M.S. in Computer Science (Bioinformatics Specialization)

The objective of the Master of Science in Computer Sciences with a Bioinformatics specialization is two-fold: 1) to prepare graduate students for advanced professional practice as bioinformaticians, and 2) to prepare graduate students for doctoral studies in bioinformatics. The program will prepare graduate students through classroom, laboratory instruction and research/project experiences based in math, computer science and engineering and biosciences. Students will be required to do a masters thesis or a master’s project. Students who want to pursue doctoral studies will be strongly encouraged to do a masters thesis. Internships with local companies will be encouraged and may be taken for credit of up to 3 course hours. The proposed specialization integrates instructional topics, problem solving, communication and teamwork.

The program focus is on advanced knowledge and skills in Design and Analysis of Algorithms, Graph Theory applications to Bioinformatics, Machine Learning, Databases and Information Retrieval systems. The program also builds a foundation in Biosciences including Microbiology, Genetics and Molecular Genetics, Molecular Phylogenetics, and Genetic Engineering. Particularly in the lab, students are expected to develop problem solving abilities, written and oral communication proficiency, and team and organizational skills. Flexibility within the program allows students to pursue a variety of related topics, such as Database and Information Systems, Computer Networking, Structural and Algorithmic Graph Theory, Information Integrity and Security, Genetic Engineering and Molecular Biology. With these attributes, graduates are prepared for pursuing doctoral studies or to take leadership positions in the bioinformatics industry.

Degree Options

Two options are available for the Master's degree in Computer Science with a Bioinformatics Specialization. Every student should discuss his/her program with an advisor before deciding on an option. The thesis option (Option I) is intended for students who intend to pursue a career in research or for those planning further graduate study. The project option (Option III) is generally recommended for students who plan on the MS being a terminal degree. Both thesis and project option students will work with a supervisory committee of three faculty members who will oversee the work and review the student's final report. A final oral exam is required of all students.

Admission Requirements

Applicants must have a Bachelor of Science degree in Bioinformatics or a Bachelor of Science degree in Computer Science and a minor in Biology, or a Bachelor of Science degree in Biology (or Master of Science in a related field, e.g. Agronomy) and a minor in Computer Science. However, students with background in only one of the two areas will also be considered for provisional admission if they have a good academic record.

The applicant shall have taken courses equivalent to the prerequisite courses listed in Table 1. An applicant who has not had all of the required background courses may be provisionally accepted and required to take the remaining courses as deficiencies. Deficiency courses (and any prerequisites thereto) may not be taken for graduate credit toward this degree. A minimum grade of B or better is required for every deficiency course.

Table 1: Required Prerequisite Courses

Course Number Course Cr. Hours
CSCE 156 Intro to Computer Sci II 3
CSCE 230 Computer Organization 3
CSCE 235 Intro to Discrete Structures 3
CSCE 310 Data Structures & Algorithms 3
CSCE 4xx Any Course in CSE Systems Track 3
MATH 106 Analytic Geometry and Calculus I 5
MATH 107 Analytic Geometry and Calculus I 5
MATH 314 Applied Linear Algebra 3
STAT 380 Statistics and Applications 3
BIOS 102 or BIOS 206 Cell Structure and Function or General Genetics 3
BIOS 431 or BIOC 321 Biomolecules and Metabolisms or Elements of Biochemistry 3

Course Requirements

The courses listed in Table 2 constitute required core courses. The requirement for a specific required course is considered satisfied if its 400-level counterpart was taken prior to admission into this degree program. In that case, the 800-level course may not be taken for degree credit. However, if the 400-level counterpart was not taken prior to admission, then the 800-level course must be taken, and counts toward the credit-hour requirements described in Subsections on Option I and Option III.

Table 2: Required Core Courses

Course Number Course Cr. Hours
CSCE 823 Design and Analysis of Algorithms 3
CSCE 871 Introduction to Bioinformatics 3
BIOS 820 or BIOC 831 Molecular Genetics or Biochemistry 4

Breadth Requirements

A student must take at least two courses in each track. There are three tracks of courses: Theory, Biosciences and Applications. The course tracks are listed here. Breadth requirements are the same for both options. The breadth requirement can be satisfied if the 400 level counterpart of any course was taken prior to admission. When CSCE 896 and 990 are taken as regular courses, the graduate committee may assign them to a track so they can fulfill breadth requirements. Any such course not so assigned cannot apply towards breadth requirements. In addition, CSCE 897, CSCE 898, CSCE 899, and CSCE 996 do not apply towards the breadth requirements.

Additionally, the student must attend at least 15 departmental colloquia, doctoral oral presentations, and/or master's thesis presentations during the M.S. program. A sign-up sheet is used during these events as proof of attendance. Note that master's project presentations may not be used to fulfill this requirement.

Depth Requirements

To satisfy the depth requirement, the student must take Thesis or Project credit hours plus at least 9 (15 for non-thesis option) credit hours of 900-level courses (or 800-level courses with no 400-level component). Within any single track, a maximum of 18 credit hours may be counted toward the degree. The total number of independent study-type courses (e.g. CSCE 896, CSCE 897, CSCE 898, CSCE 899, CSCE 990, CSCE 996) should not exceed 9 credit hours. When CSCE 896 and 990 are taken as regular courses, they do not count toward the 9-hour limit.

Thesis Option (Option I)

The requirements for this option may be satisfied by taking a total of 24 credit hours of regular courses. In addition, the student must complete a thesis under the supervision of a graduate faculty member in the department. The thesis (CSCE 899) contributes another 6 credit hours for a total of 30 credit hours. The student is also required to take at least 9 credit hours of advanced courses (900-level) in Computer Science.

A typical plan for this option consists of 9 credit hours of regular courses for each of the first two semesters, 6 credit hours of courses and an independent study (or research other than thesis) in the third semester and 6 credit hours of thesis in the final semester; however, the student should determine an exact program in consultation with the supervisory committee.

The supervisory committee for a student working on a thesis consists of three computer science faculty members approved by the graduate committee. The names of the committee members are suggested by the student in consultation with his/her advisor.

Thesis Option Requirements:
  • 24 credit hours of regular courses
  • A thesis (6 additional credit hours)
  • Total = 30 credit hours (at least 9 of which must be 900 level courses in Computer Science)

Project Option (Option III)

The requirements for this option may satisfied by taking a total of 36 credit hours. The program must include at least 3 credit hours, but no more than 6 credit hours of CSCE 897 (Masters Project). This course can not be taken with P/N option. The student must also complete a project under the supervision of a graduate faculty member in the department. The project (CSCE 897) contributes 3-6 of the 36 credit hours. The student is also required to take at least 15 credit hours of advanced courses (900-level) in Computer Science if a 6-hour MS project is presented and at least 18 credit hours if a 3-hour MS project is presented.

A typical plan for this option consists of 9 credit hours of regular courses for each of the first three semesters, and 3 (or 6) credit hours of courses and 6 (or 3) credit hours of project in the final semester.

The supervisory committee for a student working on a project consists of three computer science faculty members approved by the Computer Science Graduate Committee. The names of the committee members are suggested by the student in consultation with his/her advisor.

Project Option Requirements:
  • 30-33 credit hours of regular courses
  • A project (3-6 additional credit hours)
  • Total = 36 credit hours (12-15 hours must be 900-level courses in Computer Science)

Supervisory Committee

The examination committee for the MS degree in Computer Science with the bioinformatics specialization follows the same guidelines as for the regular CSE MS program. The MS examination committee must include two CSE faculty members, and must include at least one life-sciences faculty.

Final Oral Examination

A final oral examination is required for all students. The student must file a “Final Examination Report for Master's Degree” form at least four weeks before the required oral examination in their last semester of study. The oral examination will be scheduled for two hours and consist of a defense of the thesis or the project. The presentation is open to the public and the student is required to give an abstract (electronic copy) to the office to be used for advertising. After the public presentation and a question-and-answer period, the remainder of the examination is conducted privately by the supervisory committee. The examination is based on the thesis/project and other course work.

The supervisory committee may require the student to do additional work and the advisor is generally responsible for making sure that the work is completed. The advisor decides on the grade of the MS Thesis/Project.

Final Report

The student is expected to make the changes recommended by the supervisory committee and prepare a final copy of the thesis/report. The student is required to give a hard-bound copy to the advisor as well as the departmental office. It is also customary to offer each member of the supervisory committee a copy of the final report. Students doing a thesis must also submit two unbound copies to the Library.