Science Online 2011 tickets now on sale:
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.
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 firstname.lastname@example.org 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 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).
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/
3D Protein Structure Predicted from Evolutionary Sequence Variation
Chris Sander, Debora S. Marks
3pm 1st July 2011, University College London
The trajectory of an evolving protein through sequence space is constrained by the need to maintain structure and function. Residues in spatial proximity tend to co-evolve, yet attempts at inverting the evolutionary record to derive proximity constraints have so far been inadequate. Here we use constraints inferred from evolution to predict de novo3D protein structures, without use of homology modeling or fragments from known structures. Our evolutionary constraints tackle the major obstacle in state-of-the-art de novo prediction: the ability to sample 3D conformational space. The predicted constraints are calculated with a method borrowed from statistical physics using maximum entropy which solves the inverse problem of inferring spatial proximity from patterns of co-evolution. We report prediction for 12 proteins ranging from 20-220 residues in size at a Ca-RSMD of 2.8 – 5.1 Å. The predicted structures have excellent topological agreement with experimentally determined structures, with structural elements well placed in 3D space, suggesting they can be refined further. In this era of massive genomic sequencing across many species, the evolutionary record captured in sequence alignments provides an increasingly powerful source of predictive information, in particular for protein families that have resisted experimental structure determination.
Medawar Lankester Lecture Theatre – behind Foster Court
Mendeley Hackday thing. June 11th and 12th
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
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.
Thursday 26th May
The Flowers Building is building 31 on the campus map.
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.
Thursday 24th February
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!
March 21st 2011
£2 per person to enter.
Sciency unconference in Cambridge. Registrations open at 9am on Wednesday 2nd March: