Author Archives: londonbiogeeks

Biogeeks Christmas Drinks

Date for your diary:

The London Biogeeks Christmas Social
Thursday December 16th 6.30pm onwards.

The Miller near London Bridge:


PS. I’m looking for speakers / tutorials / demos for January’s tech meet. Give me a shout if you fancy doing something.


London-NGS: 3rd Generation Sequencing Platforms

London-NGS: 3rd Generation Sequencing Platforms

Thursday 9th December 2010

== Venue ==

Wolfson Lecture Theatre 2
MRC Clinical Science Centre
Hammersmith Hospital Campus
Du Cane road
London W12 0NN

== Program ==

From proton sequencing to 99.99% accuracy on next generation sequencing
Raimo Tanzi, Business Development Director Europe, Life Technologies

2.40 – 3.20
Ion Torrent, semi conductor sequencing for Life
Armin Winands, Vice President Sales & Support EMEA, Ion Torrent Systems, Inc.

3.20 – 4.00
PacBio RS platform
Steve Turner, founder and CTO, Pacific Biosciences

Drinks reception/networking

== Registration ==

By email:

SEGEG: Getting More from GWAS Data

Wednesday 1st Dec 2010, 1.30pm – 5pm

Roberts 106 Lecture Theatre, Univesity College London,
Roberts Building, Torrington Place, London WC1E 7JE

== Getting more from GWAS data ==

Kristin Nicodemus (Oxford) will talk on machine learning approaches to GWAS analysis

Jo Knight (KCL) will talk on Bayesian approaches to combining GWAS and annotation data

Carl Anderson (Sanger) will talk on ‘synthetic’ association and the ‘missing heritability’ problem

Doug Speed (UCL) will talk on searching for interactions in GWAS data

See for details and registration

November tech meet — RapidMiner tutorial

The next BioGeeks tech meet will be on November 25th 2010 at UCL, where Andrew Clegg will be running a workshop entitled:

RapidMiner — machine learning for the rest of us

RapidMiner is an easy-to-use and feature-packed desktop app for machine learning, data & text mining, statistical analysis and visualization.

It allows you to build workflows for your experiments, easily swap learning algorithms and evaluation methods in and out, and compare and visualize the results. It also supports parallel processing and interfaces with databases, R and Weka, all from an intuitive graphical workbench. It includes modules for dozens of different classification, clustering and regression methods, along with dozens more handy pre-and post-processing tools.

The tutorial will take you through building a learning pipeline, training and tuning models in it, applying them to new data and comparing the results, using some well-known biological data.

Andrew will also demonstrate some methods for transforming and processing your input data in ways that would take hours to script by hand.

Bring a laptop if you want to follow along or just come to watch.

N.B. If you do bring a laptop, please install RapidMiner 5 Community Edition first, in case there’s a problem getting wifi on the day.

Where: Biochemistry Lecture Theatre, Darwin Building (basement), University College London

Enter campus via Malet Place opposite Waterstones, then turn left between the Engineering and DMS Watson buildings in square C4 of this map.

When: 6pm, Thursday 25 November 2010

Followed by drinks from 7:30ish at a venue to be decided on the day (depending on numbers).

Download a poster for this event here (PDF, 125K)

Duplicate of this post because of URL mix-up, all comments there please.

Bioinformatics Openings @ the Institute of Cancer QMUL

>From Claude Chelala on the Bioconductor mailing list:

The Institute of Cancer has two bioinformatics openings:

Postdoctoral Research Assistant – Bioinformatician (1)

Postdoctoral Research Assistant – Bioinformatician (2)

Job – ICL Research Assistant / Associate

(From Anthony Rowe – ICL)

Research Assistant or Research Associate
Discovery Science Research Group

Fixed Term Appointment for up to 24 months

Research Assistant salary: £26,860 – £29,850 per annum
Research Associate salary: £30,680 per annum

The Department of Computing is a leading department of Computer Science among UK Universities. It has consistently been awarded the highest research rating (5*) in Research Assessment Exercises (RAE), coming 2nd in the 2008 RAE, and was rated as “Excellent” in the previous national assessment of teaching quality.

The Discovery Science Group is looking for an experienced and highly motivated Research Assistant/Research Associate to work as a Biological Data Analyst and play a highly visible and key role in Innovate Medicine Initiative funded Unbiased Biomarkers for Predicting Reparatory Disease Outcomes (UBIOPRED).

This is a terrific opportunity to be a part of a leading translational research project by applying analysis skills for several cutting edge technologies, such as Next-generation sequencing, systems biology, etc. The successful applicant will analyze data produced during that project to support investigators identifying biological fingerprints that combined molecular profiling technologies with clinical data.

To apply you must have a proven record in working with scientists in a research driven environment and developing analysis relevant to their research. You will also have demonstrable experience in applying a wide-variety of open-source/commercial software tools for various biomedical data processing needs and substantial experience with data analysis and data transfer/parsing/management using command-line Linux/UNIX/Mac OS X platforms and shell scripting.

For a Research Assistant post you will have an Undergraduate Degree (or equivalent) or a Masters degree (or equivalent) in an area pertinent to the research subject e.g. Biochemistry or Molecular Biology. For a Research Associate post you will have a PhD (or equivalent) in Biostatistics, Computer Science, Computational Biology, or related field with an appropriate background in data analysis.

You must have excellent communication skills and be able to organise your own work with minimal supervision and prioritise work to meet deadlines. All applicants must be fluent in English.

You will be part of the Discovery Science Research Group led by Professor Yike Guo, within the Department of Computing based at the South Kensington campus. The group is dedicated to applying
Statistics, Data Mining, Simulation and Modeling and Visualization research of the analysis of scientific data.

New Open Access Journal: Open Research Computation

Aims & Scope:

Open Research Computation publishes peer reviewed papers that describe the development, capacities, and uses of software designed for use by researchers in any field. Submissions relating to software for use in any area of research are welcome as are papers dealing with algorithms, useful code snippets, as well as large applications or web services, and libraries. Open Research Computation differs from other journals with a software focus in its requirement for the software source code to be made available under an OSI compliant license, and in its assessment of the quality of documentation and testing of the software. In addition to papers describing software Open Research Computation also welcomes submissions that review or describe developments relating to software based tools for research. These include, but are not limited to, reviews or proposals for standards, discussion of best practice in research software development, educational and support resources and tools for researchers that develop or use software based tools.