IBA » Jiří Jarkovsky, Adam Svobodnik Institute of Biostatistics and Analyses HU ML IBA IUI History Structure Collaboration Institute and Analyses: History e Since 2001 ■* group of scientists interested in analysis of biological and clinical data ■* Centre of Biostatistics and analyses 0 2006 ■* Institute of Biostatistics and Analyses ■* 45 employees and PhD students ■* 40 students in pregraduate study of Computational Biology 0 2007 ■* Integration into Research Centre for Environmental Chemistry and Ecotoxicology IÉítĚ Jarkovský, Svobod nik JSA M; 6747 625938 Institute and Analyses: Internal Structure 0 Nowadays IBA has the following structure: Department of Clinical Trials Masaryk university • Faculty of Medicine • Faculty of Science Department of ICT >epartment of Data Analysis >epartment of Environmental Informatics >♦ *A DSC Services RECETOX TOCOEN Jarkovský, Svobod nik IBA M; Institute of Biostatatistic and Analyses: Collaboration Faculty of Medicine (MU in Brno) Faculty of Informatics (MU in Brno) Faculty of Science (MU in Brno) Research Centre for Environmental Chemistry and Ecotoxicology (MU in Brno) Department of Mathematics (MU in Brno) Czech Environmental Information Agency National and Regional Centre for Persistent Organic Pollutants in Middle and East Europe Masaryk Memorial Hospital Czech Statistical Office Czech National Cancer Registry Committee for Breast Cancer Screening (Ministry of Health) Czech Oncology Society Standard professional collaboration More than 100 independent health care providers and hospitals, research institutions, environmental agencies, ministries etc. Jarkovský, Svobod nik IBA M; Institute of Biostatatistic and Analyses: Areas of interests 0 There are five main areas of interest Analysis and scientific research of clinical and other biological data Analysis and scientific research of environmental data Clinical trials and registries * Jarkovský, Svobod nik IBA M; HU ML IBA IUI Basic and advanced courses of data analysis Computational Biology Conferences Background of educational and scientific activities Basic and advanced courses of data analysis 0 18 courses for Faculty of Medicine and Faculty of Science 0 Both undergraduate and postgraduate courses with 450 students per year * Analysis of biological and clinical data ■ % Hhri Mr M* —* £«*■ id 0HT ľ^"*Tr" *l CeurMt is.munl.cz «i*- m* tfUHPJ ■■■!*■.[•, riHM.MlM MIH-lls Ei b« u.. b. n (t*— ivy-i — PJ-----Lll.ltel.IMff, : ŕ]JBMJJru*HW.I..n IT*^hJ| ...h,, i irr.sc.K, l|lhlHHl> . .nil. :m- ?■■■„ Hr ET ři.rrii □ Biostatistics □ Stochastic modelling a Multivariate data analysis □ Experimental design □ Data mining □ Etc. Clinical trials □ Design and analyses of clinical trials □ Data management in clinical trials Courses of visiting professors: International collaboration in teaching ■■■•>-* : .. u, t„. L ikK J bJl l.if™^ MŮ3/ Jarkovský, Svobod nik ÍBA ;iMJ; Computational biology 0 Computational biology is newly (since 2001) established study programme at Masaryk University with high potential in almost all biological and clinical disciplines i0 The concept of the computational biology is: -> intrinsically inter-disciplinary closely related to standard biological and clinical disciplines and their modern trends (bioinformatics, processing of large scale data from genomics to ecological biomonitoring, risk assessment, predictive modeling...). 0 We define computational biology in a broad sense as umbrella branch for all standard biological and clinical disciplines with three main branches: □ Analysis of biological and clinical data • Applied analysis of data or development of new methods □ Environmental informatics • Environmental information systems, biomonitoring etc. □ Informatics in medical sciences • Informatics in clinical trials, information systems for clinical data, clinical registry Jarkovský, Svobod nik IBA M; Conferences 0 IBA organizes several international scientific meeting and conferences * 2005 □ Summer School of Environmental Chemistry and Ecotoxicology 2005: tutorial of environmental risk assessment □ Enviroinfo 2005 - Informatics for environmental protection □ Summer School on Computational Biology * 2006 □ Summer School of Environmental Chemistry and Ecotoxicology 2006: tutorial of environmental risk assessment □ Summer School on Computational Biology: Predictive modelling and ICT in Environmental Research - September 11-13 * 2007 □ TIES: Conference of International Environmetrics Society □ Summer School on Computational Biology: Processing and Analysis of Biodiversity Data: from Genomic Diversity to Ecosystem Structure - August 13-15 Jarkovský, Svobod nik IBA M; Background of educational and scientific activities 0 Library ■* Books and journals covering almost all areas of data analysis in biology and medicine ■.................___^^^^^™ * Free access to many databases ^žl'ZL-I 75 HU ML IBA IUI Important projects m lllVlľDlAllltlllíilj JülÜlÜgilÜil lilií £' pi Üi^-LQi Di D y. V ľ b-Dbíiľ Ľll Environmental research Epidemiology Various biological research TRITON project 0 Project with Agricultural Water Management Authority 0 Software and statistical methodology of data analysis in biomonitoring networks ■* Visualisation of data Statistical analysis of time trends, biodiversity etc. Pravděpodobnostní komparace - grafické znázornění ■ ♦ * * ♦ .■■*■ Hodrwcvm vybraniho odboru n Oř [n FutihtUy í ;y - Poi(H *J"fJ 5^ i "■«rWI___I »tM , . Vítat«, mritkj ^ RBBIBB» .LV(--rfi ■■ VKijpid ofa» | >r* W^t | Vft4pffprvTŮ , . fi jfvr -S^i ifi.; ■:%■;.«■> ■/.syp '■ £ is&mm LT_ - 122 I fHSÉ F ú Jarkovský, Svobod nik ja» ^ii jdi ■»rrai-i jojL-iu han tt ;:■>- : Rfl-^itrt . . ;.-, ..;i. ■ „ i-..;-., MTMiw&ii hií"í :ir' 3 C (ÍDmparaůiímDťM d MnninDtUlli ■ t i—n "■■«■■—fc _ "■IH i \*mt IBA M ARROW project 0 Part of implementation of Water Framework Directive EU in the Czech Republic 0 IBA tasks Development of methodology and scientific research in analysis, typology and prediction of ecological state of localities -> Software implementation of analytical methodology m Loubc Lfcr-jw .obraz*. L.I.,II!I,.|I|||.IJI.I,!.III11HIIIII.1!111I1HJW1 Prejt iichř- L-(i4jiíj>. rrfctroit Nápowjds jg / ft hf-os/ř...... l-i.r»m ■:...v,f^rj--M*..hr.- -\ O *t* @, ^■>:'.-;IjF.-i.-j li-,FT>Hfad-&T-r 0Hniiam-VMiamOÉB W Wwy).™-urrrtr-t- __> 5umi fe W-Jn*i-iibyHor... _ Gumfe C-tomJff , 1 LM- Uc-UttLUv-... jj__J_rr_rnLAi«uinaá-n_ | l_JJ FterjiJi ü-n* - F^jly i J lij MmtK-1*-- ijŤ Experimental work Data analysis □ Modelling of POPs distribution and transport j Dose-response analysis □ Biodiversity analysis □ Analysis of data of biomonitoring networks □ Environmental risk assessment J GIS Compounds of interest | | Zatopené oblasti fí\/ Železnice ' Hranice povodí Dřevnice f\J Přítoky Dřevnice | |Jezera /\y Řeka Dřevnice /\J Řeka Morava /^Silnice PLAN Pilot tests (screening) Jarkovský, Svobod nik ISA M; INCHEMBIOL: Evironmental risk assessment © i Uncertainty analysis Sampling C Modelling RISK CHARACTERIZATION Bioindicators Bio-tests ; Expert judgement EXPOSURE ASSESSMENT Biota Biomonitoring Benchmarking Probability estimation EFFECTS CONCEPTUAL MODEL & SCENARIO tt**4***44*4****^ Data processing Modelling Multivariate analyses Model of area of interest Experimental design rroblem delinition Hazard identification Retrospective problem Actual / urgent situation Data gathering Data aggregation Information services Optimization & Processing in information systems & Communication Jarkovský, S* Prospective evaluation IBA Hl V) SVOD project: description 0 SVOD = EXPERT SYSTEM FOR ANALYSIS AND PRESENTATION OF EPIDEMIOLOGICAL DATA IN ONCOLOGY 0 Data of National Cancer Institute: population database of cancer epidemiology since 1970 0 Data includes incidence and mortality rates, time profiles, distribution of clinical stages, regional heterogeneity and more... "^ http:/AVWW.t..UU.L..IL - JTUIÍ Hllfli; ßrf§ REGIONAL OVERVIEWS Select a diagnose [ŽJ Display all diagnostic groups II. TUMOURS OF DIGESTIVE ORGANS ■ tvn int i • • n i ■.......-..( - .....i.-, .i- i - 015 - Malicinant neoplasm of esoohacius C1G Malicinant neoplasm of stomach C1F Malicinant neoplasm of small intestine CI B -1i .|ľ v.- .- |.|i il . t .. f. CI 3 i -|l «■ ■■ l-l II ■ i .........i H i «1 eao i ■........ .i-i .■ ■ -.■ ■ ■ ■ C21 Malicinant neoplasm of anus and anal canal C1B ľŕl - Malianant neorolasm of colon and rectum C33 Malicinant neoplasm of liver and intrahepatic bile ducts C23 -i- .p ■,<. .- pi- n . i (i .i- .i- C24 Malicinant neoplasm of other and unspecified Darts of biliar v tract nľ>i.0>4-Malicinant neoplasm of aallbladder and biliarv tract 0*5 - Malicinant neoplasm of pancreas t'.'/h ■ 1' - ir v.- ■.- ■ i -i i -it ■ r .1 .- -■ ■.. u .i-iif.- i h. - i - I K^ http://www.Birad.cz - SVOD Analyse - Mo: 'M time trend; Patient group selection l£) Sex, age Period Stage TNM classification Other parameters Other anafyses for selected diagnose and group of patients^ 3500 r 3000 r 2500 r I 2000 : i 1500 r I 1000 r 500 050,005 - Breast tunours, uonen growth index of incidence to year 1977 fcu ňnalasrt data: »=107294_________________httpi/Ai-i.sval.cz_________________Source of data: fag] Cliange diagnose Analysis «lings Other outputs ra ,ble Display report http://www.5vod.ez/analy5e.php7moduNregionprehled# Jarkovsky, Svobodnik ISA M; SVOD project: aims 0 Project aims H ■* Scientific research of epidemiology data □ General epidemiological and socio-economical analyses. □ Load of population by malignant tumours, population risks. □ Analysis of health care heterogeneity □ Approximate evaluation of the health care effectiveness according to therapeutic results. Software development □ Desktop software □ Web visualization of epidemiology data - public access http://www.svod.cz/ Teifcor -.p-ř-V Zoť-uft. ^jľ . . hrtřijywhWi.ixjd.ci/rSK-dlijJtrfllů-ia-tn ^Oífrt lei N L«*41* I «f «nu ^ ťŕeWed ip*> 0 n*m«TrW*bB* Ůtk* ty HtíwjtoYfl JYrtrtM $ L+msm V V*TnF4 jfcAv lifer... U b»^»L*Vndv » TEÍWÍ | (|^n*i*r^O¥*l«vt'it* ■„ U*:lní*jtt4«nW*y... CENIA | . SW» > tOU^m^.ll ^Th r^g S5 eotlHTBteH MJMMMV PPEJEkT^TIQI, iitiUaua * :0 !ú JW3 VH* COS selMi« ***ityini,v*i tn*fcfcni SVOD ViSéodbamfih gaiantü oraiaktu p e-a u zaMaupem p^edstimlal* iŕííchirftiiamiifili ímíri í*fli™ Ml*irtl ipi*jpr;3cu.ii[ľch matrturf {U f (1 JÍ.UO II DlriufHii iqx jjy porl.ti £ tikaetu vii as:e Hal t«du v anBfŕzuí h dpf asnŕ n*pŕlstusrŕ dngnúg niiifiríi kr#nni>in-j irriiiriifiihň nytlAniij l]*kti|itriwi 7.» pnchnpflni U.ieiUzáii'rUUUtinřr»wttíwfpDnil^iiiíJffi4niiroKr*řrřinsiJ Jarkovský, Svobod nik IBA M; INFORMATION AND ANALYTIC SEVICES OF THE SYSTEM SVOD ^JflliV^\™ iiiiiiiÉiiyiiniii mmmmiui J í J J f ľ 4 _1=____I .m — I i- I Data browser - analysis of individual parameters .VDirfr-^hjUji^hii,^! I" T *#k pfi ulinvnnl dn Mřll ifl pHl Hq -vytlili) k^>9DII> m;ii k M ImUhd h Vlil Ml- hanili» Mill »ni Jlnl p»iljirnl hanili» :i/i hlrflvl Inrolnd rirrJitninľ k**flDPI* JM t ! ;■ ■. 3H ÍBA Microarrays and analysis of their data 0 Promising technique of molecular biology, nevertheless with lots of problems on the field of data analysis 0 Analysis of expression and CGH microarrays data 0 Project in cooperation with Masaryk Memorial Hospital -> Genomic profiling in prediction of response of radiochemotherapeutic treatment in colorectal carcinoma :PR0J_all_topNNN9_9C fl.Sno (a! Sew**: brt*a Eumfvs lun** its*