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Hayden Fennell

James A. Glazier

Dept. of Intelligent Systems Engineering

and Biocomplexity Institute

Indiana University

Bloomington, IN 47408

USA

Please submit questions/concerns/suggestions via zoom chat
Group discussion will be facilitated via zoom breakout rooms
All workshop sessions will be live-streamed, recorded and distributed on YouTube
Hackathon materials can be found in the hackathon folder:

https://drive.google.com/drive/folders/19iWzpozUVRibYfl3OUMZB30Uix7Q30I_?usp=sharing

Please also join the workshop Slack workspace:

https://join.slack.com/t/compucell3dwo-dcc2973/shared_invite/zt-1dfj0gvb7-9CoER58PCzsUqvEKu1KoWA

Support: NIH NIBIB-U24EB028887, NIGMS-R01GM122424, NSF-2120200, NSF-2000281, NSF-1720625, NIGMS-R01GM076692, NIGMS-R01GM077138

CompuCell3D Workshop: Module 5.E �Day 5: Hackathon Teaming Session

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Module 5.3 Parallel Sessions�2:45–4:15 PM (EDT)

Presenter(s)	Topic	Session	Link
Shane Hutson	Computational Model of Secondary Palate Fusion and Disruption	1	https://iu.zoom.us/s/87407897836
Mrinmoy Mukherjee	Cluster size distribution of cells disseminating from a primary tumor	2	https://iu.zoom.us/j/3184813942
Juliano Gianlupi	Uploading CC3D Simulations as nanoHUB tools	3	https://iu.zoom.us/j/89666874915
Priyom Adhyapok	Cell Lineage Tracing	4	https://duke.zoom.us/j/97332356266?pwd=Z25ubGppMkdHcjFNM0t2Ni9FNlZkdz09 Passcode: 306013

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Hackathon Teaming

Please post any Hackathon discussion or teaming requests to the #hackathon channel in the Slack workspace:

https://join.slack.com/t/compucell3dwo-dcc2973/shared_invite/zt-1bupii7ww-MLhnd_i5s3dIjs0B4wrt7g

Please also add a brief description of your idea to the shared google doc. Update the document as the day goes on to reflect your teaming status�https://docs.google.com/document/d/1E6k07IwalJvs-c8M7lz9KTghPQlctsGX5--GLnWrrbc/edit?usp=sharing

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Talking About Models

Model Elements

Behaviors and Interactions

Dynamics and Events

Initial and Boundary Conditions

Objects

(Properties/State)

All models of reality, whether mental models of the players in a football game, a mathematical model of planetary orbits or a computational simulation of molecules in a solution must have four Elements:

In the constructive models we will use, NOTHING exists unless we assert it. We don’t inherit anything for free!

There are other, equally valid ways to group these concepts

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Take five minutes to map your biological problem of interest
What are the specific hypotheses you wish to test?
How can they be measured?
What are the key components you wish to model (and why?)
What are the main processes, interactions, dynamics and events you wish to model? Why are these necessary?

Exercise 2.1.2—Define a Biological Conceptual Model

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The Workflow of Model Development

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Some Thoughts on Scoping

You have 2 days to prototype your project

10.5 hours of free work time (during day)

Important questions to address:

What is the end goal for the weekend?
What is each person going to do?
How will these pieces be combined?
What don’t we know?

What do we still need to learn?
When are we going to learn it?

What is the protocol when things don’t work?

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Some Thoughts on Scoping

What are we trying to do?

What question(s) is our model trying to answer?
What hypotheses are we testing?
What is the simulation’s function?
What do we want the final result to look like?

Can the phenomenon we’re modeling be broken down into component parts?

How long will each part take to model?
Is one component enough for a 2-day project?
Which piece is most foundational? Which component do we need first?

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Open Discussion Time

Use this time for:

Asking questions about project ideas
Discussing informal project ideas
Getting to know your classmates (ask about relevant skills and background)
Project scoping

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Hackathon Details

Hackathon Dates: Saturday Aug. 6 & Sunday Aug. 7, 2022
Organizing Teams

Hackathon participants can choose their top three projects they’d like to work on
Organizers will help suggest teams at the end of the day on Wed, Aug 3rd (if you are not already on a project team)
Please work through the slack channels and use posted zooms so people can join as they are available

Check-ins Morning & Noon (EDT) with whole group
Brief written report on Saturday for feedback next morning
Short Oral Presentation & Model documentation by each group at the end

Post Hackathon support with CC3D team is available to help generate publication-quality customizations

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Hackathon Schedule

Day 1 (Saturday, Aug 6)

10:00AM–11:00AM: (Self-) Organizing Teams
11:00AM–1:00PM: Morning Work Session, Setup and Initial Model-Building
1:00PM–1:30PM: Quick Check-in in Main Session
1:30PM–5:00PM: Afternoon Work Session
5:30PM–6:00PM: First Day Reports

Day 2 (Sunday, Aug 7)

10:00 AM–10:30 AM: Check-in with full group
10:30 AM–2:00 PM: Work on models
2:00 PM–2:30 PM: Quick Check in (Report, Ask other teams for help)
2:30 PM–5:00 PM: Work on Models
5:00 PM–6:00 PM: Reports and Discussion

All times in EDT (UTC -4)