Author Archives: londonbiogeeks

May tech talks – 26th May

May’s BioGeeks tech meet will be on Thursday 26th May at Imperial College London from 6pm.
Theres going to be 3 talks and as always everyone is welcome. Talks will of course be followed by drinks and chat in a nearby pub (Hoop and Toy). Help us advertise this meeting by putting up a poster.

Knowledge Management in the U-BIOPRED Project.
Anthony Rowe
 – Department of Computing, Imperial College
U-BIOPRED is a Pan-European translational study to identify and characterize biomarkers associated to severe asthma. The project consortium is made up of 40 organisations and includes 10 large pharmaceutical partners as well as 20 academic medical centres. We are currently recruiting a cohort of 750 adults and 500 paediatric volunteers and will be profiling tissue samples from this patients with Genomic, Proteomics, Lipidomic and Breathomic approaches. This talk will discuss the processes and technology we are developing to organise and manage this highly diverse and large dataset and the strategies we are developing to analyse and interpret this data.

FigShare – Why don’t you publish all of your research?
Mark Hahnel – NHLI – Imperial College
Scientific publishing as it stands is an inefficient way to do science on a global scale. A lot of time and money is being wasted by groups around the world duplicating research that has already been carried out. FigShare allows you to share all of your data, negative results and unpublished figures. In doing this, other researchers will not duplicate the work, but instead may publish with your previously wasted figures, or offer collaboration opportunities and feedback on preprint figures.

Dexy – Documentation for Science and Code
Ana Nelson
Dexy is an open source document automation tool that can help you create documents using your favourite programming languages and your favourite software.
Programmers: Promote and improve your code with automated documentation.
Scientists: Create beautiful, reproducible documents including graphs and analysis from your raw data and code.

When?
Thursday 26th May
6pm onwards.

Where?
G47A
Flowers Building
Imperial College
London

The Flowers Building is building 31 on the campus map.

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London NGS Meeting Thursday 7th April

The next London NGS Meeting has been announced.
It will be at the Windeyer Institute, UCL at 2pm on Thursday 7th April.

AGENDA

7th april London NGS meeting Agenda.pdf

Contact Jacob Raby at UCL Genomics for more information:
http://www.genomics.ucl.ac.uk/about-us/contacts.htm

January Tech Meet

So the next BioGeeks tech meet will be on January 27th at Imperial College London at 6pm.

Multi-scale computational protein design
James MacDonald, Imperial College London
Efficiently exploring protein structure/sequence space is difficult due to the astronomical number of variables. In the case of computational enzyme design one wants to fit a given constellation of functional group residues onto a protein scaffold. I introduce a method I have been developing to explore conformational space on multiple levels of detail while annealing an “active site” on to a scaffold.

Poing: a coder’s take on protein modelling
Ben Jeffreys, Imperial College
Poing is a protein structure and folding model, designed to predict the tertiary structure of a protein from its sequence. I’ve been developing Poing for five years, after moving into computational biology from a background in software engineering. I’ve tried to keep the engineering ethos whilst dealing with the vagaries of scientific enquiry. My talk will focus on the engineering aspect, and how I’ve used a combination of C++, Python, various Python libraries, Subversion and server farms to produce a fairly slick workflow for both software engineering and developing and using the protein structure model. I will also talk about what I would have done differently with the benefit of hindsight.
Slides from Ben’s talk

Bioinformatics in the cloud
Peter Clarke, NUI Maynooth
TBC


When?

Thursday 27th January
6pm onwards.


Where?
G47A
Flowers Building
Imperial College
London

map of imperial college


Wanted: Analytical Computing Researcher

Another one from Lianda Payne at E-Resourcing Ltd. Please contact her with any enquiries.

Analytical Computing Researcher

A highly qualified individual to join a newly formed research team to build up our research on analytics applications .

Reporting to company’s Chief Innovation Officer, the qualified individual will research on data analyses methods and building proof-of-concept prototypes for company’s biological data analysis products. Support company’s scientific informatics business, you will focus on the build up analytics capacities within company’s data management and analysis product stack, especially in building analytical application for company’s cloud offering

The following qualifications are highly desirable:
-Msc/PhD in computer science, computational biology, Statistics or equivalent scientific discipline
-Be familiar with data mining technology-Ideally have experience with various omics data analysis in biomarker discovery field.
-Excellent analytical programming skills—excellent skill in bioinformatics/statistics, in building analytics applications
-Excellent people skills
-Excellent skill in Web2.0, cloud computing and internet programming

Wanted: Next Gen Sequencing Researcher

This just in, via Lianda Payne of E-Resourcing Ltd. Please contact her with any enquiries. She may have other bioinformatics posts available.

Bioinformatics Researcher

A highly qualified individual to join a newly formed research team to build up our research on NGS data analysis capabilities.

Next Generation Sequencing Data Analysis Research

Reporting to company’s Chief Innovation Officer, the qualified individual will research on data analyses methods on NGS and building proof-of-concept prototypes for company’s biological data analysis products. Support company’s translational medicine business, you will provide overview and technical presentations internally and externally, and in general be in touch with the existing and emerging thought leaders in this exciting new genomics/TR market space .

The following qualifications are highly desirable:

-PhD in molecular biology/genomics, or computational biology, biostatistics or equivalent scientific discipline
-Be familiar with high throughput genomic methods -Ideally have experience with next generation sequencing
-Publications, including publications using Next Generation Sequencing data/applications
-A knowledge of the thought leaders and leading researchers in the field of DNA sequencing, especially Next Generation Sequencing
-Excellent computer skills—excellent skill in bioinformatics/statistics-Excellent people skills
-Excellent presentation skills

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)

Job opportunity at Eisai Labs (UCL campus)

Scientist/Senior Scientist Bioinformatics, Biomarkers and Personalized Medicine Unit

Eisai bioinformatics ad (PDF, 106KB)