It is our pleasure to announce the SB3C Post-Conference Computational Workshop. This post-conference workshop provides individuals with an opportunity to receive hands-on training in open-source software after the 2022 SB3C Meeting. This event will be completely in person and will occur on June 23, 2022 from 9AM – 1PM.

This workshop will provide trainees with a focused and smaller group setting to work through demonstrative examples and work directly with software developers to address specific software questions. Attendees should expect to leave this event with a detailed understanding of the software simulation environment as well as the ability to perform end-to-end simulations using the software.

Instructional Session 1.5 hours
Coffee Break ½ hour
Instructional Session 1.5 hours
User questions and individual assistance ½ hour

There are three software workshops to choose from. Each registered attendee can attend a single day-long training session for one of the three open-source biomechanical engineering simulation workshops:

CRIMSON, the CardiovasculaR Modelling and SimulatiON Environment, is a complete software pipeline for segmenting blood vessels from medical imaging data, generating meshes, designing and specifying boundary conditions and material properties, and performing finite element simulation of blood flow on thousands of CPU cores.

Upon completing the workshop, attendees will be fully trained in image-derived patient-specific simulations of arterial blood flow. Because of CRIMSON’s focus on presenting cutting-edge modeling and simulation features via a modern and intuitive user interface, complete novices can learn to perform their first segmentation and simulation in less than half a day. The workshop will cover these introductory topics as well as teach advanced features of CRIMSON, such as custom boundary condition design tools, patient-specific cardiac performance modeling, and transitional physiology and cardiovascular control scripting.

Attendees are required to download the latest version of CRIMSON from prior to the start of the workshop.


Alberto Figueroa, University of Michigan

The FEBio workshop will offer beginning and intermediate users of FEBio a full-day course on how to setup FEBio models, run, and analyze them. All demos will be given using FEBioStudio, the new, fully integrated software environment for FEBio.

The workshop will be divided in several focused, hands-on sessions, with topics including importing geometry, creating surface and volume meshing, doing solid mechanics and biphasic analyses, handling material anisotropy, setting up contact models, performing parameter optimizations, and more. Participants will also learn proven techniques for debugging their models, avoiding common pitfalls, and improving runtime performance. There will also be opportunities for discussing specific modeling challenges with the FEBio developers, so participants are encouraged to bring their own models and questions to the workshop.

All workshop participants should download the latest version of FEBioStudio from prior to the start of the workshop.


Jeff Weiss, Universtiy of Utah
Gerard Ateshian, Columbia


SimVascular is a fully open source software package providing a complete pipeline from medical image data to cardiovascular blood flow simulation results and analysis (  It offers capabilities for image segmentation, unstructured adaptive meshing, physiologic boundary conditions, and two Navier-Stokes finite element solvers with fluid structure interaction capabilities, including large deformation motion with an Arbitrary Lagrangian Eulerian (ALE) formulation and multi-physics capabilities. An accompanying vascular model repository ( provides over 100 freely-available clinical data sets with image data and simulation results from different parts of the vasculature to enable research. Extensive online documentation and video tutorials with clinical examples are provided online.

In this workshop, we will offer focused sessions tailored to new and experienced users. New users will be guided through step-by-step tutorials, covering basic steps of model construction, meshing, flow simulations, and best practices (and pitfalls to avoid) for high quality results. For experienced users, we will cover advanced topics such as cardiac mechanics and electrophysiology, reduced order modeling, interactive surgical planning, and automated scripting via the Python interface. Users will have the opportunity to discuss current challenges from their research with the SimVascular developers and thus participants are encouraged to bring their own models and questions to the workshop.

Attendees should download the latest version of SimVascular from ( prior to the start of the workshop.


Alison Marsden, Stanford University
David Parker, Stanford University
Shawn Shadden, UC Berkeley
Nathan Wilson, Open Source Medical Software Corporation

There is a $100 registration fee for this event that is separate from the SB3C registration fee. This fee is being collected to cover the expenses of the workshop (e.g., audio/visual rental, coffee, etc.) and will not be used to financially benefit any of the participating open-source software organizations.

Registration Process

Registration for this event will be handled on a first-come, first-serve basis. The total number of attendees in each workshop will be limited to ensure the purpose of the meeting is fulfilled (hands-on training with individualized support).  Registrants MUST already be registered for the main SB3C conference in order to register for the post-conference workshop

There are two paths to register:

  1. If you have already registered for the main conference
  2. If you have NOT already registered for the main conference
    • Follow instructions for main conference registration.
    • At the end of the registration process, a URL will be provided that will allow you to continue to the post-conference registration form.
    • You will need your registration ID (sent to you in the main conference registration confirmation email).