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Explosion of biological data leads to new collaborations and bioinformatics degree at CSU San Bernardino




​​​​​​​​​Dr. Arturo Concepcion, a computer science professor at CSU San Bernardino (CSUSB), received a Curriculum Development grant from CSUPERB in 2011. In his proposal he explained that most "bioinformatics graduate programs assume that students come from a specific disciplinary program, and they may be weak in one or more area, such as biology, computer science or mathematics."  Aspirational bioinformaticians and data scientists typically fill knowledge gaps by taking individual, but uncoupled, courses in other disciplines.

The Biology, Chemistry and Biochemistry, and Co​mputer Science and Engineering​ faculty at CSU San Bernardino saw the need for and an opportunity to intentionally integrate biology, chemistry, computer science, and mathematics content to educate next generation bioinformaticians.  

The CSUPERB grant supported the development of a new bioinformatics courses based on real-world research problems. Faculty developed course content around DNA sequence analysis and numerical modeling concepts.  To provide course-based research experience, they partnered with researchers at the Center for Bio-Image Informatics at UC Santa Barbara (UCSB), the Center for Perinatal Biology​ at Loma Linda University (LLU) Medical Center, and the Bioinformatics Core Facility at City of Hope.  Researchers at UCSB, City of Hope and LLU hired CSUSB students as research interns, in addition to providing case studies and advice.  

Dr. Concepcion explains, "bioinformatics is a young discipline and the focus of study is still being defined and shifting, opportunities in current research work in this field will give the students valuable knowledge on where this discipline is going." For example George Chen, a senior bioinformatics major, is working with Dr. Christopher Wilson at LLU to develop "an infrastructure for incorporating Electronic Medical Records [EMR] associated with LLU patients in a research database using REDCap, a secure patient-oriented database that protects patient privacy. The ultimate goal of the project is to merge different patient data modalities (physiology, radiology, EMR/EHR, and genomics/transcriptomics/proteomics/epigenetics/metabolomics) into a personalized medicine profile to improve patient care and long-term outcomes."  With an up-to-the minute undergraduate education coupled with hands-on experience like this, recent CSUSB bioinformatics graduates go on to graduate school and work at companies including Amgen and Dexcom.​

In the long-term report submitted this summer to CSUPERB, Dr. Concepcion writes, "I am pleased to report that the B.S. Bioinformatics degree program at CSUSB has been approved for permanent status...I firmly believe that this is due to the offering of the new bioinformatics courses...the high-quality internship programs that our majors undertake, and the success of our graduates in finding meaningful and appropriate careers in bioinformatics."​ 

But the long-term report reveals that other things happened on campus as the new bioinformatics program developed.  

Dr. Concepcion wrote, "My own understanding of bioinformatics has improved and I have a clearer picture on how computing principles and concepts can be applied to this new field of study.​"  

He embarked on a collaborative project with Jeremy Dodsworth​, an assistant professor of biology, to develop a web-based, mobile application to visualize very large metagenomic datasets. ​ Dr. Dodsworth explains, "Bioinformatic analysis of metagenomic data using signatures such as nucleotide word frequencies can aid in the identification and separation of DNA fragments...[revealing] phylogeny ("who's there?") and predicted function ("what are they doing?")."  

    ​The project requirements led the team to cloud-based computing and distributed processing solutions.  As a result another new course on Big Data was developed and the first course taught in Computer Science and Engineering at CSUSB is now "Cloud Computing." 

    The recent 2016 Talent Integration Report emphasized the need for professionals with "proficiency in data management, data storage, analytics, bioinformatics, biostatistics and modeling."  Dr. Concepcion and colleagues at CSU San Bernardino are providing students the educational environment and multi-disciplinary opportunities to answer that call.​​