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"<span aria-label=""Short training"" title=""Short training"">:material-monitor-account:</span>",**Command Line 101: Integrating your local and cluster compute environments**,February 19,11:00AM-12:00PM,Virtual
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"<span aria-label=""Short training"" title=""Short training"">:material-monitor-account:</span>",**Command Line 101: Tips & tricks for aspiring power users**,February 12,11:00AM-12:00PM,Virtual
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"<span aria-label=""Programming and Pizza"" title=""Programming and Pizza"">:fontawesome-solid-pizza-slice:</span>",**Programming and Pizza**,February 11,4:00PM-6:00PM,Northwest Building B227.45
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"<span aria-label=""Short training"" title=""Short training"">:material-monitor-account:</span>",**Command Line 101: What's the deail with directories?**,February 5,11:00AM-12:00PM,Virtual
@@ -31,15 +31,15 @@ Is this your first time sitting down typing commands into the command line or lo
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Now that you know how to move around the cluster, let's explore how to customize your command line experience. You'll learn about using dotfiles to automatically run things upon login, save and search your command history, use terminal multiplexers like screen, and more. If you plan to spend a good amount of time running programs on the command line, this seminar will save you effort and make your experience smoother!
#### Command line 101: Integrating your local and cluster compute environments
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**Thursday February 19 2026, 11AM - 12PM**
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In this seminar, we will cover topics and allow you to seamlessly move between your local environment to the cluster computer environment by using tools like VSCode and various file transfer applications. Geared towards both beginner and intermediate users, students will learn how to use apps to help them program and process data like a pro.
#### Command line 101: Git/GitHub on the cluster and on your computer
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## Calendar
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This Google calendar will show all our upcoming office hours as well as any workshops we have scheduled.
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This calendar will show all our upcoming office hours as well as any workshops or events we have scheduled.
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<iframe
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We piloted a series of short one hour short trainings in the Fall of 2024. These sessions are designed to be quick introductions to topics that we think are useful for researchers. Sessions with content are listed below. See our [previous events page](previous-events.md) to view topics that were live demonstrations with no attached content (look for the short trainings icon: :material-monitor-account:). If you are interested in any of these topics, please let us know and we can schedule another workshop or just talk about it with you!
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#### Command Line 101 Series
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#### Command line 101
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Introductions to working on computers through text interfaces, starting with file system basics and moving to topics such as remote computing, customizing your shell environment and git from the command line.
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Introductions to working on computers through text interfaces, starting with file system basics (part 1) and moving to topics such as remote computing, customizing your shell environment (parts 2 and 3), and git from the command line (part 4).
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##### :octicons-command-palette-24: Part 1: What's the deal with directories? Intro to file systems
-##### :octicons-command-palette-24: Part 1: What's the deal with directories? Intro to file systems
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Is this your first time sitting down typing commands into the command line or logging into the Cannon cluster to do an analysis? In this one hour seminar, we'll show you how files and directories are organized on common operating systems, including the Cannon cluster. You'll learn how to navigate a file system using the command line (aka the terminal), understand file permissions, and login to a remote server. This seminar is suitable for absolute beginners to command line and cluster usage.
<!-- Is this your first time sitting down typing commands into the command line or logging into the Cannon cluster to do an analysis? In this one hour seminar, we'll show you how files and directories are organized on common operating systems, including the Cannon cluster. You'll learn how to navigate a file system using the command line (aka the terminal), understand file permissions, and login to a remote server. This seminar is suitable for absolute beginners to command line and cluster usage. -->
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##### :octicons-command-palette-24: Part 2: Tips & tricks for aspring power users
-##### :octicons-command-palette-24: Part 2: Tips & tricks for aspiring power users
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Now that you know how to move around the file system, let's explore how to customize your command line experience. You'll learn about using environment variables and aliases, dotfiles to automatically run things upon login, and using terminal multiplexers like screen. If you plan to spend a good amount of time running programs on the command line, this seminar will save you effort and make your experience smoother!
<!-- Now that you know how to move around the file system, let's explore how to customize your command line experience. You'll learn about using environment variables and aliases, dotfiles to automatically run things upon login, and using terminal multiplexers like screen. If you plan to spend a good amount of time running programs on the command line, this seminar will save you effort and make your experience smoother! -->
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##### :octicons-command-palette-24: Part 3: Integrating your local and cluster compute environments
-##### :octicons-command-palette-24: Part 3: Integrating your local and cluster compute environments
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In this seminar, we will cover topics and allow you to seamlessly move between your local environment to the cluster computer environment by using tools like VSCode and various file transfer applications. Geared towards both beginner and intermediate users, students will learn how to use apps to help them program and process data like a pro.
<!-- In this seminar, we will cover topics and allow you to seamlessly move between your local environment to the cluster computer environment by using tools like VSCode and various file transfer applications. Geared towards both beginner and intermediate users, students will learn how to use apps to help them program and process data like a pro. -->
#### Population Genomics: Getting started with SNPArcher
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</div>
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December 10, 2025, 11:00AM-12:00PM (Virtual)
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#### Introduction to single-cell RNA-seq analysis
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[Download PDF of slides :octicons-download-24:](../workshops/short-trainings/snparcher/snparcher-tutorial.pdf){ .md-button }
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Part 1 introduces students to the basics of single-cell RNA-seq analysis, including pre-processing and cleanup of data for downstream analyses.
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#### Introduction to Genome Annotation
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Part 2 covers cluster marker gene discover, cell type annotation, and for multi-sample, multi-condition experiments, assessing and correcting batch effects, and differential expression analysis across experimental conditions. Note that to run the downloadable markdown below will require generating count matrices for the samples used in the training using *cellranger count*. Until we create an option for delivering the count matrices, please contact the Informatics Group for more information.
In collaboration with the [Bauer Sequencing Core :octicons-link-external-24:](https://bauercore.fas.harvard.edu/){:target="_blank"}, we hosted a short training session on DNA sequencing with long reads. This training covered the basics of long-read sequencing technologies and analysis. We provide the necessary information for you to (1) choose the sequencing technology options best suited for your research question and/or your sample quality, (2) understand the pros and cons of a PacBio vs ONT assembly for your project, (3) anticipate decision making points in your experiment and how it might affect downstream processes.
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-##### :material-dna: Part 2
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[Download PDF of slides :octicons-download-24:](../workshops/short-trainings/long-read/Long_Read_Workshop.pdf){ .md-button }
Part 2 covers cluster marker gene discover, cell type annotation, and for multi-sample, multi-condition experiments, assessing and correcting batch effects, and differential expression analysis across experimental conditions. Note that to run the downloadable markdown below will require generating count matrices for the samples used in the training using *cellranger count*. Until we create an option for delivering the count matrices, please contact the Informatics Group for more information.
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-##### :material-chart-line: Population Genomics: Getting started with SNPArcher
-##### :material-dna: DNA sequencing with long reads
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August 27, 2025, 11:00AM-1:00PM (Virtual)
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November 19, 2025, 11:00AM-1:00PM (Virtual)
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[Download PDF of slides :octicons-download-24:](../workshops/short-trainings/onboarding-offboarding/Onboarding_Offboarding_Fall2025.pdf){ .md-button }
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In collaboration with the [Bauer Sequencing Core :octicons-link-external-24:](https://bauercore.fas.harvard.edu/){:target="_blank"}<!--, we hosted a short training session on DNA sequencing with long reads. This training covered the basics of long-read sequencing technologies and analysis. We provide the necessary information for you to (1) choose the sequencing technology options best suited for your research question and/or your sample quality, (2) understand the pros and cons of a PacBio vs ONT assembly for your project, (3) anticipate decision making points in your experiment and how it might affect downstream processes.-->
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#### Workflow managers and Nextflow demo
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[Download PDF of slides :octicons-download-24:](../workshops/short-trainings/long-read/Long_Read_Workshop.pdf){ .md-button }
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November 12, 2024, 9:30-10:30AM and November 13, 2024, 12:15-1:15PM (Northwest Building 453)
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-##### :material-source-branch: Basics of git and GitHub with GitHub Desktop
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[Download PDF of slides :octicons-download-24:](../workshops/short-trainings/workflow-managers/Workflow_managers.pdf){ .md-button }
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September 24, 2025, 12:00-1:00PM (Virtual)
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#### Plotting in R with ggplot
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[Download PDF of slides :octicons-download-24:](../workshops/short-trainings/git-github/git_github_one_hour.pdf){ .md-button }
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October 29, 2024, 9:30-10:30AM and October 30, 2024, 12:15-1:15PM (Northwest Building 453)
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-##### :material-transfer: The Baton Pass: Data onboarding and offboarding
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