THE PERVASIVE APPLICATIONS OF COMPUTER SCIENCE IN BIOMEDICINE* Igor Balsim, Ronald Eckhardt, Elie Feder, Sarwar Jahangir, Gabriel Yarmish
[email protected] Kingsborough Community College and Brooklyn College- CUNY Departments of Mathematics, Computer Science, and Biology
ABSTRACT An interdisciplinary computer science educational program is introduced in the field of biomedicine. The program is designed to be implemented in Kingsborough Community College (KCC), a two-year college, and Brooklyn College (BC), a four-year college. Motivation and various applications of the field of bioinformatics are presented. The educational structure of the program is presented and the models of a community college and four year college are discussed. 1. INTRODUCTION A recent study by UCLA's Higher Education Research Institute found a 60 percent decline between 2000 and 2004 in the number of college freshmen who planned to major in computer science. Bill Gates was perplexed by the declining enrollment in computer science programs at the nation's universities. Citing all the advances made possible by computer science, he questioned why so many people would opt for less exciting and practical careers [3]. One factor which contributed to this decrease is the increase in non-CS programs that integrate computer information technology into their curriculum [2]. This allows for students to learn computer technology in the context of other disciplines which they find more interesting. In these programs, however, students do not typically learn enough about computer science to either work in or contribute to the field as computer scientists [13]. While the number of students applying for pure computer science is decreasing, the number of students who are actively and aggressively using computers in their curricula — in the areas of mechanical engineering, electrical engineering, bioengineering and the ___________________________________________ *
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JCSC 24, 3 (January 2009) sciences — is growing [3]. One wonders if this is a crisis for computer science or merely a transformation. As modern society grows ever more dependent on computing technology, many sectors of science and industry anticipate ongoing shortages of well-trained computer scientists and engineers [13]. The gap between the foundations of computing and its research and application frontiers is considerably shorter than in many other fields. Therefore, the curriculum in computer science and engineering faces constant evolutionary pressure to integrate new critical developments. We need to re-energize our curriculum, to really understand that it takes more than just a simple solution [9]. One promising approach is the development and advancement of an interdisciplinary computer science education. This educational outlook calls for an integration of the major degree programs and course curricula in computer science with the natural sciences and business, both in style and in content [11]. Illustrating the interactions of computers with various other disciplines gives students a realistic perspective on the strengths and limitations of computers. This perspective provides insight as to the contributions and advances that computer science can offer to help solve difficult problems in a variety of fields. This paper presents a collaboration of faculty from Kingsborough Community College (KCC) and Brooklyn College (BC), a four year college that describes some of the active interdisciplinary research and curriculum development in the applications and integration of the fields of computer science and biomedicine. These programs should serve as a model for other colleges throughout the nation. 2. INTERDISCIPLINARY COMPUTER SCIENCE EDUCATION Computer science courses can be broken down into pure and applied courses. There are two types of applied computer science courses: (i) Computer Science with Applications: These are computer science courses which are centered around real-life scenarios that are solved by means of computer science; (ii) Bridge Courses: These courses present a unified combination of computer science and a related discipline, i.e., bioinformatics unifies computer science and biology. Corresponding to these applied computer science courses are two types of interdisciplinary computer science degree programs: (i) Applied Computer Science Programs: These programs offer a full-fledged computer science degree consisting of a core of pure and applied computer science courses, bridge courses, and some courses from other disciplines that utilize computer science; and (ii) Integrated Science Programs: These programs consist of a conglomerate of multiple departments and faculty. In addition to course work, students get involved in faculty-led research projects whose primary objective is to foster educational and research growth in the fields of computer science and related application sciences. These degree programs focus on training in multifaceted career development, as opposed to the traditional unilateral approach. Both of these programs must be designed such that their various courses complement each other to form a coherent, unified program. The focus of any interdisciplinary computer science program must be the integration of computer science and other disciplines in a manner which has potential for great impact [12]. 12
CCSC: Eastern Conference 3. INTERDISCIPLINARY COMPUTER SCIENCE IN TWO-YEAR AND FOURYEAR COLLEGES Even though interdisciplinary computer science educational programs often require advanced research skills and capabilities, we strongly believe that such programs are indeed appropriate for two-year colleges and should be implemented. There are many two-year college students who have a great deal of potential to advance in mathematical and science related research fields despite being in a two-year college. There are many technical barriers which lead to advanced students attending two-year colleges. Some examples are: low income, language barriers for foreign students, lack of motivation, poor high school preparation, family problems, etc. However, such obstacles could be overcome with a strong will, proper mentoring and guidance, and perseverance. This is evident from the many success stories of two-year college students who have excelled in their education and careers by transferring to top-quality universities and graduate school programs. One outstanding example of a community college student who went on to excel in a top quality university serves as a role model of what is possible for many similar students whose potential has not yet been realized. Anthony S. Tantuccio is presently enrolled with a full scholarship in the chemical engineering program at The Cooper Union in New York City. At twenty-four, despite his fears of being too old to undertake college, he enrolled at KCC, a community college. His curiosity was revived when his courses illustrated the beauty and wisdom implicit in the world. In the first semester he achieved a 4.0 G.P.A. which he maintained through his two years at the community college. Based upon his success, he was inducted as a member of Mu Alpha Theta Mathematics Honor Society. Anthony also participated in the NSF Summer 2007 Research Project: Cerium Oxide Nano-particles Increase Bone Marrow Stem Cell Proliferation by Superoxide Free Radical Scavenging.Anthony is but one example of the 1000 members of Mu Alpha Theta Mathematics Honors Society in its 35 active two-year college chapters. These 1000 members are but a small sample of the many more students at two-year colleges around the nation with unrealized talents in mathematics and computer science. We firmly believe that a strong interdisciplinary computer science program will provide the necessary motivation to help these students realize their natural talents and abilities. It is with these thoughts in mind that we introduce an applied computer science program, an integrated biomedical program, and a biotechnology program which join the students of a two-year college together with those of a four-year college. 4. MOTIVATION FOR BIOMEDICINE Recent advances in information and communication technologies have enhanced our understanding of complex medical problems and their solutions. This has increased the use of computers in healthcare settings and biomedical research, and expanded interest in learning more about biomedical computing. This technological development has provided advanced services, such as: computer-assisted radiology, telemedicine, and robotized tele-operating systems. A thorough preparation for the future advancement requires a fundamentally deep understanding of the biomedical computing and of the current and future capabilities and limitations of its technology [7]. Various computer 13
JCSC 24, 3 (January 2009) technologies have been applied to the array of problems in the biomedical fields with varying degrees of success: artificial intelligence, machine learning, neural nets, genetic algorithms, etc. The most accepted and proven methods for applying these technologies and developing information systems for users are found in the field of software engineering; a branch of Computer Science and Engineering (CSE) [4]. The wide applications of computing techniques in the biomedical environment will demand welltrained professionals to teach, design, develop, and manage the biomedical computing systems of tomorrow. The field's development has been restricted because of the limited trained personnel who are qualified to design research programs, execute experimental and developmental activities, and provide academic leadership in biomedical computing. These failings are largely due to the lack of proper communication between the biologist or health professional and the computer scientist. Interdisciplinary research and development projects are more likely to be successful if they are directed by individuals who can unify the biomedical and computing fields [8]. This suggests the development of a strong interdisciplinary educational approach to help educate such individuals. An applied computer science degree in biomedicine should be formed. This will help to train individuals who would be proficient in both computer science and biomedicine and would therefore excel in the many areas of biomedicine in which knowledge of computer science is necessary. 5. APPLICATIONS OF BIOMEDICINE In this section, we present a description of the wide range of applications of computer science techniques in the field of biomedicine. 5.1 Clinical Informatics The electronic health record is an integrated health service solution for creating an information and communication system that reduces outdated paperwork [7]. 5.2 Bioinformatics and Biotechnology Starting at the molecular level, bioinformatics analyzes how information is represented in biological systems. Clinical informatics and bioinformatics are closely related since they both deal with the management of information that is related to the delivery of healthcare in the formal case and the underlying basic biological sciences in the latter case. The increase in the needs for information storage, retrieval, and analysis in molecular biology and genomics in the past decade has spurred a rapid growth in the bioinformatics discipline. Bioinformatics is able to construct a more unified view of biological processes due to the creation of genome sequencing and the new technologies for measuring metabolic processes within cells [8].Related to the field of bioinformatics is the field of biotechnology, where computing technologies are used together with basic biological techniques. Biotechnology holds the greatest potential for fundamental discovery and job potential in the 21st century. From healthcare to the environment, the application of gene therapy, stem cell technology and cloning applications are burgeoning. It also extends from forensics, biotech pharmacy, to agriculture [10].
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CCSC: Eastern Conference 5.3 Virtual Reality Mathematical modeling and computer simulation is used to give an elegant and simple description of biological systems. Such experiments could be regulated with more flexibility to stop and start the experiment at any time or design a new model with new parameters. With this methodology statistical effects and mathematical analysis can be developed to continue with advanced research and measurements [7]. 5.4 VR in Medical Diagnostics and Visualization Biomedical Imaging techniques affect the noninvasive visual representation of human anatomy and the functional mapping of human physiology from the cellular to the organism level. The advanced 3-D graphics technology of virtual reality has expanded these visualizations by creating data-fusion of human structural imaging of human physiology and function. This is the genesis of further visualization for many other micromolecular imaging techniques, including electron microscopy and NMR-based cellular imaging [7]. 5.5 Virtual Learning Environments Computer Technology is used in healthcare education. Care2X is an open source integrated healthcare environment (IHE) that integrates data, information, functions, and workflows. Computer training is apropos for visually intensive, detail-oriented subjects such as anatomy and kinesiology, because it permits text to be combined with still and moving graphics, with full control of the display of this information [7]. 5.6 Computer Assisted Diagnosis Digital imaging is one of the essential technologies in solving many problems in diagnosis and therapy. Computer-assisted surgery and diagnosis rely on some type of image management. Functional neurosurgery is reserved for chronic neurological diseases resistant to drug therapy. Accurate localization of the surgical target and of the cortical areas that are responsible for vital brain functions is of paramount importance because imprecision in such critical brain areas can have devastating results. Functional brain mapping aims at visualizing the relationship between neural structures and their function. [7]. 5.7 Data Mining Data-mining techniques have been used for gaining diagnostic results, especially in medical fields such as kidney dialysis, skin cancer and breast cancer detection, and biological sequence classification [7].
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JCSC 24, 3 (January 2009) 6. PROGRAM DESCRIPTION This section presents the computer science course curricula and degree programs which we have implemented or plan to implement in order to realize our educational objectives. 6.1 Course Curricula We plan to revise basic computer science course curricula by including computer applications such as biomedicine, in order to illustrate the wide use of computers in the modern world. This will serve as an incentive to attract students to pursue careers related to computer science. We also will include small research projects related to computational biology and data mining in the computer science curricula. The assignments should have the character of an engineering project related to a computer application. Some significant steps in approaching these problems are: (i) a problem is given; (ii) the student prepares a written plan for solving the problem; (iii) the student builds a prototype; (iv) the student tests the prototype with the users; (v) the student refines the prototype in response to the testing; (vi) the student documents its results [5].Additionally, a new capstone course Applications in Linear Algebra and Vector Analysis has been designed for students at the community college. The course illustrates basic computing techniques in applied linear algebra including: dynamical systems modeled by linear differential equations, image processing, boundary value problems, and solution techniques such as Fourier Transform and Laplance Transform. These techniques are used in real-world problems which are encountered in applied mathematics, engineering, and science. The course also demonstrates the derivation of these mathematical techniques from fundamental mathematical principles.These innovations will be made more meaningful, even at the two-year colleges, by introducing honors courses for talented students who have demonstrated potential to excel. The objectives of these courses include: enhancing mathematical and scientific abilities, increasing awareness and interest in mathematical and science related career fields, encouraging student achievement, and instilling an appreciation and understanding of the social value of science and applied mathematics. Assessing which students are suitable for these courses is not necessarily restricted to looking at their GPA. Evaluations can also be made through other means, such as signs of creative performances or superb project presentations. 6.2 Applied Computer Science Program At both the community college (KCC) and the four year college (BC) we plan to develop an applied computer science degree with a concentration in biomedicine. As a first initiative at our community college we have already designed a bioinformatics bridge course that will be implemented in the Fall 2008. With the appropriate background, this course will prepare community college students to transfer to a senior four-year college to pursue an interdisciplinary computer science degree.
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CCSC: Eastern Conference 6.3 Integrated Science Programs Biotechnology Program: KCC and BC will be offering a jointly registered AS/BA/BS in Biotechnology Program starting in Fall 2008. During the four years of the Program, students’ studies will include basic computing technology, statistics, and mathematics through calculus. NSF is providing startup funding through an Advanced Technological Education grant. Other Federal/State/City government agencies should provide further funding to assist in placements of graduates from the Program into internships and jobs in the biotechnology industry. Biomedical Engineering Program: We are also in the process of creating a Biomedical Engineering Program at KCC. The students will take courses in the field of biomedicine and work with research mentoring faculty on independent research projects. To pursue their biomedical research careers further, they will subsequently transfer to schools of Biomedical Engineering. 7. REFERENCES 1. ACM/IEEE Joint Task Force for Computing Curricula, Overview Report, 2005. 2. Biomedical Information Science and Technology Initiative Prepared by Biomedical Computing Advisory Committee to the Director, June 3, 1999. 3. T. Bishop, “Gates Laments Decreasing Interest in Computer Science,” Seattle Post-Intelligencer Reporter, July 19, 2005. 4. C. Dubay, J. M. Brundedge, W. Hersh, and K. Spackman, Delivering Bioinformatics Training: Bridging the Gaps Between Computer Science and Biomedicine, Proceedings of the AMIA 2002 Annual Symposium, 2002, 220-224 5. P. Greespun, “What's Wrong With the Standard Undergraduate Computer Science Curriculum,” Internet 2004. 6. D. Gusfield, Algorithms on Strings, Trees, and Sequences. Computer Science and Computational Biology, Cambridge University Press, N.Y., 1997. 7. A. A. Lazakidou ed., Handbook of Research in Informatics in Healthcare and Biomedicine, Idea Group Inc., Hershey PA., 2006. 8. E. H. Shortliffe and J. J. Cimino ed., Biomedical Informatics. Computer Applications in Healthcare and Biomedicine, third ed., Springer, N.Y., 2006. 9. A. B. Tucker, Strategic Directions in Computer Science Education, ACM Computing Surveys, 28 (4), Dec. 1996. 10. UDDC, 2004. U.S. Department of Commerce, A Survey of the Use of Biotechnology in U.S. Industry, Executive Summary for the Report to Congress. 11. C. Van Loan. Introduction to Computational Science. Addison-Wesley, 1996. 12. M. Zhang, E. Lundak, C. Lin, T. Gegg-Harrison, and D.J. Francioni, “Interdisciplinary Application Tracks in an Undergraduate Computer Science Curriculum, SIGCSE'07, March 2007, Covington, Kentucky, ACM, 425-429.
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JCSC 24, 3 (January 2009) 13. J. L. Zimmerman, “Defining Biomedical Informatics Competency: The Foundations of a Profession,” Adv. Dent. Res., De. 2003, 17, 25-28.
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