2025 Move-in and Bootcamp Schedule

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The SIMCODES cohort will be arriving in Ames on 5/25. The 2025 SIMCODES Bootcamp will take place from 5/26-5/30 in Hach Hall room 1227. Attendance by cohort members is mandatory. Attendance by mentors is strongly encouraged.

Slides will be made available at https://github.com/SIMCODES-ISU/training_materials.

Sunday (5/25)

Move-In 9AM - 5PM

(Please make alternative arrangements with the PI or Co-PI if you can not move-in during normal business hours)

Location: Freddy Court

Monday (5/26)

Settle-In/Find Room 8:50 AM - 9:00 AM

  • Mentor: Ryan
  • Students should go to the main (West) entrance of Hach Hall
  • Mentors can meet at entrance or go directly to 1227 Hach Hall.

Introduction 9AM - 10 AM

  • Mentors: All
  • Topics:
    • Learn more about the mentors.
    • Learn more about the cohort members.
    • Eat delicious donuts (donuts will be provided).
  • Technologies:
    • N/A

Orientation Part 1 10 AM - 11 AM

  • Mentor: Ryan
  • Goals:
    • Abbreviations you’ll be hearing a lot.
    • Objectives of the SIMCODES program.
    • Stay safe over the summer.
    • What NSF, AMES, ISU, and SIMCODES expects.
  • Technologies:
    • N/A

15 Minute Break

Orientation Part 2 11:15 - 12 PM

  • Mentor: Ryan
  • Topics:
    • Code of conduct.
    • Intro to research integrity.
    • Learn how to get help.
  • Technologies:
    • N/A

Lunch 12 PM - 1 PM

Provided

Fundamentals of Reactions 1 PM - 4 PM

  • Mentor: Felix Rojas (on behalf of Theresa)
  • Topics:
    • Reactions
    • Basic types of reactions
    • Thermochemistry (endo- and exo-thermic)
    • Kinetics (physical state, concentration, temperature, catalyst)
    • Reaction rate expression an order
    • Reaction mechanisms (identify catalyst and intermediates)
    • Equilibrium (time permitting)

Tuesday (5/27)

Meet For AMES IDs 8:50 AM - 9:00 AM

  • Mentor: Ryan
  • Meet Outside TASF (2416 Pammel Dr) at 8:50 AM

AMES IDs 9 AM - 10 AM

  • Mentor: Ryan
  • After IDs we will travel over to Hach Hall and start SDE Setup

Software Development Environment Setup 10 AM - 11 AM

  • Mentor: Ryan
  • Topics:
    • Linux terminal.
    • Installing Python.
    • Terminal-based Python
  • Goals:
    • Get a bare-bones SDE setup.
    • Be able to write and execute simple Python scripts in Terminal.
  • Technologies we will use:
    • Terminal
    • Python interpreter

ISU IDs 11 AM - 12 PM

  • Mentor: Felix Rojas
  • Tasks:
    • Travel to 0530 Beardshear Hall.
    • Get photo taken.
    • Be issued ID
  • Technologies:
    • N/A

Lunch 12 PM - 1 PM

  • Immediately following IDs, Felix will escort the cohort to Union Drive Marketplace for lunch. Lunch uses swipe.

Version Control, Git, GitHub 1PM - 3PM

  • Mentor: Ryan
  • Topics:
    • Why do we need version control?
    • What is version control/Git?
    • Intro to git terminology.
    • Suggested git/GitHub workflow.
  • Technologies:
    • Git
    • GitHub
    • Terminal (to run Git commands)
    • Cookiecutter (for initializing a repo)

Wednesday (5/28)

Bootcamp Overview 9 AM - 10 AM

  • Mentor: Davit

Enzymes as Catalysts Part 1 10 AM - 11 AM

  • Mentor: Davit

Lunch 12 PM - 1PM

On your own.

Intro to Software Engineering: Writing code that works 1PM - 3 PM

  • Mentor: Myra
  • Topics:
    • Overview and the need for good software engineering practices
    • Documentation and team practices
    • Foundations of Software Testing - making sure our code works
    • Introduction to pytest
    • Continuous Integration
  • Technologies:
    • pytest

Thursday (5/29)

Intro to ML Part 1 9AM - 10 AM

  • Mentor: Qi and Mengdi
  • Topics:
    • Overview of machine learning.
    • Supervised vs unsupervised learning.
  • Goals:
    • Get a basic understanding of machine learning and AI

Intro to Quantum Chemistry 10 AM - 12 PM

  • Mentor: Peng
  • Topics:
    • Wave function
    • Schrodinger Equation
    • The Hamiltonian
    • Hydrogen Atom
    • Helium Atom
    • Chemical Bond
    • Intermolecular Forces
    • Fragmentation approaches
  • Technologies:
    • None

Lunch 12 PM - 1 PM

On your own.

Intro to ML Part 2 1 PM - 2 PM

  • Mentor: Qi and Mengdi
  • Topics:
    • Deep learning and neural networks
    • Pertaining and fine-tuning
  • Goals:
    • Get a basic understanding of deep learning and generative AI

Hands-on ML Practice 2 PM - 3 PM

  • Mentor: Qi and Mengdi
  • Topics:
    • scikit-learn
    • pytorch
    • Matplotlib
  • Goals:
    • Get a Colab setup.
    • Be able to train a model and perform inference on test data.
    • Be able to evaluate model performance
    • Be able to visualize data
  • Technologies we will use:
    • Colab

Friday (5/30)

Intro to Molecular Dynamics 9 AM - 10 AM

  • Mentor: Davit and Xueyu
  • Issue # 29

Hands-On Python Tutorial 10 AM - 12 PM

  • Mentor: Ryan
  • Topics:
    • Fundamentals of a Python project.
    • Creating a bare-bones Python project.
    • Test-driven development of a Python module.
    • Optimizing a Python module.
  • Technologies we will use:
    • Terminal
    • Python
    • VSCode or other IDEs at your discretion

Lunch 12 PM - 1PM

On your own.

Mentor Meeting 1 PM -

  • Mentors: All
  • Goal:
  • Mentors meet with mentees.
  • Introduce mentees to the rest of the mentor’s research group.
  • Introduce mentees to the research space.
  • Project-specific onboarding.

Boardgame and Pizza Dinner 6 PM

  • Location is 1761 Gilman Hall.

  • Ryan will bring an assortment of board games.

  • Mentor: All