LUCID Hackathon

Nov 4, 2024, 9:00 AM → Nov 5, 2024, 5:01 PM America/Chicago

Argonne National Laboratory, TCS Conference Center 1416, 9700 South Cass Avenue, Lemont, IL 60439

Rick Stevens (Argonne National Laboratory)

Hackathon Goal: Our high-level Hackathon goal is to get the LUCID team members aligned with FY2025 project priorities, and then to bring prototyping and making the prototyping available across the project using tools such as GitHub. 

Mon, November 4 ¶

1 LUCID: Hackathon Overview and Charge¶

Speaker: Rick Stevens (Argonne National Laboratory)

2 Introduction to Hackathon Breakouts¶

Here we’ll learn what we have thus far; the goal is to have each
one up and running as a service

• Variant Analysis Pipeline: Maulik to describe what we currently have and what would be needed to scale it up
• Cell Painting Pipeline: Clark and Abe to describe what we currently have and what would be needed to scale up
• Transcriptome Pipeline: Maulik to describe what we currently have and what is needed
• Signature Pipeline: NAME to describe what we currently have and what is needed
• Perturbation Test: Rick to describe what we currently have and what is needed

3 Working Lunch¶

Infrastructure and Services Breakouts: Breakout 1: Variant Analysis Pipeline¶

In these breakouts, the goal is to work on implementations and let that drive the establishment of software processes that support multi-institution code development. We can reduce the number of breakouts depending on attendance and interest. After the Hackathon, we will focus on debugging the use of our infrastructure/services with partnerships. A follow-up Hackathon will focus on predictive modeling and other explorable based on the data collected from the public and generated internally.

Infrastructure and Services Breakouts: Breakout 2: Cell Painting Pipeline¶

In these breakouts, the goal is to work on implementations and let that drive the establishment of software processes that support multi-institution code development. We can reduce the number of breakouts depending on attendance and interest. After the Hackathon, we will focus on debugging the use of our infrastructure/services with partnerships. A follow-up Hackathon will focus on predictive modeling and other explorable based on the data collected from the public and generated internally.

Infrastructure and Services Breakouts: Breakout 3: Transcriptome Pipeline¶

In these breakouts, the goal is to work on implementations and let that drive the establishment of software processes that support multi-institution code development. We can reduce the number of breakouts depending on attendance and interest. After the Hackathon, we will focus on debugging the use of our infrastructure/services with partnerships. A follow-up Hackathon will focus on predictive modeling and other explorable based on the data collected from the public and generated internally.

Infrastructure and Services Breakouts: Breakout 4: Signature Pipeline¶

In these breakouts, the goal is to work on implementations and let that drive the establishment of software processes that support multi-institution code development. We can reduce the number of breakouts depending on attendance and interest. After the Hackathon, we will focus on debugging the use of our infrastructure/services with partnerships. A follow-up Hackathon will focus on predictive modeling and other explorable based on the data collected from the public and generated internally.

Perturbation Test Breakouts: Breakout 5: Mechanistic Model 1¶

These will focus on mechanistic models related to radiation response. Topics will be discussed during the introduction. The goal is to relate AI-generated hypotheses with mechanistic models in the context of perturbations to the mechanistic model. These can become the basis for future CRISPR experiments in the laboratory. Identify genes and other entities in the mechanistic models. Identify existing computational models related to this mechanistic model. Identify hypotheses related to these models and use those to develop perturbation scenarios that can be tested experimentally and/or computationally.

Perturbation Test Breakouts: Breakout 6: Mechanistic Model 2¶

These will focus on mechanistic models related to radiation response. Topics will be discussed during the introduction. The goal is to relate AI-generated hypotheses with mechanistic models in the context of perturbations to the mechanistic model. These can become the basis for future CRISPR experiments in the laboratory. Identify genes and other entities in the mechanistic models. Identify existing computational models related to this mechanistic model. Identify hypotheses related to these models and use those to develop perturbation scenarios that can be tested experimentally and/or computationally.

Perturbation Test Breakouts: Breakout 7: Mechanistic Model 3¶

These will focus on mechanistic models related to radiation response. Topics will be discussed during the introduction. The goal is to relate AI-generated hypotheses with mechanistic models in the context of perturbations to the mechanistic model. These can become the basis for future CRISPR experiments in the laboratory. Identify genes and other entities in the mechanistic models. Identify existing computational models related to this mechanistic model. Identify hypotheses related to these models and use those to develop perturbation scenarios that can be tested experimentally and/or computationally.

4 Day 1 Concludes¶

Tue, November 5 ¶

Breakout: Report-Outs¶

5 Breakout 1: Variant Analysis Pipeline¶

6 Breakout 2: Cell Painting Pipeline¶

7 Breakout 3: Transcriptome Pipeline¶

8 Breakout 4: Signature Pipeline¶

9 Breakout 5: Mechanistic Model 1¶

10 Breakout 6: Mechanistic Model 2¶

11 Breakout 7: Mechanistic Model 3¶

12 Q&A¶

13 Day 2: Hackathon Charge¶

14 Working Lunch¶

Infrastructure and Services Breakouts: Breakout 1: Variant Analysis Pipeline¶

In these breakouts, the goal is to work on implementations and let that drive the establishment of software processes that support multi-institution code development. We can reduce the number of breakouts depending on attendance and interest. After the Hackathon, we will focus on debugging the use of our infrastructure/services with partnerships. A follow-up Hackathon will focus on predictive modeling and other explorable based on the data collected from the public and generated internally.

Infrastructure and Services Breakouts: Breakout 2: Cell Painting Pipeline¶

In these breakouts, the goal is to work on implementations and let that drive the establishment of software processes that support multi-institution code development. We can reduce the number of breakouts depending on attendance and interest. After the Hackathon, we will focus on debugging the use of our infrastructure/services with partnerships. A follow-up Hackathon will focus on predictive modeling and other explorable based on the data collected from the public and generated internally.

Infrastructure and Services Breakouts: Breakout 3: Transcriptome Pipeline¶

In these breakouts, the goal is to work on implementations and let that drive the establishment of software processes that support multi-institution code development. We can reduce the number of breakouts depending on attendance and interest. After the Hackathon, we will focus on debugging the use of our infrastructure/services with partnerships. A follow-up Hackathon will focus on predictive modeling and other explorable based on the data collected from the public and generated internally.

Infrastructure and Services Breakouts: Breakout 4: Signature Pipeline¶

In these breakouts, the goal is to work on implementations and let that drive the establishment of software processes that support multi-institution code development. We can reduce the number of breakouts depending on attendance and interest. After the Hackathon, we will focus on debugging the use of our infrastructure/services with partnerships. A follow-up Hackathon will focus on predictive modeling and other explorable based on the data collected from the public and generated internally.

Perturbation Test Breakouts: Breakout 5: Mechanistic Model 1¶

These will focus on mechanistic models related to radiation response. Topics will be discussed during the introduction. The goal is to relate AI-generated hypotheses with mechanistic models in the context of perturbations to the mechanistic model. These can become the basis for future CRISPR experiments in the laboratory. Identify genes and other entities in the mechanistic models. Identify existing computational models related to this mechanistic model. Identify hypotheses related to these models and use those to develop perturbation scenarios that can be tested experimentally and/or computationally.

Perturbation Test Breakouts: Breakout 6: Mechanistic Model 2¶

These will focus on mechanistic models related to radiation response. Topics will be discussed during the introduction. The goal is to relate AI-generated hypotheses with mechanistic models in the context of perturbations to the mechanistic model. These can become the basis for future CRISPR experiments in the laboratory. Identify genes and other entities in the mechanistic models. Identify existing computational models related to this mechanistic model. Identify hypotheses related to these models and use those to develop perturbation scenarios that can be tested experimentally and/or computationally.

Perturbation Test Breakouts: Breakout 7: Mechanistic Model 3¶

These will focus on mechanistic models related to radiation response. Topics will be discussed during the introduction. The goal is to relate AI-generated hypotheses with mechanistic models in the context of perturbations to the mechanistic model. These can become the basis for future CRISPR experiments in the laboratory. Identify genes and other entities in the mechanistic models. Identify existing computational models related to this mechanistic model. Identify hypotheses related to these models and use those to develop perturbation scenarios that can be tested experimentally and/or computationally.

15 Hackathon Concludes¶