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Q&A: Istvan Albert on Penn State's Efforts to Equip Biomedical Researchers to Use Bioinformatics Tools


NEWYORK (GenomeWeb) – Pennsylvania State University has launched a new graduate certificate in applied bioinformatics through which it intends to train biomedical researchers to apply and use algorithmic processes, tools, and techniques to explore data from omics studies.

The graduate certificate is available through Penn State World Campus, the online arm of Penn State University. Penn State's faculty, including Istvan Albert, an associate professor of bioinformatics, biochemistry, and molecular biology, and Anton Nekrutenko and Ross Hardison, both professors of biochemistry and molecular biology, will teach the 11-credit certificate program. Nekrutenko is also the principal investigator of the Galaxy project.

Applications are now being accepted for enrollment in the spring 2015 semester. People who complete the certificate should be equipped to work for pharmaceutical, biotech, and software companies as bioinformatics scientists, technicians, or statisticians; next-generation sequencing analysts; genome curators; bioanalysts; and geneticists, according to the school.

This week BioInform sat down with Albert, who is the lead faculty member for the graduate certificate, to discuss the planned curriculum and merits of the newly minted program. What follows is an edited version of that conversation.

What is the background on why you set this up?

This program is the result of a multi-year planning process. It's rooted in our efforts to establish a bioinformatics PhD program at Penn State. Most of the courses that we offer online are based on courses that we have developed for the bioinformatics and genomics PhD curriculum.

If you already have a PhD program, then why add a separate certificate option?

Our PhD program can only accommodate a small subset of those who need this type of training. We thought this way we could expand our reach and offer our training expertise to a much wider audience than at a PhD program level. In addition, because the training domain lies in computing and requires the use of numerous online resources it is well suited to an online educational environment.

Who is the target audience for the certificate?

We are targeting life scientists who need sequencing and data analytics and want to either perform the data analytics themselves or become sufficiently knowledgeable about the subject to be able to direct, supervise, and otherwise meaningfully interact with collaborators and partners offering computational assistance and support.

Would the program be suitable for lay people interested in bioinformatics and genomics and getting their feet wet?

Absolutely, it's a really good match for them as well.

What's the curriculum like?

We try to cover the all essential domains of bioinformatics and data analytics. But we do primarily focus on applications. We offer a biology and genomics-oriented course that covers the structure and function of genomes. We have a course that targets the current developments and techniques in computational biology and genomics. We have an applied bioinformatics course that trains students in the computational analysis of very large biological datasets. Finally, we have a statistical analysis course that covers the methodology required to assess and validate discoveries.

You offer about four courses according to the program website. What were some of the considerations that went into selecting these courses?

The courses that we list today are based on what we consider the key parts of the core competency of the bioinformatics curriculum here at Penn State. The online offerings are, of course, more focused but just as rigorous and comprehensive. We plan to expand these course offerings in the future depending on our experiences and the feedback that we collect. We envision that we will also add a few electives on biomedical applications, clinical genomics, proteomics, and others.

Are there specific tools you intend to teach students to use?

We plan to cover the commonly used data analysis methodologies, from command line tools through various open-source and commercial tools. We plan to give students a high-level overview of all the options that they have at their disposal.

Should applicants have some kind of background?

The current prerequisite is a bachelor's degree, but I personally believe that an advanced undergraduate close to finishing their studies would also have the necessary skill and preparation [to] successfully complete the course.

There are a lot of free programs out there that biologists and others interested in bioinformatics can take. What's the draw for a paid program?

It all depends on the amount of information that's covered, the completeness, depth, and variety of information that a program contains. I found most offerings to be focused to a narrow application domain. For example, they'll cover a subset of Bioconductor or a few specific elements of RNA-seq analysis. These programs are great as refreshers or to add to existing knowledge but do not provide the necessary basis to build a career upon. We offer a program that provides a well-rounded and complete educational experience that prepares the candidates for a much wider variety of tasks. We cover all aspects, the foundations in biology and statistics, the use of computational tools and techniques, and the scientific reasoning that needs to support every analysis. I think we provide a balanced and very comprehensive training package that is not available from any other source.

Is there a time frame for students to complete the certificate?

We plan to offer this program with a schedule that allows students to complete all required courses within a year of their enrollment. Of course, people could take a little longer if they wish.

Anything else you'd like to add as we wrap up?

I think our program is unique. I am fairly knowledgeable of other online courses and resources, and to the best of my knowledge ours is the only well-structured program that was designed for and focuses primarily on the applied aspects of bioinformatics. [This is] the most pressing need in the field [and] we recognized this from the feedback from our resident instruction, from teaching workshops and summer courses, from direct requests, and many other modes of intercommunication. This is why we have designed a series of courses to focus mainly on the practical applications. We are not planning to teach algorithms or how to write bioinformatics software. We will teach students how to choose from different implementations of algorithms, how to decide which computational tool or statistical technique to apply when faced with a particular problem set, how to customize parameters, and tune a process to match the biological problem that is to be solved.

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