M.S. in Computer Science (Bioinformatics Specialization)

The objective of the Master of Science in computer science with a bioinformatics specialization is two-fold:

1) to prepare graduate students for advanced professional practice as bioinformaticians or data scientists in bio-related fields, 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 only coursework. 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 and artificial intelligence (AI), databases and information retrieval systems. The program also builds a foundation in biosciences including microbiology, genetics, and molecular genetics, molecular phylogenetics, genomics, 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 A) is intended for students who wish to pursue a career in research or who are planning further graduate study. The coursework option (Option B) is generally recommended for students who plan on the MS being a terminal degree. Requirements for each option are given below. 

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/informatics/data sciences. 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 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 or 311

Data Structures & Algorithms

3

CSCE 4xx

Any Course in 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. 

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

To satisfy the breadth requirements each student must take at least two courses (6 credit hours) in each of the three tracks -theory; biosciences; applications. The course tracks are listed here

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.

Depth Requirements

To satisfy the depth requirement, the student must take Thesis credit hours plus the 900-level courses required for the option (see below) chosen. CSCE 896, CSCE 897, CSCE 898, CSCE 899, CSCE 996 courses taken as independent study courses usually count only towards the depth requirements. When CSCE 896 and 990 are taken as regular courses the student's supervisory committee may, if deemed appropriate, assign them to a track and they can be counted in the breadth requirements.

The total number of independent study type courses (CSCE 896, CSCE 897, CSCE 898, CSCE 899, and CSCE 996) counted toward the program may not exceed 9 credit hours. When CSCE 896 and 990 are taken as regular courses, they are not counted toward the 9-hour limit.

Option A (Thesis)

The requirements for this option may be satisfied by taking a total of 30 credit hours. The students who choose this option must complete a thesis under the supervision of a graduate faculty member in the CSE department. The thesis (CSCE 899) may be taken for 6-9 credit hours. The student is required to take at least 15 credit hours of graduate-only courses in Computer Science including thesis hours. 

Of the 30 hours, no more than 12 credit hours can include independent study type courses (CSCE 896, CSCE 897, CSCE 898, CSCE 899, CSCE 990, and CSCE 996). When CSCE 896 and 990 are taken as regular courses, they are not counted toward the 12-hour limit. Each student must take at least two courses (6 credit hours) in each of the three tracks -theory; biosciences; applications. See track listing for detailed information.

A typical plan for this option consists of 9 credit hours of regular courses for each of the first two semesters, a combination of regular courses, independent study (or research other than thesis) and thesis for 9 credit hours in the third semester and 3 credit hours of thesis in the final semester; however, the student should determine an exact program in consultation with the supervisory committee.

The student must submit a thesis based on the conducted research and pass an oral examination. The oral examination committee consists of three faculty members (three SoC bioinformatics faculty or two in SoC faculty and one life sciences faculty) approved by the Graduate Chair. The names of the committee members are suggested by the student in consultation with his/her advisor.

Additionally, the student must attend at least 15 departmental colloquia, doctoral oral presentations, and/or master's thesis presentations during the M.S. program. 

Summary of Requirements:

  • Total credit hours: 30
  • CSCE 899 (MS Thesis): 6-9 credit hours
  • Graduate-only courses: 15 credit hours (including CSCE 899 credit hours and at least 9 graduate-only courses credit hours)
  • Breadth: 6 credit hours in each of the three tracks (Theory, Biosciences, and Applications)
  • 15 colloquia, doctoral dissertation or master's thesis oral presentations
Option B (Courses Only)

The requirements for this option may be satisfied by taking a total of 30 credit hours of courses.  The program must include at least 15 hours of graduate-only courses, and at least 6 credit hours in each of the three tracks – Theory, Biosciences, and Applications. See track listing for detailed information. The courses must not include independent study type courses (CSCE 896, CSCE 897, CSCE 898, CSCE 899, CSCE 990, and CSCE 996). However, CSCE 896 and CSCE 990 may be taken as a part of the program when they are offered as regular courses. There is no research (thesis) requirement and there is no final examination. There is no advisor or supervisory committee in this option.  However, if a student does want some research experience, the student must find an advisor and can take 3 to 6 hours of independent study type courses.

A typical plan for this option consists of 9 credit hours of regular courses for each of the first three semesters, and 3 credit hours of courses in the final semester. A student may choose to take 3 credit hours in the summer and complete the program in one and a half years. 

Additionally, the student must attend at least 15 departmental colloquia, doctoral oral presentations, and/or master's thesis presentations during the M.S. program. 

Summary of Requirements:

  • Total credit hours: 30
  • Graduate-only courses: 15 credit hours
  • Breadth: 6 credit hours in each of the three tracks (Theory, Biosciences, and Applications)
  • 15 colloquia, doctoral dissertation or master's thesis oral presentations

Memorandum of Courses

The program of study is formally established by filing a “Memorandum of Courses” with the Office of Graduate Studies. The memorandum must be filed before the student has received grades in more than one-half of the prescribed program, in most cases this is before the end of the student's second semester in the MS program. The memorandum must be signed by the Advisor and submitted to the Graduate Secretary. It is then signed by the Graduate Chair, and finally by the Dean of Graduate Studies. The memorandum cannot be filed until the student has cleared all the deficiency courses listed in his or her Certificate of Admission.

Thesis Report

All students must complete a thesis under the supervision of a member of the graduate faculty. It is expected that the work done in a thesis has some original research contribution. It is expected that the work done in a thesis has some original research contribution and is of good quality.

The student is required to write the thesis in a standard style (Use the “Guidebook for Preparing your Thesis or Dissertation” available from the Office of Graduate Studies.) LaTeX templates are also available on the departmental computers.

Following the review by the advisor, copies of the thesis are given to the members of the supervisory committee. The student must give a copy to each committee member at least two weeks before the final oral examination. Students working on a thesis must also submit a copy to the Graduate Studies Office at least two weeks prior to the date of the oral examination.

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. 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 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 M.S. Thesis.

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 should upload an electronic version of the thesis/report to UNL Digital Commons. The student is required to make a hard-bound copy of the thesis/report to the advisor, unless the advisor chooses not to require one. It is also customary to offer each member of the supervisory committee a copy of the final report.

Visit unl.edu/gradstudies/current/degrees/masters#thesis for the Office of Graduate Studies' instructions on the final thesis preparation and uploading.