EpiCompare User Guide
Contents
1. BJ Delete Column Insert Column Rename Column o a fr T D amp Insert Row At Sort Table 0 s 00 00 80 00 80 0 80 s 0 0 o Help Figure 1 Data View The buttons for switching views are below the menu bar 1 The command pane 2 offers the currently available commands The currently edited cell is indicated 3 A blue table head as shown in 4 marks the currently sorted column Switching Views The pane below the menu bar is used for switching different views There are three views Data which contains a table for the used data Procedures which allows selection of calculation procedures and Results where the calculation results are displayed Click on the text in the pane or use the Back and Forward buttons to switch the views Import Data from a File Use the button in the command pane to open a file Several import options can be set e whether the file contains a header in the first line or not 66 99 e ifaCSV file is chosen the delimiter can be set In most cases this will be or Take a look at the preview table to find out if the delimiter is chosen correctly e each column in the table needs an unique name Columns that have a name assigned are displayed in white If a column has no name assigned it is displayed in a light red colour Click on a column and s2. N includes non typable values N Number of isolates that show a non missing value and that have the same value on repeated testing If both results are non typable it 1s also counted here See Hunter Gaston 1988 Struelens 1996 Ridom EpiCompare User Guide Discriminatory Index Discriminatory index is calculated with the following formula _ l i D i aa gea lV where N is the total number of strains in the sample population s is the total number of types described and 7 is the number of strains belonging to the jth type A 95 Confidence Interval CI can be calculated for D with the following formula 4 2 n Cl D 2 0 D 2 o7 with 4 5 m gt TT and De Ridom EpiCompare uses all isolates that have no missing data and are typable for calculation of discriminatory index and 95 confidence interval Isolates with missing data or isolates that are non typable are ignored in this calculation See Simpson 1949 Hunter Gaston 1988 Grundmann et al 2001 Typing System Concordance Use typing system concordance to compare the results of different typing systems For calculation pairs of the results of 2 typing systems x y x y ElIsolates of all isolates are created All pairs are arranged in a 2x2 table according to their type in both typing systems System 1 System 7 System 2 A B of pairs x y for which x of pairs x y for which x and y have the sa
3. Tol PE 7 Strain no iv and Strain no a a Figure 2 Procedures View The upper pane 1 contains the text for non typable and missing isolates Selecting attributes in 2 displays a summary statistic for this attribute Select 3 6 for calculation of 3 Typing System Concordance 4 Reproducibility 5 Typability and 6 Discriminatory Index Ridom EpiCompare User Guide Results View The results view see Figure 3 displays the calculation results of the selected procedures References for the different procedures are given The results can be saved and printed In addition they can also be exported to the clipboard and used in word processor programs like Microsoft Word DSEnicompare File Edit Table Help gt 1 Data Back N 2 Procedures 3 Results Commands Resu Its Save Results Date 8 27 07 4 34 PM Using isolates from D workspaceEbPAMiEpiComparelinstallerisample_filesiMellmann_JCM_2004 xls Print Results of isolates 42 Copy Results to Clipboard Summary MLST ST of isolates with valid value 42 of different values 14 of isolates with valid values 12 28 6 4 8 2 4 11 9 2 4 11 9 4 8 4 8 7 1 el 2 4 TA 2 4 Item isolates ho gt ol wl win a as Figure 3 Results View Use the command pane 1 to export or print the results Send Bug Report Ridom EpiCompare includes a feedback
4. have to install Java first before you are able to install Ridom EpiCompare Ridom EpiCompare can now be started by clicking the software s icon in the installed directory on the desktop or in the Start Menu Updating the Software A download option for on line updates is integrated into the software Help menu For disabling the auto update feature or for proxy settings use the Preferences dialogue from the File menu Ridom EpiCompare Help Use the button in the Help menu to view this PDF document the document includes a Quick Reference with menu and keyboard shortcuts 4 Getting Started Keyboard Shortcuts Frequent occurring actions can be conveniently invoked by keyboard shortcuts All menu commands can also be invoked e g if no mouse is available by using the Alt key in combination with a character as indicated by underscore in the menu e g for the command Open press Alt F O Ridom EpiCompare User Guide BS EpiCompare File Edit Table Help be 1 Da coa lin I f l spa lin Kreisw spa type K A o 3 s a a New Table Open CSY File Export Data to CSV File GA Print Table 2 Copy Complete Table Replace Table NES with Clipboard Content OpAON OSs goog D gt p Weee a OO w w TE 9 Tar P so e o o eo ao eo e aa a aa ol ol aaa Oooo ENN a Nn e ee
5. selected before the first column Rename Column namel A R Changes the name of the selected column Merge Columns B Alt M Merges two or more columns Delete Row HH Ctrl Del Deletes the selected table rows Insert Row tits C t r Inserts a row after the first selected row or if no row is selected Enter before the first row Sort Table aa Sorts the table according to a chosen column 11 Ridom EpiCompare User Guide Menu Item Shortcut Description Help Menu EpiCompare User Guide PDF F1 Opens the program manual PDF in an external viewer e g Adobe Reader Software Update Online Update Searches for available software updates at the Ridom web server Software Update Import Update File Imports a software update file that was manually downloaded from the Ridom web server Ridom Support Send Bug Report Feature Request Sends a bug report or a request of new feature Ridom Support Support Home Page Opens the Ridom support home page with the default WWW browser About Opens the Ridom EpiCompare version info includes also a system overview 9 Ridom EpiCompare Frequently Asked Questions FAQ Can Ridom EpiCompare open Microsoft Excel Files Microsoft Excel Files with a file name typically ending with xls can be read directly with Ridom EpiCompare For other spreadsheet programs you must convert the data into CSV fi
6. Radom bioinformatics Ridom EpiCompare Version 1 0 Contents Ms T OGUCUON aeran E aasueuneesondaseaantekeeeosenedecees 2 POIO eea E E ee ee ee eee 2 3 Installing Ridon IC ONO Al ssenari A EAA SE EEEN 3 aE ao Eee E o E ES EE E E OE eee E E E E OEE 3 CUON DETA a a E E E E 7 0 REIG ONCOS sanre EE E R E E 10 os TIO FIO Sacre iE AE S E A RE 10 OEIC RETE O e E E E E E EE 11 9 Ridom EpiCompare Frequently Asked Questions FAQ c cccccsseeeeeeeeseeeesaeeeseeeenees 12 10 End User Licence Contract for Ridom EpiCOMpare cccccececeeceeeeeeeeeeeeeeeeeeeteeees 13 Ridom and Ridom EpiCompare are registered trademarks of the Ridom GmbH in Europe U S and certain other countries All other brand names and product names are trade names service marks trademarks or registered trademarks of their respective owner Ridom GmbH Sedanstr 27 D 97082 W rzburg Germany email info ridom de Ridom EpiCompare User Guide 1 Introduction Epidemiological typing has many different applications Those include surveillance of infectious diseases outbreak control and others Often two ore more different typing methods are available There are several criteria for evaluating the power of typing methods and for comparing different methods The underlying mathematical formulas are often quite simple but the handling of the data can get demanding for large data sets The program Ridom EpiCompare can calculate variou
7. ages from loss of profit loss of business information or from any other financial loss which arises as a result of the use of this product or of the inability to use this product is expressly excluded c For damage or loss which involve death or physical injury Ridom GmbH is in no case liable for aggravated compensation for damages or penalty compensation for damages for any specific indirect coincidental damage or 1oss or consequential loss or damage arising the refrom this applies particularly but not exclusively tor bOSs of use Joss Of data Loss Of profit and for Loss of Savings and business This applies regardless of the basis of the claim or grievance d Ridom GmbH is not responsible for and makes no warranty for the product running without interruption or without error VI Place of judgement and applicable law a Place of fulfilment for all obligations arising from the contract relationship is for both contract partners Wurzburg the base of Ridom GmbH This applies even if the residence of the customer is unknown or is outside Germany VII Final provisions a Should any provision of this EULC be or become ineffective or contestable for any reason its content is not otherwise disturbed thereby Rather it is to be performed in accordance with the intent b Instead of the ineffective or contestable provision an appropriate regulation is to apply which as far as legally permissible comes as close as possible
8. dialogue to provide the user with a convenient way of sending messages directly to the developers such as features requests and bug reports This dialogue can be opened in the Help menu If an program error occurs a window opens automatically The report already contains the internal description of the error that occurred together with some system information Ridom EpiCompare version OS and Java version If the error occurred after a specific user transaction it would be of help to us in solving the problem if a description of the circumstances leading to the problem is given in the comment field Ridom EpiCompare User Guide 5 Calculation Details Typability The typability is the proportion of strains that are assigned a type by the typing system The formula reads with N the number of isolates assigned a type and N the number of isolates tested Ridom EpiCompare uses N Number of isolates that show a non missing value N Number of isolates that show a non missing typable value See Hunter Gaston 1988 Struelens 1996 Reproducibility Reproducibility is the ability of a typing system to assign the same type to a strain tested on independent separate assays The formula reads IN R N with N the number of isolates assigned the same type on repeated testing and N the number of isolates tested Ridom EpiCompare uses the following data N Number of isolates that show a non missing value
9. discriminating among Staphylococcus aureus isolates implications for use of a single marker to detect genetic micro and macrovariation J Clin Microbiol 42 792 799 2004 10 Ridom EpiCompare User Guide 8 Quick Reference Menu Functions Menu Item Icon Shortcut Description File Menu New Table 5j Ctrl N Replaces the current table with a new one Open File me Ctrl O Opens a file MS Excel or CSV Export Data L Ctrl E Exports the current table to a file MS Excel or CSV Print Table m Ctrl P Prints the current table Save Results As S Ctrl S Saves the results of the calculation as a HTML file Print Results A Ctrl P Prints the results of the calculation Preferences oA Preferences for automatic updates and proxies Exit Ctrl Q The preferred way to exit the program Edit Menu Copy Complete Table B Ctrl Shift C Copies table to clipboard in MS Excel format Replace Table with Ctrl V Replaces the table with clipboard content Table in clipboard must Clipboard Content E be in MS Excel format Copy Results to Clipboard Ctrl C se results of calculation to clipboard Clipboard content can e used further e g in word processor programs Table Menu Delete Column Ei Altt Del Deletes the selected table columns Insert Column iE I t Inserts a table column after the selected column or if no column nter is
10. elect a predefined name or specify a name by selecting the command Enter Column Name from the context menu Import Data from Clipboard It is also possible to import a table from the clipboard This feature supports Microsoft Excel clipboard format This means that you can select a table _ or parts of it in MS Excel copy it to the clipboard and paste it into the program Press the WEB button to replace the table with the current clipboard content You will be asked if the first row should be used for selecting column names If this applies and two or more columns have the same name numbers are attached to the names to make them unique Ridom EpiCompare User Guide Data View In the Data View see Figure 1 each row contains one isolate and each column contains a specific attribute The attribute names are unique this means that two columns cannot have the same name The table columns can be moved by dragging them with the left mouse button Table columns can be selected by clicking their column head Multiple columns can be selected by pressing the Ctrl key while clicking the column head To edit the table double click a cell The Tab key can be used to traverse the table s cells while editing The Table menu contains functions for modifying and sorting of the table It 1s also possible to sort the table by double clicking a column head with the left mouse button The head of the sorted column appears blue It is possible to mer
11. ge two or more columns with the Merge Columns button A new column 1s created with a name made out of the names of the merged columns and the new column is filled with the concatenated values of these columns Be careful with cells containing non typable values Check that the merged cells contain the correct data for your usage Procedures View Figure 2 shows the view that is used for selecting the procedures See next chapter for calculation details A pane allows the input of strings for missing or not non typable values The default for missing is empty text and for non typable values NT Change these if your dataset uses other strings It is possible to select multiple lines 1n the lists by using the Ctrl key while clicking with the mouse button Typing system concordance and reproducibility can only be calculated for two attributes at once File Edit Table Help 1 Data 2 Procedures 3 Results Hint Use ctrl key to select multiple elements String For non typable NT String For missing data empty cells amp C Show Summary for C Show Typability for Strain no Strain no Origin Origin Epidemiologic implication Epidemiologic implication PFGE Smal PFGE Smal jaa MLST ST ow Concordance Rand s and Wallace s Coefficients For C Show Discriminatory Index for rain no K and Strain no Strain no i Origin Epidemiologic implication C Show Reproducibility for PFGE Smal
12. hotographs animations video audio text and applets which are included in the software product the accompanying printed material and each copy of the software product are the property of Ridom GmbH All rights and intellectual property rights in and to content which can be accessed with the aid of this software product are the property of the respective owners of the content and may be protected by applicable intellectual property rights laws and other laws and agreements on intellectual property This EULC does not grant the licensee the right to use such content III Scope of Licence a The licensee is entitled to install the software product the demo version or an earlier version on several computers workstations portable PCs or another digital electronic device b The software product is licensed as a unitary product The licensee is not entitled to separate its components for use c The licensee is not entitled to reverse develop to decompile or to disassemble the software product No changes to the existing source code neither any re use of parts of it are permitted d The licensee is not entitled to resell the software product or in any other way to transfer the software product for a counter value The licensee is not entitled to rent the software product to lease it or to sell it e Without prejudice to its other rights Ridom GmbH is entitled to terminate this EULC insofar as the licensee contravenes the provisions of thi
13. ing multiple typing methods by application to macrolide resistant Streptococcus pyogenes J Clin Microbiol 44 2524 2532 2006 Grundmann H Hori S Tanner G Determining confidence intervals when measuring genetic diversity and the discriminatory abilities of typing methods for microorganisms J Clin Microbiol 39 4190 4192 2001 Hunter P R and Gaston M A Numerical index of the discriminatory ability of typing systems an application of Simpson s index of diversity J Clin Microbiol 26 2465 2466 1988 Simpson E H Measurement of diversity Nature 163 688 1949 Struelens M J Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems Clin Microbiol Infect 2 2 11 1996 7 Example Files There are two example datasets included as MS Excel and CSV files They contain example data from the following publications Mellmann JCM 2004 Mellmann A Mosters J Bartelt E Roggentin P Ammon A Friedrich A Karch H and Harmsen D Sequence based typing of flaB is a more stable screening tool than typing of flaA for monitoring of Campylobacter populations J Clin Microbiol 42 4840 4842 2004 you will note a small calculation error in this publication Sorry for the error but we did not had Ridom EpiCompare available at that time Koreen JCM 2004 Koreen L Ramaswamy S V Graviss E A Naidich S Musser J M and Kreiswirth B N spa typing method for
14. les comma separated values The procedure xyz is missing Will it be included in future releases Maybe But first we must know that someone wants the procedure xyz to be included If you are interested in new procedures or new features you can write an email to info ridom de or use the Send Bug Report Feature Request command from the help menu to contact Ridom GmbH 12 Ridom EpiCompare User Guide 10 End User Licence Contract for Ridom EpiCompare Permission is granted to anyone to use this software FREELY for any purpose subject to the following restrictions I General a This End User Licence Contract KULC forms a legally binding contract between you the licensee and Ridom GmbH the licensor for the Ridom EpiCompare software and related media materials and documentation the software product b If you do not agree to these conditions you are not entitled to use the software c The person who concludes this EULC assures and makes warranty that he is entitled to declare a legally binding contract on behalf of his employer as the licensee d The software product is licensed not given away II Copyright a The software product distributed by Ridom GmbH is protected both by copyright laws and international copyright treaties and also by other laws and agreements concerning intellectual property b Ownership and copyright of the software product including but not restricted to images p
15. me type in and y have the same type in System 1 and in System 2 System 2 and a different type in System 1 System 2 C D of pairs x y for which x of pairs x y for which x and y have the same type in and y have a different type in System 1 and a different System 1 and in System 2 type in System 2 Ridom EpiCompare User Guide A D A B C D This value is also known as Rand s coefficient However if comparing two random data sets concordance calculation does not approach the value 0 Therefore when calculating the Adjusted Rand coefficient a correction factor is used to take into account the presence of chance agreement ADH A B C D n n n 1 n 1 gt n n 1 gt nt 2 gt 3 L ao oa oo The ratio is the frequently called in publications the typing system concordance Adjusted Rand with where n represents the total number of isolates and represent the numbers of isolates with values and j for System 1 and System 2 Wallace s coefficients are calculated by A A B and A W A AFC They represent the probability that a pair of isolates that have the same type in System also have the same type in System 2 and vice versa See Carrico et al 2006 Ridom EpiCompare User Guide 6 References Carri o J A Silva Costa C Melo Cristino J Pinto F R de Lencastre H Almeida J S Ramirez M Illustration of a common framework for relat
16. s EULC In such a case the licensee is obliged to destroy all copies of the software f Ridom GmbH reserves all rights not expressly granted The individual provisions of this licence agreement can only be changed by Ridom GmbH The written form is required for this without any exception IV Warranty and assurances a This software is provided as 1is without any express or implied warranty In no event will the Ridom GmbH be held liable for any damages e g hardware damages loss of data or miscalculations arising from the use of this software b The software product is supplied in accordance with the current development status Ridom GmbH draws attention to the fact that 1s not possible in the current state of technology to create computer software such that it works 13 Ridom EpiCompare User Guide without errors in all applications and combinations The subject of this contract is therefore only software which is in principle usable in the sense of the program descriptions and user manual c Statements contained in brochures advertisements and similar documents represent only descriptions and do not contain any assurance of properties or guarantees V Limitation of liability a The licensee bears the responsibility for the selection and for the consequences of use of the software product together with the results thereby intended or achieved b Liability for damages of any kind included without restriction are dam
17. s criteria for data of different typing techniques It combines easy calculation with ease of data handling Ridom EpiCompare can calculate the following parameters Typability is the percentage of distinct microbial strains which can be assigned a positive typing marker Reproducibility is the percentage of strains that give the same result on repeated testing Discriminatory power of a typing method is its ability to distinguish between unrelated strains Typing system concordance helps to compare different independent typing systems 2 Features Import data from files MS Excel CSV and from Clipboard Easy handling of data edit sort reorder print Calculation of different performance criteria for data Typability Reproducibility Discriminatory Index Typing System Concordance Export results as HTML file Export via clipboard or files MS Excel CSV Ridom EpiCompare User Guide 3 Installing Ridom EpiCompare System Requirements An installed Java Runtime Environment 1 5 or higher is required to run Ridom EpiCompare Java is freely available from www java com An installed PDF Viewer e g Adobe Reader www adobe com is needed for viewing the manual Ridom EpiCompare was tested with Java 1 5 on Windows NT4 0 2000 XP and Vista Installing Instructions Download from www ridom de the latest version of Ridom EpiCompare Double click the downloaded file and follow the on screen instructions please remember you
18. to that which the parties who concluded the contract intended or would have intended in accordance with the sense and purpose of this contract if they had considered the point when concluding this contract The same applies in the event of a lacuna in this contract This also applies even if the ineffectiveness of a provision rests in any way on a measure of the performance and the time period or date prescribed in the contract A legally permissible measure of the performance or time date or period which comes as close as possible to that which was intended shall then be deemed to be agreed Ridom EpiCompare license version 1 1 July 2005 14
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