BNFO   201. Computing Skills and Concepts for Bioinformatics. 3 Hours.

Semester course; 3 lecture hours. 3 credits. Prerequisite: MATH   151 or 200 with a minimum grade of C, or satisfactory score on the VCU Mathematics Placement Test within the one-year period immediately preceding the beginning of the course. An introduction to computation in bioinformatics, including basics of data representation, and computer organization, as well as programming in PERL or other appropriate scripting language. Bioinformatics applications in the literature will be discussed. Guest speakers will share bioinformatics career experiences and opportunities.

BNFO   251. Phage Discovery I. 2 Hours.

Semester course; 4 laboratory hours. 2 credits. Corequisite: BIOL   151 or 152. An exploratory laboratory where students will purify phage from soil, visualize phage using electron microscopy and isolate genomic material for nucleic acid sequencing. Registration by override only. Crosslisted as: LFSC   251.

BNFO   252. Phage Discovery II. 2 Hours.

Semester course; 4 laboratory hours. 2 credits. Corequisite: BIOL   151 or 152. An exploratory laboratory where students will learn about the genomes of viruses infecting bacteria. Students will be given the genome sequence of a novel virus, which will be the basis for a series of computer-based analyses to understand the biology of the virus and to compare it with other viruses that infect the same host. Registration by override only. Crosslisted as: LFSC   252.

BNFO   292. Independent Study. 1-2 Hours.

Semester course; variable hours. 1-2 credits. May be repeated for a maximum total of 6 credits. Prerequisite: permission of instructor. A course designed to provide an opportunity for independent readings of the bioinformatics literature under supervision of a staff member.

BNFO   300. Molecular Biology Through Discovery. 3 Hours.

Semester course; 3 lecture hours. 3 credits. The course aims to expand students' "ignorance," a prerequisite for success in science, by confronting them with the interface between the known and the unknown, stressing the process by which the boundary is traversed. It will do so using as the raw material the study of molecular biology, an essential groundwork for bioinformatics.

BNFO   301. Introduction to Bioinformatics. 3 Hours.

Semester course; 3 lecture hours. 3 credits. Introduction to the basic concepts, tools and possibilities of bioinformatics, the analysis of large bodies of biological information. The course stresses problem-solving and integrative projects, making extensive use of exercises in class that draw on bioinformatics resources on the Web and on local servers. Graded as pass/fail. Crosslisted as: BIOL   351.

BNFO   380. Introduction to Mathematical Biology. 4 Hours.

Semester course; 3 lecture and 2 laboratory hours. 4 credits. Prerequisites: MATH   200 and BIOL   151, or permission of instructor. An introduction to mathematical biology. Various mathematical modeling tools will be covered and implemented in a range of biological areas. Additionally, the collaborative research process will be presented and discussed. Crosslisted as: MATH   380/BIOL   380.

BNFO   420. Applications in Bioinformatics. 3 Hours.

Semester course; 2 lecture and 2 laboratory hours. 3 credits. Prerequisites: CMSC   245 or 255 and BNFO   301. Capstone course. Students will integrate biological, computational and quantitative skills to complete bioinformatics projects in a professional team-problem-solving context. Course includes explicit instruction in the conduct of research as well as a review of applicable strategies, methods and technologies. Written and oral presentation is emphasized, with systematic feedback and practice opportunities provided.

BNFO   440. Computational Methods in Bioinformatics. 3 Hours.

Semester course; 2 lecture and 2 laboratory hours. 3 credits. Prerequisites: CMSC   255 and 256; BNFO   301, or permission of instructor. An introduction to mathematical and computational methods in bioinformatics analysis. Topics include but are not limited to operating systems, interfaces, languages, SQL, search algorithms, string manipulation, gene sequencing, simulation and modeling, and pattern recognition. Students will be exposed to Maple, Matlab, SPSS, E-cell, BioPerl, Epigram and C as part of the requirements of this course.

BNFO   491. Special Topics in Bioinformatics. 1-4 Hours.

Semester course; variable hours. 1-4 credits. Prerequisites: permission of instructor and adviser. An introductory, detailed study of a selected topic in bioinformatics unavailable as an existing course. Students will find specific topics and prerequisites for each special topics course listed in the Schedule of Classes. If multiple topics are offered, students may elect to take more than one. Adviser's approval is required for counting each special topics course toward meeting specific requirements of the B.S. program.

BNFO   492. Independent Study. 1-4 Hours.

Semester course; variable hours. A minimum of three hours of supervised activity per week per credit is required. 1-4 credits. May be repeated for a maximum total of 6 credits. Prerequisite: BIOL 218. Projects should include data collection and analysis, learning bioinformatics-related research techniques, and mastering experimental procedures, all under the direct supervision of a faculty member. A final report must be submitted at the completion of the project. Graded as pass/fail.

BNFO   496. Undergraduate Teaching Assistantship in Bioinformatics. 1-2 Hours.

Semester course; variable hours. 1-2 credits. May be repeated for a maximum total of 2 credits. Prerequisites: permission of instructor and a minimum grade of B in the course the student will TA. Student will work with course instructor to implement course objectives. Typical duties involve media preparation, answering questions, providing feedback on course assignments and peer mentoring. Provides exposure to the practice, possibilities, rewards and responsibilities of the act of teaching.

BNFO   497. Research and Thesis. 1-4 Hours.

Semester course; variable hours. A minimum of three hours of supervised activity per week per credit is required. 1-4 credits. May be repeated for a maximum total of 6 credits. Prerequisites: BIOL 218, junior or senior status. Projects should include data collection and analysis, learning bioinformatics-related research techniques, and mastering experimental procedures, all under the direct supervision of a faculty member. A written thesis of substantial quality is required at the completion of the research.

BNFO   501. Introduction to Physical Implementation of Databases. 1 Hour.

Semester course; 1 lecture hour. 1 credit. Prerequisite: permission of instructor. Basic searching and sorting algorithm design, and advanced data structures including hashing and B-trees.

BNFO   505. Essentials of Statistics in Bioinformatics. 2 Hours.

Semester course; 2 lecture hours. 2 credits. Prerequisites: Statistics and permission of instructor. An intensive course designed for graduate students in either the biology/genomics or the computational science tracks of the bioinformatics program, aimed at providing the background in statistical concepts necessary for them to participate in graduate-level courses involving statistics. The course will focus on areas of particular interest in bioinformatics, including probability, combinatorics and linear models.

BNFO   507. Essentials of Molecular Biology in Bioinformatics. 2 Hours.

Semester course; 2 lecture hours. 2 credits. Prerequisites: Cell biology and permission of instructor; Pre- or corequisite: Organic chemistry or permission of instructor. An intensive course designed for graduate students in either the quantitative/statistics or the computational science tracks of the bioinformatics program, aimed at providing the background in molecular biology necessary for them to participate in graduate-level courses involving molecular biology. The course will focus on areas of particular interest in bioinformatics, including DNA, RNA and protein synthesis, gene structure, function and regulation, protein structure, activity and regulation, and the tools by which formation in these areas has been discovered.

BNFO   508. Introduction to Bioinformatics Research. 2 Hours.

Semester course; lectures and 3 laboratory hours. 2 credits. Prerequisites: graduate status and permission of instructor. Introduction to all active research programs in bioinformatics. Presentations of research programs by investigators and rotation of students through track-appropriate faculty labs to gain direct exposure to individual research projects. Graded as S/U/F. Required of all first-year students pursuing the thesis option (M.S.).

BNFO   530. Bioinformatics and Genomics in Drug Research. 3 Hours.

Semester course; 3 lecture hours. 3 credits. Covers the basic elements of cellular pathways and drug interactions, and how modern genomics comes into play. Presents bioinformatics principles being used every day in data-intensive fields of research. Introductory and concept-oriented, the course will prepare students for grasping how bioinformatics is being used in many areas of biomedical sciences. Geared toward students coming from a variety of backgrounds in biology, biochemistry and chemistry. While many of the analytical approaches are statistical in nature, there is no requirement for a background in statistics or mathematics. Each student will have the opportunity to design a small project applying bioinformatics concepts. Crosslisted as: MEDC   530.

BNFO   540. Fundamentals of Molecular Genetics. 3 Hours.

Semester course; 3 lecture hours. 3 credits. Prerequisite: BIOL   310 or consent of instructor. The basic principles and methodologies of molecular biology and genetics are applied to genome organization, replication, expression, regulation, mutation and reorganization. Emphasis will be placed on a broad introduction to and integration of important topics in prokaryotic and eukaryotic systems. Crosslisted as: BIOL   540.

BNFO   541. Laboratory in Molecular Genetics. 2 Hours.

Semester course; 1 lecture and 4 laboratory hours. 2 credits. Pre- or corequisite: Molecular genetics. Experiments are designed to apply advanced techniques and concepts of molecular biology and genetics using prokaryotic and eukaryotic systems. Emphasis will be placed on experimental design, integrating results throughout the semester, making use of relevant published literature, scientific writing and providing hands-on experience with advanced equipment and methodologies. Crosslisted as: BIOL   541.

BNFO   591. Special Topics in Bioinformatics. 1-4 Hours.

Semester course; variable lecture hours. 1-4 credits. Adviser's approval is required for counting each special topics course toward meeting specific requirements of the master's program. An introductory, detailed study of a selected topic in bioinformatics unavailable as an existing VCU course. If multiple topics are offered, students may elect to take more than one. Graded as "S," "U" or "F." Students will find specific topics and prerequisites for each special topics course listed in the Schedule of Classes.

BNFO   592. Independent Study. 1-9 Hours.

Semester course; variable lecture hours. Variable credits. Determination of the amount of credit and permission of instructor, adviser and curriculum committee must be obtained prior to registration for this course. Designed to provide an opportunity for independent study at an introductory graduate level in a bioinformatics-related area of interest and significance to the student outside what is available through the courses and other options in the Bioinformatics Program. Graded as "S," "U" or "F.

BNFO   600. Basic Scripting Languages. 2 Hours.

Semester course; 2 lecture hours. 2 credits. Prerequisite: permission of instructor. Basics of programming in PERL or other appropriate scripting language.

BNFO   601. Integrated Bioinformatics. 3 Hours.

Semester course; 3 lecture hours. 3 credits. Prerequisite: permission of instructor. Presents major concepts in bioinformatics through a series of real-life problems to be solved by students. Problems addressed will include but not be limited to issues in genomic analysis, statistical analysis and modeling of complex biological phenomena. Emphasis will be placed on attaining a deep understanding of a few widely used tools of bioinformatics. Crosslisted as: BIOL   601.

BNFO   620. Bioinformatics Practicum. 3 Hours.

Semester course; 3 lecture hours. 3 credits. BNFO   601/BIOL   601 or permission of instructor. Practical application of bioinformatics to genomic, proteomic and pharmacogenomic analyses. Students will work in small groups to plan, develop and execute a project designed to solve practical challenges in the realm of bioinformatics. Proficiency in various aspects of bioinformatics will be developed.

BNFO   621. Business and Entrepreneurship Essentials for Life Scientists. 3 Hours.

Semester course; 3 lecture hours. 3 credits. Consists of presentations on the core concepts of business, including intellectual property, patents and patent law, entrepreneurship, launching a "start up," raising capital, financial management, marketing, managerial accounting, planning, and project management. Course includes lectures and discussions on core concepts of business and their real-world application. Students will develop a business plan and/or a plan to manage a research project. Business case studies and team projects with presentations are required. Focus is on the biotechnology and pharmaceutical industries.

BNFO   637. Networks Biology. 3 Hours.

Semester course; 2.5 lecture hours. 3 credits. Prerequisite: prior course work in cell biology or molecular biology, or permission of instructor. Covers in detail networks as a basic tool for the systems biology approach to biology and medicine, particularly on the molecular level. Qualitative and quantitative aspects of biological systems and processes will be identified and analyzed. The course focuses on the biochemical networks formed in the cell from genes, proteins and metabolites. Network structure and dynamics will be characterized proceeding from graph theory and other mathematical methods. Essential part of the course is the practical work with basic software for building, manipulation and analysis of biological networks, as well as for identifying structural motifs and modules, and comparative network organisms (human, drosphila, yeast, C. elegans).

BNFO   650. Sequence Analysis in Biological Systems. 3 Hours.

Semester course; 1 lecture and 2 laboratory hours. 3 credits. Prerequisite: BNFO   601/BIOL   601 or permission of instructor. This course will treat the computational theory behind algorithms that are used for nucleic acid and protein sequence analysis. Students will be exposed to the theory and methodology of computational biology that has led to the development of current sequence analysis software. The objective of the course is to provide students with a basic knowledge of how current software tools have been developed and how they function, which will permit them to then apply this knowledge to the development of new algorithms and technology.

BNFO   653. Advanced Molecular Genetics: Bioinformatics. 3 Hours.

Semester course; 3 lecture hours. 3 credits. Prerequisites: Cell/molecular biology or permission of instructor. An advanced course on contemporary bioinformatics. Topics covered include the principles and practice of DNA, RNA and protein sequence analysis, computational chemistry and molecular modeling, expression array analysis and pharmacogenomics. The course includes lectures, reading, computer lab, homework problem sets and projects. Crosslisted as: MICR   653.

BNFO   690. Seminars in Bioinformatics. 1 Hour.

Semester course; 1 lecture hour. 1 credit. Presentation and discussion of research topics of current interest in the field of bioinformatics. Graded as "S," "U" or "F.

BNFO   691. Special Topics in Bioinformatics. 1-4 Hours.

Semester course; variable hours. 1-4 credits. Adviser's approval is required for counting each special topics course toward meeting specific requirements of the master's program. An advanced, detailed study of a selected topic in bioinformatics unavailable as an existing VCU course. If multiple topics are offered, students may elect to take more than one. Students will find specific topics and prerequisites for each special topics course listed in the Schedule of Classes.

BNFO   692. Independent Study. 1-9 Hours.

Semester course; variable hours. Variable credit. Determination of the amount of credit and permission of the instructor, adviser and curriculum committee must be obtained prior to registration for this course. A course designed to provide an opportunity for independent study in a bioinformatics-related area of interest and significance to the student outside what is available through the courses and other options in the Bioinformatics Program.

BNFO   697. Directed Research in Bioinformatics. 1-9 Hours.

Semester course; variable hours. 1-9 credits. May be repeated for credit. Directed research leading to the M.S. degree in bioinformatics. Graded as S/U/F.

BNFO   700. Externship in Bioinformatics. 1,2 Hour.

Semester course; variable hours. 1 or 2 credits. Prerequisites: BNFO   601/BIOL   601 and BNFO   620, or permission of instructor. Typically off-campus planned experiences for advanced graduate students designed to extend professional competencies, carried out in a professional setting under supervision of an approved professional. Externship activities monitored and evaluated by university faculty. Plan of experience designed by extern and external adviser with prior approval of department. An externship class will meet weekly using online technology to accommodate students doing out-of-town summer externships. Each externship will be a defined project leading to a required final report or product and offering real potential benefits to the sponsoring company/lab. Subsequent to the externship, a presentation to program faculty and students is required.