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!
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'
**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)
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If you use Docker, you can
docker pull
, and thendocker 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.
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Download the VM Ware image that has additional software such as Komodo edit and BlazeGraph installed (see instructions below)
Dear Students,
You will take this course using a VMWare Virtual Machine. You should do the following:
- CREATE AN ACCOUNT ON GitHub (this website) if you haven't already got one...
- 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
- 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
- Unzip the virtual machine
- Start VMWare Player and select the virtual machine - start it (PASSWORD IS osboxes.org)
- In the top-right corner of the VM Desktop, you can select either US-style or Spanish-style keyboard
- Browse to: https://github.com/CBGP-UPM-INIA-PUBLIC/Accelerated_Intro_to_CompBio_Part_1
- In the top-right corner, click "Fork", to make a copy of this repository in your own GitHub account
- Browse to the copy in your GitHub account (you should already be there after Forking)
- Click the big green "Clone" button and copy the address to your clipboard
- open a terminal window in your Virtual Machine
- type:
git clone http://github.com/yoruaccountname//Accelerated_Intro_to_CompBio_Part_1.git
(whatever you copied in step 9) - after it is cloned, cd into the "Lectures" folder and type
jupyter notebook
to start the interactive Jupyter session - Browse to Lesson 1 and... let's get started!