News Archive

31 May 2016

EASTBIO DTP PIPS Coordinator, Caroline Pope has recently reported on PIPS.

This is an exciting time for the new 2015 cohort of EASTBIO students. Many have innovative PIPS ideas. The deadline for submitting the ‘PIPS Planning Sheet’ is September 31st 2016. To help with this students are encouraged to

  • Read the 'EASTBIO brochure' and ‘PIPS Student Guide’
  • Agree PIPS timing with PhD supervisor
  • Review the skills audit to assess what skills and experience you wish to use PIPS to develop
  • Attend networking events and discuss with a Careers Advisor
  • Explore online existing 'Internship' schemes etc.

The 2014 cohort are busy approving their ‘PhD Internship Agreement’ which outlines the parties, roles and responsibilities and project details of their internship. Professional internships are being developed in Scottish organisations such as: Parkure, Ingenza, Snygenta, Elsevier, GSK, the Scottish Government as well as further afield in Canada and Germany. Congratulations to all of our 2013 cohort who have completed their PIPS and are now submitting the online the post ‘PIPS BBSRC DTP PIPS Placement Report’.


31 May 2016

First-year student Hamish Todd (U o Edinburgh) has been working with the Protein Data Bank to integrate his virtual reality program onto their website: that way he will be enabling people to look at any protein they like in VR!

Proteins and nucleic acids are complex three-dimensional structures. In order to learn, research, or speak about them, we are often required to internally “picture” them - and if we are interested in docking, substrate binding, or point mutations, our ability to picture them will be sorely tested.

In collaboration with the protein data bank, he intends to use virtual reality technology to improve the way that biomolecules are illustrated. If you can find your protein of interest on the protein data bank, he intends that the user will simply have to click one button to be taken to a VR representation of it, which may be twisted arbitrarily and docked to other proteins. By allowing multiple people to view a person interacting with a protein in a single environment, the vision is to bring something very new to biology teaching.

Here's a visualisation on it.

31 May 2016

In January this year Ben Rutter (U of Aberdeen) attended a 2-week ‘workshop on genomics’ in Cesky Krumlov, Czech Republic. It was a very intensive course which was ‘developed in response to the increasing demand for training on how to effectively analyze and manage data generated by modern sequencing technologies’.

The reason for him going to this was to be able to learn how to assemble a genome De Novo. After this course and just recently he has, he told us, assembled the genomes of two fungi that have never had their genomes sequenced before, using the command line.

Ben has never had any experience of the command line and now he feels very confident about this. Hewanted to make others aware of this course for analysing any sort of sequencing data - it covers many topics and not just whole genome sequencing.

For more info on the course, see here.

31 May 2016

Congratulations to another one of our third-year, Douglas Pyott (U of Edinburgh) for his research paper! Details and abstract below or for a link, click here.

Pyott, DE, Sheehan, E, Molnar, A. ‘Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants.’ Mol Plant Pathol. 2016 Apr 21. doi: 10.1111/mpp.12417.


31 May 2016

Congratulations to our third-year student Audrey Henderson (U of St Andrews) for her research paper, which came out in April 2016:

Henderson, A. J, Holzleitner, I. J., Talamas, S. N., Perrett, D. I, ‘Perception of Health from Facial Cues’. Philosophical Transactions of the Royal Society.

The paper investigates which facial cues are important when making judgements of how healthy a person looks. The contributors found that multiple cues are improtant: skin colour (particularly yellowness), adiposity levels and expersions (how smiley or dowturned a mouth looks) were all influenceing how healthy faces were judged to be. See here for more details.

31 May 2016

Katherine Bassil, a final year biology undergraduate with the American Lebanese University, made contact with Edinburgh University through Jane Haley (Edinburgh Neuroscience) to set up a lab placement at the Roslin Institute in Rona Barron's lab with final year Eastbio PhD student Kirsty Ireland.

26 May 2016

We hope you will enjoy reading the May 2016 BBSRC DTP/ICP Newsletter. Input by some of the EASTBIO students features here!

Please click on the image below.


3 May 2016

The EASTBIO Symposium 2016 on Bioscience Research is to be held at the University of St Andrews on the 13-14 June 2016.

For EASTBIO students and supervisors: To register, please click here.

To view a draft programme, click on the Symposium poster, below.


2 May 2016

Lawrence Picton, who recently graduated from the University of St Andrews where he completed his PhD funded by the EASTBIO DTP - he is actually the first EASTBIO student who completed his doctoral studies - has contributed to The Neuroethology of Predation and Escape, with Keith T. Sillar and William J. Heitler (Wiley Blackwell).

For the book flier and an order form, please click on the image on the right.

Congratulations to Lawrence for a marvellous start to his post-doctoral career!

2 May 2016

Six BBSRC Research Experience Placements 2016 were awarded across the EASTBIO DTP to:

Alex Websdale, sponsored by Professor Carol Munro (School of Medicine, Medical Sciences and Nutrition, University of Aberdeen), to do a BfH project "Investigating Candida albicans echinocandin drug susceptibility with gain of function mutants”

Manuel Blank, sponsored by Professor Frank Sargent (School of Life Sciences, University of Dundee), to do an IBB project "Carbon capture and storage using engineered bacteria"

Robyn Macrae, sponsored by Dr Melissa Cudmore (Centre for Cardiovascular Science, University of Edinburgh), to do a BfH project "The role of VEGF receptor interactions during vascular morphogenesis”

Emma Lund, sponsored by Dr Steven Pollard (Centre for Regenerative Medicine, University of Edinburgh), to do a BfH project "Genome editing in mouse neural stem cells"

29 Feb 2016

At the recent EASTBIO DTP 2016 PIPS QA Event in Dundee (12 February), our second-year students were treated to a number of presentations by students who have completed their PIPS and gave some useful insights into actual experiences of placements.

Fraser Murphy (Dundee-based third-year student) shared his slides with us; click on the image below to get a sense of his talk.


22 Feb 2016

Our second-year students will be taking part in a live 'Speed Science' event, which is part of the British Science Week activities in the partner University of Aberdeen on the 17-18 March 2016.

This is an interactive element of their EASTBIO Science Communication training run this year by the University of Aberdeen, where students will be putting into practice skills developed in the two-day workshop in front of a live audience.

More details to be published here soon.

10 Feb 2016

EASTBIO third-year student Christopher Johnston, based at the University of Aberdeen, wrote a report for the Scottish Government during his PIPS internship which got published and hit the national news.

One of the first studies to use the full data set of survey results between 1990 and 2013, shows lowest levels of smoking amongst 13 and 15-year old pupils in Scotland.

Congratulations to Chris on a fine job, with plenty of impact!


7 Oct 2015

We are currently revising our Training Programme and wish to draw the attention of our students and supervisors - existing and new ones - to the changes in requirements and timelines for each of the four EASTBIO student cohorts.

Please go to our Programme page to see a variety of guides for students and supervisors or click on the child pages to see year-by-year views of our Training.

Browse the revised EASTBIO Student Handbook 2015 for more insights into the thinking and interconnection of the different strands of our training.

As we are finalising the details of some of the optional training open to EASTBIO students across the partnership, we would appreciate the input by partners and colleagues. Please check these pages regularly for updates and contact us at EASTBIO if you spot any mistakes, obvious omissions or wish to offer a suggestion.

22 Sep 2015

The EASTBIO website is currently being moved to a different server. As a result, remote access to it for registered users (EASTBIO students and supervisors) may be blocked. Students and supervisors not based at the University of Edinburgh may not be able to access some of its pages during this week.

We hope that the reconfiguration will be complete by the end of this week (21-28 September). Apologies for the inconvenience.

For any query, please email EASTBIO.

3 Sep 2015

Our Induction Day for students who start their PhD in 2015 and hosted by the University of Dundee (28 September 2015) will be followed this year by a Foundation Masterclass on Statistics and Experimental Design (29 September), delivered by Dr Margo Chase-Topping (Centre for Immunity, Infection and Evolution, University of Edinburgh).

Find more details here.

20 Jul 2015

Edinburgh Genomics runs an Introduction to Variant Analysis of NGS Data in Edinburgh on Thursday 22 and Friday 23 October 2015. The workshop is aimed at researchers, postdocs and PhD students who want to learn how to do variant analysis of next generation sequencing data.

The aim of the 2-day workshop is to familiarise researchers with and to initiate them in the variant analysis of NGS data by providing lectures and practicals on analysis methodologies. In the practicals Illumina-generated sequencing data and various widely used software programs (e.g. FastQC, FastqMcf, Bowtie2, TopHat2, Picard, RSeQC, samtools, IGV, GATK, DeNovoGear, MuTect, RVtests, VEP, SnpEff, ANNOVAR) will be used. The workshop will be focused on human and in the practicals data sets from human will be used.

The workshop will be given by Marta Bleda and Ignacio Medina of the University of Cambridge.

For this workshop we will do participant selection. The application deadline is Thursday 24 September 2015 noon.

16 Jul 2015

We will be welcoming our new students and supervisors at our Induction Day 2015 which will be hosted by the University of Dundee on Monday the 28th of September 2015 at the West Park Conference Centre.

The Induction Day will be followed by an EASTBIO masterclass on "Statistics and Experimental Design" course on Tuesday the 29th September 2015.

The programme for both days and general information will be posted on our Induction Day page soon. Email EASTBIO for any questions.

9 Jun 2015
Edinburgh Genomics offers two 5-day workshops on Python for Biologists, one at introductory and the other at advanced level. Both courses to be held in August in Edinburgh (King's Buildings) on a first come first served basis. Please note the registration deadlines and read carefully the information on the links provided below.
For further information, please contact Bert Overduin.
5-day Introduction to Python for Biologists
Date: Mon 3 - Fri 7 August 2015
Price: £500
Registration deadline: Mon 20 July 2015
This workshop is first come, first served.
5-day Advanced Python for Biologists
Date: Mon 17 - Fri 21 August 2015
Price: £500
29 Apr 2015

Places are still available for SysMIC, an online course in systems biology.

The course provides introductory and advanced training in maths and computing, based around biological examples. Participants will gain an understanding of programming MATLAB to model and simulate biological systems and the R package to run statistical analysis of results.

Every topic includes code examples, exercises and quizzes, with hands-on support provided by online tutors.

There are three modules available to study, each lasting six months and requiring about five hours work per week.

1 - Basic Skills

2 - Advanced topics and applications

3 - Project work

You can find the full course details here.

We issue a suggested schedule to help participants complete in 6 months, in time for certification, but the deadlines are flexible as SysMIC is a self-directed course.

Module 1 for the spring 2015 cohort started on the 20th of April 2015.  The next cohort will be around October/November 2015.