Bylaws

Article I. Objective

A. Degree(s) offered by the program

PhD

B. Discipline: A brief statement on the discipline(s) of the program

The Biological and Medical Informatics (BMI) Graduate Program at the University of California, San Francisco (UCSF) trains diverse students to become scientific leaders at the interface between computation, statistics, biology, and medicine. The program equips PhD students with skills and knowledge in computer science, clinical informatics, statistics, machine learning, physics, chemistry, and biology to study the structure, function, and evolution of biological systems across molecular, cellular, and systems levels in health and disease. These quantitative skills are essential for scientific progress given the massive biological and clinical data sets being generated across domains.

C. Mission of the program

The goal of the program is to train the next generation of biological and medical informatics researchers for academia and industry. Students are trained to gather, store, analyze, predict, and disseminate their data, results, and algorithms in rigorous, open, and reproducible pipelines.

Article II. Membership

A. Criteria for membership in the graduate program

The Executive Committee has authority to define criteria for faculty membership in the BMI program, including criteria for inclusion, exclusion, and removal, unless otherwise specified. Further, the Executive Committee has authority to propose and administer bylaws governing faculty participation and conduct. Membership is independent and separate from academic department appointments. Membership is based upon disciplinary expertise and active research, so members throughout campus are eligible for consideration to membership in the group.

B. Voting rights

Graduate program matters will be determined by a vote of the Executive Committee. All members of the Executive Committee will have an equal vote.

C. Application for membership

1. Types of BMI faculty membership: There are two types of membership in the BMI Program: core and affiliate. Core faculty may be primary mentors of BMI PhD students and receive full high-performance computing privileges. They additionally have priority for student funding, pizza talk slots, and other opportunities. Affiliate faculty may co-mentor BMI PhD students with a core faculty member. Their students receive high-performance computing privileges, but the lab does not get additional resources beyond student quotas.

2. How faculty may apply:

   To become a member of the BMI Program, faculty must formally apply to the program by email to the Program Manager and Program Director(s) and have their application approved by the BMI Executive Committee. Membership in the BMI training program is considered a privilege and a responsibility. Faculty should submit their CVs and a short description elaborating: 1) how they will be active participants in the program; 2) their ability to mentor students on computational projects; 3) their available resources to financially support students; and 4) whether they want to be Core or Affiliate members. (See anticipated contributions below). A Core BMI faculty member must also support the nomination.

3. Transitioning between core and affiliate membership. Faculty may transition between core and affiliate membership by submitting the application materials outlined above with explanation of the motivation for the change to the Program Manager and Program Director(s). The change in membership must be approved by vote of the Executive Committee.
4. Anticipated contributions that all graduate faculty members will perform as a member.
   1. Participation in program activities: Faculty in the BMI program are expected to demonstrate their commitment to the training program by regularly participating in program activities. These may include teaching in courses, serving as a coach for the journal club series, serving as an academic advisor, serving on thesis and qualifying examination committees, outreach and other activities that promote diversity and inclusivity in the BMI program, participating in recruitment and interviews, regular attendance at program events, and BMI committee service.
   2. Mentoring and teaching in the lab: Program faculty are expected to maintain a productive and inclusive training environment for thesis students. Relevant measures may include evidence that the laboratory environment is welcoming to and supportive of trainees from all backgrounds; that lab students produce rigorous and reproducible publication-worthy research; that research is conducted in the spirit of open science including depositing work on preprint servers and publishing in open-source journals, when appropriate; that lab students complete their degrees in a timely manner; and that students successfully transition into careers in the scientific workforce.
   3. Participation in faculty mentor development activities: Program faculty must regularly participate in mentoring training and development activities. Specifically, each faculty member with a BMI student in their lab must take part in at least one mentorship development activity of their choosing each year. Faculty must have met this requirement to host a rotation student. Typically, an “activity” will be a university-sponsored training program, such as the courses offered by the Graduate Division (mentoring.ucsf.edu/trainings). However, the development of strong mentorship skills is an ongoing process that extends beyond any single course, and faculty are encouraged to seek mentorship development opportunities in different ways. Faculty who undertake significant activities outside of the University-sponsored training may petition the program to allow these activities to satisfy the mentor development activity requirement in a given year.

   4. Core faculty roles and expectations: Core members must have deep expertise in bioinformatics and/or computational biology for teaching and mentoring BMI PhD students. Each year they must participate in:

      1. At least one mentoring/diversity training (organized and recorded by the Graduate Division).

      2. At least two of the following activities: coaching journal club; participating in student recruiting by interviewing candidates, giving talks if invited, attending events; or serving on qualifying exam, mini-qual, and/or thesis committees.

      3. At least one of the following: Teach a BMI course or mini-course (1+ week of class) or another course with significant BMI registration (>1 BMI student per year). Serve on one or more of the following BMI committees: Executive Committee, Admissions Committee, Curriculum Committee, Student Success Committee, Committee for Building and Sustaining Diversity, Equity, and Inclusion (IDEA), or significantly contribute to graduate education beyond BMI (e.g., direct another PhD program).

   5. Affiliate faculty roles and expectations: Each year affiliate faculty must participate in at least two of the following activities: coaching journal club; participating in student recruiting by interviewing candidates, giving talks if invited, attending events; or serving on qualifying exam, mini-qual, and/or thesis committees.

5. Compliance with University policies and Program values

   Program faculty are expected to comply with all university policies and uphold the values of the training program, including but not limited to the University Code of Conduct (APM-016) (PDF, 7 pages, 182 KB); UC Policy on Sexual Violence and Sexual Harassment; the UC Policy on Discrimination, and the Harassment, and Affirmative Action in the Workplace; scientific misconduct and/or financial improprieties.

D. Emeritus status

Emeritus faculty with active research programs may remain members of the program and are afforded the following rights: they may attend and participate in program activities (including meetings and administrative committees), may teach graduate courses, and may serve on student committees. Emeritus faculty on the Executive Committee may vote on policy and bylaw issues related to the program.

E. Review of membership

The criteria for reviewing members of the program is the same for all members. Each faculty member’s contributions to the program shall be reviewed once every three years for the purpose of identifying faculty members who are not providing an acceptable level of service to the program.

1. Obtaining relevant information

   To ensure compliance with these requirements, the Program Director(s) and Executive Committee need to have the relevant information about faculty conduct. Given the different types and sources of information that are needed, the BMI Program will track compliance with these requirements in multiple ways, including data from the Graduate Division and University, surveys, and conversations with faculty and students.

2. Violations of program expectations for faculty conduct

   The Graduate Program Directors, Executive Committee, and Program Coordinators are in frequent communication with trainees, faculty, the Graduate Division, and the University administration to monitor for compliance with all membership policy requirements. This can include reports from the Bias Response Team (once it has been established) or other communications from the Graduate Division, and communications from the University administration about faculty violations of the University Code of Conduct. The Executive Committee will promptly revoke program membership upon learning about faculty conduct detrimental to the program or the safety and welfare of its members. Examples of evidence of this type of detrimental conduct include (but are not limited to), official findings by the University that a faculty member has violated Title VII or IX, or legal determinations of guilt (including settlements out of court) that may not have resulted in a University sanction.

   In addition, faculty may also be put on suspension or removed from the program for conduct that has not resulted in a University or legal sanction but nonetheless has been determined by the Executive Committee to be detrimental to the program or the safety and welfare of its members. This may include serious or sustained actions that create a hostile work environment such as a pattern of racist, sexist, or homophobic remarks or behavior, or a significant lack of professionalism or integrity. The BMI program expects all its faculty members to represent and uphold UCSF values of Professionalism, Respect, Integrity, Diversity and Excellence.

   The Executive Committee will develop a course of action on a case-by-case basis. For example, faculty who are found to have violated Title VII or IX will be removed from the program immediately and are generally not eligible to reapply (but may appeal as outlined in Section II.F). The plan of action to address less severe violations may include interventions by program leadership, mediation, additional training, etc. before a decision to suspend or remove a faculty member from the program is reached. In any of these cases, the program may seek guidance from University offices and resources, such as the Office of Academic Affairs, the Office of the Ombuds, and the Graduate Division.

F. Membership appeal process

If membership is denied or not renewed, faculty can appeal to the Executive Committee for reconsideration. Majority vote of the Executive Committee will determine the outcome.

Article III. Administration

The administration of the program and its activities will be vested in the Program Director(s), Program Manager, and the Executive Committee.

Article IV. Graduate Program Director

A. Director appointment process

When a Program Director position is open, nominations will be sought from the BMI community. The graduate Program Director will be selected in consultation with the Executive Committee and approved by a 2/3 vote of the Executive Committee. The Executive Committee may decide that the program would benefit from having co-Directors or an Associate Director. In such cases, the appointment, terms, and review will be conducted as for the Director.

B. Director terms of service

The Director commits to serving a four-year term unless extenuating circumstances call for a shorter term. Program Directors will be renewed every four years by vote of the Executive Committee. There is no limit on the number of terms a Program Director may serve, and it is expected that they will serve multiple terms to ensure stable administration and program continuity. If there are concerns about a Program Director, the Executive Committee will meet with the Program Director, raise the concerns, and give an opportunity for the Program Director to respond to the concerns. The Executive Committee (excluding the Director under review) may remove a Program Director after this hearing with a 2/3 vote.

C. Duties of the director(s)

The Director(s): a) provides overall academic leadership for the program; b) develops and implements policies for the program; c) represents the interests of the program to the campus and University administrators; d) calls and presides at meetings of the Executive Committee; e) calls and presides at meetings of the program; f) is responsible for coordinating all administrative matters with the Graduate Division and the program administrators; g) provides guidance on the use of program funds; h) takes responsibility for the submission of competitive and non-competitive renewals of the training grant, if applicable (and is often the Lead PI of the training grant); i) submits course change or approval forms; and j) is responsible for the accuracy of all publications related to the program including web pages and catalog copy. If the program has Co-Directors or an Associate Director, the distribution of these responsibilities will be determined by the Directors at the start of each academic year, in consultation with the Program Manager and Executive Committee if necessary. Any disagreements will be resolved by vote of the Executive Committee.

D. Duties of the program manager

The Program Manager’s job duties are defined by their manger(s) in the home department in consultation with the Program Director(s).

Article V. Committees

A. Executive Committee

The Executive Committee shall consist of the Program Director(s) plus at least five faculty selected from the Core membership, and one student who has advanced to candidacy. The student member is nominated by the students (including self-nominations) and selected by the Executive Committee. All members have voting rights, including the student representative, unless the student does not participate in the discussion due to the nature of the topic (see below). The faculty members of the Executive Committee shall be elected for a three-year term, which is renewable. The student member will serve a one-year term and may be re-nominated.

Election of faculty members of the Executive Committee: Upon an Executive Committee vacancy, nominations will be sought from the Core BMI members. Candidates can self-nominate by e-mail to the Program Director(s) or the Program Manager. Elections will be conducted by a vote of the Executive Committee.

The principal duties of the Executive Committee are to: determine and implement policy for the good of the program, determine program membership, and represent the interests of the program generally to various universities and other agencies. This committee has responsibilities and authorities over all other committees. The primary roles of the Executive Committee are to facilitate decision making on programmatic changes as needs arise and to vote on: new faculty members, faculty continuation, mediating role switching (core/affiliate), and changes to program bylaws. Faculty members on the Executive Committee are expected to have shown substantial dedication to the BMI graduate program and have typically served on one or more other committees or taught core BMI courses prior to nomination to the Executive Committee.

Any Executive Committee member may rule that an item of business is inappropriate for discussion in the presence of the student representative. That item of business will then be discussed in the absence of the student member of the Committee. More generally, the chair of any committee with a student member must excuse the student representatives from meetings during discussion about personnel actions or disciplinary issues relating to faculty, during rankings of existing students for funding, discussions of student welfare, and for disciplinary issues related to students.

The Executive Committee shall meet at least annually. Additional meetings and executive sessions may be held as deemed necessary, or upon petition by five members of the program. Discussion, votes, and decisions on many issues (e.g., membership, student petitions) can be made by email without calling a meeting of the committee members.

B. Admissions Committee

The Admissions Committee will consist of at least ten faculty members and two students. The committee members will review and rank the written applications to select applicants for an interview and will assess interview evaluations to select applicants for admission. The Committee’s tasks are to publicize the program, holistically process and evaluate written applications, coordinate and conduct interviews and select the most qualified applicants. The committee emphasizes “Distance Traveled” at each stage of review, enabling students who have overcome early disadvantages to be competitive for the BMI program. The Admissions Chair is named by the Executive Committee and coordinates student admission with assistance from the Program Director(s) and Program Manager. Each year, the BMI Program Manager and Admissions Committee chair solicit faculty and student volunteers for the admissions committee. Student voices are treated equally at all stages of review. Faculty and student members will serve for one-year renewable terms. The Admissions Committee will meet at least once in Fall quarter to discuss written applications and once in Winter quarter to discuss in-person interviews.

C. Educational Policy Committee

The BMI Educational Policy (aka Curriculum) Committee is composed of the Program Directors, course directors of required BMI courses (BMI 203 and 206), a faculty volunteer, and up to two students. This committee determines the structure of the training environment of the program, reviews student course evaluations, and ensures that the evolving needs of BMI students are met by course offerings. The Educational Policy Committee will meet at least once per year.

D. Other Standing Committees

Student Success Committee

Ensuring students have the resources they need for success is para- mount for our graduate program. The Student Success committee will consist of at least four faculty and the Program Director(s). This committee provides academic advising for first-year students; reviews comments from student self-evaluations, qualifying exams, and thesis committee evaluations to identify additional resources that could help students progress in our program as early as possible; and reviews petitions (e.g., 6th year+, exceptional qual/thesis committee members). This committee will regularly review the written criteria for expectations and acceptable progress through the program. Members will be elected to three-year renewable terms. Due to the sensitive nature of this committee, students are not permitted. The Student Success Committee will meet at least once per year.

Inclusion, Diversity, Equity, and Anti-racism (IDEA) Committee

The BMI Program condemns racism and sexism in all forms. The Inclusion, Diversity, Equity, and Anti-racism (IDEA) Committee oversees progress toward building and sustaining a diverse, equitable, and inclusive graduate program for all in the computational sciences. This committee consists of the Program Directors, three faculty, and up to three students to continually develop, refine, and implement approaches for the recruitment and retention of diverse students. The IDEA Committee will determine the cadence of meetings annually, with the expectation of meeting at least once per year.

Article VI. Student Representatives

Student representatives on all committees are self-nominated or nominated by the students, typically in response to a Committee Service Announcement sent out by email at the start of each academic year. The nominees submit a short description of their interest in the position and particular qualifications, if applicable. The Program Director(s) or Committee Chair will select the student representative from the list of nominees as appropriate. The term of service and voting rights of the student representative will be determined by the Chair of the committee.

Article VII. Graduate Advisers

Each year, BMI assigns Academic Advisors to the incoming class. MSTP students joining will keep their MSTP advisors and receive a BMI advisor. Students must meet with their assigned Academic Advisor quarterly during Year One, and at least twice during Year Two. The purpose of these meetings is to discuss the student’s coursework, lab rotations, academic progression, lab selection at the end of the first year, and qualifying exam procedures in the second year. The Academic Advisor is intended to be an outside neutral person to discuss issues that may be uncomfortable to discuss with a rotation or thesis PI. The Academic Advisor can be an important ally during the student’s time in the program in case of conflicts with faculty, postdocs or other students. Advisors will focus on career advice rather than scientific advice, so students may be paired with advisors outside of their field of interest.

Article VIII. Meetings

The BMI Program will have at least one annual meeting with the Program Director(s), Program Manager, and the students, either at the Program Retreat in the Spring, or during the regularly scheduled full-program BMI 222 Research Talks course. At this meeting, the Program Director(s) will summarize recent programmatic changes, climate survey results (if applicable), and updates, and will open the floor for input from the students. Suggestions from this meeting will be taken into consideration by the Program Directors as they set policy for the coming year and will be discussed with the Executive Committee. The Program Director(s) and Manager will also meet with each cohort individually in the fall to address specific milestones and progression.

Article IX. Quorum

All issues that require a vote must be:

• Supported by at least half of the Executive Committee Membership eligible to vote.
• On graduate program matters other than amendment/revision of bylaws, passage requires a supporting vote by at least half of the members voting.
• On amendments and revision of bylaws: passage requires a supporting vote by at least two thirds of the members voting.

If balloting is conducted via e-mail or web-based technology, seven days must be provided for expression of opinions about the proposal prior to the acceptance of votes; the program must allow seven days for votes to be returned or before the "polls are closed."

Article X. Order of Business for Meetings

The BMI Program does not have a set order of meetings.

Article XI. Amendments

Amendments to these bylaws may be made in accordance with program’s quorum policy in Article VIII. Program members may propose amendments by petition to the Program Director(s). The Program Director, or relevant Executive Committee member, may ask for revisions from the faculty who submitted proposed amendments before forwarding the revisions to the membership for review and voting. Quorum, voting and passage is described in Article VIII. All amendments and revisions must be submitted to the Graduate Council for review and approval; changes in the bylaws will become effective upon approval by the Graduate Council.