NOTE: Registration has closed due to capacity limit.

Monte Carlo Simulation in Medicine with TOPAS

September 16 - 18, 2020,  12 - 5:15 PM Eastern Daylight Time
Online via Zoom

Cost: Free

Registration: Closed. We have reached capacity for this course.


Format/Educational methodsA 15 hour on line course divided evenly over three days (5 hours a day with a 15-minute break) with lectures and practical examples. The students will use the TOPAS system hands-on to simulate the examples shown by the instructors and observe the effect of changing parameters used in the different simulations.

Participants must have a computer capable of running TOPAS.

  • Mac OSX 10.12 or newer
  • Linux Debian 8, 9 or 10 or a Debian 8, 9 or 10 variant
  • CentOS 6, 7 or 8 or a CentOS 6, 7 or 8 variant
  • Other OS with a Virtual Machine system pre-installed and one of the above Linux variants
    (note: Windows 10 already comes with an appropriate Linux subsystem)
Target audienceMedical physicists with basic knowledge of Monte Carlo simulations. The course is designed for new as well as experienced TOPAS users.

Requirement: Participants are required to complete the 2-hour on-line TOPAS introductory course and have TOPAS installed on their computer prior to the course. Sign-up for the introductory course is available at Installation instructions are given as part of the course.

Course objectivesTo provide the background necessary for participants to reliably use the TOPAS Tool for Particle Simulation for Monte Carlo simulation in medicine. Participants will learn the fundamentals of the Monte Carlo method and its application in medicine. They will then learn through lectures and examples how TOPAS provides a simple, effective means to access the Geant4 Monte Carlo toolkit. Participants will leave the course with practical knowledge on how to use TOPAS for their own application.

Registration period: August 3, 2020, closing August 7, 2020 (or when reach 50 participants, first come first served). The course might be cancelled if fewer than 20 participants register.

Registration method: Register online at

Activity location: The course will be given online. The institutions of the instructors are listed below.

Zoom: Zoom login information and password will be distributed to registered participants prior to the course. 

CAMPEP application statement: This meeting has applied to CAMPEP for approval of 15 MPCEC hours. The online system to be used will allow tracking of attendance. 

Sources of support: This course is supported under NIH grant U24CA215123.

Instructors (in alphabetical order):

  • Bruce Faddegon, Ph.D., TOPAS U24 PI, UCSF (Bruce)
  • Harald Paganetti, Ph.D., Director of Physics Research, MGH (Harald)
  • Joseph Perl, Chief TOPAS architect, SLAC (Joe)
  • Jose Ramos Mendez, Ph.D., TOPAS Developer, UCSF (Jose)
  • Jan Schuemann, Ph.D., Head of Multi-Scale Monte Carlo lab, MGH (Jan)
  • Aimee McNamara, Ph.D., TOPAS Developer, MGH (Aimee)
  • Jungwook Shin, Ph.D., TOPAS Developer, MGH (Jungwook)
  • KyungDon Choi, Ph.D., TOPAS Developer, UCSF (KyungDon)

TOPAS Course Outline


Every time is given in both Pacific Time (San Francisco) and Eastern Time (Boston).

So you will see two start times listed for each session as PT /  ET.

Each lecture includes time for questions.

Each day will include some exercises for you to continue working on your own.

Then for the first hour of days 2 and 3, we will have three separate zoom rooms where you

can get help, one room for each of three exercises you were given the day before.

So, while for each day there will be one main Zoom room,

there will be additional zoom rooms for the first hour of days 2 and 3.

Day 1 (Wednesday, September 16, 2020) Jan Schuemann, chair

Introduction to Monte Carlo and TOPAS simulation of x-ray and electron therapy

      PT       /     ET

  9:00 am  / 12:00 pm Welcome and introductions (Joseph, Bruce, Harald) 

  9:15 am  / 12:15 pm Lecture 1 - Review of fundamentals of the Monte Carlo method (Jose) 

10:00 am  /   1:00 pm Lecture 2 - Monte Carlo in x-ray and electron therapy (Bruce) 

11:00 am  /   2:00 pm Example 1 - Linac treatment head simulation (KyungDon)

12:00 pm  /   3:00 pm Break

12:15 pm  /   3:15 pm Example 2 - Variance reduction for a generic x-ray linac (Jose)

  1:15 pm  /   4:15 pm Example 3 - Patient simulation: DICOM interface (Jungwook)

  2:15 pm  /   5:15 pm Adjourn - Participants work on problems from example sessions

Day 2 (Thursday, September 17, 2020) Aimee McNamara, chair

TOPAS simulation of proton therapy

      PT       /     ET

  9:00 am  / 12:00 pm Breakout sessions: Examples 1-3

10:00 am  /   1:00 pm Lecture 3 - Monte Carlo in proton therapy (Harald) 

10:45 am  /   1:45 pm Lecture 4 - TOPAS advanced capabilities, Part I (Joseph)

11:30 am  /   2:30 pm Example 4 - Double-scattering proton treatment head (Joseph)

12:15 pm  /   3:15 pm Break

12:30 pm  /   3:30 pm Example 5 - Extensions (Jose)

  1:30 pm  /   4:30 pm Example 6 - Proton patient dose, LET and RBE

                                        calculation using pre-made extensions (Jan) 

  2:15 pm /    5:15 pm Adjourn – Participants work on problems from example sessions

Day 3 (Friday, September 18, 2020) José Ramos Méndez, chair

TOPAS advanced capabilities and examples

      PT       /     ET

  9:00 am 12:00 pm Breakout session: Examples 4-6

10:00 am /   1:00 pm Lecture 5 - Geant4 and TOPAS (Jan)

11:00 am /   2:00 pm Lecture 6 - TOPAS advanced capabilities, Part II (Joseph)

11:30 am /   2:30 pm Example 7 - Target tracking in a scanning proton beam (Joseph)

12:30 pm /   3:30 pm Break

12:45 pm /   3:45 pm Example 8 - Advanced extension: TOPAS-nBio (Aimee)

  2:15 pm /   5:15 pm Adjourn