Category Archives: techmeet

June Tech Meet

KCL Logo

SLaM Logo
 
 
 

This month’s tech meet, organised in association with the KCL Bioinformatics Interest Group (BIG) and the Biomedical Research Centre for Mental Health (BRC-MH), will be at King’s College London, Guy’s Campus (London Bridge) in the Large Committee Room of the Hodgkin Building from 6pm on Thursday 23rd June.

We’ll have some tables booked at The Miller afterwards for more biogeeky chat and beers.

Important!

We only have space for 35 people to participate in the WGCNA talk / workshop, and we expect it to be a popular event, so please email london.biogeeks@gmail.com if you want to be sure of a space.

If you can’t make it to the workshop, feel free to come along to the pub afterwards. We’ll be there from around 7.30.


Steve Horvath

 

Speaker

We’re excited to announce that this month’s meet up will feature Steve Horvath from the Biostatistics Department at UCLA.

Steve is a Professor in Human Genetics and Biostatistics and his group develops biostatistical, computational, and systems biologic methods for studying complex phenotypes. Recent research has focused on the development and application of systems biologic and systems genetic methods for addressing biological, genetic and clinical questions. He’ll be giving us an overview of Weighted Gene Co-Expression Network Analysis (WGCNA).

Bring along a laptop with R and WGCNA installed so you can play along!

 
 


WGCNA

WGCNA

Weighted gene co-expression network analysis (WGCNA) facilitates a systems biologic view of gene expression data. The network framework makes it straightforward to integrate gene expression data with other types of data, e.g. clinical traits and genetic marker data. This talk covers several theoretical topics including network construction, module definition, network based gene screening, and differential network analysis. The methods are illustrated using several applications including i) screening for cancer genes, ii) comparing human and chimp brains, and iii) complex disease gene mapping. Related articles and material can be found at the following webpage http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/


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.

March Tech Meet – 24th, UCL

March’s BioGeeks tech meet will be on Thursday 24th March at University College London, Bloomsbury Campus, from 6pm.
We’ll have 2 talks. All welcome!

Be aware: the first 20 people to enter the conference room will receive a voucher for 2 free drinks and some food after the meeting!
Help advertise this event, put up a Poster!

The £495 desktop supercomputer
Ian Ozsvald
, Artificial Intelligence consultant (Mor Consulting Ltd.)
We’ll take a look at NVIDIA’s CUDA architecture which gives us a massively parallel supercomputer for the cost of a conventional PC gaming graphics card. We’ll take a look at the C++ and Python interfaces along with some mathematical and physics simulator case studies showing 100* speed-ups. The talk is high level and won’t dwell on the programming.

Disease gene identification by network analysis and data fusion
John Pinney, Imperial College London
The inference of novel causal and associated genes, given a disease of interest, is an important task at the interface between medicine and the biological sciences. Genes relate to each other in many ways, each type of information revealing another aspect of a complex picture. For example, data on human gene-gene relationships is now available from analyses of multiple transcriptomics and proteomics experiments, from genome annotations via the concept of semantic similarity, and more generally through text mining resources. Although several tools are available to produce lists of candidate genes to be tested for roles in a particular disease, existing methods are often based on a restricted number of input data types, and as such cannot integrate all of the available evidence. Tools that do exploit multiple data sources do so in a uniform manner, so that each data source is considered to have the same importance as the others, across all diseases. We have recently developed an integrated, network-based approach, in which the evidence from each data source is combined with that of the others in proportion to its predictive value for a particular set of input genes, leading to better results and supporting a greater understanding of the different causal pathways of genetic diseases.

Supported by the Developer Community Supporting Innovation Project (DevCSI) funded by JISC based at UKOLN, University of Bath

The talks will be followed by a discussion on possible future workshops.

When?
Thursday 24th February
6pm onwards.

Where?
University College London,
Engineering, Room 1.03
Malet Place
London, WC1E 6BT

7:30 – Print Room Cafe’, UCL Bloomsbury Campus, South Junction
Vouchers for 2 free drinks and food will be given to the first 20 people to enter the conference room!

Feb Tech Meet Talks

Videos of the Feb tech meet talks. Apologies for the quality, we had a camera failure and had to record them on mobile phones. Many thanks to Mahendra from UKOLN for emergency camera-work!

Slides from Nathans talk


Slides from Spiros’s talk


Slides from Will’s talks

Feb Tech Meet

Will be on Thurs 24th Feb, 6pm at King’s College London. We’ll have talks from Nathan Harmston, Spiros Denaxas and Eagle Genomics.

More details soon!

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)

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.

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).

Summer tech meets poll

Hi everyone,

So we’re trying to decide how often to run tech meets over the summer (from June till Sept’ish) / if at all. In the spirit of democracy we thought we’d put it to a vote (I’m sorry but PollDaddy doesn’t support AV). After this months tech meet at Imperial the next one is going to be a Kings.

Hopefully this poll will return a clear majority ;)