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UC San Diego Teams up With Illumina to Launch Bioinformatics Specialization on Coursera

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NEW YORK (GenomeWeb) – The University of California San Diego is launching a new Bioinformatics specialization, developed in part with researchers at Illumina, on the educational technology website Coursera that is designed to teach core bioinformatics principles and concepts to biologists and computer scientists interested in analyzing and exploring genomic data.

The six-course specialization, which officially begins on Aug. 31, succeeds an earlier course launched in 2013 on bioinformatics algorithms that was initially offered by the institution. The extended program teaches identical content to what's taught in a core class in UC San Diego's bioinformatics and systems biology program, but ultimately covers twice as much material as would be taught in the actual class, according to Pavel Pevzner, a professor of computer science and engineering at UCSD. Pevzner co-developed the specialization with Phillip Compeau, who was previously a postdoctoral researcher at USCD and is now an assistant teaching professor at Carnegie Mellon University. These researchers are also responsible for developing Rosalind, a bioinformatics education platform that challenges users to solve problems that address concepts in biology and programming.

"Online education is developing so quickly" and multi-course specializations are emerging as standard within the space, "[which] is why we transferred our offering into this standard," Pevzner told GenomeWeb this week.

They also wanted to break down their much longer course into smaller manageable chunks, he said. Previously, their single course ran for 10to 12 weeks, but now it's been broken down into smaller four-week courses under the new specialization. The longer sequence also allows UCSD to offer a capstone course that will test the skills that students have learned over the course of the program.

Students who sign up for the newly-minted specialization will have their pick of one of two tracks. There's a so-called "hacker track," which targets students with backgrounds in primarily computational disciplines, who may not have had formal biology training and don't necessarily understand biological questions or know how best to use their skills in the space.

Statistics gathered on students enrolled in the preceding bioinformatics course showed that at least 40 percent had advanced degrees in computer science, physics, and similar disciplines, Pevzner said. However, no specific programming language is required for the hacker track, he noted.

A second option targets wet lab biologists who are primarily interested in understanding how popular bioinformatics tools, such as Blast, work and learning to apply them to interesting research questions.

There are some similarities between this and the Genomic Data Science specialization offered by researchers at Johns Hopkins University. For example, both aren't intended to replace traditional degree programs but provide useful training that helps learners explore large genomic datasets. They also target the same demographic — wet lab biologists who want to learn to apply useful computational skills, or individuals from more of a straight computational background who are interested in genomics. However, they do have different focuses, according to Pevzner. He described the UCSD specialization as more akin to a classic course on bioinformatics, one that more closely mimics the sort of content taught in bioinformatics courses at various universities. Ultimately, both options have their merits, he added. 

Each course in the UCSD bioinformatics specialization will last for about four weeks — courses in the Genomic Data Science specialization also last four weeks. Courses in the UCSD specialization cover topics such as comparing genes and protein, exploring molecular evolution, and finding mutations. The content draws on a bioinformatics textbook Pevzner initially published in 2004, but which has been updated to reflect the new realities of the space and adjusted based on feedback received from previous participants in the course, he said. A second edition of the textbook dubbed Bioinformatics Algorithms: An Active-Learning Approach is being published this month.

The specialization concludes with a capstone project centered on challenges in the personalized medicine space that students will be expected to work on. They won't be expected to pass all of the projects, but they will be required to meet a certain grade threshold in order to successfully pass the specialization, Pevzner told GenomeWeb.

The capstone will focus on current challenges faced by researchers in the biotech and pharmaceutical industry. "Each section of the capstone will include a motivating example illustrating how the emerging field of personalized medicine has contributed to decoding the causes of mysterious diseases that traditional approaches failed to diagnose," Pevzner said in a statement.

A sample project might, for example, focus on detecting mutations in cystic fibrosis, which will require students to use various tools and databases and test their ability to apply the skills and expertise that they've picked up over the 24-week specialization. "There's enormous need for these type[s] of skills," and that need is only going to grow in the coming years, he said. "I honestly believe that in five years from now, the ability to program will become a job requirement for nearly all biologists. We are basically preparing them for this transition."

Pevzner and Compeau developed the capstone component in collaboration with researchers within Illumina's enterprise informatics business unit, who came up with many of the problems that are included in the capstone and are providing free access to analysis workflows and datasets that will be used for this portion of the course.

Students will have access to Illumina's BaseSpace cloud infrastructure, where all the datasets will reside, as well as applications for resequencing, RNA-Seq, de novo assembly, tumor/normal analysis, and several others that are available in the cloud, Semyon Kruglyak, Illumina's senior director of informatics research, told GenomeWeb in an email. As part of the course, "students will sign up for BaseSpace accounts, review the available data sets, then run the appropriate apps to answer the questions posed in the challenges," he said.

Furthermore, "because the course content is highly relevant to the real world problems that are our focus, Illumina will be offering job interviews to some of the top performers in the course," Kruglyak added.

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