README.md - BS32010 University of Dundee

Overview

This repository contains teaching materials used in delivering the BS32010 bioinformatics course lecture and workshops on “Comparative Genome Analysis and Visualisation” at the University of Dundee, March 2016

The format has changed since 2015, and now takes the form of:

• One introductory lecture (1hr)
• Two workshops (2hr each)

The lecture notes and slides can be found in the lecture subdirectory, and the material for the workshops can be found in workshop_1 and workshop_2.

Getting Started

You can grab a local copy of all the files for this workshop/lecture using git clone:

$ git clone https://github.com/widdowquinn/Teaching-Dundee-BS32010.git

Prerequisites

The exercises and examples have been written, and are known to run, with the following software, but they may also run happily on other versions:

• Python 3.5.1
• Jupyter 4.06
• Biopython 1.66
• Pandas 0.17.1
• i-ADHoRe 3.0.01
• NCBI BLAST 2.2.31+
• MUMmer 3.23
• MCL 14-137

Executing notebooks

To start the notebooks in your browser, execute

$ jupyter notebook

at the command-line.

You will be able to read the HTML sessions in your browser, but the work for these will be done largely in the terminal or standalone applications.

Licensing

Presentation

The presentation/lecture components are licensed under the Creative Commons Attribution ShareAlike license:

• https://creativecommons.org/licenses/by-sa/4.0/

summarised below

You are free to:

Share — copy and redistribute the material in any 
        medium or format
Adapt — remix, transform, and build upon the 
        material for any purpose, even commercially.

The licensor cannot revoke these freedoms as long 
as you follow the license terms.

Under the following terms:

Attribution — You must give appropriate credit, 
             provide a link to the license, and 
             indicate if changes were made. You 
             may do so in any reasonable manner, 
             but not in any way that suggests the 
             licensor endorses you or your use.                  
ShareAlike — If you remix, transform, or build 
             upon the material, you must distribute 
             your contributions under the same 
             license as the original.
No additional restrictions — You may not apply 
             legal terms or technological measures 
             that legally restrict others from 
             doing anything the license permits.

Notices:

You do not have to comply with the license for 
elements of the material in the public domain or 
where your use is permitted by an applicable 
exception or limitation.

No warranties are given. The license may not give 
you all of the permissions necessary for your 
intended use. For example, other rights such as 
publicity, privacy, or moral rights may limit how 
you use the material.

Software and code

Unless otherwise indicated, all code is subject to the following agreement:

(c) The James Hutton Institute 2014-2016
Author: Leighton Pritchard

Contact: leighton.pritchard@hutton.ac.uk

Address: 
Leighton Pritchard,
Information and Computational Sciences,
James Hutton Institute,
Errol Road,
Invergowrie,
Dundee,
DD2 5DA,
Scotland,
UK

The MIT License

Copyright (c) 2014-2016 The James Hutton Institute

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.