Hope Computer Science News

Computer Science students present research in San Diego at ASBMB

Wed, 25 Apr 2012 12:57:26 GMT

by Matthew DeJongh.

Hope College Computer Science students Josh Kammeraad, Nick Hazekamp and Ben Bockstege worked with Prof. Matt DeJongh on the CytoSEED plugin for metabolic model visualization during the Summer 2012 research program. Their work was selected for presentation at the ASBMB conference in San Diego on April 22, 2012, and won an Honorable Mention in the undergraduate student poster competition. CytoSEED is a freely available plugin for the Cytoscape framework for complex network visualization. CytoSEED enables viewing and manipulating the metabolic models generated by the Model SEED resource.

Computer Science students successful in International Physics Competition

Fri, 16 Mar 2012 13:51:26 GMT

by Ryan McFall.

A team of three Hope College students has won a bronze medal, placing in the top half among 77 teams from around the world participating in the 2011 University Physics Competition for undergraduate students. The Hope team consisted of junior Andrew McCubbin, a computer science and physics major and mathematics minor from Galesburg (far right); junior Matthew Eiles, a physics and mathematics major from Beaverton, Ore.; and senior Caitlin Taylor, a physics major and mathematics minor from Kalamazoo. In addition to Andrew McCubbin, Matt Eiles has also been active in the Hope Computer Science department.

For more information, see the Hope College press release.

Jipping Gives Talk at Hope's Winter Happening

Fri, 09 Mar 2012 13:53:29 GMT

by Michael Jipping.

Professor Mike Jipping made a presentation at Hope's Winter Happening, a series of seminars that is open to Holland's general public. Dr. Jipping's talk focused on his research on assistive technology and it's implementation on Android mobile phone platforms.

Jipping's talk was titled "Helping People See Better with Mobile Phones." The focus of the seminar was the work he and Dr. McFall did during the summer of 2012 to allow mobile phones to read real-world images and to provide this as assistance to those with low vision. There are approximately 400 million people suffering from the challenges of visual impairment around the world. There are over 5 billion mobile phones in use around the world. The ubiquity, power, and flexibility of mobile phones combine to provide a unique opportunity in the search for technological assistance for visual impairment: a computing platform already accessible to many. The challenge in providing this kind of assistance is in the rendering of real-world images.

Jipping's talk drew approximately 60 people from the Holland community.

Computer Science students publish bioinformatics software

Fri, 20 Jan 2012 14:33:26 GMT

by Matthew DeJongh.

Hope College Computer Science students Josh Kammeraad, Nick Hazekamp and Ben Bockstege have published bioinformatics software that is now in use by scientists around the world. Working together with Professor Matt DeJongh during the Summer 2011 on-campus research program, Josh, Nick and Ben completed the first version of the CytoSEED software package that enables viewing, manipulating and analyzing metabolic models created using the Model SEED. The release of CytoSEED represents the culmination of three years of work by Professor DeJongh, over a dozen computer science students, and one local high school student. CytoSEED is released for free on SourceForge.net, and has been downloaded hundreds of times since the end of the summer. In addition, Professor DeJongh and his students have published a paper on CytoSEED that has recently appeared in the journal Bioinformatics. The development of CytoSEED was funded by grants from the National Science Foundation, and its ongoing support and development is funded by the Department of Energy's Systems Biology Knowledgebase project.

Hope alums named Holland Small-Business Persons of the Year

Fri, 11 Nov 2011 11:12:13 GMT

by Ryan McFall.

Mat Nguyen and Mike Harris, who graduated from Hope College with Computer Science degrees in 2001, were recently honored by the Holland Chamber of Commerce as Small Business Persons of the Year. Nguyen and Harrison are co-owners of Worksighted, an IT support and services provider located in Holland.

Congratulations to Mat and Mike! More information is available in the Holland Sentinel story about the award.

Hope College Part of Department of Energy Knowledgebase Collaboration

Thu, 13 Oct 2011 21:48:53 GMT

by Matthew DeJongh.

The US Department of Energy has formed a collaboration of researchers that it has tasked with developing a systems biology database that will enable comparative genomics research for scientists studying plants, microbes, and the environment.

DOE's Office of Science recently announced that the team, which includes Hope College's Matthew DeJongh, Associate Professor of Computer Science and Aaron Best, Associate Professor of Biology, and is spread across eight institutions around the country, will work together to develop the Systems Biology Knowledgebase, which is designed to enhance collaborative computational research.

Initiated with $3 million in funding from the 2009 American Recovery and Reinvestment Act, the Knowledgebase project will provide new capabilities for researchers to evaluate data-driven theories of microbial and plant systems and to generate new data, protocols, algorithms, and testable models.

The first round of funding supported development of a mapping strategy, architecture, and pilot software projects for the database.

The DOE's Office of Science 2012 budget request to Congress seeks $12 million to fund the build-out of the Knowledgebase, which will include extensive software development, data capture, and integration efforts.

"Hidden in the mountains of biology data we are accumulating today are the secrets of Nature's solutions to a broad range of challenges we face in energy and the environment," said Sharlene Weatherwax, DOE's associate director of science for biological and environmental research (BER). "The Knowledgebase will accelerate our ability to unlock those secrets and help take systems biology to a new level."

Funded through BER's Genomic Science division, the Knowledgebase will use capabilities and supercomputing facilities within the DOE's national lab complex including the Joint Genome Institute, the BioEnergy Scientific Computing Center at Lawrence Berkeley National Laboratory, the Magellan testbed, and other DOE facilities.

The Knowledgebase project will be led by principal investigator Adam Arkin, director of the Physical Biosciences Division of the Lawrence Berkeley National Lab.

The collaborators will include researchers at Argonne National Laboratory; Oak Ridge National Laboratory; Brookhaven National Laboratory; the University of California, Davis; Hope College; the University of Illinois at Urbana-Champaign; Cold Spring Harbor Laboratory; and Yale University.

Summer Research 2011 Ends with 6 Successful Projects

Thu, 15 Sep 2011 20:31:03 GMT

by Michael Jipping.

The summer research program for 2011 wrapped up on July 29, 2011. This was 20th year of our summer research, having started in 1992, with each year supported by the National Science Foundation. We had 15 students this summer, working on 6 different research projects. We were able to support 10 Hope students and 5 students from outside Hope.

In addition to our four faculty members, we were joined by Ravi Agarwal, a faculty member from St. Norbert's College in Depree, Wisconsin.

Chuck Cusack conducted one team on a project called "Algorithms for Graph Pebbling". The project involved developing and testing algorithms for graph pebbling problems. Hope students Tim Lewis and Dan Simpson were joined by Sam Taggart from Oberlin College on this project.

Chuck Cusack also conducted a team on a project called "Human Computing Games for Graph Problems". This project worked on ways to inform the automated solution of graph problems by learning from how humans play computing games. Hope students Hsiang Lin and Russel Zinn participated in this project.

Matt DeJongh worked on a project entitled "Modeling Bacterial Metabolism and Genetic Regulation" This project combined biology, computer science, and mathematics in interdisciplinary research in systems biology. The goal of systems biology continues to be building computer models that use genetic information about an organism to simulate and predict its behavior. Matt's research students were all from Hope: Ben Bockstege, Josh Kammeraad, and Nick Hazekamp.

Mike Jipping and Ryan McFall worked together on a project called "Assistive Technology with Android on Mobile Phones." This project used the technology of Android mobile phones to build an application that will assist people with visual impairment. David Fish from Emory University and Eric Ostrowski from Grand Valley State University were the students on the project.

Ryan McFall also worked on a project called "Building an online survey system" with three students. This project involved continuing development, testing and deployment of a free, open source software system to administer and analyze online surveys, similar to services such as SurveyMonkey. Ryan was joined by Hope students Michael Henley, Matt Johnson, and Josh Kamstra.

Ravi Agarwal brought his team from St. Norberts. His team worked on "Android Robotics: Android makes Robots Smarter". They explored possibilities of using an Android powered device attached to a robot to control and navigate the robot. Students Chris Gusman and Derek Harrington worked with Ravi.

Each student will be presenting the results of their projects at their respective schools. Congratulations to all on a great summer of research!

Summer Research Begins May 31

Wed, 04 May 2011 12:38:33 GMT

by Michael Jipping.

The Computer Science department's summer research program is set to begin on May 31, 2011. This summer program is in its 20th year and has been funded by the National Science Foundation for each of those years. This summer, we will have 15 students involved: 10 from Hope College and 5 from off-campus.

This summer, our four faculty members will be joined by Ravi Agarwal, a faculty member from St. Norbert's College in Depree, Wisconsin.

Our research will focus on six different areas:

Chuck Cusack will conduct one team on a project called "Algorithms for Graph Pebbling". The project will involve developing and testing algorithms for graph pebbling problems.
Chuck Cusack will also conduct a team on another project, called "Human Computing Games for Graph Problems". This project attempts to inform the automated solution of graph problems by learning from how humans play computing games.
Matt DeJongh will be working on a project entitled "Modeling Bacterial Metabolism and Genetic Regulation" This project intertwines biology, computer science, and mathematics students and faculty in interdisciplinary research in systems biology. The goal of systems biology is to build computer models that use genetic information about an organism to simulate and predict its behavior.
Mike Jipping will be conducting a team working on "Assistive Technology with Android on Mobile Phones" This project will use the technology of Android mobile phones to assist people with visual impairment.
Ryan McFall will be working a a project called "Building an online survey system" with a team. This project will involve continuing development, testing and deployment of a free, open source software system to administer and analyze online surveys, similar to services such as SurveyMonkey.
Ravi Agarwal will be working with his team on a project called "Android Robotics: Android makes Robots Smarter". This project will explore possibilities of using an Android powered device attached to a robot to control and navigate the robot.

Graph Games presented at Meaningful Play 2010

Fri, 03 Dec 2010 23:14:54 GMT

by Charles Cusack.

Professor Cusack, Hope College students Jeff Largent, Ryan Alfuth, Matt Jara, and Dan Simpson, and Hope College graduate Kim Klask presented their research related to Graph Games at the Meaningful Play conference held at Michigan State University in October, 2010. Meaningful Play is an international interdisciplinary conference that brings together scholars and industry professionals to understand and improve upon games to entertain, inform, educate, and persuade in meaningful ways.

Graph Games is a collection of human computing games. In general, human computing games leverage certain abilities possessed by humans that computers lack. Most such games solve problems like sound and image recognition--problems which are typically trivial for humans to solve but very difficult for computers to solve. Graph Games takes this concept one step further, attempting to solve problems which do not have obvious answers. In particular, the problems of interest are those that can be represented on graphs. Most of these problems can be solved by computers, but not very quickly. The thought behind the games is that humans may have specific problem solving strategies that will allow them to determine solutions to certain problems more quickly than the best-known algorithms.

At the conference, the entire group presented the games as part of the games competition. Although Graph Games did not win a prize, people were very intrigued by the idea. It turns out that most people have never thought of the concept of using games to solve problems. Typically researchers in the field of "serious games" think about games for education, training, and persuasion--all things which focus on what the player gets out of the experience. Human computing games reverse this and ask what the players can contribute. This makes perfect sense because playing just about any game requires problem solving. Human computing games simply insert a "real" problem into the game for the players to solve.

Professor Cusack also presented a paper, written with Jeff Largent, Ryan Alfuth, and Kim Klask, that focused on the original Graph Games: The Pebble It games. These games solve graph pebbling problems, which are related to resource allocation and distribution problems. They were inspired by conversations with Professor Bekmetjev from the Mathematics Department.

Graph Games can be played by going to http://graph.computinggames.org.

DeJongh and Frybarger publish bioinformatics paper in leading journal

Fri, 15 Oct 2010 12:51:31 GMT

by Matthew DeJongh.

New software developed with the involvement of faculty and student researchers at Hope College is helping to speed dramatically the time-intensive, painstaking task of transforming the immense amount of genomic data being collected worldwide into working models of how organisms function at a fundamental level.

Professor Matt DeJongh in the Computer Science department, and student Paul Frybarger (middle), contributed to the development and publication of the Model SEED, a web-based resource for the automatic generation, optimization and refinement of microbial metabolic models.

The work was recently highlighted in an article published in the August issue of the prestigious monthly scientific journal "Nature Biotechnology." In 2009, the journal ranked first in biotechnology and applied microbiology for its "impact factor" - a measure of the frequency with which the publication's articles are cited elsewhere - as determined by Thomson Reuters Journal Citation Reports.

According to Hope faculty members Dr. Aaron Best (Biology Department) and DeJongh, co-leaders of the Hope research team, the web-based "Model SEED" resource, which is available at http://www.theseed.org/models, can reduce to 48 hours most of the calculations that used to take a year to render manually - and the research team is working on speeding up the rest. Even as the Model SEED is already being used by scientists internationally, they noted that the team is also looking at a further step: how to use the models in examining a variety of questions, from the way that some bacteria cause diseases to how other bacteria produce energy and clean up pollution.

The resource reflects collaboration between researchers at Argonne National Laboratory - where Model SEED is based - the University of Chicago and Hope. The "Nature Biotechnology" article's six co-authors, representing the three institutions on the research team, include three from Hope: DeJongh, who is an associate professor of computer science; Best, an associate professor of biology; and recent graduate Paul Frybarger, who worked on the project as a student. Lead author is Christopher S. Henry of Argonne National Laboratory and the University of Chicago; the other authors, Ben Linsay and Rick L. Stevens, are both with the University of Chicago as well.

DeJongh noted that the impetus for the Model SEED grew from the reality that the tools for working with genomic information haven't kept up with the explosion in data collection made possible by advances in biotechnology.

"The capability of generating data has been outpacing the ability to analyze it, so we've needed software to analyze this genome-level data," he said. "That's where the tools that we've created come in."

"This kind of work used to take a person about a year to do on a manual basis," DeJongh said. "We can effectively do 80 to 90 percent of that work in 48 hours now, and we're working on tools to assist scientists doing that remaining 10 to 20 percent by hand."

Combined, the speed and analytical capabilities are an important new tool, Best explained.

"A particularly valuable outcome of this work is that the software provides a powerful framework for comparing how different organisms perform certain functions or respond to conditions. This is a framework that has been lacking," he said. "A resource like this allows researchers to, for instance, look at two very closely related strains of bacteria--one that causes disease, another that doesn't - and better understand the differences in how they function."

The Model SEED is accessible to researchers around the globe through the RAST (Rapid Annotation using Subsystems Technology) genome analysis service available through Argonne National Laboratory. The SEED project is a nationwide, open-source effort to develop and share genomic data.

Best and DeJongh and Hope students have been working on the project for about five years. In addition to receiving National Science Foundation (NSF) grant support for their work, Best and DeJongh both received Towsley Research Scholar awards from Hope and funding from a multi-purpose Howard Hughes Medical Institute grant to Hope.

In developing and testing the Model SEED, the research team generated 130 models of a variety of forms of bacteria - life forms that involve thousands of distinct biochemical processes. Subsequent comparison of the models with real-life data has found the system to be 87 percent accurate.

"It is remarkable that this level of agreement between model and experimental data is achieved with little manual input into the model-building process and for a very diverse group of bacteria," Best said. "As researchers begin to focus in on models for individual bacteria, not only will this accuracy increase, but the models have the potential to reveal and predict important behaviors that will help us understand how these bacteria interact with their environment."

The overall effort is currently supported by two major grants from the NSF. The first, awarded to Best and DeJongh in 2008, has supported the development of the models and modeling software, and will continue through this spring as the team seeks to automate some of the remaining analysis. The other, a two-year award that Best and DeJongh received with colleague Dr. Nathan Tintle of the mathematics faculty, is supporting taking the simulation further, from creating a model that accurately reflects the systems being represented to using the model to see how the systems respond to different situations.

"The new grant builds on this resource to use these models to analyze other kinds of data," DeJongh said. "What can we get out of it when we start feeding it environmental data and make simulations and statistical predictions?"