www.exeter.ac.uk/biomedicalhub biomedical informatics hub

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www.exeter.ac.uk/biomedicalhub Biomedical Informatics Hub Slide 2 WELLCOME TRUST ISSF BIOMEDICAL INFORMATICS HUB Dr Konrad Paszkiewicz Slide 3 Contents Wellcome Trust ISSF Background Seed Corn Fund Aims Biomedical Informatics Hub Purpose Expertise Resources Training Seminars Project booking/Prioritisation Sustainability Slide 4 Institutional Strategic Support Fund A 1.5 million Wellcome Trust award.......match funded by the University to enhance institutional strategies for the biomedical sciences to support scientific progress, translation and interdisciplinary collaboration to encourage greater efficiency, effectiveness and accountability in the stewardship of Wellcome Trust funding Slide 5 University of Exeter ISSF project Create a virtual Biomedical Informatics Hub to maximise output from emerging technologies and large datasets Establish an ISSF Seed Corn Fund to support highly-talented researchers to generate preliminary data in support of independent fellowship and grant applications 8 projects supported in 2012 University match-funding = new academic posts that will utilise the Hub to enable major advances in interdisciplinary biomedical research Slide 6 Seed Corn Fund Slide 7 Round 3: Who? outstanding postdoctoral researchers - to generate preliminary data to support independent Fellowship applications early career academics - to generate preliminary data in support of research grant applications mid-career and senior academics seeking pump priming support for new activity that will lead to a Wellcome Trust application (first time applicants to the Trust particularly encouraged) Slide 8 Round 3: What? Must be in the Wellcome Trusts remit 5 to 7 projects (up to 12 months) Up to 20k (30k for senior researchers) Closing date = 1st Feb 2013 Assessment criteria track record proposed project outputs Contact Allison McCaig (a.mccaig@exeter.ac.uk) Slide 9 Biomedical Informatics Hub Slide 10 Purpose 1. Supply informatics expertise in bioinformatics, mass-spectrometry, imaging and statistics 2. Train researchers through existing and newly developed programs to make best use of their data 3. Supply PhD students, postdocs and junior researchers with the tools and expertise to produce 4* research 4. Provide leadership, governance and coordination to leverage and extend Exeter's IT research infrastructure 5. Support researchers with access to centralised computational infrastructure and equipment 6. Act as a central point of contact for initial research ideas Slide 11 Expertise 1.Bioinformatics Medical - Marcus Tuke, Anna Murray & Mike Weedon (Prof. Tim Frayling) Bioscience - Dr Christine Sambles (Sequencing Service) 2.Metabolomics/Proteomics Dr Venura Perera (Dr Hannah Florance) 3.Image analysis Dr Jeremy Metz (starting November) (Prof. Rob Beardmore) 4.Tomography and EM TBC (Prof. Gero Steinberg) 5.Statistics TBC (Prof. Tim Frayling) 6.Computational modelling/sensor-based networks Dr Mahmood Javaid (Prof. Ed Watkins) Slide 12 Resources Sequencing Service (Konrad Paszkiewicz, Karen Moore) Illumina HiSeq 2000 Mass-spectrometry Service (Hannah Florance) Agilent QQQ Agilent QTOF Metabolomics/Proteomics Imaging (Martin Schuster, Gero Steinberg) Confocal, EM Tomography, SEM, TEM Computational Resources Zeus cluster Slide 13 Resources Zeus Systems Biology cluster 19 nodes with 144 cores Nodes have between 24Gb and 192Gb RAM 150TB of storage Designed for serial jobs, not MPI/OpenMP jobs Upcoming 150k upgrade Contact Konrad for access Slide 14 Hub Training Courses Training courses currently offered: 1.Amazon EC2 cloud computing 2.Unix & Perl 3.Short read genomics 4.Phylogenetics 5.Use of R statistical package 6.RNA-seq New courses in 2013 Slide 15 6. Seminars Monthly seminars/workshop meetings Scope: bioinformatics, statistics, image analysis, programming Slide 16 Submitting requests You can approach Hub members informally for initial discussions about projects If youre unsure email me Slide 17 Submitting requests BUT before they undertake any work for you: You must apply via bioinformatics-hub.ex.ac.uk Await approval by the head of discipline (no more than a few days) You need to specify up-front outcomes in terms of grant applications and/or publications and when you expect to achieve these Allison McCaig will review outputs. Users who use Hub time and do not publish or apply for grants outcomes will be penalised in future hub applications. Slide 18 Some screenshots..... Slide 19 Project proposal submission bio-informaticsHub.ex.ac.uk Slide 20 Project proposal submission bio-informaticsHub.ex.ac.uk Slide 21 Project proposal tracking bio-informaticsHub.ex.ac.uk Slide 22 Prioritisation Wellcome Trust remit projects have priority to achieve extraordinary improvements in human and animal health....... we support the brightest minds in biomedical research and the medical humanities. See Research Challenges at www.wellcome.ac.ukwww.wellcome.ac.uk 1.Seed Corn Fund projects 2.Existing Wellcome Trust funded projects 3.Wellcome Trust remit research 4.Other research Slide 23 Sustainability Funding via the Wellcome Trust ISSF for up to three years (annual approval) To continue the Hub, we need to ensure members are costed into grant applications now Any projects which use Hub expertise and subsequently apply for a grant need to cost relevant members Slide 24 Hub team presentations Slide 25 Ven Perera Slide 26 Who Am I Dr Venura Perera Located Room: M01 Mezzanine Floor Biosciences College of Life and Environmental Sciences Geoffrey Pope Background: PhD in Systems biology/Bioinformatics Using mathematical methods for analysis of untargeted mass profiling data sets. Applied mathematics Use of numerical methods for forecasting and predictive modeling of non-linear systems Data drive techniques for parameter optimization Ordinary and partial differential equations for system modeling Slide 27 My skills Applied Mathematics Use of Numerical models for data modeling Development of dynamic models using numerical methods Statistical Modeling using non-parametric methods Large Data Sets Analysis Focus on Untargeted Metabolite data New methods to solve any question Metabolite Pipeline ExSpec Development of metabolite centers untargeted pipeline Programming Java Data Modeling R Mainly for data visualization Matlab Data Modeling and Visualization HTML, PHP, MySQL and basic Java Script Slide 28 Further the use of MS techniques Numerical methods for data modelling Using probabilistic methods for data driven coupled systems Development of techniques for the MS fingerprinting Using MS methods for polygenetic tree reconstruction My research interests Slide 29 Targeted Targeted / Quantitative Analysis Multiple Reaction Monitorin g Statistical analysis, Modelling and ClusteringSample Comparis on Quantificatio n Non-targeted Exploratory Non-targeted Analysis Extract Data Molecular Feature Extraction (MFE) and data pre- processing My Work Small Molecule analysis: Untargeted profiling and Targeted quantification Slide 30 Targeted Targeted / Quantitative Analysis Multiple Reaction Monitoring Statistical analysis, Modelling and ClusteringSampleComparisonQuantification Non-targeted Exploratory Non-targeted Analysis Extract Data Molecular Feature Extraction (MFE) and data pre- processing Slide 31 Example Project Two groups of patient types : Healthy Cancer Three patients Project Aim: Using a variety of techniques both targeted analysis as well as untargeted profiling to determine key components which are effected by the cancer Slide 32 Example Project Slide 33 Patient 24 had a large amount of inflammation causing the control and cancer tissue to share a great deal of features similarities. Slide 34 http://biosciences.exeter.ac.uk/facilities/spectrometry/ http://bio-massspeclocal.ex.ac.uk/ Nick Smirnoff (Director of Mass Spectrometry) N.Smirnoff@exeter.ac.ukN.Smirnoff@exeter.ac.uk Hannah Florance (MS Facility Manager) H.V.Florance@exeter.ac.uk Venura Perera (Bioinformatics and Mathematical Support) V.perera@exeter.ac.uk Slide 35 Numerical Dynamic Modeling Reaction scheme: A K : known substrate of B (can be removed if un-mapped A U : Unknown substrate of B B : Substrate to model E : Enzyme(s) controlling the reaction C : Known product of B C U : Unknown product of B B U : Unknown substrate of C AkAk AkAk AUAU AUAU B B CUCU CUCU C C E E BUBU BUBU Slide 36 Example of Substrate-Product combo Substrate-Product combo: Switch profiles show delayed affect indicating possible reaction scheme Profiles visually illustrate similarity AkAk AkAk AUAU AUAU B B CUCU CUCU C C E E BUBU BUBU Slide 37 Anna Murray & Mike Weedon Slide 38 Mike Weedon, PhD Lecturer in Bioinformatics and Statistics, Exeter Medical School, St Lukes Campus M.N.Weedon@exeter.ac.uk Graduate in Biochemistry and Molecular Biology PhD in molecular genetics of type 2 diabetes, Peninsula Medical School Postdoc on genetics of complex traits, Peninsula Medical School Current research interests genome-wide investigations of monogenic and polygenic traits Anna Murray, PhD Senior Lecturer in Human Genetics, Exeter Medical School, St Lukes Campus A.Murray@exeter.ac.uk Graduate in Biology PhD in molecular biology of T cell receptor rearrangement in coeliac disease in Southampton Postdoc on population genetics of Fragile X syndrome in Salisbury/Southampton Current research interests Genetics of female reproductive lifespan Slide 39 Slide 40 Whole exome/genome sequencing ENCODE and other projects to annotate non- coding genome Genome-wide SNP and expression array studies Biological pathway analysis Statistical analysis of large datasets Slide 41 Marcus Tuke Slide 42 Background Computer Science Graduate University of Exeter Medical School Supercomputer systems administrator 8 months working on projects at the Wellcome Trust Centre for Human Geneti


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