diff --git a/README.md b/README.md index 0acc5a3..3019299 100755 --- a/README.md +++ b/README.md @@ -47,7 +47,7 @@ You can view the information in Module 0 in your browser by clicking on the Gith Additional information on how to [create an Azure account](https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateAzureMLNotebooks.md) is provided by the NIGMS in abbreviated form for those with a subscription to Azure. -* Video directions can be viewed at ____________ +* Video directions can be viewed at [Learning Modules for Cloud-Based Biomedial Research.](https://www.youtube.com/playlist?list=PLXaEJPtnQ4w7Vu7vqWbttBjUGrPp4Qa7b) ## **Software Requirements** @@ -74,7 +74,7 @@ Data will be obtained from online databases (e.g., NCBI) or will be in folders i ## **Module Outline** **Module 0 - Intro to Cloud Computing and Git** -- Lecture (coming) +- Lecture (upcoming) - Tutorial 1: Github Download *how to get the tutorials* - Tutorial 2: Jupyter Notebooks *how to navigate these tutorials* @@ -88,7 +88,7 @@ Data will be obtained from online databases (e.g., NCBI) or will be in folders i Learn core concepts, diverse applications, introductory algorithms, ethical considerations, and data challenges. -- Lecture (coming) +- Lecture (upcoming) - - Tutorials - Tutorial 1: Python Overview diff --git a/Submodule 0/Submodule_0_Tutorial_1_GithubDownload.ipynb b/Submodule 0/Submodule_0_Tutorial_1_GithubDownload.ipynb index 3313e26..b5b133c 100755 --- a/Submodule 0/Submodule_0_Tutorial_1_GithubDownload.ipynb +++ b/Submodule 0/Submodule_0_Tutorial_1_GithubDownload.ipynb @@ -74,7 +74,15 @@ "\n", "You are likely familiar with cloud data storage, for example with your files saved on OneDrive (Microsoft) or Google Drive (Google). Cloud *computing* takes that a step farther and carries out data processing and runs programs on computers that are located in some distant site. \n", "\n", - "The advantage of \"cloud computing\" is that the computational speed and power is not limited by what you have in *your* desktop or laptop. Rather, cloud computers are very FAST computers with substantially more memory (to work on big biological data sets). Additionally, the providers of cloud computing can make more (or fewer) processors available to your job, depending on the need. " + "The advantage of \"cloud computing\" is that the computational speed and power is not limited by what you have in *your* desktop or laptop. Rather, cloud computers are very FAST computers with substantially more memory (to work on big biological data sets). Additionally, the providers of cloud computing can make more (or fewer) processors available to your job, depending on the need. \n", + "\n", + "

\n", + " \n", + " \"NIH/NIGMS\n", + " \n", + "
\n", + " Click above image to watch introductory video \n", + "

" ] }, { @@ -83,6 +91,15 @@ "metadata": {}, "source": [ "## What you see when you arrive at the \"Sandbox\"\n", + "\n", + "

\n", + " \n", + " \"NIH/NIGMS\n", + " \n", + "
\n", + " Click above image to watch introductory video \n", + "

\n", + "\n", "It is possible that you are reading this file having already navigated to the \"Sandbox.\" \n", "\n", "The [Sandbox](https://github.com/NIGMS/NIGMS-Sandbox) is housed at github.com. Github is a collaboration tool/website/repository that is being used by NIGMS as a great way to share materials.\n", diff --git a/Submodule 0/Submodule_0_Tutorial_4_GitHub4You.md b/Submodule 0/Submodule_0_Tutorial_4_GitHub4You.md index 91b6212..5106ce4 100755 --- a/Submodule 0/Submodule_0_Tutorial_4_GitHub4You.md +++ b/Submodule 0/Submodule_0_Tutorial_4_GitHub4You.md @@ -4,6 +4,23 @@ ## Overview Git is a powerful version control tool that helps track changes to your data files over time. While Git is traditionally used for computer code, it can be just as effective for managing structured data by recording each change, allowing you to compare versions and collaborate efficiently. +

+ + NIH/NIGMS Sandbox Foundations of Python Video 1 + +
+ Click above image to watch introductory video +

+ +

+ + NIH/NIGMS Sandbox Foundations of Python Video 12 + +
+ Click above image to watch introductory video +

+ + ## Learning Objectives By the end of this lesson, you will be able to: - Define FAIR data practices @@ -45,6 +62,15 @@ The key word: *AUTOMATICALLY* though we'll not get to THAT until the next tutori Version control tools like Git provide a structured way to track, manage, and document changes to data over time, ensuring that every update, correction, or modification is properly recorded. +

+ + NIH/NIGMS Sandbox Foundations of Python Video 2 + +
+ Click above image to watch introductory video +

+ + ### Why Version Control for Research Data?
1️⃣ Ensuring Data Integrity Over Time
@@ -89,6 +115,7 @@ Now that we understand why research labs need version control, let's set up Git Before you can start using GitHub for your materials, you need to create an account. GitHub is a platform that allows you to store, share, and collaborate on code. It is widely used by developers, students, and organizations for managing software projects using Git, a version control system that tracks changes in your code. + To get started, you need to sign up for a free GitHub account. This will give you access to your own profile, repositories, and collaboration tools. Follow the steps below to create your GitHub account. - Go to GitHub's website @@ -97,6 +124,15 @@ To get started, you need to sign up for a free GitHub account. This will give yo - Click Create an account and follow the instructions. - GitHub will send a verification email. Click the link in the email to verify your account. +

+ + NIH/NIGMS Sandbox Foundations of Python Video 4 + +
+ Click above image to watch introductory video +

+ + ## Step 2: Setting Up a GitHub Account & Installing GitHub Desktop Before tracking your data, you need to install GitHub Desktop, a user-friendly application that simplifies version control without needing command-line commands. @@ -107,6 +143,13 @@ Before tracking your data, you need to install GitHub Desktop, a user-friendly a 2. Install GitHub Desktop and sign in with your GitHub account. 3. Set up your GitHub profile with your name and email (important for tracking contributions) from the account you set up in step 1. +

+ + NIH/NIGMS Sandbox Foundations of Python Video 5 + +
+ Click above image to watch introductory video +

## Step 3: Creating a Repository for Your Research Data A repository (A "repo") is like a folder where you store your research data and track changes over time. @@ -121,11 +164,35 @@ A repository (A "repo") is like a folder where you store your research data and 5. Check “Initialize this repository with a README” (important for documenting your dataset). This is the appropriate spot to include summary information about this particular repository's purpose 6. Click Create Repository. +

+ + NIH/NIGMS Sandbox Foundations of Python Video 5 + +
+ Click above image to watch introductory video +

+ +

+ + NIH/NIGMS Sandbox Foundations of Python Video 10 + +
+ Click above image to watch introductory video +

+ Now, you have a version-controlled folder on your computer where you can store and track your research data. ## Step 4: Adding Data Files to GitHub Desktop Once your repository is set up, you can start adding data files like Excel, CSV, or JSON datasets. +

+ + NIH/NIGMS Sandbox Foundations of Python Video 9 + +
+ Click above image to watch introductory video +

+ ### Instructions: 1. Open your repository folder *on your computer.* 2. Copy or move your data files (e.g., temperature_data_2024.csv) into the folder. @@ -167,4 +234,40 @@ Now, every protocol update is documented and timestamped, ensuring full transpar ## Managing a lab group using the same git repository It is rather unlikely that ONLY one person would be the involved in collecting all of the data for a research lab. In order to control and protect overwriting, Git provides clear management tools. That is covered in the next tutorial. +### Additional Resources: + +

+ + NIH/NIGMS Sandbox Foundations of Python Video 13 + +
+ Click above image to watch introductory video +

+ +

+ + NIH/NIGMS Sandbox Foundations of Python Video 14 + +
+ Click above image to watch introductory video +

+ +

+ + NIH/NIGMS Sandbox Foundations of Python Video 15 + +
+ Click above image to watch introductory video +

+ +

+ + NIH/NIGMS Sandbox Foundations of Python Video 16 + +
+ Click above image to watch introductory video +

+ + + Go to the [next tutorial](Submodule_0_Tutorial_5_ManagingGit.md) \ No newline at end of file diff --git a/Submodule 0/Submodule_0_Tutorial_5_ManagingGit.md b/Submodule 0/Submodule_0_Tutorial_5_ManagingGit.md index 0423746..088edcd 100755 --- a/Submodule 0/Submodule_0_Tutorial_5_ManagingGit.md +++ b/Submodule 0/Submodule_0_Tutorial_5_ManagingGit.md @@ -19,6 +19,14 @@ Please complete tutorial 4 before tutorial 5. ## Why use Git for your research lab team *DATA?* In a research lab environment, managing data properly is just as important as collecting it. Labs often deal with long-term datasets, changing protocols, and *multiple* contributors, which can lead to data integrity issues if not properly managed. +

+ + NIH/NIGMS Sandbox Foundations of Python Video 11 + +
+ Click above image to watch introductory video +

+ 🧪 GitHub Repo Management Guide for Science Lab PIs 🎯 Goal: @@ -74,6 +82,15 @@ In Branch name pattern, type: main (or master, depending on your repo) +

+ + NIH/NIGMS Sandbox Foundations of Python Video 8 + +
+ Click above image to watch introductory video +

+ + **Check the following boxes:** ✅ Require pull request reviews before merging diff --git a/Submodule_1/Submodule_1_Tutorial1_PythonOverview.ipynb b/Submodule_1/Submodule_1_Tutorial1_PythonOverview.ipynb index 9645fde..87be95c 100755 --- a/Submodule_1/Submodule_1_Tutorial1_PythonOverview.ipynb +++ b/Submodule_1/Submodule_1_Tutorial1_PythonOverview.ipynb @@ -9,13 +9,21 @@ "\n", "This section of the introductory module gives you the foundations for understanding how Python works. \n", "\n", + "

\n", + " \n", + " \"NIH/NIGMS\n", + " \n", + "
\n", + " Click above image to watch introductory video \n", + "

\n", + "\n", "
Attention: This page is for novices!.
\n", "\n", "## Learning Objectives\n", - "- Describe a Python program\r", + "- Describe a Python program\n", "- Recognize and create comments\n", "- Find help for Python Tools\n", - "- Use functions and methods on variables (at a beginner level)\r\n", + "- Use functions and methods on variables (at a beginner level)\n", "## Prerequisites\n", "NONE\n", "\n", diff --git a/images/CreateGitHubAccount.png b/images/CreateGitHubAccount.png new file mode 100644 index 0000000..93fdd64 Binary files /dev/null and b/images/CreateGitHubAccount.png differ diff --git a/images/CreatingandPopulatingNewRepo.png b/images/CreatingandPopulatingNewRepo.png new file mode 100644 index 0000000..b4eae97 Binary files /dev/null and b/images/CreatingandPopulatingNewRepo.png differ diff --git a/images/CreatingandPopulatingNewRepoExample.png b/images/CreatingandPopulatingNewRepoExample.png new file mode 100644 index 0000000..34f0806 Binary files /dev/null and b/images/CreatingandPopulatingNewRepoExample.png differ diff --git a/images/DeleteLocalRepoDesktop.png b/images/DeleteLocalRepoDesktop.png new file mode 100644 index 0000000..c30f47c Binary files /dev/null and b/images/DeleteLocalRepoDesktop.png differ diff --git a/images/DeleteRepoGitHub.png b/images/DeleteRepoGitHub.png new file mode 100644 index 0000000..533eeb5 Binary files /dev/null and b/images/DeleteRepoGitHub.png differ diff --git a/images/DesktopTutorialRepo.png b/images/DesktopTutorialRepo.png new file mode 100644 index 0000000..7059122 Binary files /dev/null and b/images/DesktopTutorialRepo.png differ diff --git a/images/GenerateGitHubAcctToken.png b/images/GenerateGitHubAcctToken.png new file mode 100644 index 0000000..32a1f0f Binary files /dev/null and b/images/GenerateGitHubAcctToken.png differ diff --git a/images/GitHubDesktopInstall.png b/images/GitHubDesktopInstall.png new file mode 100644 index 0000000..f4896c3 Binary files /dev/null and b/images/GitHubDesktopInstall.png differ diff --git a/images/GitIntro.png b/images/GitIntro.png new file mode 100644 index 0000000..4d4da56 Binary files /dev/null and b/images/GitIntro.png differ diff --git a/images/InstallGit.png b/images/InstallGit.png new file mode 100644 index 0000000..e5456c7 Binary files /dev/null and b/images/InstallGit.png differ diff --git a/images/IntroPythonforBioinfo.png b/images/IntroPythonforBioinfo.png new file mode 100644 index 0000000..0e24a76 Binary files /dev/null and b/images/IntroPythonforBioinfo.png differ diff --git a/images/TourofGit.png b/images/TourofGit.png new file mode 100644 index 0000000..488ae78 Binary files /dev/null and b/images/TourofGit.png differ diff --git a/images/TourofGitHub.png b/images/TourofGitHub.png new file mode 100644 index 0000000..22bab89 Binary files /dev/null and b/images/TourofGitHub.png differ diff --git a/images/TypicalCollabProcess.png b/images/TypicalCollabProcess.png new file mode 100644 index 0000000..89bb46b Binary files /dev/null and b/images/TypicalCollabProcess.png differ diff --git a/images/UsingGitwithGitHub.png b/images/UsingGitwithGitHub.png new file mode 100644 index 0000000..e10cf48 Binary files /dev/null and b/images/UsingGitwithGitHub.png differ diff --git a/images/VersionControl.png b/images/VersionControl.png new file mode 100644 index 0000000..8ae4db3 Binary files /dev/null and b/images/VersionControl.png differ diff --git a/images/WhatIsGitHub.png b/images/WhatIsGitHub.png new file mode 100644 index 0000000..e9c6658 Binary files /dev/null and b/images/WhatIsGitHub.png differ