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Undergraduate Catalog 2012

Bioinformatics and Computational Biology

Faculty

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Professors

Charles J. Bieberich
Thomas Cronin
Phillip J. Farabaugh
Lasse Lindahl
Phyllis R. Robinson
Suzanne O. Rosenberg
Phillip S. Sokolove
Richard E. Wolf, Jr.

Associate Professors

Daphne Blumberg
Rachel Brewster
Mauricio M. Bustos
Nessly C. Craig
David M. Eisenmann
Jeffery W. Leips
Tamra Mendelson
Stephen M. Miller
Kevin Omland
Harold J. Schreier

Assistant Professors

Ivan Erill
Maricel Kann
Weihong Lin
Bernard Lohr
Hua Lu
Michelle Starz-Gaiano

Senior Lecturers

Steven Caruso
Esther Fleischmann
Bryan MacKay
James W. Sandoz
Julia B. Wolf

Lecturers/Instructors

Lark Claassen
Reagan Lake
Sarah Leupen
Cynthia Wagner

Chemical and Biochemical Engineering

Mariajose Castellanos
Douglas D. Frey
Mark R. Marten
Govind Rao

Chemistry And Biochemistry

Bradley R. Arnold
C. Allen Bush
Richard L. Karpel
Michael F. Summers

Computer Science and Electrical Engineering

Hillol Kargupta

Mathmatics and Statistics

Kathleen Hoffman
Florian Potra

Senior Research Scientist

Janice Zengel

Information Systems

Anthony F. Norcio
Carolyn Seaman

Courses in this program are listed under BIOL and MATH and STAT and CHEM and PHYS and CMSC .

This program offers comprehensive training in the fields of Bioinformatics and Computational Biology by combining courses in the areas of biology, chemistry, physics, computer science and mathematics. Graduates will acquire the necessary skills for automated querying and data analysis using complex databases, extraction of essential information from genomic and proteomic data, modeling of biological systems, as well as the design and development of software and algorithms to support these activities. Students also have the opportunity to engage in independent research in the lab, the field or off-campus, working one-on-one with a faculty mentor. The curriculum consists of 88-92 credits in biology, computer science and related disciplines (chemistry, information systems, mathematics and physics), complemented by two specific courses on Bioinformatics and Computational Biology. This program is appropriate for any student desiring a rich and multidisciplinary grounding in all the essential elements of bioinformatics and computational biology.

Career and Academic Paths

An undergraduate degree in bioinformatics and computational biology from UMBC provides students with an excellent background for employment in industry, academics, government or for graduate studies in the areas of bioinformatics, biology, computational biology or molecular biology. For specific requirements regarding graduate programs, students should consult the Graduate Catalog of the institution they are interested in attending. Major itineraries and their associated career pathways are outlined in the requirements worksheet for the Bioinformatics and Computational Biology requirements worksheet.

Academic Advising

Bioinformatics and computational biology majors who have not yet completed their gateway requirements will be advised by the undergraduate academic advisor for life sciences (see the description of degree requirements for details regarding the gateway). Subsequently, they will be assigned to one of the full-time faculty for advising. Students are required to see their advisors at least once each semester. Academic progress is monitored through graduation.

Bachelor of Science (B.S.)

The B.S. curriculum consists of 88-92 distributed as follows:

A. Biology 29

  • BIOL 141 - Foundations of Biology I
  • BIOL 142 - Foundations of Biology II
  • BIOL 300L - Experimental Biology Lab
  • BIOL 302 - Molecular & General Genetics
  • BIOL 303 - Cell Biology
  • BIOL 430 - Biological Chemistry
  • BIOL 313 - Introduction to bioinformatics
  • BIOL 495 - Seminar in Bioinformatics +

B. Chemistry 11

  • CHEM 101 - Principles of Chemistry I
  • CHEM 102 - Principles of Chemistry II
  • CHEM 351 - Organic Chemistry I

C. Physics & Math 19

  • PHYS 121 - Introductory Physics I
  • MATH 151 - Calculus & Analytical Geometry I
  • MATH 152 - Calculus II
  • MATH 221 - Linear Algebra
  • STAT 355 - Intro to Prob & Stats for Sci/Eng

D. Computer Science 17

  • CMSC 201 - Computer Science I for Majors
  • CMSC 202 - Computer Science II for Majors
  • CMSC 203 - Discrete Structures
  • CMSC 341 - Data Structures
  • CMSC 461 - Database Management Systems

E. Electives 12-16

  • 1 List A Elective
  • 1 List B Electives
  • 2 List A/B Electives

List A Electives

Any List A recommended course or any BIOL 4xx / CHEM 4xx course approved by a BINF advisor.

Recommended list A electives:

  • BIOL 304 - Plant Biology
  • BIOL 305 - Comparative Animal Physiology §
  • BIOL 411 - Bacterial Physiology
  • BIOL 414 - Eukaryotic Genetics and Molecular Biology
  • BIOL 418 - Human Molecular Biology
  • BIOL 426 - Approaches to Molecular Biology
  • BIOL 428 - Computer Applications in Molecular Biology
  • BIOL 434 - Microbial Molecular Genetics
  • BIOL 442 - Developmental Biology
  • BIOL 444 - Development and Cancer
  • BIOL 466 - Population and Quantitative Genetics
  • BIOL 483 - Evolution: From Genes to Genomes
  • BIOL 486 - Genome Science
  • CHEM 301 - Physical Chemistry
  • CHEM 303 - Physical Chemistry for the Biochemical Sciences
  • CHEM 352 - Organic Chemistry II
  • CHEM 420 - Computer Applications in Chemistry
  • CHEM 431 - Chemistry of Proteins
  • CHEM 432 - Advanced Biochemistry
  • CHEM 433 - Biochemistry of Nucleic Acids
  • CHEM 438 - Comprehensive Biochemistry II
  • CHEM 455 - Introduction to Biomedicinal Chemistry
  • CHEM 444 - Molecular Modeling in Biochemistry 

List B Electives

Any List B recommended course or any CMSC 4xx / IS 4xx / MATH 4xx / STAT 4xx course approved by a BINF advisor and the corresponding department/instructor.

Recommended list B electives:

  • CMSC 433 - Scripting Languages
  • CMSC 441 - Design and Analysis of Algorithms
  • CMSC 442 - Information and Coding Theory
  • CMSC 445 - Software Engineering
  • CMSC 453 - Applied Combinatorics and Graph Theory
  • CMSC 455 - Numerical Computations
  • CMSC 471 - Artificial Intelligence
  • CMSC 472 - Knowledge - Based Systems
  • CMSC 473 - Introduction to Natural Language Processing
  • CMSC 475 - Introduction to Neural Networks
  • CMSC 476 - Information Retrieval
  • CMSC 478 - Introduction to Machine Learning
  • IS 413 - GUI Systems Using JAVA
  • IS 428 - Data Mining Techniques and Applications formally
  • IS 448 - Markup and Scripting Languages
  • MATH 341 - Computational Methods
  • STAT 419 - Introduction to Biostatistics
  • STAT 420 - Statistics for Bioinformatics
  • STAT 432 - Statistical Computer Packages and Their Applications
  • STAT 433 - Statistical Computing
  • STAT 451 - Introduction to Probability Theory
  • STAT 453 - Introduction to Mathematical Statistics
  • STAT 454 - Applied Statistics
  • STAT 614 - Environmental Statistics

A majority of the required biology courses must be completed in residence at UMBC. In fulfilling major requirements in Bioinformatics and Computational Biology, a student must obtain a grade of “C” or higher in all required courses used to fulfill major requirements for the B.S. Under certain circumstances and after petitioning, students may be able to graduate with a grade of “D” in a single (not retaken) course, provided that they have an overall “C” average in all required courses upon approval of the Undergraduate Committee of the Department of Biological Sciences. Prerequisites and co-requisites for all courses will be enforced. Prerequisites must be satisfied with a grade of “C” or better. Students will be allowed only two attempts to earn a grade of “C” or better in all required biology (BIOL XXX) courses. Students who have not earned a grade of “C” or better (including a grade of “W”) after two attempts will no longer be eligible for the B.S. in Bioinformatics and Computational Biology, and must change their major. The department will adhere to university policies that limit to two the number of times a student may register for the same course.

Gateway requirements

Students must complete the courses below with a Grade Point Average (GPA) no lower than 3.0 and with no grade lower than “C” in any of the courses. At least three of these courses must be completed at UMBC. A course may be repeated once to meet gateway requirements, but both grades will be used to compute the gateway GPA. (e.g. a student receiving a grade of “B” in all six gateway courses with one enrollment in each course will have a gateway GPA of 3.0. A student receiving an initial grade of “C” and a repeated grade of “B” in CHEM 101, with a “B” in all other gateway courses, will have a gateway GPA of 2.86).

BIOL 141 - Foundations of Biology I

BIOL 302 - Molecular and General Genetics           

CHEM 101 - Principles of Chemistry           

CHEM 102 - Principles of Chemistry II

CMSC 201 - Computer Science I for Majors

MATH 151 - Calculus & Analytical Geometry I

Students who do not meet the above criteria (e.g. transfer students who transfer in more than three of the above courses) may petition the BINF steering committee for admission to the program.

Honors Program

Bioinformatics and computational biology majors who have completed the following requirements will be eligible to enter the Biological Sciences Departmental Honors Program. The following courses, or acceptable transfer equivalents thereof, must have been completed with a cumulative GPA of 3.5: BIOL 141, 142, 302, 303, 302L or 303L; CHEM 101, 102, 102L, 351; MATH 151 and STAT 355. Additionally, the student must maintain a minimum GPA of 3.5 in the major and 3.25 overall.

This program, in addition to the regular requirements for the major, includes the following nine credits of coursework:

  • BIOL 499H Honors Independent Research (Two semesters for a minimum total of six credits)
  • BIOL 497H Honors Capstone (One semester)

Eligible students should apply to the Biological Sciences Departmental Honors Committee. Forms are available in the biological sciences office.

Special Opportunities

Talented upper-class undergraduates committed to performing quality independent research are encouraged to apply for a variety of research opportunities offered by UMBC’s outstanding faculty. Under the guidance of faculty mentors, student research assistants work on their own lab research projects and help their mentors with important research. These unique, intensive experiences allow students to sharpen their critical thinking skills, learn how to write and read scientific papers, and expand their scientific understanding of computational biology concepts.

Tutorial Center

Bioinformatics students are invited to use the facilities of the Biological Sciences Tutorial Center, located in room 011 of the Biological Sciences Building. The center has 12 computer workstations for student use and two workstations for faculty. The center is open for students to study in groups and to access course Web pages and other information on the Web. Tutors are available for the biology core courses (Concepts of Biology, Ecology and Evolution, Molecular and General Genetics, Cell Biology, Plant Biology and Animal Physiology).

Student Organizations

Biology Council of Majors (BIO/COM) All bioinformatics majors are welcome to join the Biology Council of Majors (BIO/COM). This very active student organization strives to promote the achievement of the professional ambitions of its members and to serve as a means of social contact among them.