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software carpentry teaching

Software Carpentry Workshop, Oxford, 9-10 January 2017

Earlier this week I instructed the first Software Carpentry workshop run by the Reproducible Research Oxford project. This is a one-year project supported by the IT Innovation Challenges Fund and the Social Sciences Division. It is led by Laura Fortunato and I’m a member of the project team. One of the main aims of the […]

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teaching

DTC Bioinformatics Module – Hackathon!

Last month I organised the Bioinformatics Module for the Oxford Interdisciplinary Bioscience Doctoral Training Partnership – this immediately followed the DTC Programming Module, which I also taught part of. This was the first year I’ve organised this three-week module and was fortunate that we had five teams of lecturers from the previous year who were […]

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teaching

DTC Programming Module – Feedback

Last month I finished lecturing part of the Programming Course that all the Doctoral Training Centre DPhil students do at the start of their first year. It is the first time I’ve helped teach the course so I thought I’d record some of the feedback I collected here. Overall the course introduces C and Python […]

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teaching

DTC Programming Course

Advanced Resources for the Curious http://software-carpentry.org http://www.datacarpentry.org http://rosalind.info Comics http://xkcd.com http://phdcomics.com Installing python on your laptop A good guide is to follow SciPy’s instructions. On my Mac I install python and its modules using MacPorts. For Windows I’d use Enthought Canopy or Anaconda. These work on Mac and Linux as well and give you python + […]

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teaching

2017 PhD projects advertised

If you are interested in helping combat antibiotic resistance and want to work on an interdisciplinary computational project with the possibility of strong public engagement (through bashthebug.net), please check out this project Antibiotic resistance in Tuberculosis: Predicting de novo the effect of individual genetic mutations. Supervised by me and Sarah Walker. These are part of […]

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antimicrobial resistance clinical microbiology teaching tuberculosis

Cheltenham Science Festival

A bit over a week ago I helped run the Modernising Medical Microbiology stall at the Cheltenham Science Festival. This was my first time helping explain about antibiotic resistance to, well, anyone and everyone. As I come from a molecular background and we didn’t have any information about protein structure, I thought I’d put together […]

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meetings molecular dynamics teaching

Analysing Simulation Data CECAM Workshop, Jülich, 14-15 October 2015

This two day workshop on Analysing Simulation Data was part of the larger CECAM Macromolecular Simulation Software Workshop at the Forschnungzentrum, Jülich that I co-organised. It was the second workshop and immediately followed an introductory Software Carpentry workshop. Prior to a few years ago I analysed all my simulation data using either VMD, often by […]

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computing meetings software carpentry teaching

Software Carpentry Workshop, Jülich, 12-13 October 2015

Last week, myself and David Dotson from ASU, ran a 2 day Software Carpentry workshop to kick off the CECAM Macromolecular Simulation Software Workshop at the Forschnungzentrum, Jülich. The idea was to give participants who were less well versed in python and working collaboratively with e.g. git a crash course to bring them up to […]

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computing meetings molecular dynamics software carpentry teaching

CECAM Macromolecular simulation software workshop

I’m co-organiser of this slightly-different CECAM workshop in October 2015 at the Forschungszentrum Jülich, Germany. Rather than following the traditional format of 3-4 day populated by talks with the odd poster session, this is an extended workshop made up of six mini-workshops. Since it is focussed on python-based tools for biomolecular simulations, of which there are an increasing number, the […]

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computing meetings skills teaching

HackDay: Data on Acid

Every year the Software Sustainability Institute (SSI) run a brilliant meeting called the Collaborations Workshop, usually in Oxford. This is an unconference lasting two days. At first glance it doesn’t look like it would be relevant to my research, but I always learn something new, meet interesting people and start, well, collaborations. The latest edition was last […]