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Getting that first job in the field of software engineering is difficult. Employers want to see tangible results of projects the applicant has performed, preferably working with a program that must produce real-world results.

That’s why Michael Scott Brown, program chair for UMUC’s Software Engineering specialization, is pleased with the alliance he and adjunct professor Mir Mohammed Assadullah have built with Cytoscape, a leading biological modeling tool used in research.

Software engineering master’s degree students use their capstone project to build applications that add to Cytoscape’s software tools for biomedical and other types of research, such as cancer research, gene modeling and cell modeling.

Begun in 2002 by a research lab in Seattle, Cytoscape now is maintained by a consortium of a dozen academic groups led by Trey Ideker at the University of California at San Diego.  It is a non-profit, open-source tool so any researcher can use its apps to create ways to visualize data in a research project. While it was originally designed for biological research, Cytoscape has become a general platform for complex network analysis and visualization.

Collecting and analyzing data is fine, Brown said but making people understand the importance of that data is difficult unless a researcher also can find a way for people to see data. That’s what

Cytoscape does.  It’s a group of modeling tools that allows researchers to build pictures. Raw data is loaded into it, and out comes these models.

Brown, who does research in biotechnology, said he was at an academic conference four years ago when a presenter from the University of Toronto talked about this tool used extensively in biology and other fields.

“The lightbulb went on,” Brown said.  “When it was coffee time, I talked to him.”

One thing led to another, and now UMUC graduate students work closely with Cytoscape.

Students attracted to a master’s in software engineering come from two different sources, Brown said.

About half are professional software developers who work for companies like IBM and Lockheed. They know a lot about programming, but they don’t know what goes into building software, such as project management, requirement documentation, and testing. They need the bigger picture.

The other half are people—accountants or English teachers for example—who want to change careers and are ready for the next challenge in life.  They want to learn enough to get jobs as requirement analysts, software testers and developers. They need enough knowledge and experience to get through an interview for that first crucial job in software engineering. They know once they pass that hurdle, advancing in the field is much less difficult.

One of the things that separate UMUC from most university software engineering programs is the opportunity for students to get practical, on-the-job experience, Brown said. Finding

opportunities for the students, such as working with Cytoscape, expands their knowledge in the practical aspects of software development.

“The relationship is a win-win,” Brown said.  “Cytoscape gets new functionality.  Our students get real-world experience.”

Cytoscape’s core software can be extended by apps, each of which can be developed by four or five master’s degree students during a 12-week UMUC term.

“UMUC students can put this on their resume and a lot of employers see it as real-world experience, which is important to get a job,” Brown said.  “In software, there is a textbook way to do things, but you have to adapt it to real-world situations.  When you only have 12 weeks, you have to focus on the most important things, and that’s building a knowledge base employers want to see.”

For example, he said, a biology teacher who had come to the program as a career switcher, applied for a job that required testing experience. He had never worked in the software engineering field, but when he explained what he had done with Cytoscape, the employer told him that work counts. It gave him the minimum experience needed to get the job.

For Cytoscape, working with UMUC students also is a plus, said Alexander Pico, a staff research scientist at the Gladstone Institutes, and vice president of Cytoscape's managing consortium.

UMUC students don’t have to start from scratch with Cytoscape because the basic computer architecture already has been developed, he said, and they can build from that with a group of mentors who help them along the way.

Of the three projects already completed, Pico said, UMUC students were able to enrich the entire Cytoscape tool set that adds to the ecosystem of free and open source works.

Having students work with Cytoscape also helps improve its quality, he said.  While mentors are teaching them how to use the tool, they run across hard places that need to be smoothed out to make it more efficient.

“We see this as training and mentoring developers on how to work with the Cytoscape code base,” he said.  “That’s an investment for us because they may end up working on Cytoscape again as their careers progress.”

Pico also works with the National Resource for Network Biology, which provides additional training and resources.  Mentoring UMUC students is part of its mission, so students get assistance from it as well as Cytoscape.

“We’re really happy with the relationship with UMUC,” he said, “and we hope to continue it in the future.”