> For the complete documentation index, see [llms.txt](https://igb.mit.edu/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://igb.mit.edu/mini-courses.md).

# Mini Courses

- [Schedule](https://igb.mit.edu/mini-courses/schedule.md)
- [Previous Teaching](https://igb.mit.edu/mini-courses/schedule/previous-teaching.md)
- [Introduction to Unix](https://igb.mit.edu/mini-courses/introduction-to-unix.md)
- [Why Unix?](https://igb.mit.edu/mini-courses/introduction-to-unix/why-unix.md)
- [The Unix Filesystem](https://igb.mit.edu/mini-courses/introduction-to-unix/the-unix-filesystem.md)
- [The Unix Tree](https://igb.mit.edu/mini-courses/introduction-to-unix/the-unix-filesystem/the-unix-tree.md)
- [Network Filesystems](https://igb.mit.edu/mini-courses/introduction-to-unix/the-unix-filesystem/network-filesystems.md)
- [The Unix Shell](https://igb.mit.edu/mini-courses/introduction-to-unix/the-unix-shell.md)
- [About the Unix Shell](https://igb.mit.edu/mini-courses/introduction-to-unix/the-unix-shell/about-the-unix-shell.md)
- [Unix Shell Manual Pages](https://igb.mit.edu/mini-courses/introduction-to-unix/the-unix-shell/unix-shell-manual-pages.md)
- [Using the Unix Shell](https://igb.mit.edu/mini-courses/introduction-to-unix/the-unix-shell/using-the-unix-shell.md)
- [Viewing the Unix Tree](https://igb.mit.edu/mini-courses/introduction-to-unix/the-unix-shell/using-the-unix-shell/viewing-the-unix-tree.md)
- [Traversing the Unix Tree](https://igb.mit.edu/mini-courses/introduction-to-unix/the-unix-shell/using-the-unix-shell/traversing-the-unix-tree.md)
- [Editing the Unix Tree](https://igb.mit.edu/mini-courses/introduction-to-unix/the-unix-shell/using-the-unix-shell/editing-the-unix-tree.md)
- [Searching the Unix Tree](https://igb.mit.edu/mini-courses/introduction-to-unix/the-unix-shell/using-the-unix-shell/searching-the-unix-tree.md)
- [Files](https://igb.mit.edu/mini-courses/introduction-to-unix/files.md)
- [Viewing File Contents](https://igb.mit.edu/mini-courses/introduction-to-unix/files/viewing-file-contents.md)
- [Creating and Editing Files](https://igb.mit.edu/mini-courses/introduction-to-unix/files/creating-and-editing-files.md)
- [Manipulating Files](https://igb.mit.edu/mini-courses/introduction-to-unix/files/manipulating-files.md)
- [Symbolic Links](https://igb.mit.edu/mini-courses/introduction-to-unix/files/symbolic-links.md)
- [File Ownership](https://igb.mit.edu/mini-courses/introduction-to-unix/files/file-ownership.md)
- [How Unix File Ownership Works](https://igb.mit.edu/mini-courses/introduction-to-unix/files/file-ownership/how-unix-file-ownership-works.md)
- [Change File Ownership and Permissions](https://igb.mit.edu/mini-courses/introduction-to-unix/files/file-ownership/change-file-ownership-and-permissions.md)
- [File Transfer (in-progress)](https://igb.mit.edu/mini-courses/introduction-to-unix/files/file-transfer-in-progress.md)
- [File Storage and Compression](https://igb.mit.edu/mini-courses/introduction-to-unix/files/file-storage-and-compression.md)
- [Getting System Information](https://igb.mit.edu/mini-courses/introduction-to-unix/getting-system-information.md)
- [Writing Scripts](https://igb.mit.edu/mini-courses/introduction-to-unix/writing-scripts.md)
- [Schedule Scripts Using Crontab](https://igb.mit.edu/mini-courses/introduction-to-unix/schedule-scripts-using-crontab.md)
- [Advanced Utilization of IGB Computational Resources](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources.md)
- [High Performance Computing Clusters](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/high-performance-computing-clusters.md)
- [Slurm](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/slurm.md)
- [Checking the Status of Computing Nodes](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/slurm/checking-the-status-of-computing-nodes.md)
- [Submitting Jobs / Slurm Scripts](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/slurm/submitting-jobs-slurm-scripts.md)
- [Interactive Sessions](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/slurm/interactive-sessions.md)
- [Package Management](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/package-management.md)
- [The System Package Manager](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/package-management/the-system-package-manager.md)
- [Environment Modules](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/package-management/environment-modules.md)
- [Conda Environments](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/package-management/conda-environments.md)
- [SSH Port Forwarding](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/ssh-port-forwarding.md)
- [SSH Port Forwarding Jupyter Notebooks](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/ssh-port-forwarding/ssh-port-forwarding-jupyter-notebooks.md)
- [Containerization](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/containerization.md)
- [Docker](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/containerization/docker.md)
- [Docker Installation](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/containerization/docker/docker-installation.md)
- [Running Docker Images](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/containerization/docker/running-docker-images.md)
- [Building Docker Images](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/containerization/docker/building-docker-images.md)
- [Singularity](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/containerization/singularity.md)
- [Differences from Docker](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/containerization/singularity/differences-from-docker.md)
- [Running Images in Singularity](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/containerization/singularity/running-images-in-singularity.md)
- [Running Nextflow / nf-core Pipelines](https://igb.mit.edu/mini-courses/advanced-utilization-of-igb-computational-resources/running-nextflow-nf-core-pipelines.md)
- [Python](https://igb.mit.edu/mini-courses/python.md)
- [Introduction to Python for Biologists](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists.md)
- [Interactive Python](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/interactive-python.md)
- [Types](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/types.md)
- [Strings](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/types/strings.md)
- [Lists](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/types/lists.md)
- [Tuples](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/types/tuples.md)
- [Dictionaries](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/types/dictionaries.md)
- [Control Flow](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/control-flow.md)
- [Loops](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/loops.md)
- [For Loops](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/loops/for-loops.md)
- [While Loops](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/loops/while-loops.md)
- [Control Flows and Loops](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/control-flows-and-loops.md)
- [Storing Programs for Re-use](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/storing-programs-for-re-use.md)
- [Reading and Writing Files](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/reading-and-writing-files.md)
- [Functions](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/functions.md)
- [Biopython](https://igb.mit.edu/mini-courses/python/biopython.md)
- [About Biopython](https://igb.mit.edu/mini-courses/python/biopython/about-biopython.md)
- [Quick Start](https://igb.mit.edu/mini-courses/python/biopython/quick-start.md)
- [Basic Sequence Analyses](https://igb.mit.edu/mini-courses/python/biopython/quick-start/basic-sequence-analyses.md)
- [SeqRecord](https://igb.mit.edu/mini-courses/python/biopython/quick-start/seqrecord.md)
- [Sequence IO](https://igb.mit.edu/mini-courses/python/biopython/quick-start/sequence-io.md)
- [Exploration of Entrez Databases](https://igb.mit.edu/mini-courses/python/biopython/quick-start/exploration-of-entrez-databases.md)
- [Example Projects](https://igb.mit.edu/mini-courses/python/biopython/example-projects.md)
- [Coronavirus Exploration](https://igb.mit.edu/mini-courses/python/biopython/example-projects/coronavirus-exploration.md)
- [Translating a eukaryotic FASTA file of CDS entries](https://igb.mit.edu/mini-courses/python/biopython/example-projects/translating-a-eukaryotic-fasta-file-of-cds-entries.md)
- [Further Resources](https://igb.mit.edu/mini-courses/python/biopython/further-resources.md)
- [Machine Learning with Python](https://igb.mit.edu/mini-courses/python/machine-learning-with-python.md)
- [About Machine Learning](https://igb.mit.edu/mini-courses/python/machine-learning-with-python/about-machine-learning.md)
- [Hands-On](https://igb.mit.edu/mini-courses/python/machine-learning-with-python/hands-on.md)
- [Project Introduction](https://igb.mit.edu/mini-courses/python/machine-learning-with-python/hands-on/project-introduction.md)
- [Supervised Approaches](https://igb.mit.edu/mini-courses/python/machine-learning-with-python/hands-on/supervised-approaches.md)
- [The Logistic Regression Model](https://igb.mit.edu/mini-courses/python/machine-learning-with-python/hands-on/supervised-approaches/the-logistic-regression-model.md)
- [K-Nearest Neighbors](https://igb.mit.edu/mini-courses/python/machine-learning-with-python/hands-on/supervised-approaches/k-nearest-neighbors.md)
- [Unsupervised Approaches](https://igb.mit.edu/mini-courses/python/machine-learning-with-python/hands-on/unsupervised-approaches.md)
- [K-Means Clustering](https://igb.mit.edu/mini-courses/python/machine-learning-with-python/hands-on/unsupervised-approaches/k-means-clustering.md)
- [Further Resources](https://igb.mit.edu/mini-courses/python/machine-learning-with-python/hands-on/further-resources.md)
- [Data Processing with Python](https://igb.mit.edu/mini-courses/python/data-processing-with-python.md)
- [Pandas](https://igb.mit.edu/mini-courses/python/data-processing-with-python/pandas.md)
- [About Pandas](https://igb.mit.edu/mini-courses/python/data-processing-with-python/pandas/about-pandas.md)
- [Making DataFrames](https://igb.mit.edu/mini-courses/python/data-processing-with-python/pandas/making-dataframes.md)
- [Inspecting DataFrames](https://igb.mit.edu/mini-courses/python/data-processing-with-python/pandas/inspecting-dataframes.md)
- [Slicing DataFrames](https://igb.mit.edu/mini-courses/python/data-processing-with-python/pandas/slicing-dataframes.md)
- [Selecting from DataFrames](https://igb.mit.edu/mini-courses/python/data-processing-with-python/pandas/selecting-from-dataframes.md)
- [Editing DataFrames](https://igb.mit.edu/mini-courses/python/data-processing-with-python/pandas/editing-dataframes.md)
- [Matplotlib](https://igb.mit.edu/mini-courses/python/data-processing-with-python/matplotlib.md)
- [About Matplotlib](https://igb.mit.edu/mini-courses/python/data-processing-with-python/matplotlib/about-matplotlib.md)
- [Basic Plotting](https://igb.mit.edu/mini-courses/python/data-processing-with-python/matplotlib/basic-plotting.md)
- [Advanced Plotting](https://igb.mit.edu/mini-courses/python/data-processing-with-python/matplotlib/advanced-plotting.md)
- [Seaborn](https://igb.mit.edu/mini-courses/python/data-processing-with-python/seaborn.md)
- [About Seaborn](https://igb.mit.edu/mini-courses/python/data-processing-with-python/seaborn/about-seaborn.md)
- [Basic Plotting](https://igb.mit.edu/mini-courses/python/data-processing-with-python/seaborn/basic-plotting.md)
- [Visualizing Statistics](https://igb.mit.edu/mini-courses/python/data-processing-with-python/seaborn/visualizing-statistics.md)
- [Visualizing Proteomics Data](https://igb.mit.edu/mini-courses/python/data-processing-with-python/seaborn/visualizing-proteomics-data.md)
- [Visualizing RNAseq Data](https://igb.mit.edu/mini-courses/python/data-processing-with-python/seaborn/visualizing-rnaseq-data.md)
- [R](https://igb.mit.edu/mini-courses/r.md)
- [Intro to R](https://igb.mit.edu/mini-courses/r/intro-to-r.md)
- [Before We Start](https://igb.mit.edu/mini-courses/r/intro-to-r/before-we-start.md)
- [Getting to Know R](https://igb.mit.edu/mini-courses/r/intro-to-r/getting-to-know-r.md)
- [Variables in R](https://igb.mit.edu/mini-courses/r/intro-to-r/variables-in-r.md)
- [Functions in R](https://igb.mit.edu/mini-courses/r/intro-to-r/functions-in-r.md)
- [Data Manipulation](https://igb.mit.edu/mini-courses/r/intro-to-r/data-manipulation.md)
- [Simple Statistics in R](https://igb.mit.edu/mini-courses/r/intro-to-r/simple-statistics-in-r.md)
- [Basic Plotting in R](https://igb.mit.edu/mini-courses/r/intro-to-r/basic-plotting-in-r.md)
- [Advanced Plotting in R](https://igb.mit.edu/mini-courses/r/intro-to-r/advanced-plotting-in-r.md)
- [Writing Figures to a File](https://igb.mit.edu/mini-courses/r/intro-to-r/writing-figures-to-a-file.md)
- [Further Resources](https://igb.mit.edu/mini-courses/r/intro-to-r/further-resources.md)
- [Version Control with Git](https://igb.mit.edu/mini-courses/version-control-with-git.md)
- [About Version Control](https://igb.mit.edu/mini-courses/version-control-with-git/about-version-control.md)
- [Setting up Git](https://igb.mit.edu/mini-courses/version-control-with-git/setting-up-git.md)
- [Creating a Repository](https://igb.mit.edu/mini-courses/version-control-with-git/creating-a-repository.md)
- [Tracking Changes](https://igb.mit.edu/mini-courses/version-control-with-git/tracking-changes.md)
- [Exercises](https://igb.mit.edu/mini-courses/version-control-with-git/tracking-changes/exercises.md)
- [Exploring History](https://igb.mit.edu/mini-courses/version-control-with-git/exploring-history.md)
- [Exercises](https://igb.mit.edu/mini-courses/version-control-with-git/exploring-history/exercises.md)
- [Ignoring Things](https://igb.mit.edu/mini-courses/version-control-with-git/ignoring-things.md)
- [Remotes in Github](https://igb.mit.edu/mini-courses/version-control-with-git/remotes-in-github.md)
- [Collaborating](https://igb.mit.edu/mini-courses/version-control-with-git/collaborating.md)
- [Conflicts](https://igb.mit.edu/mini-courses/version-control-with-git/conflicts.md)
- [Open Science](https://igb.mit.edu/mini-courses/version-control-with-git/open-science.md)
- [Licensing](https://igb.mit.edu/mini-courses/version-control-with-git/licensing.md)
- [Citation](https://igb.mit.edu/mini-courses/version-control-with-git/citation.md)
- [Hosting](https://igb.mit.edu/mini-courses/version-control-with-git/hosting.md)
- [Supplemental](https://igb.mit.edu/mini-courses/version-control-with-git/supplemental.md)
- [Research Computing on Engaging with VSCode](https://igb.mit.edu/mini-courses/research-computing-on-engaging-with-vscode.md)
- [Connecting to Engaging via OnDemand](https://igb.mit.edu/mini-courses/research-computing-on-engaging-with-vscode/connecting-to-engaging-via-ondemand.md)
- [Files](https://igb.mit.edu/mini-courses/research-computing-on-engaging-with-vscode/connecting-to-engaging-via-ondemand/files.md)
- [Shell Access](https://igb.mit.edu/mini-courses/research-computing-on-engaging-with-vscode/connecting-to-engaging-via-ondemand/shell-access.md)
- [Interactive Apps](https://igb.mit.edu/mini-courses/research-computing-on-engaging-with-vscode/connecting-to-engaging-via-ondemand/interactive-apps.md)
- [Engaging Desktop](https://igb.mit.edu/mini-courses/research-computing-on-engaging-with-vscode/connecting-to-engaging-via-ondemand/interactive-apps/engaging-desktop.md)
- [Jupyter Notebook](https://igb.mit.edu/mini-courses/research-computing-on-engaging-with-vscode/connecting-to-engaging-via-ondemand/interactive-apps/jupyter-notebook.md)
- [RStudio Server](https://igb.mit.edu/mini-courses/research-computing-on-engaging-with-vscode/connecting-to-engaging-via-ondemand/interactive-apps/rstudio-server.md)
- [VSCode](https://igb.mit.edu/mini-courses/research-computing-on-engaging-with-vscode/vscode.md)
- [Basic Guide](https://igb.mit.edu/mini-courses/research-computing-on-engaging-with-vscode/vscode/basic-guide.md)
- [SSH Configuration](https://igb.mit.edu/mini-courses/research-computing-on-engaging-with-vscode/vscode/ssh-configuration.md)
- [Connecting to Engaging](https://igb.mit.edu/mini-courses/research-computing-on-engaging-with-vscode/vscode/connecting-to-engaging.md)
- [LLM Support](https://igb.mit.edu/mini-courses/research-computing-on-engaging-with-vscode/vscode/llm-support.md)
- [Running Containerized RStudio](https://igb.mit.edu/mini-courses/research-computing-on-engaging-with-vscode/running-containerized-rstudio.md)