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 |
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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: Pre-workshop software installation and cluster setup Instructors: Adam Lamson/Reza Farhadifar |
Day 2 (Tuesday 6/6) | aLENS (part 1) |
2:00PM | Introduction to aLENS (what can it do?) Speaker: Adam Lamson |
2:30PM | A peek into the numerical methods behind aLENS Speaker: Bryce Palmer |
3:00PM | Break |
3:10PM | Tutorial: Running aLENS for the first time Instructor: Adam Lamson |
~3:45PM | Tutorial: Paraview and visualizing Instructor: Adam Lamson/Bryce Palmer |
~4:00PM | Break |
~4:10PM | Parameter explanation and playing with simulations Instructor: Adam Lamson |
Day 3 (Wednesday 6/7) | aLENS (part 2) |
9:00AM | Current projects (Flexible filaments and transient networks) Speaker: Adam Lamson |
9:30AM | Current projects (Semi-flexible and growing filaments) Speaker: Dimitrios Vavylonis |
10:00AM | Break |
10:10AM | Current projects (Bacterial growth) Speaker: Taeyoon Kim |
10:40AM | Tutorial: Analysis package for aLENS and free play Instructor: Adam Lamson |
~11:10AM | Break |
~11:20AM | Tutorial: Analysis package for aLENS and free play Instructor: Adam Lamson |
Day 4 (Thursday 6/8) | SkellySim (part 1) |
9:00AM | Intro to SkellySim Speaker: Robert Blackwell |
9:30AM | Computational methods of SkellySim Speaker: David Stein |
10:00AM | Break |
10:10AM | Tutorial: Running SkellySim for the first time Instructor: Robert Blackwell |
~11:00AM | Break |
~11:10AM | Free play Speaker: Coordinators |
~11:40AM | Visualizing with Blender Speaker: Reza Farhadifar |
Day 5 (Friday 6/9) | SkellySim (part 2) |
9:00AM | Current projects (Oocyte flows) Speaker: Reza Farhadifar |
9:30AM | Current projects (Rotating centrosomes) Speaker: David Stein |
10:00AM | Break |
10:10AM | aLENS or SkellySim: Free play Instructors: Coordinators |
~11:10AM | Break |
~11:20AM | Free play Instructors: Coordinators |
Day 6 (Monday 6/12) | PDE solvers/methods (part 1: Dedalus) |
9:00AM | Intro to Dedalus Speaker: Keaton Burns |
9:45AM | Current projects (Oscillating active dipolar flows) Speaker: Brato Chakrabarti |
10:10AM | Break |
10:20AM | Current projects (Heterochromatin condensation) Speaker: Alex Rautu |
10:40AM | Tutorial: Running Dedalus Instructor: Keaton Burns |
~11:10AM | Break |
~11:20AM | Tutorial: Visualizing Dedalus and free play (active fluid simulations) Instructor: Keaton Burns |
Day 7 (Tuesday 6/13) | PDE solvers/methods (part 2: General surfaces) |
2:00PM | Computational methods (Function intention) Speaker: David Stein |
2:30PM | Compuational methods (Surfacefun) Speaker: Dan Fortunato |
3:00PM | Break |
3:10PM | Current projects (Cell polarization) Speaker: Pearson Miller |
3:40PM | Tutorial: Using Surfacefun Instructor: Dan Fortunato |
~4:10PM | Break |
~4:20PM | Tutorial: IPDE Instructor: David Stein |
Day 8 (Wednesday 6/14) | Advanced cluster usage |
9:00AM | Running programs and environment management Speaker: Chris Edelmaier |
10:00AM | Break |
10:10AM | Tutorial: Slurm Instructor: Chris Edelmaier |
10:30AM | Tutorial: Large batch runs with DisBatch Instructor: Nick Carriero |
~11:00AM | Break |
~11:10AM | Testing code for correctness and efficiency Speaker: Vickram Muligan |
Day 9 (Thursday 6/15) | Free play and/or walkthroughs with instructors to help |
9:00AM | Current projects (Contractile matter) Speaker: Shahriar Shadkhoo |
9:30AM | Tutorials/Free play Instructors: Coordinators/Mentors |
Day 10 (Friday 6/16) | Free play and/or walkthroughs with instructors to help |
9:00AM | 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