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Biomedical Informatics Hub. Wellcome Trust ISSF Biomedical Informatics Hub. Dr Konrad Paszkiewicz. Contents. Wellcome Trust ISSF Background Seed Corn Fund Aims Biomedical Informatics Hub Purpose Expertise Resources Training Seminars - PowerPoint PPT Presentation


Wellcome Trust ISSF Biomedical Informatics Hub Informatics Hub

Wellcome Trust ISSF Biomedical Informatics HubDr Konrad PaszkiewiczContentsWellcome Trust ISSFBackgroundSeed Corn FundAimsBiomedical Informatics HubPurposeExpertiseResourcesTrainingSeminarsProject booking/PrioritisationSustainability

Institutional Strategic Support FundA 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

University of Exeter ISSF projectCreate a virtual Biomedical Informatics Hubto maximise output from emerging technologies and large datasetsEstablish an ISSF Seed Corn Fund to support highly-talented researchers to generate preliminary data in support of independent fellowship and grant applications8 projects supported in 2012University match-funding = new academic posts that will utilise the Hub to enable major advances in interdisciplinary biomedical research

Seed Corn FundRound 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 applicationsmid-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) Round 3: What?Must be in the Wellcome Trusts remit5 to 7 projects (up to 12 months)Up to 20k (30k for senior researchers)Closing date = 1st Feb 2013Assessment criteriatrack recordproposed projectoutputs Contact Allison McCaig (

Biomedical Informatics HubPurpose1. Supply informatics expertise in bioinformatics, mass-spectrometry, imaging and statistics2. Train researchers through existing and newly developed programs to make best use of their data3. 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 infrastructure5. Support researchers with access to centralised computational infrastructure and equipment6. Act as a central point of contact for initial research ideas

ExpertiseBioinformaticsMedical - Marcus Tuke, Anna Murray & Mike Weedon (Prof. Tim Frayling)Bioscience - Dr Christine Sambles (Sequencing Service)Metabolomics/ProteomicsDr Venura Perera (Dr Hannah Florance)Image analysisDr Jeremy Metz (starting November) (Prof. Rob Beardmore)Tomography and EMTBC (Prof. Gero Steinberg)StatisticsTBC (Prof. Tim Frayling)Computational modelling/sensor-based networksDr Mahmood Javaid (Prof. Ed Watkins)ResourcesSequencing Service (Konrad Paszkiewicz, Karen Moore)Illumina HiSeq 2000 Mass-spectrometry Service (Hannah Florance)Agilent QQQAgilent QTOFMetabolomics/ProteomicsImaging (Martin Schuster, Gero Steinberg)Confocal, EM Tomography, SEM, TEMComputational ResourcesZeus cluster

ResourcesZeus Systems Biology cluster

19 nodes with 144 coresNodes have between 24Gb and 192Gb RAM150TB of storageDesigned for serial jobs, not MPI/OpenMP jobsUpcoming 150k upgrade

Contact Konrad for access

Hub Training CoursesTraining courses currently offered: Amazon EC2 cloud computingUnix & PerlShort read genomicsPhylogeneticsUse of R statistical packageRNA-seqNew courses in 2013

6. SeminarsMonthly seminars/workshop meetingsScope: bioinformatics, statistics, image analysis, programming

Submitting requestsYou can approach Hub members informally for initial discussions about projectsIf youre unsure email me

Submitting requestsBUT before they undertake any work for you:You must apply via 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 theseAllison 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.

Some screenshots.....Project proposal submission proposal submission proposal tracking 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

Seed Corn Fund projectsExisting Wellcome Trust funded projectsWellcome Trust remit researchOther research

SustainabilityFunding 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 nowAny projects which use Hub expertise and subsequently apply for a grant need to cost relevant members Hub team presentationsVen PereraWho Am IDr Venura PereraLocated Room: M01 Mezzanine FloorBiosciencesCollege of Life and Environmental SciencesGeoffrey PopeBackground:PhD in Systems biology/BioinformaticsUsing mathematical methods for analysis of untargeted mass profiling data sets.Applied mathematicsUse of numerical methods for forecasting and predictive modeling of non-linear systemsData drive techniques for parameter optimizationOrdinary and partial differential equations for system modeling

My skillsApplied MathematicsUse of Numerical models for data modelingDevelopment of dynamic models using numerical methodsStatistical Modeling using non-parametric methodsLarge Data Sets AnalysisFocus on Untargeted Metabolite dataNew methods to solve any question Metabolite Pipeline ExSpecDevelopment of metabolite centers untargeted pipelineProgrammingJava Data ModelingR Mainly for data visualizationMatlab Data Modeling and VisualizationHTML, PHP, MySQL and basic Java Script

Further the use of MS techniquesNumerical methods for data modellingUsing probabilistic methods for data driven coupled systemsDevelopment of techniques for the MS fingerprintingUsing MS methods for polygenetic tree reconstructionMy research interests

Targeted / Quantitative Analysis

Multiple Reaction MonitoringStatistical analysis, Modelling and ClusteringSampleComparisonQuantification

Exploratory Non-targeted AnalysisExtract DataMolecular Feature Extraction (MFE) and data pre-processingMy WorkSmall Molecule analysis: Untargeted profiling and Targeted quantificationData Reduction extracted data loaded into the pipeline which Ven will explain29Targeted / Quantitative Analysis

Multiple Reaction MonitoringStatistical analysis, Modelling and ClusteringSampleComparisonQuantification

Exploratory Non-targeted AnalysisExtract DataMolecular Feature Extraction (MFE) and data pre-processing

Example ProjectTwo groups of patient types : HealthyCancerThree patientsProject Aim: Using a variety of techniques both targeted analysis as well as untargeted profiling to determine key components which are effected by the cancer

Example Project

Example ProjectPatient 24 had a large amount of inflammation causing the control and cancer tissue to share a great deal of features similarities.33

Nick Smirnoff (Director of Mass Spectrometry) Florance (MS Facility Manager) Perera (Bioinformatics and Mathematical Support)

Numerical Dynamic ModelingReaction scheme:

AK: known substrate of B (can be removed if un-mappedAU: Unknown substrate of BB : Substrate to modelE : Enzyme(s) controlling the reactionC : Known product of BCU: Unknown product of BBU : Unknown substrate of CAkAUBCUCEBUExample of Substrate-Product combo

Substrate-Product combo: Switch profiles show delayed affect indicating possible reaction schemeProfiles visually illustrate similarityAkAUBCUCEBUAnna Murray & Mike Weedon

Mike Weedon, PhDLecturer in Bioinformatics and Statistics, Exeter Medical School, St Lukes in Biochemistry and Molecular BiologyPhD in molecular genetics of type 2 diabetes, Peninsula Medical SchoolPostdoc on genetics of complex traits, Peninsula Medical SchoolCurrent research interests genome-wide investigations of monogenic and polygenic traits Anna Murray, PhDSenior Lecturer in Human Genetics, Exeter Medical School, St Lukes in BiologyPhD in molecular biology of T cell receptor rearrangement in coeliac disease in SouthamptonPostdoc on population genetics of Fragile X syndrome in Salisbury/SouthamptonCurrent research interests Genetics of female reproductive lifespan

Whole exome/genome sequencingENCODE and other projects to annotate non-coding genome

Genome-wide SNP and expression array studiesBiological pathway analysis

Statistical analysis of large datasetsMarcus Tuke

BackgroundComputer Science Graduate University of Exeter Medical SchoolSupercomputer systems administrator8 months working on projects at the Wellcome Trust Centre for Human GeneticsMSc Bioinformatics

42Expertise I can offer

Human Next Generation Sequence data processing and analysisHuman RNA-Seq processing and analysisComputational expertise4343Expertise I can offer

Human RNA-Seq processing and analysisHuman Next Generation Sequence data processing and analysisComputational expertise4444

Computational expertise

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