General Information

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

The workshop is funded by NERC as part of the Advanced Training Short Courses programme. Priority will thus be given to NERC-funded PhD students and early career researchers from the environmental sciences who should contact Jon Mound for booking information. Some funding to cover travel and accommodation costs of these participants is avalable. Any unallocated spaces will be made generally avalable in early August

Who: The course is aimed at postgraduate students and other scientists who are familiar with basic programming concepts (like loops, conditionals, arrays, and functions) but need help to translate this knowledge into practical tools to help them work more productively. Priority will be given to NERC-funded PhD students and early career researchers from the environmental sciences.

Where: School of Earth and Environment, University of Leeds, Leeds, LS2 9JT. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail J.E.Mound@leeds.ac.uk for more information.

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Schedule

Etherpad: https://etherpad.mozilla.org/2015-08-26-leeds.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

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Syllabus

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Setup

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser. Once you are done installing the software listed below, please go to this page, which has instructions on how to test that everything was installed correctly. We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

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Before the workshop

There are a three extra tasks to undertake before the workshop in order to help make sure things run smoothly. Please try to do the following.

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During and after the workshop

We have gathered together the various links you will need and useful information below. These will remain accessable after the workshop and we will add to this list as the workshop progresses. Please read and abide by the code of conduct.

We will make use of this etherpad during the workshop. Please use this to keep collaborative notes and ask (and answer) each others questions. Feel free to tweet from the workshop using #SWCLeeds.

Workshop material

Much of the material we will be using during the workshop can be found online and you will need copies of this on your laptop. In order to download the material for the first session (and to check you have a working system with internet access) please start a new shell and type the following commands:

cd 
cd Desktop
git clone https://github.com/andreww/2015-08-26-leeds-bash.git
cd 2015-08-26-leeds-bash

(typing return after each line). You should see something like "repository successfully cloned". Let us know if this does not work for you.

Archived material for bash, python and defensive programming can be downloaded as zip files. Aaron's git material can be found at http://aaren.me/2015-08-26-git/

Stuck somewhere new?

If you find yourself in a shell that you don't recognise, or in an editor that you can't get out of then see recognising prompts and how to exit.

Useful links

Software Carpentry online lessions:

• The Unix Shell
• Version Control with Git
• Programming with Python

Git:

• GitHub interactive Git tutorials
• Git pretty - a flowchart about how to recover from mistakes.
• Changing History, or How to Git pretty - slides relating to the above.

Python:

• basemap introduction and an updated version
• matplotlib examples gallery - includes source code.
• SciPy Cookbook - examples of how to do useful stuff using numpy, scipy, matplotlib, interfacing, etc.
• Scientific Python lecture notes

Training:

• ARCHER Training - free HPC training all over the UK.
• Code Academy - free online programming courses

Papers

Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, et al. (2014) Best Practices for Scientific Computing. PLoS Biol 12(1): e1001745. doi:10.1371/journal.pbio.1001745.

Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013) Ten Simple Rules for Reproducible Computational Research. PLoS Comput Biol 9(10): e1003285. doi:10.1371/journal.pcbi.1003285.

Noble WS (2009) A Quick Guide to Organizing Computational Biology Projects. PLoS Comput Biol 5(7): e1000424. doi:10.1371/journal.pcbi.1000424.

Ram K (2013) "git can facilitate greater reproducibility and increased transparency in science", Source Code for Biology and Medicine 2013, 8:7 doi:10.1186/1751-0473-8-7.

Glass, R. (2002) Facts and Fallacies of Software Engineering, Addison-Wesley, 2002. (PDF).