> 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 and KI Computational Resources](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources.md)
- [Basic Unix](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/basic-unix.md)
- [Why Unix?](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/basic-unix/why-unix.md)
- [The Unix Tree](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/basic-unix/the-unix-tree.md)
- [The Unix Terminal and Shell](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/basic-unix/the-unix-terminal-and-shell.md)
- [Anatomy of a Unix Command](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/basic-unix/anatomy-of-a-unix-command.md)
- [Basic Unix Commands](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/basic-unix/basic-unix-commands.md)
- [Output Redirection and Piping](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/basic-unix/output-redirection-and-piping.md)
- [Manual Pages](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/basic-unix/manual-pages.md)
- [Access Rights](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/basic-unix/access-rights.md)
- [Unix Text Editors](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/basic-unix/unix-text-editors.md)
- [nano](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/basic-unix/unix-text-editors/nano.md)
- [vi / vim](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/basic-unix/unix-text-editors/vi-vim.md)
- [emacs](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/basic-unix/unix-text-editors/emacs.md)
- [Shell Scripts](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/basic-unix/shell-scripts.md)
- [Software Installation](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/software-installation.md)
- [Module](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/software-installation/module.md)
- [Conda Environment](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/software-installation/conda-environment.md)
- [Slurm](https://igb.mit.edu/mini-courses/introduction-to-unix-and-ki-computational-resources/slurm.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)


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://igb.mit.edu/mini-courses.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.