BIOS 258: Reproducibility through effective coding and data management

Course Information

Course Description

This course introduces science reproducibility through effective coding and data management. Students will complete team projects on a statistical or simulation topic of their choosing and publish them on GitHub. Instructors will guide students in learning to use R, R markdown,and GitHub to collaborate with peers as they advance their project. By the end of the course, students will learn effective coding practices, data management, version control and collaboration, and sharing analytical results. The course aims to provide students with the tools and knowledge to help make their research reproducible and easily accessible. No prerequisites required.

Course Instructors

Lucas A. Nell
Biology Department
216 Bass Biology Building


Magdalena L. Warren
Biology Department
216 Bass Biology Building


Emails will be responded to within 24 to 48 business hours.

Learning Objectives

At the completion of this course, students will be able to:

  1. Implement effective coding practices, including functional and defensive code.
  2. Organize datasets in ways that improve functionality for the researcher and for others that may access those datasets.
  3. Use version control to transparently track changes in code
  4. Collaborate on coding projects using Github.
  5. Share coding output and visualizations via reports in R markdown.
  6. Create simple R packages

Course Expectations

  1. Students will be evaluated on class participation and the final Github presentation.
  2. Class will be a combination of lecture, discussion, and project work.
  3. When readings are assigned, students will prepare before class so that in-class discussion is facilitated (and fun!).

Course Materials

Course materials and resources will be linked at our class website: https://lucasnell.github.io/pranga/. Here’s an overview of what we will be covering over our three weeks together.

Date Topic
11/13/2023 Git and Github
11/15/2023 File management and workflow
11/17/2023 Data management
11/27/2023 R basics and intro to functional coding
11/29/2023 Sourcing files and R packages
12/1/2023 Data visualization
12/4/2023 R markdown reports
12/6/2023 Workshop project materials
12/8/2023 Github project presentations

Absence Policy and Expectations

It is the student’s professional responsibility to review the absence policy and specific attendance requirements for all courses, clerkships and curricular activities in which they are involved. Students should avoid scheduling or participating in activities that directly conflict with required sessions, courses, or clerkships.

Required Courses

  1. Students are expected to be present at ALL required-attendance sessions and final exams. It is the student’s responsibility to be aware of the attendance expectations for each course. For students with disabilities who have registered with OAE, work with the course leadership (e.g., course director and course manager), at the beginning of courses to receive accommodations.

  2. If a student anticipates missing a required-attendance session, they must communicate and receive approval from the course director at a minimum of two-weeks in advance. In cases involving illness and unexpected emergencies, students should notify their course director as soon as possible submit a notification form (see below) thereafter.

    • All students are required to complete the online notification form regardless of whether the absence has been approved. If the student and course director are unable to agree on the appropriateness of an absence for a required session, they are encouraged to schedule a meeting with the course director and their assigned Advising Dean to discuss the absence further. In addition, the course may require the student to complete an internal notification form.

    • Approval of all absences is at the discretion of the course director.

    • If an absence is not approved it is expected that the student will make the necessary arrangements to change their schedule to be present.

  3. Students are responsible for the content and work associated with all missed sessions. Students are also expected to meet the participation requirement and contribute to their group’s learning, even for sessions missed, and must work out an equitable solution that balances the individual student’s needs with the needs of the group. Under no circumstances will an absence relieve a student of meeting all of the academic requirements of the course. If the absence request conflicts with a session or sessions that cannot be otherwise made up or completed, the student is advised that the absence may affect their performance evaluation in the course.

  4. The following are considered professionalism issues that may result in a referral to Committee on Performance, Professionalism, and Promotion (CP3):

    • Absence from a required session without obtaining advance approval. In cases of emergency, it is the student’s responsibility to contact the course as soon as possible.

    • Failure to communicate with the course director

    • Failure to complete the online absence notification

    • Trend in number of absences across courses

Please note that each student is responsible for requesting approval for their own absence; no group approvals will be granted.

End Quarter Period and Policy Statement

The End Quarter Period and the administration of exams have been significantly impacted by COVID. If you have questions about specific exam policies and procedures, please consult your course Canvas page, your course syllabus, or reach out to your Course Director.

The End Quarter Policy Statement

The End-Quarter Period is a time of reduced social and extracurricular activity preceding final examinations. Its purpose is to permit students to concentrate on academic work and to prepare for final examinations.

During the End-Quarter Period, classes are regularly scheduled and assignments made; this regular class time is used by instructors in whatever way seems best suited to the completion and summation of course material. Instructors should neither make extraordinary assignments nor announce additional course meetings in order to “catch up” on course presentations that have fallen behind. They are free, however, and even encouraged to conduct review sessions and to suggest other activities that might seem appropriate for students preparing for final examinations.

Students are expected to remain on campus during the end-quarter period and are advised to avoid planning activities that might conflict with course commitments and final exam preparation during this week.

No final examinations should be given during the End-Quarter Period except:

  1. In classes where graded homework assignments or quizzes are routine parts of the instruction process.
  2. In classes with laboratories where the final examination will not test the laboratory component. In such a case, the laboratory session(s) during the End- Quarter Period may be used to examine students on that aspect of the course.
  3. In Practice of Medicine, in which previously scheduled standardized patient (SP) assessments are permitted during the End-Quarter Period.
  4. In Science of Medicine, in which assessments may be maximally spread out in order to account for student wellness.

Major papers or projects about which the student has had reasonable notice may be called due in the End-Quarter Period. Take-home final examinations, given in place of the officially scheduled in-class examination, may be distributed in the End-Quarter Period. Although the instructor may ask students to return take-home examinations early in the final examination period, the instructor may not call them due until the end of the regularly scheduled examination time for that course. Such a policy respects the principle that students’ final examinations are to be scheduled over a period of several days.

Please note: In the COVID-era, there may be marked changes to the above policies. Our procedures will need to adapt to the changing landscape of county, state, and university regulations.

Final Examinations: Courses

Final examinations are scheduled by the Office of Medical Education, which posts tentative dates and times by the end of the previous quarter and final schedules by the end of the second week of the quarter. Students anticipating conflicts in examination schedules should seek to resolve them with course instructors.

Students are expected to remain on campus during the final exam period and should not book travel or other plans until they have confirmed the dates that they must sit for their final exams. Final exams should take priority over other commitments and students are advised to plan accordingly.

Final examinations are governed by the regulations below:

  1. Students are expected to take the final examination unless at least 24 hours prior to the examination they have received formal written approval for either dropping the course from the course director or for obtaining an incomplete from an Advising Dean. Incompletes are given for significant personal or medical reasons beyond the student’s control. If a student does not appear for the examination and has not been granted a drop or an incomplete, the student will receive a fail.

  2. Students are expected to report for their examinations at the time and place designated by the Office of Medical Education or the course director, unless the course director has made alternative arrangements. While examinations are not “proctored” as such, students must take the examination in the designated location within the prescribed examination time. Students are expected to adhere to the Honor Code at all times during examinations.

  3. When the final examination or its appropriate substitute is not an in-class examination (e.g., when an instructor assigns a take-home examination, paper, or project in lieu of an in-class examination), the schedule and format of the final examination, or its substitute, will be determined no later than the end of the second week of the quarter and, if changed subsequently, may be only a modification approved by a majority of the students in the class.

  4. Students with documented disabilities who have registered with and been determined by the Office of Accessible Education (OAE) to require special examination accommodations are responsible for notifying both the School of Medicine Learning Strategies Education Specialist and their course directors at the beginning of the quarter or when their accommodation letter is given that they will need accommodations. Unless students receive accommodations mid- quarter, they must let the School of Medicine Learning Strategies Education Specialist and their course directors know of their accommodations needs no later than the end of the second week of the quarter for which they are receiving accommodations. Reminder: students needing exam accommodations are to contact the OAE first, prior to notifying their course director(s).

  5. Feedback on written examinations is to be as complete as practicable. Please note: In the COVID-era, there may be marked changes to the above policies. Our procedures will need to adapt to the changing landscape of county, state, and university regulations.

Exam Policy for Required MD Pre-Clerkship Courses

Per the Stanford University Honor Code faculty can determine the best exam environment for their tests and make any requirements they see fit with regard to how students take the exam.

To uphold the spirit of the University’s Honor Code and to create consistency across courses in the pre-clerkship curriculum, the Office of Medical Education provides the following guidelines for closed-book examination environments in our required MD courses:

Stanford Medicine Bring Your Own Device Policy

Policies and Resources for Device Encryption, Security and Use can be found here:

https://med.stanford.edu/md/mdhandbook/section-3-md-requirements-procedures/section-3-12-policies-and-resources-for-mobile-devices.html

Stanford Medicine will begin the transition towards becoming a “Bring Your Own Device (BYOD)” campus. What does this mean for you?

The School of Medicine EdTech team will provide support before and during examinations to ensure a smooth experience. Please visit BYOD at Stanford Medicine for the latest details on system requirements and Stanford Medicine’s transition to BYOD. If you have any questions, please contact EdTech at .

Evaluation of Performance in Courses

The complete list of Evaluation Completion Requirements can be found at:

https://med.stanford.edu/md/mdhandbook/section-5-assessment-of-student-academic-performance/section-5-2-evaluation-of-performance-in-courses.html

All pre-clerkship MD program courses are graded on a pass/fail basis. It is the prerogative of each course director to determine the best method for assessing student performance for their course. Learning activities such as quizzes, short papers, laboratory exercises, problem sets, presentations, and group discussions, may be offered on a graded or ungraded basis at the discretion of the course director.

Attendance and participation may be required for some sessions, e.g. where small group interaction is essential to mastery of material in the course. Course directors are expected to announce criteria for passing a course by the end of the second week of the quarter.

Grading System

The following grading system is used to report on the official transcript the performance of students in all courses and clerkships taken while an MD degree candidate:

  • Pass (+) indicates that a student has demonstrated to the satisfaction of the responsible department or teaching group that they have mastered the material taught in the course.
  • Incomplete (I) indicates that extenuating medical or personal circumstances beyond the student’s control have prevented completion of course requirements. An incomplete can be corrected in a manner specified by the department or teaching group and must be corrected within one year (unless the Committee on Performance, Professionalism and Promotion specifies an earlier date). When a student takes a final or makeup examination following an incomplete, it becomes a pass, marginal pass or fail. If the student does not attempt to correct the incomplete within the agreed-upon time, it becomes a fail.
  • Continuing (N) indicates that the course has not concluded and that the student is continuing the course or that a minor component of a course (as defined by the course director) is pending.
  • Grade Not Reported (GNR) indicates that a grade has not been reported by the instructor.

A student may not receive credit for repeating a course unless the content has changed significantly, as determined by the course director.

In addition to these transcript-related grades, additional designations are used internal to the School of Medicine to report on academic progress:

  • Marginal Pass (MP) indicates that a student has fallen short of meeting minimal performance standards for a pass but has done better than a fail at the end of the academic quarter, and that additional work or remediation is necessary to achieve a pass. MP grades are tracked internally in the School of Medicine through the Medical Education Platform (MEP), and should be entered as an N grade in Axess.
  • Fail (-) indicates that a student has not met the minimum performance standards for the course. A course in which a student has received a fail grade does not show up on the official transcript. A course in which a student has received a fail grade must be repeated, and the student must achieve a passing grade within one year of the failure or prior to beginning clerkships, whichever is sooner.

Mid-Quarter Feedback for Pre-Clerkship Courses

All required pre-clerkship courses must provide students formal mid-quarter feedback of performance. Mid-quarter feedback must be provided early enough to allow a student the opportunity to improve their performance before the end of the course. Mid-quarter feedback should be provided by the mid-point of the course, and by the end of the 5th week for standard 10-week courses. Mid-quarter feedback is recorded in the Medical Education Platform (MEP) student record system.

Narrative Assessment in Pre-Clerkship Curriculum

Narrative assessment is provided to medical students in courses where the primary mode of instruction includes small group activities (typically up to 12 students per group), small clinical reasoning, clinical skills, and/or team-based learning where attendance is required and there is longitudinal direct contact with an individual faculty member for at least 10 hours during the course.

In other pre-clerkship courses, where the primary mode of instruction takes place in lectures with occasional small group activities narrative assessments may be provided at the end of the course if attendance for the sessions is required and individual faculty have had at least 10 hours of direct contact time with the student during the course.

In addition, faculty may provide narrative comments if they so choose when submitting mid-quarter feedback for each student via MEP (Medical Education Platform).

Disability Accommodations

Information about Disability Accommodations can be found at:

https://med.stanford.edu/md/mdhandbook/section-3-md-requirements- procedures/section-3-5-disability-accomodations.html

As outlined on the Office of Accessible Education (OAE), Stanford University has an institutional commitment to providing equal educational opportunities for qualified students with disabilities in accordance with state and federal laws and regulations, including the Americans with Disabilities Act of 1990 and 2008, and Section 504 of the Rehabilitation Act of 1973. To provide equality of access for students with disabilities, accommodations (including auxiliary aids and services) will be provided to the extent necessary to comply with state and federal laws. For each student, these accommodations will specifically address those functional limitations of the disability which adversely affect equal education opportunity.

Medical students who may need an academic accommodation based on the impact of a disability must initiate the request with the OAE. Professional staff within OAE will evaluate the request with required documentation, recommend reasonable accommodations, and prepare an Accommodation Letter for faculty dated in the current quarter in which the request is being made. Students should contact the OAE as soon as possible since timely notice is needed to coordinate accommodations. The Associate Dean of Medical Student Affairs serves as the liaison with the OAE and is available to assist in the facilitation of accommodations. coordinates with the Office of Accessible Education to facilitate accommodations.

Student Responsibilities

Each student bears the responsibility of initiating a disability-related request for accommodations with the OAE prior to the time such an accommodation is needed. In addition, and more specifically, it is the responsibility of the student to:

  • As early as possible, register with the OAE and submit documentation of disability as a prerequisite to receiving accommodations.
  • Notify the OAE immediately when an accommodation is not being provided correctly.
  • Notify the OAE immediately when discontinuing an accommodation (e.g., notetaking) or dropping a course for which alternate format materials are required.
  • Provide timely notification to faculty of approved accommodations by submitting the OAE Accommodation Letter.
  • Provide for personal disability-related needs or services such as “personal care attendants,” transportation off campus, housekeeping, golf cart rental, wheelchair repair, etc.
  • Meet the same standards—academic, technical, performance and behavior— expected of all Stanford students.

Faculty Responsibilities

  • Notify students that accommodations are available.
  • Refer Students with Questions about Accommodations to the OAE
  • Do not seek to arrange accommodations by yourself with the student.
  • Protect Student Privacy and Confidentiality
  • Maintain student confidentiality and treat all disability-related information as confidential.
  • Although faculty do not have the right to ask about the nature of the disability, if students choose to disclose their disability, this information should be treated confidentially.
  • Refrain from identifying the student with a disability in class or openly discussing accommodations or disability issues in front of others.
  • Meet privately with a student when presented with and reviewing the Accommodation Letter.
  • Collaborate with Student and OAE Staff in Arranging and Providing Accommodations
  • Consult with the OAE staff if the academic accommodation(s) recommended appear to violate the goals or requirements of the course. Recommended accommodations are open for negotiation.
  • Permit the Use of Approved Accommodations
  • Provide accommodations only to students who are registered with the OAE and who have submitted an Accommodation Letter.

Process for Accommodations

Students who need accommodations must first register with OAE. OAE then sends an accommodations letter to Dr. Mijiza Sanchez Guzman, Associate Dean in the Office of Medical Student Affairs, for official record keeping. We cannot support accommodations from students who are not registered with OAE.

Students are then responsible for letting instructors know that they will need accommodations at the beginning of the quarter, or as soon as possible if accommodations are given mid-quarter. It is up to the student to advocate for him/herself in a timely manner. The instructor may choose to deny accommodations if they feel the accommodations will interfere with the essential elements of what the course is trying to teach or what is being assessed.

The Stanford School of Medicine MD Program Handbook

Students enrolled in the MD program may wish to access the program handbook to review the overall learning goals of the program as well as program policies and procedures. The handbook is available at: https://med.stanford.edu/md/mdhandbook.html

Course Communications

All official course communications must use “stanford.edu” emails. Students should not be using gmail, yahoo, etc. accounts.