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Getting Started – Research Workflow & Environment Setup

Introduction to the Computational Simulation Workflow

Installing WSL and Ubuntu on Windows

Installing FEniCS in WSL (Windows)

Installing FEniCS using Conda/Docker (macOS/Linux)

Testing Your FEniCS Installation

Working with Containers – Docker for Scientific Computing

Introduction to Docker – Why It Matters

Installing Docker

Images, Containers, and Registries

Running FEniCS Inside Docker

Managing Containers

Building Custom Images

Using Docker Volumes

Sharing Docker Images

Docker Compose

Best Practices for Reproducibility

Essential Research Tools – VS Code, GitHub, and Obsidian

Installing VS Code

VS Code Interface – Panels & Buttons

Setting Up Python in VS Code

Extensions for Scientific Computing

Running FEniCS Code in VS Code

Git Basics

GitHub Workflow

Branch, Commit, Push, Pull

Pull Requests & Issues

Introduction to Obsidian

Building a Research Vault

Communication & Documentation Skills

Why Communication Matters

Taking Effective Screenshots

Recording Demo Videos

Progress Updates on Slack

Writing Commit Messages

Maintaining a Project Journal

Creating Codebase Docs

Sharing Results & Asking for Feedback

Reporting Bugs Clearly

Presenting Results Professionally

Terminal & Linux Essentials

Navigating the File System

Creating & Managing Files

Working with Directories

Permissions & Ownership

Package Management

Process Management

Searching with grep, find, awk

Compression & Archiving

Remote Access & scp

Automating with Bash Scripts

Introduction to Salome – Geometry & Meshing

Installing Salome

Salome Interface Overview

Creating Basic Geometries

Boolean Operations

Working with Sketcher

Parametric Geometries

Meshing Basics

Creating Meshes

Exporting Meshes

Automating Geometry with Python

ParaView for Visualization and Post-Processing

Installing ParaView

Pipeline & Interface Overview

Loading VTK/VTU Files

Visualizing Scalar Fields

Visualizing Vector Fields

Using Filters

Plotting & Extracting Data

Time-Dependent Results

Customizing Visual Styles

Exporting Visualizations

Workflow Integration – From Geometry to Results

Full Workflow Overview

Project Management Best Practices

Automation with Shell & Python

Integrating Docker & CI/CD

Common Troubleshooting Tips

Working with Cloud & Remote Servers

Introduction to Remote Computing & Cloud

Setting Up SSH Keys & Config

Secure File Transfer (scp & rsync)

tmux & screen for Long Jobs

VS Code Remote-SSH

Remote Python Development & Debugging

Port Forwarding & Jupyter

ParaView Client–Server Mode

Remote Job Submission (SLURM/PBS)

End-to-End Remote Workflow

Scientific Reporting and Documentation

Introduction to Scientific Reporting

LaTeX Basics and Setup

Structuring a Well-Written Report

Guidelines for Figures and Graphs

Creating Professional Graphs with Veusz

Visual Design with Affinity Designer

Standard Guidelines and Best Practices

Capstone Exercises and Mini Projects

FEniCS Installation Exercise

Docker Container Exercise

GitHub Branch Exercise

VS Code Demo Recording

Obsidian Workflow Documentation

Geometry & Mesh Exercise (Salome)

FEniCS Elasticity Problem

ParaView Visualization Exercise

Automation & Remote Execution

Capstone Project

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Standard Guidelines And Best Practices

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This section will cover key concepts and practical examples related to standard guidelines and best practices.

Overview

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Key Concepts

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Practical Examples

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Summary

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Next Steps

In the next section, we'll explore...

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