The 2nd Workshop on Monte Carlo eXtreme for Biomedical Optics Research (MCX OSA'18)
- 1. Summary
- 2. Event agenda
- 3. Instructions on preparing your laptop
- 4. Organizer contact info
- The Diplomat Beach Resort, RM307, Hollywood, FL, USA
- April 2, 2018
- See our 1st MCX Training Workshop here: http://fanglab.org/news/MCXWorkshop2017.html
- How much it costs
- Free! We thank the funding support from the NIH/NIGMS under Award# R01-GM114365. This event is not possible without this support!
- What do you need
- A laptop that can be connected to the Internet using Wifi/cable. We will have a post-workshop reception/poster session, we encourage attendees to present poster for their related research.
- How to register
- The registration was closed. Please email the organizer if you still want to sign up.
2. Event agenda
- 8:00-9:00 Breakfast (provided), user laptop preparation
- 9:00-9:15 Opening (Monte Carlo algorithm, MCX project overview)
- 9:15-11:00 MCX Studio Training
- 9:15-9:45 Basics of MCX Studio (GUI, built-in demo, remote execution, visualization, use binary data)
- 9:45-10:15 Designing complex domains using MCX Studio
- 10:15-11:00 Hands-on session on MCX Studio
- 11:00-12:30 MCXLAB Training
- 11:00-11:15 MCXLAB Introduction
- 11:15-11:45 MC simulation in Digimouse using MCXLAB
- 11:45-12:30 Hands-on session on MCXLAB
- 12:30-1:30 Lunch Break (lunch on your own)
- 1:30 - Starting MMC/iso2mesh training session
- 1:30-2:45 Iso2Mesh/Brain2Mesh training
- 1:30-1:45 Introduction to Iso2Mesh and basic mesh generation
- 1:45-2:15 Hands-on session on Iso2Mesh basic meshing features
- 2:15-2:30 Generating high-quality human brain 3D meshes
- 2:30-2:45 Hands-on session on Brain2mesh
- 2:45-3:30 MMCLAB Training
- 2:45-3:00 MMC algorithm and simulation basics
- 3:00-4:00 Hands-on session on MMCLAB for brain simulations
- 3:30-4:00 (in parallel) User problem troubleshooting and additional user practices
- 4:00-6:00 Post-workshop reception and poster session (light refreshment provided)
3. Instructions on preparing your laptop
Our MC simulation software delivers the best efficiency when running on more capable hardware (such as later generations of GPUs). We will give users opportunities to experience fast simulations using our GPU resources in our lab. On the other hand, we also recognize that our participants will benefit the most from setting up a stand-alone simulation environment on our own computers.
For the above reason, we strongly recommend our participants to try our first approach:
- Method A (recommended) - Running everything from your laptop (or remote server in your own lab)
This way, you will have a working system after getting back from the workshop and ready to run new simulations.
In the event that your laptop is too old, or have driver issues and unable to use the CPU/GPU for our simulations, we will ask you to try the alternative approach:
- Method B - Use remote GPU via MCXStudio from your laptop
If the above approach (Method B) still unable to allow you to connect and run simulations, we will have to use our preconfigured Linux-based environment, this is our fall-back plan:
- Method C - Run simulations over the remote desktop of our Linux GPU server
Because of limited network bandwidth, we do not recommend Method C to everyone, but only use it when the previous two approaches fail.
If you have difficult configuring your laptop, please consider borrowing another laptop or run a remote server in your home institution. Please test connections if you decide to run the simulations on your server.
4. Organizer contact info
If you have any questions regarding this event, please feel free to contact the organizers. Their contact info is listed below.
- Xin Sun (workshop coordinator)
- Email: sun.xin1 at husky.neu.edu
- Phone: 857-272-4545 (cell)
- Prof. Qianqian Fang
- Email: q.fang at neu.edu
- Phone: 617-407-5769 (cell), 617-373-3829 (office)
- Office: ISEC 223