Category Archives: Meeting

Eagle Genomics to Sponsor Christmas Social

The lovely people at Eagle Genomics have kindly offered to donate some money towards beer and food for the Biogeeks Christmas Social!

In return, go take a look at their website. They’re doing some cool stuff around open-source bioinformatics. Everything from basic telephone support for tools like Ensembl to designing and implementing big grid/cloud based bioinformatics pipelines.

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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)

Biogeeks Christmas Drinks

Date for your diary:

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

The Miller near London Bridge:
http://www.beerintheevening.com/pubs/s/20/20918/Miller_of_Mansfield/Borough

Cheers,
Cass.

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

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.

October Tech Meet – Sequencing


Help promote this event: stick a couple of posters up around campus. Thanks!


Experience in variant calling from exome sequencing
Francesco Lescai, Elia Stupka
UCL Genomics, University College London

Sequencing whole exomes in order to identify high penetrant variants in few individuals is becoming relatively easy, and calling variants
is apparently an easy push-one-button procedure. However, understanding data quality and filtering out potential false positives in SNP calling is far more difficult. We will give a tour among the key QC and filtering issues, and discuss our experiences in calling variants from exome sequencing projects at UCL Genomics.

Analysing sequencing data on the NGS Cloud
Caroline Johnston, Matteo Turilli

The generation of large next-generation sequencing datasets is rapidly becoming a standard procedure in biology, but the resulting data requires compute resources beyond those normally available in a lab. The National Grid Service’s prototype Cloud is a first step towards a non-commercial, scalable solution for UK researchers. We will give a brief introduction to the NGS and to the Cloud prototype and will run a demo to process some short read data.

AQuA-NGS: A Quality Assessment Tool for Next Generation Sequencing Data
Zabeen Patel

The recent advancement of high-throughput sequencing enables the experimentalist to generate huge amounts of data at the genomic, transcriptomic, and epigenetic levels. However, as this is a relatively new technology, the methods for assessing the quality of the data are still limited. The AQuA-NGS system was developed as a platform-independent, desktop application for the viewing of quality assessment metrics generated by the R/Bioconductor package, ShortRead. These metrics are stored in a MySQL database, together with run and sample metadata. Using the flash-based GUI, the Bioinformatician may submit new data, browse the database, view metrics via interactive tables and charts, and directly compare QA metrics across samples, on the basis of multiple criteria. The system in its present, foundational state can perform the basic functions of generating, viewing, and comparing a limited set of QA metrics generated from Illumina/Solexa export files. It requires additional development to make it ready for public release, such as the ability to process non-Solexa files, and work with remote destinations. Once complete, it will hopefully be incorporated into the pre-processing pipeline of multiple next generation sequencing platforms.


When?

Thurs 21st October
6pm onwards.


Where?
G47A
Flowers Building
Imperial College
London

map of imperial college


Pub

After the talks (around 7.30 if you want to meet us there), we will be going to the Eastside Bar on Princess Gardens.

BioGeeks @ the Pub — August 19th

Since so many people are on holiday or have other arrangements at the moment, the August tech meet at UCL has been cancelled.

Instead, we’re getting together for a social evening at the Miller of Mansfield pub — same date (Thursday 19th August), from 6pm.

Map to Miller of Mansfield

Miller of Mansfield, 96 Snowsfields Road, London Bridge, SE1 3SS

We’ll try to book a table in the usual place. See you there!

June Tech Meet: Fri 18th @ KCL


Help promote this event: stick a couple of posters up around campus. Thanks!


We’re very pleased to announce that Cameron Neylon will be giving our main talk at the June Tech Meet:

What has the public ever done for us?
Why return on investment and engagement need to matter to scientists.

Public engagement and measures of impact, economic or otherwise, are
becoming an increasing burden for working scientists. At the same time
public distrust in science fuelled by scandals over data release and a lack
of understanding of the scientific process appears to be increasing. The
web, however offers us the greatest opportunity in history to actively
engage people in the process of carrying out science, and the greatest
opportunity since the printing press to radically improve the efficiency of
scientific communication and scientific process. I will argue that if we
take the approach of maximising return on the public investment on science
in terms of economic, social, and scientific outcomes that we have an
opportunity to solve all these problems. And that if we do not we will fail
to make the argument for scientific research as a key area for public
investment in the 21st century

Cameron works at the Science and Technology Facilities Council and is a well known proponent of open science and open data.


We will also have a series of 5-10min lightning talks:

Matt Arno – Unexpected presence of mycoplasma probes on human microarrays

James Campbell – Predicting proteotypic peptides for targetted quantitative proteomics

More to be announced…


When?

Fri 18th June
6pm onwards.


Where?

King’s College London
Seminar Room 2.21,
Waterloo Bridge Wing, Franklin-Wilkins Building
Waterloo Campus, Stamford Street
London SE1 9NH


Pub

We have tables reserved upstairs at the Rose and Crown, Colombo St, SE1 EDP
(marked on map above).