The document provides instructions and forms for students in the Biomedical Informatics Training Program at Stanford University to complete progress reports. It details the required sections and deadlines for progress reports each academic year. Students must meet with their advisors and submit student information, milestones, coursework assessments, research summaries, and course waiver records. The forms are designed to track student progress toward degree requirements over multiple years.

1. Stanford University BIOMEDICAL INFORMATICS TRAINING PROGRAM
Biomedical Informatics MEDICAL SCHOOL OFFICE BUILDING, X215
251 CAMPUS DRIVE, STANFORD, CA 94305-5479
Russ B. Altman, MD, PhD, Director
Lawrence M. Fagan, MD, PhD, Co-Director PHONE (650)723-6979, FAX (650)725-7944
Mark A. Musen, MD, PhD, Co-Director
Betty Cheng, PhD, Associate Director
Mary Jeanne Oliva, MA, Student Services Officer
Darlene Vian, Program Administrator
Progress Report Forms for the Biomedical Informatics Training Program
Preface
This file contains all of the progress report forms for all co-terminal MS students. You will not need to fill out every page
for every progress report. The information for this form is cumulative. Simply add data as you progress through the
program. If you lose your file, start with a blank. We will maintain each version of your report in your student folder.
Failure to submit this report will affect the availability of funds for student travel.
Table of Contents
Preface - Instructions for the Progress Report Forms p. 1
Front page – Student Information and Advisor Signatures p. 2
Student Milestones p. 3
Review of academic progress p. 4
Development of research focus or interests (for 1st year students) p. 5
Assessment of rotation/research experience (Optional) p. 6
Instructions for the BMI Unit Flowsheet and Record of Course Waivers p. 7-8
Course waivers granted (all 1st year students to complete) p. 9
BMI Unit Flowsheet (all students taking classes) p. 10
All students will need to schedule a meeting with their advisors before submitting the progress report. Since scheduling
meetings with faculty may be difficult, we recommend starting the scheduling early.
Year Action December Deadline Action June Deadline
Submit these pages Submit these pages
One Meet with your p. 2, 3, 4, 5, 6 and Meet with your academic, p. 2, 3, 4, 5, 6 and
academic, and/or p. 9-10 rotation and/or research p. 11 - 12
research advisors advisors
Two Meet with your p. 2, 3, 4, 6 and Meet with your academic, p. 2, 3, 4, 6 and
academic, rotation p. 9-10 rotation and/or research p. 9-10
and/or research advisors advisors
Staple sheets together or submit electronically to the BMI student service office, Mary Jeanne Oliva
(mjoliva@stanford.edu), MSOB, room x-204.

2. BMI Progress Report
Front Page – For All Students and Advisors to Complete for all Progress Reports
Student Name
Student ID
Date
Academic Advisor Name
Research Advisor Name
Research co-Advisor Name
For Students with employment (consultancies) other than RA/TA-ship
Supervisor Name Company Name
Address Hours worked per week:
Phone Other Contact Information Duration of Employment
Describe your activities briefly:
Advisor’s Signatures
Students still enrolled in classes will need their academic advisor’s signature.
Academic Advisor: Has this student made sufficient academic progress this period? (Y/N)
Signature:
Date:
For all students who have chosen a research advisor.
Research Advisor: Has this student made sufficient research progress this period? (Y/N)
Signature:
Date:
updated March 2010 2

3. BMI Progress Report
Student Milestones
All students add to this section with every progress report. Enter the quarter and year of completion or
anticipated completion for each of the following:
This section for Coterminal MS students
Quarter & Year Action Item Comment
Date of Matriculation
Request course waivers immediately Schedule advising session with Betty Cheng
File Masters Program Proposal Form Required for MS students. Due by the end of 1st qtr of matriculation.
BMI coursework completed
Choose Research Advisor (optional)
Volunteer TA for one course (optional) Course Title:
Submit Research Report (optional) Discuss with your research advisor
Graduate
updated March 2010 3

4. BMI Progress Report
Review of academic progress for students in years 1-3. For the academic advisor to complete
Assessment of Academic Progress after First Academic Year
Assessment of Academic Progress after Second Academic Year
Assessment of Academic Progress after Third Academic Year
Additional Comments
updated March 2010 4

5. BMI Progress Report
Development of research focus or interests in first year students. For academic advisors (and research advisors if
chosen) to complete.
Comments (e.g. change in research focus?)
Proposed Area of Research:
Proposed Breadth Areas:
Review of current skills in math, statistics, computer science, engineering
Additional Comments?
updated March 2010 5

6. BMI Progress Report
Optional: Assessment of research progress. For student and research advisors to complete.
Assessment of First Research Experience
Assessment of Second Research Experience
Assessment of Third Research Experience
List Oral Presentations (include Colloquiums), Posters and Publications
Plan for finding a research mentor (if desired)
Plan for Summer Quarter (internship?)
Future Plans
updated March 2010 6

7. BMI Progress Report
Instructions for the BMI Unit Flowsheet and Record of Course Waivers Granted
According to University policy, no graduate student may take a class number 99 or below and have it count towards the graduate degree. You may take such classes only if those
units will not be used to fulfill any degree requirement. No more than 50% of your academic units may come from class numbered 100 – 199. Graduate level classes are numbered
200 and above.
The BMI unit flowsheet reflects the requirements and restrictions for classes in the 5 domains required for the degree, the requirement to maintain your GPA and the requirements
for the final plan of study needed to complete the requirements for the PhD. The complete set of requirements is listed in the Stanford Bulletin under the section for Biomedical
Informatics. A concise version follows for your convenience. When in doubt, the instructions in the Bulletin supersede these instructions.
17 units in Biomedical Informatics (BMI) are required. Biomedin 200, 201, 204, 205, 206, 299, 301, 302, 303, 390 A,B,C may not be counted towards these 17 units
Biomedin 210, 211, 212, 214, 217 are required. CS 228, CS 262, 273 and other classes in biocomputation may be substituted if required classes have been waived.
Biomedin 201 is required. One other seminar class with high relevance to biomedical informatics is required - Biomedin 201, 205, or Chemeng 459 Frontiers in
Interdisciplinary Biosciences are examples
9 units of Computer Science (CS)
o Complete a class which incorporates significant programming and knowledge of machine architectures. For example, CS 108 Object-Oriented Systems Design
o Complete a class in artificial intelligence or related topic. Examples include CS 121, 224N, 227, 228, CS 229
o CS 161 Design and Analysis of Algorithms
9 units of Probability, Statistics, Decision Science, Machine Learning or Experimental Design (P/S/DS/ML/ED)
So long as classes fall into one of these five categories, you may take any combination or sequence of classes. Examples of suitable classes include: MS&E 120/220 (graduate
students take 220), Stats 116, followed by 200, Stats 202, or Stats 315 A & B, CS 228 or 229. Decision analysis – MS&E 152, 252 or BMI 432
6 units of Biomedical (BM) Domain Knowledge – choose six units of graduate level biology (courses labeled 200 or above are graduate level)
4 units of Social & Ethical (S&E) issues – Med 255 Responsible Conduct of Research is required. For the remaining 3 units, consider classes that examine the impact of
technology, with emphasis on biomedical technologies, on social and ethical issues.
The BMI executive committee reviews course waiver requests for new students annually. You will receive a message from the Executive Committee about the status of your
request after the full review process. For the benefit of your academic advisor and the Student Services Officer, both of whom must review your progress towards the degree,
please enter the course waiver information. See the example below.
BMI Courses Course Grade Course description Sem/Qtr & Number of Date Recommendations by the Exec.
or Core areas Number Year units waiver
waived/substit and Title waived granted for
ution BMI
program
CS Artificial CS 121 A- See Stanford bulletin Aut, 1998 3 Aut, 2003 Take 3 more units of
Intelligence graduate level CS
class
BM domain Biology GPA for See transcript & bulletin 6 Aut 2003 Student may take any
knowledge undergrad grad bio elective class in any of the 5
classes = required areas. CS is
Took 5 3.75 recommended.
graduate
level bio
classes
updated March 2010 7

8. BMI Progress Report
The BMI Unit flowsheet
The BMU unit flowsheet has been designed to allow you to review your progress towards the degree using the same sheet for the duration of your classes. A highly abbreviated sample version of the
sheet is shown below. Enter each class on a separate row. If you enroll for a class twice, you may enter the information on the same row. Enter the number of units for the class under the term you
took the class, i.e., Year one, Aut Qtr. Enter the grade for your class. Once you have entered all your classes for the quarter, go to the bottom and enter the total number of units. If you do not have 10
units for the quarter, sign up for Biomed 299 Directed Reading and Research. Calculate your GPA for each of the five areas required for the degree. Then calculate the total GPA including all classes.
Sample (sheet has been abbreviated) – Pseudo data for first progress report entered
BMI Unit Flowsheet Year One Year Two
Waiver(y/n) Aut Win Spr Sum Aut Win Spr Sum Grade Units
Biomedical Informatics (17 units)
Enter Dept and course number Enter
numbe
r of
course
units
Biomedin 201 1 1 A 1) Not counted towards the 17 required units of
BMI, 2 ) Enter the average grade
Biomedin 205 2 A Not counted towards the 17 required units of BMI
Biomedin 210 3 A-
Biomedin 211 3 A
Biomedin 299 Directed Reading & 1 A Not counted towards the 17 required units of BMI
Research
Computer Science (9 units) Must maintain a BMI GPA of 3.0 or above BMI GPA 3.85 Total Required Biomedin units 6
class in Artificial Intelligence or 3 B
Machine Learning (CS 228 selected)
CS 161 3 B+
A class with significant 3 A-
programming and knowledge of
machine architectures, e.g. CS 107
or 108. Other classes with
appropriate focus may be
substituted with the permission of
the BMI exec
Must maintain a CS GPA of 3.0 or above CS GPA 3.3 Total CS units 9
Total units per quarter [if less than 10 10 Grand Total units (equal to or greater than 54?)
10, add biomedin 299 units]
Total GPA (equal to or greater than 3.0?)
updated March 2010 8

9. BMI Progress Report
BMI Course Waivers (duplicate this page if you need more room)
BMI Courses Course Number and Title Grade Course description Sem/Qtr & Number of Date Recommendations by the Exec.
or Core areas Year units waiver
waived/substit waived granted for
ution BMI
program
updated March 2010 9

10. BMI Progress Report
BMI Unit Flowsheet Year One Year Two Year Three Units
Waived(y/n) Aut Win Spr Sum Aut Win Spr Sum Aut Win Spr Sum Grade
1 Biomedical Informatics (17 units)
Biomedin 201 (Student Journal Club)
Required Seminar
Biomedin 210
Biomedin 211
Biomedin 214
Biomedin 217
Biomedin 212
2 Computer Science (9 units) Maintain BMI GPA of 3.0 BMI GPA Total Biomedin units
Artificial Intelligence or Machine Learning
CS 161
programming and knowledge of machine
architectures class, e.g. CS 107
3 P/S/DS/ML/ED (9 unit) Maintain CS GPA of 3.0 CS GPA Total CS units
4 Biomedical Domain (BM) Knowledge (6 units) Maintain P/S/DS/ML/ED GPA of 3.0 P/S/DS… GPA Total Prob/Stat/DS/ML/ED units
5 Social and Ethical Issues (3 units for coterms) Maintain BM domain GPA of 3.0 BM GPA Total units Biomedical Knowledge
Med 255 required for research only
6 Additional Courses Maintain S&E GPA of 3.0 S&E GPA Total Social & Ethical units
Total Other units
7 Total units per quarter Grand Total units (equal to or greater than 45?)
8 Total GPA (equal to or greater than 3.0?)
updated March 2010 10