from Intel and two from Microsemi.

“People here are really excited about the things they are making,” said Aayush Pathak, a silicon architecture engineer from Intel who attended HWeekend as a mentor. “And to be a part of it and share what I have seen in my school and life — it’s a proud feeling.”

Staff from both the College of Business and the College of Engineering also helped mentor students through the creation and marketing of their projects.

“It’s an incredibly valuable partnership between business and engineering,” said Dale McCauley, the makerspace manager for the College of Business. “The students are getting the chance to build relationships that ordinarily wouldn’t form. If you get business students to understand how engineers think and vice versa, I think that is valuable.”

At the end of the weekend, the students received group awards for their dedication and hard work. The Executors award goes to the team that produces the best engineering execution of their idea to create the most polished final product, the Helping Hand is for the team that contributes the most to other teams, and the InnovationX Pitch awards go to two teams who had the best business pitches for selling their prototypes.

Photo of temperature-based alarm clock team.
The temperature-based alarm clock team works out their design.

Award winners

Executor: Temperature Based Alarm Clock team. The team included members Noah Hoffman, Taylor Johnston, Alexia Patterson, and Abdurrahman Elmaghbub.

Helping Hands: Checkpoint team. The team included members Andrey Kornilovich and Graham Barber

InnovationX Pitch: Checkpoint team and Temperature Based Alarm Clock team.

Story by Taylor Mrzena

Ziad EldebriGraduate student Ziad Eldebri was the winner of the Lattice Hackathon Contest hosted by Lattice Semiconductor. He was awarded the grand prize of $5,000 and a trip to the Consumer Electronics Show 2017 in Las Vegas, Nevada. Eldebri competed against other students across the country to create an original idea on how to improve a battery powered device using Lattice FPGA. Eldebri’s winning idea was to develop a LIPO battery charger that could be used in any product that uses Lattice FPGAs.

“It was awesome, because I got to attend the Consumer Electronics Show and see state of the art electronics that ranged from 3D printed cars to drones that will talk to you,” Eldebri said. “I also got to learn more about Lattice Products and FPGAs.”

The goal of the competition was to create new ideas on how we can use FPGAs to improve our lives and the electronic devices that we use every day.

Story by Taylor Mrzena

Rey Pocius
Rey Pocius had a great experience as an intern at Metal Toad as a freshman.

Guest Post by Rey Pocius

As a freshman it’s pretty difficult to land an internship because most companies are looking for people with more experience or students who will be graduating soon. But it is possible! This summer I had the opportunity to work for Metal Toad, a software consulting company in Portland, Oregon that offers technical consulting, product development, application support, and managed cloud services to a broad set of clients such as major TV networks, non-profits, health institutions, cultural institutions (such as The Emmys and Golden Globes), and corporations in the technology sector.

I took the initiative to email the marketing manager which eventually led to a phone conversation. I found that professionals in the Portland software community are surprisingly very willing to spend time talking with you. We talked about what the company did and the culture of the company. After some time I was able to speak to the director of human resources and we talked about the internship program, the logistics, and how I could fit into the company as an intern. This led to a phone interview and then a second interview at the company site.

The interview was different from what I had expected — it was less technical, and more centered on cultural fit. I then followed up with email thanking them all for their time and saying that I was looking forward to hearing back to them about the position. About a week later they replied to me asking me if I was still available to take the position.

It was a learning experience for all of us. The company is relatively small and their internship program is still growing and changing, so I was their first intern “guinea pig.” I was new to the formal workplace and was doing something completely new to me — DevOps.

My First Day

I took the internship without having seen the office where I’d be working. It was not what I expected. There were no cubicles, but rather it had an open floor plan. Software developers and other professionals sat next to each other. I was to contribute my expertise to the cloud services (or DevOps) team. Our job was to configure custom cloud services to help align with what the software developers are doing and what the clients want.

I immediately asked for things to do and I was given task after task by my mentor, who was the senior engineer on the team. It seemed like there was an endless amount of things for me to do if I was willing to learn, so I took on whatever I could, even if I had no knowledge about it.

Our team used the Kanban methodology, which produces tickets or tasks from a list of things to do. The Kanban methodology is similar to having a wall covered in sticky “to-do” notes. Members of teams then finished tasks on a first come first serve basis. This methodology worked very well for the small and experienced DevOps team. Everyone on the team was capable of taking on anything coming their way.

Lessons Learned

I took advantage of the resources that I had to learn as much as I could over the 12-week internship. I contributed to several internal DevOps along with working on some client side projects. One experience that students don’t always have access to during undergraduate course work is seeing how a consulting firm, such as Metal Toad, interacts with the clients continuously to create and maintain great products. Being at a small software company allowed me to see all sides of the operations, which was invaluable. Not only was I able to learn and get advice from my mentors, but I was able to learn about the business end of things along with how our work affects our clients and software developers.

Extra-Curricular Fun

Being in the city exposed me to other software companies in the area. Our company was part of the Portland Tech Intern Experience which is a collaborative effort to give a voice to Portland’s growing and diverse tech industry. I would highly recommend this organization to gain greater access to players in the Portland tech industry. The program offered several different networking events and lunch learning sessions that helped unite and nurture the Portland tech scene. During these network events, I met and learned from former interns, and was exposed to future technologies areas of computer science such as deep learning. I also met CEOs, angel investors, and recruiters.

The networking experience that I gained from this internship is invaluable to me. It really opened my eyes to the special software company culture that Portland has. The CEO of Metal Toad encouraged the interns to message people on LinkedIn who they want to learn more about, and ask them for 30 minutes of their time for coffee, or for anything. Driven interns, even “guinea pigs” who can convince companies they’re able to learn and tackle just about any new task, will find that people are more than willing to help you.


Author biography:

Rey Pocius grew up in Elmhurst, IL, where he attended York Community High School. He moved to Oregon in pursuit of the growing tech scene in Portland and the thriving programs at Oregon State. He is also the President of the Oregon State University Association for Computing Machinery student chapter (OSU ACM).

He is very passionate about informing others about the ever growing tech field and helping people find the help they need to launch their careers. He is also particularly interested in deep learning and robotics. He hopes to focus his research and efforts into those two areas.

Outside of academia he enjoys playing tennis and spending a lot of time hiking around the Corvallis area. So don’t be surprised if you find him on some of the local trails. He also enjoys painting and working on software side projects.