Professor McFall completes sabbatical as an "intern"

Picture of Professor Ryan McFallProfessor Ryan McFall spent his fall semester sabbatical as an application development intern with Open Systems Technologies in Grand Rapids.   While there, he was part of a team of OST employees who were charged with building a new web site to drive the operations of the client. 

Ryan spent his days learning about current technologies in the world of software development, and will be bringing many of those technologies back into his spring courses. He also found time to bring a group of senior Computer Science students on a tour of OST, which led to one December graduate landing a full-time position and another student beginning an internship in December running through the spring semester.

The idea of a college professor serving as an intern caught the interest of the local media, and was featured in several news outlets, including the Grand Rapids Business Journal, the Grand Rapids Press, and WGVU radio.

Posted Fri, 17 Jan 2014 19:28:13 GMT

Computer Science Students Place in Regional Programming Contest

Team PhotoOn Saturday November 9th, Hope College computer science students Timothy LewisJoshua Kammeraad, and Shinnosuke Kondo competed in the 2013 ACM ICPC East Central North America Regional Programming Contest.  They competed at the Grand Valley State University Site, one of four in the region.  During the five hour competition they were able to write programs to solve 4 of the 9 problems they were given which was good enough to earn them 16th place out of 126 teams in the region and 3rd place out of 23 at the site.  The second place team at the site also solved 4 problems, but were able to do it in less time (the tie-breaker).  The top team at the site (2nd place in the region) solved 7 problems.

ACM Programming Contests are very competitive.  Teams spend a significant amount of time preparing for each competition, with some schools having local competitions to decide who gets to compete in the regional contests. Schools with a long and consistent history of competing seem to do the best. Since Hope hasn't had a team compete since the 1990s, the team was formed less than a month before the competition, and was only able to have a couple of practice sessions lasting only a few hours each, their performance in the contest was impressive. The team's coach, Dr. Charles Cusack, told them before the contest that they might be able to solve maybe as many as four or five, but that they should be happy even if they only solved one or two problems since it is not uncommon for well over half of the teams to solve no more than one problem. In fact, he agreed to buy them dinner if they got three correct. Apparently they were hungry.

Posted Fri, 15 Nov 2013 18:24:05 GMT

NSF Funds Integrated Metabolic and Regulatory Modeling Grant

Bioinformatics LabA major, multi-year grant from the National Science Foundation (NSF) will support a significant new step in an on-going research project at Hope College that is developing and refining computer-based models of metabolic activity.If the team’s previous work provided a road map, researchers Dr. Aaron Best and Dr. Matthew DeJongh say, the new effort should yield the equivalent of an online navigation system.Best, who is the Harrison C. and Mary L. Visscher Associate Professor of Genetics at Hope, and DeJongh, who is an associate professor of computer science, have received the new three-year, $400,000 grant as part of an NSF collaborative award totaling $650,000 with Dr. Nathan Tintle of the mathematics faculty at Dordt College. Best, DeJongh and Tintle have worked together on the research since Tintle’s days as a Hope colleague from 2005 to 2011.
The researchers have collaborated for nearly a decade, with support from a series of NSF grants, to build and improve a computer program that creates genome-scale metabolic models, condensing into a few hours a process that required about a year when done manually. The research at Hope has been conducted in collaboration with Argonne National Laboratory as part of an open-source initiative that has made the tool available to scientists around the world. The software, named “Model SEED,” has been applied to thousands of microbial genomes. DeJongh and a team of Hope students also developed “CytoSEED,” a software package that enables viewing, manipulating and analyzing metabolic models created using the “Model SEED” and which itself is used around the globe.
Through the new award, the research team will add the ability to model how the organisms behave in response to changes in their environment. “The first years of the project were designed to allow us to build models efficiently, but the models are at some level starting points,” Best said. “One of the primary activities that this grant will fund is increasing the sophistication of the model: from the capabilities the organism has, to layering on top of that information about when the organism uses those capabilities.”
“We talk about our models as being like roadmaps,” DeJongh said. “A road map tells you how to get from point A to point B. What we’re trying to do now is use real-time data to figure out how the organism is using different capabilities at different times,” DeJongh said. “We’re hoping to develop statistical tools to elucidate parts of the system that we don’t understand yet.”
Crucially, the grant is also enabling the researchers to test and improve the accuracy of the computer models through laboratory work. “We can make predictions using the model, and then grow a sample in the lab and use genetic sequencing to determine whether or not those conditions are actually happening,” Best said.
A key component of the project, Best and DeJongh noted, is that the research will continue to involve students at both Hope and Dordt. Students at Hope work directly as collaborative researchers with Best and DeJongh during both the school year and summer, but the project is also integrated into the academic program in other ways. For example, computer science students at the college revised the “CytoSEED” program to make it compatible with a new version of the platform on which it operates, and the researchers envision involving students in biology courses to conduct laboratory validation of the computer models.

Posted Thu, 07 Nov 2013 21:36:57 GMT

Computer Science Junior Maria Equiluz Chosen for National Research Program

Maria EguiluzHope College sophomore Maria Eguiluz of Redford was chosen to participate in the Summer 2013 national “Exceptional Research Opportunities Program” (EXROP) of the Howard Hughes Medical Institute (HHMI). Eguiluz is a biology and computer science double-major. Eguiluz has been active in research at Hope since even before her freshman year began. As a high school student, she participated in the college’s REACH (Research Experiences Across Cultures at Hope) program, which engages high school students in collaborative research at the college full-time for several weeks during the summer. Following her freshman year, during the summer of 2012, she conducted research full-time at Hope in the laboratory of biologist Dr. Aaron Best, in a collaborative project with computer scientist Dr. Matthew DeJongh.

Hope College sophomore Maria Eguiluz of Redford was chosen to participate in the Summer 2013 national “Exceptional Research Opportunities Program” (EXROP) of the Howard Hughes Medical Institute (HHMI).

EXROP provides outstanding summer research experiences to undergraduate students from disadvantaged backgrounds or from groups traditionally underrepresented in the sciences to encourage them to pursue careers in academic science. Last year, 60 students nationwide participated in the highly selective program.

The participating students are matched with HHMI scientists around the country who have volunteered to provide mentored research experiences for 10 weeks during the summer. EXROP students also attend meetings at HHMI headquarters, where they present their research in a poster session, network with their peers and HHMI scientists, and hear from scientists from various backgrounds and in various stages of their careers. Selection includes a $4,500 award.

Eguiluz is a biology and computer science double-major. Through EXROP this summer, she conducted research at Cold Spring Harbor Laboratory in New York with Dr. Gregory Hannon, whose lab works primarily on mechanisms and applications of RNA interference and is also interested in cancer biology, in particular in developing tools to understand cancer initiation and progression.

Eguiluz has been active in research at Hope since even before her freshman year began. As a high school student, she participated in the college’s REACH (Research Experiences Across Cultures at Hope) program, which engages high school students in collaborative research at the college full-time for several weeks during the summer. Following her freshman year, during the summer of 2012, she conducted research full-time at Hope in the laboratory of biologist Dr. Aaron Best, in a collaborative project with computer scientist Dr. Matthew DeJongh.

During her first year at Hope, she was enrolled in the research-based, year-long “Phage Genomics Research Initiative,” a freshman-level laboratory class established through an award to the college from HHMI. Also as a freshman last year, she participated in the college’s FACES (Fostering A Community of Excellence in Science) peer-mentoring program for first-year students interested in careers in the natural and applied sciences who are from groups traditionally underrepresented nationally in such careers. This year, she is one of the upperclassmen mentoring one of the college’s freshman students. Both REACH and FACES are initiatives in science education at Hope funded through grants to the college from HHMI.

Eguiluz’s activities at the college also include the orchestra. She is a 2011 graduate of Zeeland East High School, and the daughter of Luis and Maria Eguiluz of Redford.

The Howard Hughes Medical Institute is a nonprofit medical research organization that ranks as one of the nation’s largest philanthropies. HHMI plays a prominent role in advancing biomedical research and science education in the United States.

Founded in 1953 by aviator and industrialist Howard R. Hughes, HHMI is headquartered in Chevy Chase, Md., and employs more than 3,000 individuals across the U.S. HHMI has an endowment of $16.1 billion, of which the institute spent $800 million for research and distributed $119 million in grant support for science education in fiscal year 2012

Posted Tue, 01 Oct 2013 12:52:05 GMT

Computer Science Department T-Shirts

CS@HopeThe Computer Science Department unveiled new t-shirts this fall.  Every student and faculty member in the department was given one during the first colloquium of the year and asked to wear it every Tuesday to show their pride in being a member of one of the most burgeoning departments on Hope's campus.
What students didn't know was that there was a message encoded in the anchor logo.  That fact was revealed two weeks ago.  What is the message and how was it encoded?  That's still a secret. The department is offering rewards for each student who successfully decodes the message within the next several weeks.  So far 2 students have been able to decode it, one of them before we even told them that there was a message!  

If you want to try to decode it, you can find a higher resolution version of the logo here.  If you are able to decode the message, send an e-mail to Dr. Cusack ( with the decoded message along with a brief description of how you decoded it.

Posted Mon, 30 Sep 2013 20:08:29 GMT

September 17 Summer of Fun Colloquium available on CS web site

In case you missed out, check out the video on this page (lower right hand corner):

Next Tuesday at 11 AM we'll have those two guys from Google I told you about with us for an hour - you won't want to miss it. I'll send out details soon, but in the meantime, wash your Computer Science@Hope College T-Shirt and get ready for the fun to continue!


Posted Fri, 27 Sep 2013 13:19:03 GMT

Pearson Student Coding Contest

Dear Professor DeJongh,

Pearson is excited to announce our first ever Pearson Student Coding Contest. The Contest is open to undergraduate students in the United States and is designed to reward contestants who develop relevant, innovative, creative, and original apps that integrate with Pearson APIs.

Contest Details
Students will submit their Idea Proposal from September 3 - September 30. Contestants will be notified by October 8 if their Idea Proposal has been accepted. Contestants with approved Idea Proposals have from October 8 - November 30 to develop and submit their Entry.


We're also offering:

3 internship positions for summer 2014 at eCollege in Denver.

An opportunity to interview for the Pearson Leadership Development Program—a highly selective program that Pearson uses to recruit the most talented college grads.

Use the following resources to notify your students about this amazing opportunity!

Full Contest details are available online: Download a PowerPoint slide or flyer to use during class. Feel free to print and distribute, or post on your course website. If you have any questions, please feel free to contact me directly.

We hope that you encourage your students to participate in the Contest.



Gregory O. Smith, PhD
Publisher’s Representative
Professional & Career
Higher Education

D: 614-841-3632
T: 800-228-7854 x3632

Always Learning
Learn More: Catalog & Instructor Resources
Learn How: MyLab Help & Training | Tech Support
Learn About Me: LinkedIn

Posted Tue, 24 Sep 2013 12:39:11 GMT

SoftwareGR Meeting in Grand Rapids Tuesday Night

Please share the upcoming Software GR Speaker Series line up with your students.

If you have any questions, please let me know.


John Rumery

Today myself, tomorrow the neighborhood, then the world.
(616) 240-2813

Posted Mon, 23 Sep 2013 19:58:00 GMT

22nd Summer Research Program Successfully Completes

The summer program for 2013 wrapped up on July 19, 2013. This was 22nd year of our summer research, having started in 1992, with each year supported by the National Science Foundation. We had 12 students, working on 4 ifferent projects. In addition, we continued with a program in software development, modeled after the research program.
Chuck Cusack worked with Hope student Matt Barbour and with Scott Hoelsema from Covenant College and Seth Yoder from Goshen College.  They continued Chuck's work in volunteer computing games, adding more functionality to the Graph Games Web site.  Chuck also worked with  Hope student Tim Lewis to produce various theoretical results connected to NP-completeness of graph pebbling algorithms.

Matt DeJongh worked with two Hope students on a project entitled "Modeling Bacterial Metabolism and Genetic Regulation."  This project worked toward building computer models that use genetic information about organisms to simulate and predict their behavior.  Matt's research students were Carl Deeg and Shinnosuke Kondo.
Mike Jipping worked with three students on a program based on structure recognition.  His project was built on Android devices and layered data and functions onto live video images that matched preconfigured photographs.  Mike work with Hope students Brant Bechtel and Kevin Hartsfeld and with Alek Szilagy from Maravian College.
In addition to these research projects, the department also continued a program from the summer of 2012 in software development.  The goal of this program, called the Hope Software Institute, is to give students the same rich experience in software development that students get in research projects.  This summer's project was the development of an Android app for use with the College's Health Dynamics class for tracking exercise and fitness activities and a tablet app for viewing fitness data entered by students. The group went on field trips to a variety of organizations, studying their methods of software development.  These organizations included TechSmith in Okemos, and Collective Idea in Holland.  Each organization had different types of clients and different methods for coordinating groups efforts.  The summer program included three Hope students: B.J. Schulz, Brennen Sieck, and Taylor Brushwyler.

Posted Fri, 30 Aug 2013 13:50:07 GMT

Computer Science department featured in News from Hope College

Picture of students Michael Henley and Matt Johnson, along with Prof. Ryan McFallThe work of the Computer Science department students and faculty was recently featured in a News from Hope College article, highlighting the way that student projects are impacting the life of the college.  This includes a diverse set of projects which touch the lives of Hope students, faculty and staff.

The article can be found here.

Posted Thu, 06 Dec 2012 10:52:24 GMT