Part 2 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 weeks (~24 hours) of material, taught by Mark Wilkinson.
In this part of the course we cover:
- Jupyter Notebooks (a bit more detail)
- Introduction to Docker
- Introduction to Databases (mySQL), including Docker installation
- SQL (and perhaps other kinds of DBs, time permitting)
- Introduction to Python
A BioRuby-based bioinformatics course (still under-development - not recommended for ANY purpose!)
** CURRENTLY DISABLED ** 1) Binder is a way to interact with the Jupyter notebooks inside of this repository - try it!
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If you use Docker, you can
docker pull, and thendocker runthis course as a Docker image as follows:docker pull markw/upm_compbio_masters_programmedocker run -p 9000:9000 -it markw/upm_compbio_masters_programme jupyter notebook --ip 0.0.0.0 --port 9000Open 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_2
- 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_2.git(whatever you copied in step 9) - after it is cloned, cd into the "Lectures" folder and type
jupyter notebookto start the interactive Jupyter session - Browse to Lesson 1 and... let's get started!