Collection of resources for the Biophysical Modeling Software Summer School
Quickly acquaint new personel with compuational tools developed at Flatiron to model biophysical phenomena. 1. Understand the strengths and limitations of methods when applied to scientific problems. 2. Learn how to debug, troubleshoot, and analyze data from simulations. 3. Be comfortable submitting large jobs to the Flatiron cluster.
| Day 1 (Monday 6/5) | General Introduction |
|---|---|
| 9:00AM | Welcome and Introduction of BPM and CCB Speaker: Mike Shelley |
| 9:20AM | Go around presentation (~5 min/person) Speaker: Students |
| 10:10AM | Break |
| 10:20AM | Intro to resources available to SCC and Cluster Speaker: Geraud Krawezik |
| ~11:00AM | Tutorial: Cluster setup and IDE usage Instructors: Adam and Reza |
| Day 2 (Tuesday 6/6) | aLENS (part 1) |
| 2:00PM | Introduction to aLENS (what can it do?) Speaker: Adam |
| 2:30PM | Computational methods and code structure of aLENS Speaker: Bryce |
| 3:00PM | Break |
| 3:10PM | Tutorial: Running aLENS for the first time Instructor: Adam |
| ~3:45PM | Tutorial: Paraview and visualizing Instructor: Adam/Bryce |
| ~4:00PM | Break |
| ~4:10PM | Tutorial: Explanation of parameters and playing with simulations Instructor: Adam/Bryce |
| Day 3 (Wednesday 6/7) | aLENS (part 2) |
| 9:00AM | Variations and current projects (Flexible filaments and transient networks) Speaker: Adam |
| 9:30AM | Variations and current projects (Semi-flexible and growing filaments) Speaker: Dimitrios |
| 10:00AM | Break |
| 10:10AM | Variations and current projects (Bacterial growth) Speaker: Taeyoon/Bryce |
| 10:40AM | Analysis package for aLENS and free play Instructor: Adam |
| ~11:10AM | Break |
| ~11:20AM | Analysis package for aLENS and free play Instructor: Adam |
| Day 4 (Thursday 6/8) | SkellySim (part 1) |
| 9:00AM | Intro to SkellySim Speaker: Robert |
| 9:30AM | Computational methods and code structure Speaker: David |
| 10:00AM | Break |
| 10:10AM | Tutorial: Running SkellySim for the first time (visualize with matplotlib) Instructor: Robert |
| ~10:40AM | Tutorial: Explanation of parameter files and free play Instructor: Robert |
| ~11:00AM | Break |
| ~11:10AM | Free play Speaker: Coordinators |
| ~11:40AM | Visualizing with Blender Speaker: Reza |
| Day 5 (Friday 6/9) | SkellySim (part 2) |
| 9:00AM | Current projects (Oocyte flows) Speaker: Reza |
| 9:30AM | Current projects (Rotating centrosomes) Speaker: David |
| 10:00AM | Break |
| 10:10AM | Tutorial: Analysis of SkellySim Instructor: Reza |
| ~11:10AM | Break |
| ~11:20AM | Free play Speaker: Coordinators |
| Day 6 (Monday 6/12) | PDE solvers/methods (part 1: Dedalus) |
| 9:00AM | Intro to Dedalus Speaker: Keaton |
| 9:30AM | Current projects (Oscillating active dipolar flows) Speaker: Brato |
| 10:00AM | Break |
| 10:10AM | Current projects (Heterochromatin condensation) Speaker: Alex |
| 10:30AM | Tutorial: Running Dedalus Instructor: Keaton |
| ~11:00AM | Break |
| ~11:10AM | Tutorial: Visualizing Dedalus and free play (active fluid simulations) Instructor: Keaton |
| Day 7 (Tuesday 6/13) | PDE solvers/methods (part 2: David’s, Dan’s, and Alex’s method) |
| 2:00PM | Computation methods (Fast spectral solver) Speaker: David |
| 2:30PM | Computation methods (Fast spectral solver continued) Speaker: Dan |
| 3:00PM | Break |
| 3:10PM | Current projects (Polarization of cells) Speaker: Pearson |
| 3:40PM | Tutorial: Solving PDEs on curved surfaces Instructor: Dan |
| ~4:10PM | Break |
| ~4:20PM | Tutorial: Solving PDEs on curved surfaces (continued) Instructor: David |
| Day 8 (Wednesday 6/14) | Advanced cluster usage |
| 9:00AM | Getting programs running/environment management Speaker: Robert/Chris |
| 10:00AM | Break |
| 10:10AM | Tutorial: Slurm Speaker: Chris |
| 10:30AM | Tutorial: Large batch runs with DisBatch Instructor: Nick |
| ~11:00AM | Break |
| ~11:10AM | Testing code for correctness and efficiency Speaker: Vickram |
| Day 9 (Thursday 6/15) | Free play and/or walkthroughs with instructors to help |
| 9:00AM | Current projects (Contractile matter) Speaker: Shai |
| 9:30AM | Tutorials/Free play Instructors: Coordinators/Mentors |
| Day 10 (Friday 6/16) | Free play and/or walkthroughs with instructors to help |
| 9:00AM | Current projects (Tissue mechanics) Speaker: XinXin |
| 9:30AM | Tutorials/Free play Instructors: Coordinators/Mentors |
- Docker desktop
- Sign up at docker hub https://hub.docker.com/
- Download docker desktop https://www.docker.com/products/docker-desktop/
- (Optional) Docker engine
- paraview https://www.paraview.org/download/
- HDFview
- Sign up for service https://www.hdfgroup.org/register/
- Download at https://www.hdfgroup.org/downloads/hdfview/#download