Category Archives: News

Workshop for Research Software Engineers

We’re organising a workshop for Research Software Engineers with the Software Sustainability Institute on September 11th in Oxford.

You might not consider yourself a “Research Software Engineer” but the workshop is aimed at anyone who develops software in an academic research context. If any of the following are true you might want to attend:

  • Are you employed to develop software for researchers?
  • Are you a researcher who now spends more time developing software than conducting research?
  • Are you employed as a postdoctoral researcher, even though you predominantly only on software development?
  • Are you the “person who does computers” in your research group?
  • Are you not named on research papers despite playing a fundamental part in developing the software used to create that research?
  • Do you lack the metrics needed to progress your career in research – like papers and conference presentations – despite having made a significant contribution with software?

The workshop will be a chance to network with and learn from people in similar roles, find out what methods and tools other people are using, discuss ways to improve the long term maintenance and sustainability of academic software, reproducibility of research and academic career recognition of the work that goes into software dev.

More details here:

and registration here:

New MSc Genes, Environment and Development

From Dr. Cathy Fernades:

More details: MSc_GED_advert

Announcing our new one year, full time master’s programme, MSc Genes, Environment and Development, taught at the Medical Research Council (MRC) Social, Genetic and Developmental Psychiatry (SGDP) Centre at the Institute of Psychiatry, King’s College London.

This is a unique, brand new course starting in September 2013, which will provide an unrivalled learning opportunity from internationally renowned researchers in a range of behavioural genetics topics and research methods relevant to psychology and psychiatry.

This innovative MSc programme offers specialised interdisciplinary graduate training in social, genetic (both quantitative and molecular), epigenetic, developmental and cognitive approaches to psychiatry and psychology. It also provides a thorough practical training in a range of research methods and their application.
The programme equips you with the appropriate training for further full‐time study; our graduates make strong candidates for PhDs, or careers in academic, clinical or pharmaceutical organisations or in the field of science communication. Our student make‐up is diverse; you may come to us with a background in social science, psychology, psychiatry, biology, mathematics and other degrees.

GATE course

I hope everyone who attended the GATE text analytics course this week had fun and found it useful.

Course materials are now available from the GATE website:

I’ve also created a googlegroup (!forum/kcl-gate-course) so we can continue to discuss the practicals and any other GATE questions you have. If you haven’t received an invite, drop me an email.

We would also appreciate your feedback:


Biomedical Text Analytics Course

We are delighted to announce that we will be running a 5-day course on text analytics in conjunction with the GATE (Generalised Architecture for Text Engineering) team from the University of Sheffield.

The course will run in the first week of July at the SGDP, Institute of Psychiatry, Denmark Hill and will equip participants with the skills they need to develop text-mining/analytics applications using the GATE framework. There will be a focus on biomedical applications, however the techniques will be applicable to any text engineering problem and applicants from other fields are welcome to apply.

Please see the Event Page for more details.

Exome Chip Rare Caller Pipeline

A pipeline for running Zcall and Opticall on Illumina Exome Chip Datasets. This workflow will handle all the file parsing and run both callers and compare the output bed files.


Author: Amos Folarin
Organisation: KCL/SLaM



1) Sun Grid Engine
2) Zcall
3) Opticall


1) Read notes (GenomeStudio.SOP.v1.2.docx – the most up-to-date SOP are on the confluence page ) on processing the data in GenomeStudio
2) Generate the GenomeStudio Report file (as required for by Zcall, parses this as input for both Zcall and Opticall rare callers):

i) In GenomeStudio select ‘Full Data Table’ tab.
ii) Click on ‘Column Chooser’ icon.
iii) In Displayed Columns select ‘Name’, ‘Chr’,’Position’, and all your samples.
iv) In Displayed Subcolumns select ‘GType’, ‘X’ and ‘Y’.
v) Hit OK then click on ‘Export displayed data to a file’ icon.

3) Copy the into a working directory
4) Edit the paths as indicated in this script for your installations of Zcall and Opticall etc.
5) Specify the datapath and basename variables for the GenomeStudio Report generated in step (2)
6) Execute the pipeline bash script (