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Collection of resources for the Biophysical Modeling Summer School at the Flatiron Institute

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BPM Summer School

Collection of resources for the Biophysical Modeling Software Summer School

Goal

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.

Schedule

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: 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

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