Th is is the lab template: The context is a biological context based on a real biological problem. And a given hypothesisI don’t use computer science, strong word.When you read this template, you have a different view than an informatician.You want to understand the process to build the used tools.The architecture of the systemThe algorithm implementationThe quality of the resulting dataAnd so on
Session ii g3 lab behavior science mmc
Information Management Systemsin Behavior ScienceTheme: Statistic, Epidemiology Modeling and DiabetesLab #2Etienne Z. GnimpiebaBRIN WS 2013Mount Marty College – June 24th 2013Etienne.firstname.lastname@example.org
Context0. Specification & AimsLab #2Statement of problem / Case study: Interdisciplinary and transversal research development invites each scientific field to initiate an evolution toward integration to /for other field. Thebioinformatics and computational biology used in Behavior science remain difficult to describe. We propose here to use Information management tools (data collected, mining, load, statisticanalysis) and systems Biology modeling (epidemiology modeling) as key point for that translational interaction. Epidemiology is the study of the distribution and determinants of health-relatedstates or events (including disease), and the application of this study to the control of diseases and other health problems. Various methods can be used to carry out epidemiological investigations:surveillance and descriptive studies can be used to study distribution; analytical studies are used to study determinants.Bioinformatics and Information Management in Behavior ScienceAim: The aim of this lab is to create a broaderunderstanding of behavioral science data analysisand mining using statistic tools. As a part of lifescience area, we propose here to useBioinformatics and Systems Biology tools inEpidemiology modeling to predict disease spread.Acquired skillsOnline Server Tools:- Survey design (from hypothesis to questionnaire)- Google Apps (design forms, updating questions)- Data analysis, data learning, data mining- Using NetLogo (modeling approach)2Resolution ProcessT1. Creating a Google SurveyObjective: Learn how to make a Google surveyT2. Descriptive and Inference Statistics in ExcelObjective: Extract Load and Treat (ELT) data set for excel statistics used.T1.1. Setting up the SurveyT1.2 Creating the QuestionsT1.3. Collected Data and Visualize the SummaryT2.1. Import/edit/export from different formats (text, tab, xml, …)T2.2. Descriptive analysis in excel (max, min, typos, count, Stde, average, sum) anddata visualization in excel (histogram, scatter plot, …)T.2.3. Case Study: Social Reajustment Rating Scale (SRRS) question on diabeteT4. Epidemiology ModelingObjective: How to use modeling approach to analyze the epidemiology problemsT4.1. Using NetLogoT4.2. Running epiDEM simulationT3. Inference statistics in Tanagra (data mining)Objective: learn, extract knowledge from data using data mining tools (associations rules,clustering, neuronal network) in Tanagra.T3.1. Data Mining using Associaton Rule on DatasetT3.2. K-Means Clustering Method for Data Learning
Information Management in Behavior ScienceT1. Creating a Google SurveyObjective : Learn how to make a Google SurveyT1.1. Setting up the SurveyOn the Google website: http://www.google.como Click on “Drive” tabo Login or create an accounto Click on the red “Create” button and select the “Form”o In “Title” you name your survey. You can also select your desired theme. For our example we will name oursurvey “Diabetes”o Click “Ok” to begin creating your surveyo A screen will open and you can complete an number of functions such aso Providing a descriptiono Titling your questionso Providing help text if neededo Choosing you question typeo Adding more questionso When you are finished with your survey questions click “Done”o You can now choose the options too Show link to submit another responseo Publish and show the link to the results of the form to all the responderso Allow responders to edit responses after submittingo You can now share the link of your survey through Google +, Facebook, and twitter, or sending forms via e-mail.o When finished selecting recipients click “Done”Etienne Z. GnimpiebaBRIN WS 2013Mount Marty College – June 24th 2013T1.2. Creating the QuestionsT1.3. Collected Data and Visualize the SummaryStatistics in Behavior Science
Information Management in Behavior ScienceT2. Descriptive and Inference Statistics in ExcelObjective: Extract Load and Treat (ELT) data set for excel statistics usedT2.1. Import/Edit/Export from different Formats (text, tab, xml…)Etienne Z. GnimpiebaBRIN WS 2013Mount Marty College – June 24th 2013o Open Excel and go to the “Data” tab. Click on “From Text” and select the file “data_lab8” from the student folder.o Click “Next” Under “Delimiters” select only the “comma” Click “Finish” and “OK”o Click on the column letter you want to sort by and click on “Sort and Filter” on the top left of the “Data” tab.o Select the “Sort A though Z” Make sure “Expand with selection is selected and click “Sort”T2.2. Descriptive Analysis in Excel and Data Visualisation in Excelo Click on the cell under the title “Average” Under the “Formulas” tab click on “More Functions”, “Statistical” and “Average”o To find the average of the cars that traveled enter “D2:D21” in “Number 1” and click “OK”o To find the standard deviation of the number accidents select the cell under the title “Stdev” and click on “More Functions”, “Statistical”,and “STDEV.S”. In “Number 1” put “E2:E21”.o Highlight the data under “Cars Travel” (D2:D21) Go to the “Insert” tab and click on “Line” and select the first dot line option giveno You can edit the chart multiple ways and change the looks of in by going under the tabs that show up when the chart is selectedo Under the “Layout” tab you can add titles for the X and Y axiss.o Right click the chart and select “Change Chart Type…” if you want a different type of graphT.2.3. Case Study: Social Reajustment Rating Scale (SRRS) question on Diabeteso Open “Case Study-Diabetes” from your student foldero Select cell C2 and type in the equation “=$B2*$B2” and press enter.o Hover your mouse over the lower right corner and drag the black box down to C7 to apply this equation to the rest of the cells.o Select cell E2 and type in the equation “=$D2*$D2” and again drag down until cell E7o Select cell F2 and type in the equation “=$B2*$D2” and again drag down until cell F7o Select cell B8 and click on the button “Math and Trig” and select “SUM” Type in “Number 1” “B2:B7” and then press “OK”o Drag the black box across to F8. Now your table should be completeo Click on the “Insert” tab and pull down the “Scatter” button and select the first chartStatistics in Behavior Science
Statistics in Behavior Science Information Management in Behavior ScienceT3. Inference statistics in TanagraObjective: learn, extract knowledge from data using data mining tools (associations rules,clustering, neuronal network) in Tanagra.Data MiningEtienne Z. GnimpiebaBRIN WS 2013Mount Marty College – June 24th 2013T3.1. Data Mining using Association Rule on Dataseto Open Tanagra. Pull down “File” and select “Open…” Pull down “Files of Type” and select “Binary data mining diagram(*.bdm) Then open the file “T41Bin_transactions.bdm” in your student foldero Click on the “Define Attributes Status” icon [ ] Select all “Attributes” by clicking on [ ] and move over into “Input”by clicking on the arrow. Click “OK”o Right click “Define Status 1” on the left and select “Execute”o Click on “Association” on the bottom. Pull “A priori” on the top of “Define Status 1” on top left. Then double click “A priori 1”to see the resultsT3.2. K-Means Clustering Method for Data Learningo Open Tanagra, pull down “File” and click on this icon [ ] Then click on this icon [ ]Change file type to “Excel File..”and open the file “cars” from your student folder. Click “Open”o Click on this icon [ ] Move “MPG”, “Weight”, and “Drive Ratio” into the “Input” and click “OK”o Click on “Clustering” at the bottom, and pull “HAC” on top of “Define status1” Then right click “HAC 1” and change “BestClusters” to “Detect”o You can open the “Dendrogram” tab on the top of the view window. Move back to the “Report” viewo Add another “Define Status” under “HAC 1” and select all of the “Attributes” into “Input” except “Car” ad“Cluster_HAC_1”o Open “Target” tab and put “Cluster_HAC_1” ino Click on “Statistics” and put “Group characterization” under “Define status 2”o Click on “Factorial Analysis” and put “Principal Component Analysis 1” under “HAC 1” Add a “Define status” under“Principal Component Analysis 1” as well. Change the “Parameters” for the new “Define status 3” by putting “MPG”,“Wieght”, “Drive_Ration”, “Horsepower”, “Displacement”, and “cylinders” in “Input” and “PCA_1_Axis _1” and“PCA_1_Axis_2” in “Target.o Click on “Data Visualization” and put “Correlation scatterplot” under “Define status 3” In any top right pull down in thevieww window select “Cluster_HAC_1”. In the other two pull downs put “PCA_1_Axis_1” and “PCA_1_Axis_2”
Information Management in Behavior ScienceT4. Epidemiology ModelingObjective : How to use modeling approach to analyze the epidemiology problemsT4.1 Using NetLogoo Click “Run epiDEM Travel and Control in you browser” to launch ito You can change the parameters of the system as you please and simulate the experimento Click “Setup” and the system will automatically build a populationo Execute by clicking “Go”o You will be able to see the results of the population changes in the left graphso Right Click and select “Copy Image” in order to copy the image of your resultsEtienne Z. GnimpiebaBRIN WS 2013Mount Marty College – June 24th 2013T4.2. Running epiDEM SimulationOn the NetLogo website: http://ccl.northwestern.edu/netlogo/ (Make sure you are usingChrome browser)o Click on “Library” and scroll to the bottom of the page and select “epiDEM Travel and Control”Statistics in Behavior Science
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