Monthly Archives: March 2014

Evoldir software message of interest to lab

I work with population genetics and population structure of honey
bees. Therefore I had been writing some R scripts for my personal use
and someone recently suggested that I make it into a package that can
be shared. Therefore I have recently put together some useful stuff into
an R package called pophelper.

Basically, this R package does what STRUCTURE HARVESTER does. pophelper
works with structure and TESS output files. I think it may be useful
for people working with STRUCTURE, TESS and R. This package requires
some basic R skills to use. pophelper can be used to tabulate runs,
summarise them, perform Evanno method, export to CLUMPP format, generate
barplot figures etc.

The package can be installed from github for the moment. Once a stable
version is established, it will be uploaded to CRAN.

https://github.com/royfrancis/pophelper

I would very much appreciate if you could share this with the community. I
am also hoping people are willing to give this a try and provide some
feedback/comments/suggestions/criticisms etc. Feel free to contact me
at roy.m.francis@outlook.com if you run into any issues or have any
questions etc.

Sincerely,Roy Francis

IST Postdoctoral Fellowships

Next deadline is 15 March. See http://ist.ac.uk/istfellow

FREE Sheffield Research computing – Monday 31st March

Message from Terry:

I want to encourage anyone who has used Iceberg to present a poster on their work – Iceberg is having an £800k “refresh” and it is important that we show that we are productive users so that our needs are catered for.

You are invited to attend the prestigious research computing event HPC@Sheffield2014. The event is free to Sheffield researchers and takes place on Monday 31 March 2014 9:30-4:30.

HPC@Sheffield2014 will be introduced by the Vice Chancellor and has the themes High Performance Processing, Big Data and Visualisation.

It will comprise of a series of presentations, poster competition, vendor exhibits and demonstration which will help to explain how researchers may take advantage of the e-infrastructure and the HPC facilities provided in order to enhance and advance their research.

Complete the form on www.eventbrite.co.uk/e/hpcsheffield2014-tickets-10644637397 to reserve your place.

Full programme:

  • 10:00  Opening and Welcome – Prof. Sir Keith Burnett, Vice Chancellor, University of Sheffield
  • 10:15  Making Progress with High Performance Computing, The Institute for Inisilico Medicine – Prof. D. Lacroix
  • 10:45  What  is Big Data and How is it Managed? The Bioinformatics Hub – Prof. Roy Chaudhuri
  • 11:15  Coffee
  • 11:45  A New Approach to Bringing Industry and The University Together, The Advanced Computing Research Centre – Prof. Mike Holcombe
  • 12:05  Solver Enhancements in Finite Element Analysis with Abaqus – Mr. Clint Davies-Taylor, Dassault Systems
  • 12:30  Poster Session and Lunch
  • 14:00  GPU Accelerated Computing – Mr. J. Purches NVIDIA Ltd.
  • 14:30  Big Data Challenges in Particle Physics, Beyond the Higgs Boson – Dr Kerim Suriliz
  • 14:50 Using the N8 Facility for the Simulation of Turbulent Flow Structures for Engineering Applications – Miss Wei Wang.
  • 15:15  Coffee
  • 16:00  Forthcoming Developments in Research Computing – Prof. John Harding, Co. Chair of Research Computing Advisory Group
  • 16:30  Close

DNA from feathers

Hi everyone!
I have recently met a research fellow, Rachael Shaw, who is studying cognition in New Zealand North Island robins, and she is about to start her fieldwork sampling. The conservation manager she is working with routinely takes feather samples when banding, and Rachael was wondering whether these could be used for sexing and microsat genotyping for parentage analysis? Does anyone have any experience genotyping from feathers, what extraction methods worked best, and whether there was an optimal way to store the feathers to minimise degradation?
Many thanks for any help you can offer!
Anna Santure (a.santure@auckland.ac.nz)

Editorial job

Dear Colleagues

I am going to be taking paternity leave again for the second half of 2014, so we are looking for a locum Ecology and Evolution Editor to start in June. It would be great if you could pass this job posting on to anyone you know who might be interested:

http://www.nature.com/naturejobs/science/jobs/386707-locum-ecology-and-evolution-editor

Many thanks for your help.

Best wishes

Patrick

Patrick Goymer, DPhil

Senior Editor

Nature

Software preferences for Windows 7 computers

As the lab computers are getting upgraded to Windows 7 I would like to get feedback on software that people may particularly want installed on them. Each computer will have MS office and Firefox but will also have Genemapper (installed on the virtual platform VMware and running on XP). If anybody has suggestions as to what other software may be needed please email me at g.horsburgh@sheffield.ac.uk.

Thanks

University of Sheffield Three Minute Thesis competition

Share your research with the world

How long would it take you to explain your thesis to somebody who’s not an expert in your subject? Well, too bad: you’ve got three minutes!

This year, the University of Sheffield is challenging all postgraduate researchers to take part in the national Three Minute Thesis competition. You’re passionate about your research, but can you pass on that enthusiasm to an audience of non-specialists?

Public engagement is a crucial part of academic research, irrespective of your discipline; by taking part in the University of Sheffield’s Three Minute Thesis you will have the opportunity to take your research into the wider community, raising your academic profile locally, nationally and even internationally.

This is the first year that University of Sheffield has taken part in this competition and, as well as competing against other researchers to represent the University at the UK final of Three Minute Thesis in September, you will also be competing for a University prize of up to £750 to spend on a conference or other academic/professional development activity.

All postgraduate researchers are eligible to take part. If you’re interested, your first step is to submit a short (max 350 words) summary of your research, suitable for a non-specialist audience, by 14th March.

All the information you need about eligibility, rules, prizes, key dates and judging criteria is available on the University of Sheffield’s Three Minute Thesiswebpage, as well as some examples of winning Three Minute Thesis entries.

ENTER NOW:

www.sheffield.ac.uk/icoss/training/thinkahead/3mt

This event is coordinated by Sarah Bell, sarah.j.bell@sheffield.ac.uk

Lab meeting tomorrow 10am B52

Dear everyone,

Our next molecular ecology lab meeting will be tomorrow 4th March at 10am in room B52. Our two speakers will be:

Anja Westram. Genomic signatures of adaptive divergence in Littorina snails
Nyil Khwaja. Wrens with benefits: inclusive fitness and kin recognition in the rifleman

Available dates for giving a talk are the following:
April 1st
May 6th
June 3rd
August 5th
September 2nd

I especially encourage people who have never given a talk at one of these meetings to present their work, even if you feel it is not yet finished. These meetings are a great opportunity not only to let people know what you are working on, but also to get valuable feedback about your project. You can also use these meetings as a rehearsal for talks that you will present somewhere else (conferences, symposia, VIVA, applications, etc.).

Finally, please let me know if there are new people that need to be added to this list.

All the best,

Mauricio Montaño-Rendón

HPC@sheffield2014 – Monday 31st March, Firth Hall

This year’s HPC@sheffield event will provide another opportunity for researchers, post graduates and final year undergraduates to hear about latest projects that take advantage of the state-of-the-art high performance computing facilities, provided both locally and also nationally, in an effort to expand the frontiers of science.

The event will comprise of a series of presentations, poster competition, vendor exhibits and demonstration which will help to explain how researchers may take advantage of the e-infrastructure and the HPC facilities provided in order to enhance and advance their research.
The emphasis of the 2014 event will be around the themes of high performance processing, big-data and visualisation.
Abstract for posters should be e-mailed to hpchub@sheffield.ac.uk
The prize for the best poster is a Titan GPU, kindly donated by Nvidia.
Attendance is by registration: