3. Dashboards - AlkaBenawra/MDMAPR GitHub Wiki
The Mapping Dashboard is used to perform geospatial analysis on qPCR run samples. On this page, an interactive map displays location markers for qPCR run sample collection locations and allows for filtering of markers by Cq intensity, date, location, taxon details, machine type, project, and assay. Hovering above a certain marker will display a pop-up menu that shows information about the specific marker. As well, the page contains a data table which shows detailed information about the markers on the map. The data table will update based on the used filters. A copy of the data table can be downloaded as a CSV by pressing the 'Download Mapped Markers Metadata' button.
Users can directly upload their own qPCR data on the page to view on the map. The user must upload a raw qPCR Experimental Fluorescence File and the filled in Metadata file. The qPCR machine types that are currently supported by the system include MIC, StepOnePlus, and Biomeme two3/Franklin. Information on the required files for the application is available on the Data page.
The Data Overview page is used to analyze individual tube/well samples and facilitates the quality control inspection of data. The page has four tabs, which include the 'Presence/Absence Samples', 'Amplification Plot', 'Standard Curve Data Overview', and 'Standard Curve Plot'. The 'Presence/Absence Samples' tab displays a table which indicates if a target sequence was detected in a tube/well based on its Cq Value. The 'Amplification Plot' shows the amplification curve associated with a specific well sample from the 'Presence/Absence Samples' tab. The 'Standard Curve Data Overview' tab displays a table with information related to the standard curve used for the samples in the 'Presence/Absence Samples' tab. Lastly, the 'Standard Curve Plot' tab shows the standard curve plot of the data from the 'Standard Curve Data Overview' tab.
Users can directly upload their own qPCR data on the page to analyze. The user must upload a raw qPCR Experimental Fluorescence File, a raw Standard Curve Fluorescence File, and the filled in Metadata file. The qPCR machine types that are currently supported by the system include MIC, StepOnePlus, and Biomeme two3/Franklin. Information on the required files for the application is available on the Data page.
The Data Submission page is used to format qPCR fluorescence data and associated metadata into a format that is acceptable to be added to the MDMAPR 2.0 database for storage. On this page, a raw qPCR Experimental Fluorescence File, a raw Standard Curve Fluorescence File, and the filled in Metadata file are required. The Data Submission tool will parse the data into 13 CSV files. A preview of the tables is viewable on the page. A zipped file of the CSVs can be downloaded by pressing the 'Download Data Submission Files' button. NOTE: Before you can upload the generated CSV data files into their respective tables in the MDMAPR 2.0 database, the ID columns (projectID, geographicRegionID, siteID, stationID, replicateID, extractID, assayID, runID, pcrChemistryID, resultID, standardCurveID, and SCresultID) must be manually changed from alphabetical characters to unique numeric IDs.
Information on the required files for the application is available on the Data page.