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I cannot attend. Would it be possible to access the materials that will be given in the bootcamp?

Slides are at It is worth noting that we're basing our workshop on the Software Carpentry series of training workshops, and their materials are open source and licensed to the creative commons at 


Is the required software simply an SSH terminal, or are there specific packages, libraries, distributions, etc that we need to install beforehand? 

The minimum requirement is that you can use ssh to log into CLEAR where we'll have relevant software installed.

If you would like to follow along on your laptop, we're doing tutorials on general Linux proficiency, Python, and R. If you have a laptop running Linux (or can install a Linux VM on your laptop), Fedora or CentOS would be the best analog for the Red Hat Enterprise Linux distribution we run on all campus machines.

Virtual Machines and installation of Fedora/CentOS are beyond the scope of our workshop.


Where I can find the secure shell client to install?

For Windows users, please see SSH with X11 forwarding on Windows. For all other (modern) operating systems, pull up a terminal and follow Using SSH to Login and Copy Files

Software Bootcamp  Schedule

9:00-9:30 Registration, Admin

9:30-10:00 Introduction

10:00-11:00 Version Control and Data Management

  • Core concepts of version control:

    • Repository vs. working copy

    • Check out/in

    • Logs and revisions

    • Conflict management

  • Subversion (Rice)

    • Why Subversion?

    • Creating a repo at Rice

    • Subversion clients (gui/cli)

  • Git (non-Rice)

    • Didn’t I just learn Subversion??

  • Data Management

  • Databases - RDBMS Relational / NO-SQL Non-Relational Database Primer

11:00-11:30 HPC Resources

  • Local Resources


11:30-12:30 Lunch

12:30-1:30 RHEL/ Linux shell basics

  • Everything’s a file

  • Pipes and redirection

  • Scripts

  • Finding/installing software

    • Configure, Make, Install

  • Secure Shell

1:30-3:00 Python

  • How to explore the interactive interface

  • Flow Control

  • In/Out

  • Variables

  • Functions

  • Regular Expressions

  • Libraries

3:00-3:15 Break

3:15-4:45 R


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