/Accelerated_Intro_to_CompBio_Part_1

Part 1 of the "Accelerated intro to Computational Biology for Biologists" course for the Master's Programme in Computational Biology, Universidad Politecnica de Madrid. This covers the first 2 days (~6 hours) of material, taught by Mark Wilkinson.

Primary LanguageJupyter NotebookOtherNOASSERTION

Accelerated Introduction to Computational Biology for Biologists - Part 1

Part 1 of the "Accelerated intro to Computational Biology for Biologists" course for the Master's Programme in Computational Biology, Universidad Politecnica de Madrid. This covers the first 2 days (~6 hours) of material, taught by Mark Wilkinson.

This is the basics of the basics, just to get you started!

In this course we cover:

  • Setting-up your Virtual Machine
  • The Linux Operating System - basic basics
  • GitHub - getting this course!

WHAT YOU NEED TO DO BEFORE THE FIRST DAY

Windows VMWare Player: https://my.vmware.com/en/web/vmware/free#desktop_end_user_computing/vmware_workstation_player/14_0 Mac VirtualBox: https://www.virtualbox.org/

You should download and unzip the Virtual Machine we have created for this course: https://doi.org/10.5281/zenodo.1147435

WINDOWS: Start VMWare, and select "open virtual machine". Browse to the folder that you just unzipped. Double-click.

MAC: After unzipping, there is a file with the extension .vmdk. You need to start VirtualBox, then follow these instructions: Open VirtualBox and create a new virtual machine. Click the "Settings" button Click Storage Click SATA Controller Click Add Hard Disk Navigate to and double-click on the VDMK file. Click OK to save the setting. Now your virtual machine will be using the virtual hard disk I created for the course.

Once the virtual machine starts, your default password is 'osboxes.org'

3 ways to run this course:

**CURRENTLY DISABLED ** 1) Binder is a way to interact with the Jupyter notebooks inside of this repository - try it!
![Binder]

(http://mybinder.org/badge.svg)

  1. If you use Docker, you can docker pull, and then docker run this course as a Docker image as follows:

    docker pull markw/upm_compbio_masters_programme

    docker run -p 9000:9000 -it markw/upm_compbio_masters_programme jupyter notebook --ip 0.0.0.0 --port 9000

    Open the link displayed to begin browsing the (interactive) course in your Web browser.

  2. Download the VM Ware image that has additional software such as Komodo edit and BlazeGraph installed (see instructions below)

UPM Students - INSTRUCTIONS

Dear Students,

You will take this course using a VMWare Virtual Machine. You should do the following:

  1. CREATE AN ACCOUNT ON GitHub (this website) if you haven't already got one...
  2. Download VMWare Player (if you haven't already got it): https://my.vmware.com/web/vmware/free#desktop_end_user_computing/vmware_workstation_player/14_0
  3. You should download the VMWare Virtual Machine that I have created for this course, which is in this Zenodo deposit: https://doi.org/10.5281/zenodo.1147435
  4. Unzip the virtual machine
  5. Start VMWare Player and select the virtual machine - start it (PASSWORD IS osboxes.org)
  6. In the top-right corner of the VM Desktop, you can select either US-style or Spanish-style keyboard
  7. Browse to: https://github.com/CBGP-UPM-INIA-PUBLIC/Accelerated_Intro_to_CompBio_Part_1
  8. In the top-right corner, click "Fork", to make a copy of this repository in your own GitHub account
  9. Browse to the copy in your GitHub account (you should already be there after Forking)
  10. Click the big green "Clone" button and copy the address to your clipboard
  11. open a terminal window in your Virtual Machine
  12. type: git clone http://github.com/yoruaccountname//Accelerated_Intro_to_CompBio_Part_1.git (whatever you copied in step 9)
  13. after it is cloned, cd into the "Lectures" folder and type jupyter notebook to start the interactive Jupyter session
  14. Browse to Lesson 1 and... let's get started!