Applicable only to students admitted during the 2018-2019 academic year.

Bioinformatics

Interdepartmental Program
College of Letters and Science

Graduate Degrees

The Bioinformatics Program offers the Master of Science (M.S.) and Doctor of Philosophy (Ph.D.) degrees in Bioinformatics.

Admissions Requirements

Master’s Degree

Advising

All academic affairs for graduate students in the program are directed by the program’s faculty graduate adviser, who is assisted by staff in the Graduate Student Affairs Office. Upon matriculation, students are assigned a three-faculty guidance committee by the faculty graduate adviser.

The chair of the guidance committee acts as the provisional adviser until a permanent adviser is selected. Provisional advisers are not committed to supervise examination or thesis work and students are not committed to the provisional adviser. Students select a permanent adviser before establishing a comprehensive examination or thesis committee.

Areas of Study

Field 1: Bioinformatics

This field of study provides exposure primarily to biological and algorithmic advances in genomics, proteomics, and other related fields. Study consists of a core curriculum, computer science, mathematics, and statistics.

Field 2: Biomedical Informatics

This field of study exposes students to foundational concepts in clinical informatics and bioinformatics, providing a background in big data management and analysis. Study comprises of an introduction to computational methods, clinical and biomedical knowledge representation, and exposure to core bioinformatics topics.

Field 3: Computational & Systems Biology

This field provides for studies in the subfields of dynamic systems biology; systems bioinformatics; neurosystems; computers and biosystems; or biomedical systems. Core curricula consist of studies in applied mathematics, including probability and statistics; in engineering systems, including signals, feedback and control systems methodologies; in computer science; and in physiology and biochemistry. The curriculum is tailored to the subfield chosen by the student.

Foreign Language Requirement

None.

Course Requirements

Students must be enrolled full time and complete a minimum of 36 units (nine courses) of graduate (200 or 500 series) or upper division (100 series) course work for the master’s degree. Within this overall requirement, students must complete 20 units (five courses) at the graduate level for a letter grade. Of these five required graduate courses, four must be in the 200 series and one may be in the 200 or 500 series. Courses must be taken for a letter grade, unless offered on S/U grading basis only.

Field 1: Bioinformatics

Students must complete all of the following: (1) at least three of the following five core courses: Bioinformatics M221,  Bioinformatics M222, and Bioinformatics M223, Bioinformatics M224, Bioinformatics M225 (additional core courses may be used towards the requirement for three approved elective courses); (2) three approved elective courses; (3) enrollment in Bioinformatics 201 is expected throughout study for the master’s degree; (4) enrollment in Bioinformatics 596 research units, although no more than two courses (eight units) of 596 may be applied toward the requirements for a master’s degree.

Field 2: Biomedical Informatics

Students must complete all of the following: (1) three core courses Bioengineering M226, M227, and M228; (2) three approved elective courses; (3) Microbiology, Immunology, & Molecular Genetics C234; (4) 8 units of Bioinformatics 596; (5) 2 units of 200-level seminar or journal club courses approved by the program.

Field 3: Computational & Systems Biology (CASB)

All students must complete: MIMG CM234 or Biomathematics M261 (research ethics) and 8 units of Bioinformatics 596. Depending on the chosen subfield, students in this field are also required to take a minimum of 20 units of graduate course work and 8 units of upper division course work, chosen from the following lists (minimum 28 units):

CASB-Systems Biology Subfield

Students must complete all of the following: (1) 3 core courses chosen from: Physiological Science 125 (Molecular Systems Biology), Biomathematics 202, 204, 213, M220, M234, M270, Computer Science CM286, Mechanical and Aerospace Engineering 279 (Dynamics and Control of Biological Oscillations), Ecology & Evolutionary Biology 219A, and Chemical Engineering 246; and (2) approved elective choices chosen from: Biomathematics 106, 108A, Bioinformatics M223, MCDB 266C, Mathematics 134, 136, 151B, 171, Chemistry 153A; Molecular, Cell, & Developmental Biology 138, 144; Ecology & Evolutionary Biology 219B, Bioengineering 110; Chemical Engineering 145; Electrical Engineering 131B, 136.

CASB-Systems Bioinformatics Subfield

Students must complete all of the following: (1) 3 core courses chosen from: BioinformaticsM221, M222, M223, M224, M225, Physiological Science 125 (Molecular Systems Biology), Biostatistics 202; and (2) approved elective choices chosen from: Biostatistics M280, Biomathematics M234, Mathematics 113, 134, 151B, Computer Science 143.

CASB-Neurosystems Subfield

Students must complete all of the following: (1) 3 core courses chosen from: Physiological Science 125 (Molecular Systems Biology), Neuroscience M145, M148, M101C, M201, M203, M204, 205, Bioengineering M260, Mechanical and Aerospace Engineering 279 (Dynamics and Control of Biological Oscillations); and (2) approved elective choices chosen from: Electrical Engineering 113, 113D, 131B, 142, CM250, Mathematics 134, Psychology 119A, Chemical Engineering CM245.

CASB-Biomedical Systems Subfield

Students must complete all of the following: (1) 3 core courses chosen from: Pharmacology M248, Physiological Science 125 (Molecular Systems Biology), Ecology & Evolutionary Biology 219A, Bioengineering CM202, CM203, Physiological Science 166, Ecology & Evolutionary Biology 170; Biomathematics 220, 230, Computer Science CM286; and (2) approved elective choices chosen from: Mathematics 134, 136, 151B, 164, 171, Bioengineering 210, 220, Electrical Engineering 136.

CASB-Computers and Biosystems Subfield

Students must complete all of the following: (1) 3 core courses chosen from: Bioinformatics M221, M222, M223, M224, M225, Computer Science 240A, Statistics 201A, B, C, Physiological Science 125 (Molecular Systems Biology), 260A; and (2) approved elective choices chosen from: Computer Science 149, 150, 151B, 181, 213A, 214, 215, 219, 229S, 230, Statistics 101B, C.

Teaching Experience

Not required.

Field Experience

Not required.

Capstone Plan

The master’s capstone is an individual project in the format of a written report resulting from a research project.  The report should describe the results of the student’s investigation of a problem in the area of bioinformatics under the supervision of a faculty member in the program, who approves the subject and plan of the project, as well as reading and approving the completed report. While the problem may be one of only limited scope, the report must exhibit a satisfactory style, organization, and depth of understanding of the subject. A student should normally start to plan the project at least one quarter before the award of the M.S. degree is expected. The advisory committee evaluates and grades the written report as not pass or M.S. pass and forwards the results to the faculty graduate adviser.

Field 1: Bioinformatics

No additional requirements.

Field 2: Biomedical Informatics

No additional requirements.

Field 3: Computational & Systems Biology

The capstone plan is not available for students pursuing this field of study.

Thesis Plan

Every master’s degree thesis plan requires the completion of an approved thesis that demonstrates the student’s ability to perform original, independent research.

Field 1: Bioinformatics

Students must choose a permanent faculty adviser and submit a thesis proposal by the end of the third quarter of study. The proposal must be approved by the permanent adviser who served as the thesis adviser. The thesis is evaluated by a three-person committee that is nominated by the program and appointed by the Graduate Division. Students must present the thesis in a public seminar.

Field 2: Biomedical Informatics

The thesis plan is not available for students pursuing this field of study.

Field 3: Computational & Systems Biology

Students in the research-oriented Computation and Systems Biology Field 3 are required to follow the M.S. thesis plan, leading to successful completion of a master’s thesis prior to graduation.

Time-to-Degree

Field 1: Bioinformatics

Normative time-to-degree is five quarters.

Field 2: Biomedical Informatics

Normative time-to-degree is five quarters.

Field 3: Computational & Systems Biology

Normative time-to-degree is five quarters.

DEGREE	NORMATIVE TIME TO ATC (Quarters)	NORMATIVE TTD	MAXIMUM TTD
M.S.	3	5	5

Doctoral Degree

Advising

The Bioinformatics Advising Committee, chaired by the Faculty Graduate Advisor, functions to advise students during the first year and is available to students throughout their tenure of their study.

Upon entering their second year in the Bioinformatics IDP Program, students will select a mentor who will serve as their dissertation chair, research advisor, and primary graduate advisor.  Together the student and the mentor will convene a doctoral committee who will guide the student throughout their research, the University Oral Qualifying Exam, Doctoral Dissertation Defense, and will approve the final dissertation.

Major Fields or Subdisciplines

These fields include computer science, genomics, molecular evolution/comparative genomics, mathematics, neuroinformatics, proteomics and statistics.

Foreign Language Requirement

None.

Course Requirements

Students must complete all of the following: (1) at least three of the following five core courses: Bioinformatics M221, Bioinformatics M222, Bioinformatics M223, Bioinformatics M224, Bioinformatics M225 (additional core courses may be used towards the requirements for three approved elective courses; (2) MIMG C234; (3) Enrollment in Bioinformatics 201 is expected throughout the first two years; (4) Bioinformatics 202 in the Fall of the first year and the Spring of the first and second years; (5) three laboratory rotations (enrolling in six units of Bioinformatics 596 during each rotation;(6) students must complete three approved elective courses by the end of the second year.

Students are required to enroll full-time in a minimum of 12 units each quarter. In addition to basic course requirements, all students are required to enroll in Bioinformatics 596 or 599 each quarter.

Students who have gaps in their previous training may take, with their thesis adviser’s approval, appropriate undergraduate courses. However, these courses may not be applied toward the required course work for the doctoral degree.

Teaching Experience

One quarter of teaching experience is required by the end of the third year.

Written and Oral Qualifying Examinations

Academic Senate regulations require all doctoral students to complete and pass university written and oral qualifying examinations prior to doctoral advancement to candidacy. Also, under Senate regulations, the University Oral Qualifying Examination is open only to the student and appointed members of the doctoral committee. In addition to university requirements, some graduate programs have other pre-candidacy examination requirements. What follows in this section is how students are required to fulfill all of these requirements for this doctoral program.

All committee nominations and reconstitutions adhere to the Minimum Standards for Doctoral Committee Constitution.

Doctoral students must complete the core curriculum before they are permitted to take the written and oral qualifying examinations. Students are required to pass a written qualifying examination that consists of a research proposal outside of their dissertation topic and the University Oral Qualifying Examination in which they defend their dissertation research proposal before their doctoral committee. Students are expected to complete the written examination in the summer following the first year and the oral qualifying examination by the end of fall quarter of the third year. The written qualifying examination must be passed before the University Oral Qualifying Examination can be taken.

During their first year, doctoral students perform laboratory rotations with program faculty whose research is of interest to them and select a dissertation adviser from the program faculty inside list by the end of their third quarter of enrollment. By the end of their second spring quarter, students must select a doctoral committee that is approved by the program chair and the Graduate Division.

Written Qualifying Examination

The Written Qualifying Examination (WQE) must take place in the summer following the first year of doctoral study. In order to be eligible to take the WQE, students must have achieved at least two passing lab rotation evaluations, as well as at least a B average in all course work. Students are expected to formulate a testable research question and answer it, by carrying out a small, well-defined and focused project over a fixed one-month period. It must include the development of novel bioinformatic methodology. The topic and methodologies are to be selected by the student. The topic requires advance approval by the faculty committee, and may not be a project from a previous course, a rotation project, a project related to the student’s prior research experience, an anticipated dissertation research topic, or an active or anticipated research project in the laboratory of the student’s mentor. The WQE must be the student’s own ideas and work exclusively. Students are expected to complete a WQE paper of publication quality (except for originality), with a maximum length of 10 pages, single-spaced, excluding figures and references. This paper is submitted to the Student Affairs Office and graded by a faculty committee on a pass or no-pass basis. Students who do not pass the examination are permitted one additional opportunity to pass, which can take place no later than the end of the summer of the first year.

Oral Qualifying Examination

The University Oral Qualifying Examination must be completed and passed by the end of the fall quarter of the third year. Students prepare a written description of the scientific background of their proposed dissertation research project, the specific aims of the project, preliminary findings, and proposed bioinformatic approaches for addressing the specific aims. This dissertation proposal must be written according to NIH R-21 grant application format, with a maximum length of 6 pages, excluding references, and is submitted to the students’ doctoral committee at least 10 days in advance of the examination. Exclusive of their doctoral committee members, students are free to consult with their thesis adviser, or other individuals in formulating the proposed research. The examination consists of an oral presentation of the proposal by the student to the committee. The student’s oral presentation and examination are expected to demonstrate: (1) a scholarly understanding of the background of the research proposal; (2) well-designed and testable aims; (3) a critical understanding of the bioinformatic, mathematical or statistical methodologies to be employed in the proposed research; and (4) an understanding of potential bioinformatic outcomes and their interpretation. This examination is graded Pass, Conditional Pass, or Fail. If the doctoral committee decides that the examination reflects performance below the expected mastery of graduate-level content, the committee may vote to give the student a Conditional Pass. At the committee’s discretion, a student who receives a Conditional Pass will be required to modify or re-write their research proposal, so as to bring it up to required standard. In the case of a Conditional Pass, the student will be permitted to seek the advice of their committee in modifying or re-writing the proposal. Any required re-write or modification will be submitted to, and reviewed by the doctoral committee. The signed Report on the Oral Qualifying Examination & Request for Advancement to Candidacy will be retained in the Graduate Student Affairs Office until the student has satisfied the doctoral committee’s request for revision or re-write.

Advancement to Candidacy

Students are advanced to candidacy upon successful completion of the written and oral qualifying examinations.

Doctoral Dissertation

Every doctoral degree program requires the completion of an approved dissertation that demonstrates the student’s ability to perform original, independent research and constitutes a distinct contribution to knowledge in the principal field of study.

Final Oral Examination (Defense of the Dissertation)

Required for all students in the program.

Time-to-Degree

Students are expected to complete the written qualifying examination in the summer following the first year of study and the University Oral Qualifying Examination by the end of fall quarter of the third year. Normative time-to-degree is five years (15 quarters).

DEGREE	NORMATIVE TIME TO ATC (Quarters)	NORMATIVE TTD	MAXIMUM TTD
Ph.D.	7	15	22

Program Participation

Individual Development Plan:

Beginning with a mandatory training workshop in the first quarter of graduate study, students are required to generate an Individual Development Plan via myIDP Website: http://myidp.sciencecareers.org/ in order to map out their academic and professional development goals throughout graduate school. The myIDP must be updated annually, and the resulting printed summary discussed with and signed by (Year 1) the student’s advising committee member, or (Years 2-5) thesis adviser, and then turned in to the Graduate Student Affairs Office to be placed in the student’s academic file each year by June 1.

Annual Committee Meetings:

Beginning one year after advancement to doctoral candidacy, and in each year thereafter until completion of the degree program, students are required to meet annually with their doctoral committee. At each meeting, students give a brief, 30-minute oral presentation of their dissertation research progress to their committee. The purpose of the meeting is to monitor the student’s progress, identify difficulties that may occur as the student progresses toward successful completion of the dissertation and, if necessary, approve changes in the dissertation project. The presentation is not an examination.

Annual Progress Report:

All students are required to submit a brief report (a one-page form is provided) of their time-to-degree progress and research activities indicating the principal research undertaken and any important results, research plans for the next year, conferences attended, seminars given, and publications appearing or manuscripts in preparation. Annual Progress report must be submitted to the Bioinformatics IDP Student Affairs Office for review by the Program Director.

Termination of Graduate Study and Appeal of Termination

University Policy

A student who fails to meet the above requirements may be recommended for termination of graduate study. A graduate student may be disqualified from continuing in the graduate program for a variety of reasons. The most common is failure to maintain the minimum cumulative grade point average (3.00) required by the Academic Senate to remain in good standing (some programs require a higher grade point average). Other examples include failure of examinations, lack of timely progress toward the degree and poor performance in core courses. Probationary students (those with cumulative grade point averages below 3.00) are subject to immediate dismissal upon the recommendation of their department. University guidelines governing termination of graduate students, including the appeal procedure, are outlined in Standards and Procedures for Graduate Study at UCLA.

Special Departmental or Program Policy

Students must receive at least a grade of B- in core courses or repeat the course. Students who received three grades of B- in core courses, who fail all or part of the written or oral qualifying examinations twice (the examination committee determines the form of re-examination for students who fail all or part of the written examination), or who fail to maintain minimum progress may be recommended for termination by vote of the entire interdepartmental program committee. Students may appeal a recommendation for termination in writing to the interdepartmental program committee and may personally present additional or mitigating information to the committee, in person or in writing.