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User Guide - Ecologie Microbienne Lyon

1. To add some but not all worksheet entries to the data list click and drag or press Shift and the Up or Down arrow keys to select contiguous rows Once they are highlighted click the Add Selected Plates button in the middle of the page Note If you want to add non contiguous MicroPlates click the Add Selected Plates button separately for each contiguous group selected The groups are added cumulatively to the data list 4 To delete MicroPlates from the data list select the wells you want to delete then click Delete Selected Plates To clear all entries from the data list you must do this to begin creating a new data list click Clear all Plates If you ve already created and saved a data list and wish to recall that list click Load at the bottom left of the page All entries existing at the time you last saved will appear in the data list If you have added or deleted MicroPlates from the data list you may want to recalculate the average plot of the replicates To do so click Average Replicates at the bottom of the page If you encounter any replicates with a Plate Revision Letter that is different from the first one a warning will appear Click OK for each warning A progress bar will show the advancement of the averaging and plotting process When you are satisfied with the results of your search as displayed in the data list click Save to retain the data list for future use and or parametric analysis A Windows Sav
2. reference and yellow both e In Display Options Colors click Form Color Lavender White This allows you to toggle the background color of the entire program page from pale purple to white Change display colors here SETUP PAGE x Page 25 OmniLog PM User Guide 1 November 03 Comparing Data Lists and Generating Reports Basic colors mir Tel eee mM ST eee oe ee ie nu BEE EEE ES BEERS mi Custom colors BEEBE ee ee EEE Eee ee Define Custom Colors gt gt Cancel COLOR SELECTION DIALOG 3 Use the MicroPlate navigation tool List Status across the bottom of the page to select which MicroPlate number you want to display Small carets appear immediately to the left and right of the selected number Viewing multiple MicroPlates The software also gives you the option of viewing 20 MicroPlates types at once This enables you to easily scan many kinetic plots and see patterns of differences and similarities These distinctions stand out because the list and reference data plots are superimposed over each other As you work with your data you will likely navigate frequently between the 1 Plate Data page to the 20 Plate Data page 1 Click 20 Plate Data tab on the menu bar 2 Right click on any well to view a description of the chemical contained in that well along with the mode of action 3 Double click on any of these descriptions to go directly to the on line KEGG website
3. Page 26 OmniLog PM User Guide 1 November 03 Comparing Data Lists and Generating Reports Each grid is a smaller version of the MicroPlate displayed on the 1 Plate Data page 20 PLATE DATA PAGE Selecting parameters OmniLog PM enables you to reduce the multitude of data on your data lists by extracting specific parameters that focus on one or more aspects of the plot depending on your areas of interest The parameters are numerical characteristics of the plots displayed Selecting specific parameters helps you find out more about the characteristics of an organism as well as conduct statistical analyses of these parameters The most commonly selected parameters are described here see Advanced Functions for descriptions of the other parameters Click one of these radio buttons to select a specific parameter Adjust this down a few hours to eliminate plot anomalies if necessary Check this checkbox to display parametric or derivative plots 1 PLATE DATA PAGE SHOWING KINETIC PLOTS FOR ONE MICROPLATE ON THE REFERENCE DATA LIST Page 27 OmniLog PM User Guide 1 November 03 Comparing Data Lists and Generating Reports MOST COMMONLY SELECTED PARAMETERS What it is Parameter What to Click Height e the average height of the plot in white light absorption values e the blue lines represent a parametric plot which is a graphical representation of the minimum value maximum v
4. C source carbohydrate PM01 A05 Succinic A 176 07 C source carbohydrate PM02 F03 Melibionic 161 93 C source carbohydrate PM01 G11 D Malic A 268 62 C sou arboxylate PM 1 G12 L Malic Ac 247 96 C sou carboxylate PM01 F05 Fumaric A 246 13 C sou c tate PMO1 co3 O L Malic 241 4 C source cart oxylate PRINTOUT OF PARTIAL PAGE OF SPREADSHEET REPORT IMPORTED INTO EXCEL Exporting parameter values OmniLog PM enables you to export your parameter values into Excel as multi worksheet xls files This is done one data list at a time These worksheets organize the parameters according to MicroPlate number or display format 1 With the data list to be exported loaded as Data List 1 also called the test data list in the 1 Plate data page select the Max Hour setting desired 2 Click the Export tab on the menu bar Click the Go Export to XLS button at the bottom of the page L PM A Parametric Click here to export a parameter values list into multi worksheet xls file EXPORT PAGE Page 35 OmniLog PM User Guide 1 November 03 Comparing Data Lists and Generating Reports 4 Name and save the file as desired average PRINTOUT OF PARTIAL PAGE OF XLS WORKSHEET EXPORTED INTO EXCEL WHAT S ON EXPORTED MULTI WORKSHEETS Meta Params worksheet MicroPlates 1 8 listed from well A1 through H12 reporting all 12 parameters with each parameter in its own column pH Salt Params w
5. Click the Data File Rename Dialog button at the bottom middle of the page Click here to convert file name format Page 6 3 The pop up dialog displays two Windows file directory trees the Origin directory on the left and the Destination directory on the right The Origin directory is the one that contains the data files to be copied and renamed though the data file names will not be listed on the page The Destination directory is the one in which you want the copies to ultimately reside Most often you will want the Origin and Destination directories to be the same the software will do this by OmniLog PM User Guide 1 November 03 x Page Defining Data Lists and Displaying Rinetic Plots default but you do have the option of saving the renamed data files to a new directory Navigate through the directories by double clicking until you find the desired Origin directory Note You may want to keep Windows Explorer open at the same time so you can view the individual data files in a given folder and make sure you are selecting the desired folder 4 Click the Copy Rename Data Files button The software will automatically rename the data files assigning each one an 1 1 field file name The old data files are not overridden the software simply creates a new set of data files with new names All the information in the old file name is contained in the new file name with additional helpful identifiers at the front
6. Dialog pops up Select the desired color by clicking on that color then click OK x Page 12 OmniLog PM User Guide 1 November 03 Defining Data Lists and Displaying Rinetic Plots Basic colors Tee ME mM om ee ADETE E ee i AEE EEEE g BEE Eee ee Custom colors BEE EEE ee BEE EEE ee Define Custom Colors gt gt Cancel COLOR SELECTION DIALOG 2 Select a MicroPlate type you d like to begin with in the data list on the Define Data List page by selecting that row 3 Click the Kinetic Plot tab on the menu bar The wells will fill with graphical data Wait until the entire display appears before clicking anything else 4 Visually scan the display for gross experimental errors e Flat lines indicate no growth Look for flat lines in wells where you would expect growth e Look for growth graphical data in unexpected wells 5 Visually scan the color plots for indications of experimental reproducibility The display can show up to 10 colors replicates in excess of 10 are still displayed but not in different colors The closer those colored lines lie on top of each other the greater the reproducibility 6 The software allows you to view graphical data in a number of ways Page 13 OmniLog PM User Guide 1 November 03 Defining Data Lists and Displaying Rinetic Plots 1 1 MicroPlate well J well 1 MicroPlate Heavy vertical lines Heavy vertical lines days i Thin horizontal lines KINETIC
7. Mode groupbox click GN gram negative to display MicroPlates PM 1 20 In the Fixed Selection Mode groupbox click GP gram positive to display MicroPlates PM 1 10 and 31 40 In the Fixed Selection Mode groupbox click YT yeast to display MicroPlates PM 1 10 and 21 30 In the Fixed Selection Mode groupbox click User to display the first 20 MicroPlate types in each data list 2 At the bottom of the page click on the List Status grid to select which MicroPlate type you want to show in the kinetic plots Row L1 displays every MicroPlate type available in the test data list Row L2 displays every MicroPlate type available in the reference data list Row L1 amp L2 displays only MicroPlate types contained in BOTH lists Row S to displays only those you selected in Fixed Selection Mode Row 20 displays only the MicroPlate types common to the test list the reference list and Fixed Selection Mode Viewing single MicroPlate comparative plots Comparing test and reference plots one MicroPlate at a time is useful for selecting the specific parameters by which you want to characterize your data and for visually inspecting superimposed plots to determine a desirable threshold The 1 Plate Data page is the place where you will refine the specifics of your plots and parameters 1 Click the 1 Plate Data sub tab on the menu bar The program displays the kinetic plots for the test data list by default You ll note that the List 1 r
8. PLOT PAGE intervals of 100 W A units MicroPlate navigation tool Plate tab Click to CE EE E E EE P hola fe ta ha ls re lir re ls 20 on 22 les 124 2s les 127 fes 29 a0 or 32 os 24 as es az es 29 a0 display different MicroPlates EE Kinetic Plat Setup Export Close Display options ai FATIGRian amp Kathy Kinetic ecol_BW26115_run2__1_36_ZEC_138_Dec 03 2002_A_ D1Aoka Info tab change graphical colors here MICROPLATE NAVIGATION TOOL KINETIC PLOT DISPLAY OPTIONS MicroPlate navigation allows you to select which MicroPlate in click on the number of the tool the current data list you want to view MicroPlate you want to view 1 40 graphically small carets appear immediately to the left and right of the displayed file Min Day Max Day allows you to narrow the span of days click the radio button desired for each displayed for example if your of Min Day and Max Day experiment spanned 7 days but there was no growth on days 1 3 and excessive growth on days 6 and 7 you can choose to view only days 4 5 if desired Max Value adjusts the vertical scale of the display click the desired radio button for you can adjust this value to show the Max Value plots on a maximal scale without being out of range x Page 14 OmniLog PM User Guide 1 November 03 Defining Data Lists and Displaying Rinetic Plots the number you select the faster the graphical display c
9. Software shall be used only in the conduct of Licensee s own business and Licensee shall not permit any third party to use the Software Licensee shall make available implementation computer equipment and software configurations approved by Licensor as adequate for implementation of the Software Ownership The Software and all modifications thereto and all copies thereof are proprietary to Licensor and title thereto remains in Licensor All applicable rights to patents copyrights know how trademarks and trade secrets in the Software and any modifications made thereto are and shall remain in Licensor Licensee shall not sell transfer publish disclose display or otherwise make available the Software or copies thereof to others Licensee agrees to secure and protect each module software product and related documentation in a manner consistent with the maintenance of Licensor s rights therein and to take appropriate actions by instruction or agreement with its employees or consultants who are permitted access to the Software to satisfy its obligations hereunder Any copies made by Licensee of the Software and other programs developed hereunder including translations compilations partial copies with modifications and updated works are the property of Licensor Violation of any provision of this paragraph shall be the basis for immediate termination of this Agreement No copying or transmission of the Software is permitted TABLE OF CONT
10. edit data Step 3 Assemble data lists and display kinetic plots Step 4 Display parameters and compare data lists OmniLog PM User Guide 1 November 03 Introducing the OmniLog PM System Step 1 Generate data The Data Collection program operates the OmniLog reader via the dedicated OmniLog computer After you have inoculated a PM panel load the MicroPlates into the OmniLog to begin data collection The software guides you through the MicroPlate loading process reads MicroPlates every 15 minutes during a user defined incubation period and walks you through the unload process Step 2 View and Edit Data The Data Management program lets you view and edit MicroPlate information fields in the kinetic data files on a plate by plate basis This allows you to correct any errors entered in the MicroPlate information fields during loading in the Data Collection program This part of the software also lets you view the kinetic data for an individual MicroPlate and offers data visualization and reports tools for specialty MicroPlates and reports You can skip this step unless you need to edit MicroPlate information fields or view a special individual MicroPlate Step 3 Make data lists and kinetic displays The File Management Kinetic portion of the software lets you assemble several MicroPlates of data into a unified set called a data list Data lists are the data file organizational format for the OmniLog PM software T
11. hours x Page 28 OmniLog PM User Guide 1 November 03 Setting a threshold is an art interive process What you view as a strikingly different will vary from experiment to experiment Page 29 Comparing Data Lists and Generating Reports Setting a threshold The software allows you to set a threshold value of significance as you analyze your data set Thresholds provide a rapid way to select wells that are significantly different while excluding insignificant ones 1 Display the desired MicroPlate on the 1 Plate Data page 2 Select the desired parameter for example Height 3 Look for wells with strikingly different plots For example a well might have a reference plot with a height of 211 and a height of 33 a difference of 178 4 Once you have a numerical value in mind for what you consider a significant difference for that data set click the Setup tab on the menu bar gt es o Fr Adjust these numbers Mer to set the threshold Form Calor Lavender White F Grid Unes F Outline Cotte Te en SETUP PAGE 5 At the right of the page you ll see the Distance Limit edit boxes The PM 1 8 distance limit covers metabolic MicroPlates while the PM 11 36 distance limit covers sensitivity MicroPlates Use the Up and Down arrows to adjust these numbers as desired Remember the purpose of changing the threshold is to create a more obvious visual aid to help you identify wells of scient
12. will fall above the thresholds you set for that experiment Wekume Define Data List Export Setsp Close Phenotypes Define Data Set 20 Plate Data 1 Piste Date Report gained by the test strain Phenotypes lost by the test strain SPREADSHEET REPORT 5 To export this information into Excel click the Export Report button at the bottom right corner of the page Name the file as desired and click Save to save as a csv file Page 34 OmniLog PM User Guide 1 November 03 Comparing Data Lists and Generating Reports Report Date 4 14 2003 10 39 20 AM Name Strain Nu Other Test E coli dpt20 2 control 20821 Ref E coli dptO1 Phenotypes Gained Faster Growth Resistance PM Wells Tes Differenc Mode of Action PM14 All Sanguinari 177 37 ATPase Na K and Mg PM14 C06 1 Hydroxy 232 98 chelator lipophilic PM14 G06 Potassium 155 04 oxidizing agent PM19 G06 G07 Dihydrostr 602 44 protein synthesis aminoglycoside PM16 E03 E04 Streptomy 458 67 protein synthesis aminoglycoside PM11 A04 Amikacin 158 06 protein synthesis aminoglycoside PM13 E08 Geneticin 157 18 protein synthesis aminoglycoside PM14 002 003 Cadmium 377 65 transport toxic cation PM14 F06 FO7 Piperacilli 430 77 wail lactam Phenotypes Lost Slower Growth Sensitivity PM Wells Test Differenc Mode of Actior PM01 A07 L Asparts 248 96 C source amino acid PMO01 D01 L Asparag 162 74 C source amino acid PM01 Al2 Duicitol 208 59
13. BIOLOG OmniLog Phenotype MicroArray Software Release 1 2 User Guide 2003 Biolog Inc All rights reserved Printed in the United States of America OmniLog and MicroPlate are trademarks of Biolog Inc Microsoft Windows Windows 2000 Windows 98 Windows 95 Windows NT and Microsoft Excel Word Power Point and Access are registered trademarks of Microsoft Corporation Technical Service For technical assistance contact us at Address 3938 Trust Way Hayward CA 94545 U S A Email PMtech biolog com OmniLog Phenotype MicroArray Software Release 1 2 User Guide Writer Designer Robin Solit LICENSE AGREEMENT Notice This is a legal agreement between you an individual or entity Licensee and Biolog Inc Licensor By purchasing or using this software whether it is on a diskette or preinstalled on a computer you agree to be bound by this agreement If you do not accept this agreement please immediately return the unopened envelope containing the complete contents as well as any computer on which such contents were preinstalled to Licensor or other place of purchase License Licensor grants Licensee the right to use the enclosed copy of Licensor s OmniLog PM Software the Softvvare at the single microbiology laboratory at one physical location for which this license is granted the Site The Software shall include all related materials and documentation provided by Licensor The
14. ENTS 1 INTRODUCING OMNILOG PM SOFTWARE uuu cccsscscssessssscsesscsscsssseeseees 1 OMNILOG PM S SUITE OF PROGRAMS ccccssesescecccccccesssscsescccccscsssussseececcssssuuensseseeccesesauenenenesses 1 2 DEFINING DATA LISTS AND DISPLAYING KINETIC PLOTGS 4 CONVERTING FILE FORMAT ccccccccccccccccssssssceccccccesesscsceccsssessussesesccsessssuusessceccsssessuuuessesceeseeees 5 POPUEATING A WORKSHEET LUIS TL EE E TEE 7 ASSEMBLINGA DATA EST el sees Moca ssishes a a a aen deve Gonwatelshcatiestecdeviehes terse 9 DISPLAYING KINETIC PLOTS cie its nem tecimisltastimenteemielsimnii 12 AVERAGING DATA cuenta te autenticitat gest 15 EXPORTING DATA tia et tiets ne deies 17 3 COMPARING DATA LISTS AND GENERATING REPORTS 20 COMPARING DATA LISTS vissicsi czccnssorccshdadescdedeacccssaheacanagonecebesd cdcheas S E aebieh aceasta ees 20 SAVING GRAPHICAL DISPLAYS AND VIEWING SAVED FILES ccccssssssecsccccccesessssscsccecceessseneeeees 32 GENERATING NON GRAPHICAL REPORTS ssssssseccccccccesssssscecccsccessssssececccssssuusesecsccssseuseneeseeees 33 EXPORTING PARAMETER VALUES cccssececcccsscccccsssceccessecccanseccesssceceussecccaussceceuaesesceaueseseeans 35 Introducing the OmniLog PM System 1 Introducing OmniLog PM Softvvare In this section The OmniLog Phenotype MicroArray PM system and software include gt OmniLog everything you need to incubate microbes OmniLog PM is a ded
15. adio button is selected in the Display Mode groupbox which corresponds to the test data list OmniLog PM User Guide 1 November 03 Comparing Data Lists and Generating Reports 1 MicroPlate vvell 1 MicroPlate Heavy vertical lines days Thin vertical line time Thin horizontal lines intervals of 100 units e Click the List 2 radio button to display one MicroPlate from the reference data list e Click the List 1vs2 radio button to display superimposed plots and areas of overlap between the test and reference data e Use the MicroPlate navigation tool across the bottom of the page to move from one MicroPlate to another click on the number of the MicroPlate you want to display p r alo Makama Define Date Unt sers Essen ose E Black lines above and Dats Set 20 Plate Dats 1 Plate Data Report at below the edge of the eee space filling plot are Graph te Clipboard standard deviation plots quc ents The colored edge of each space filling plot is the average value i eeueeee Display modes Click here to display test reference or both plots MicroPlate navigation tool 1 PLATE DATA PAGE SHOWING KINETIC PLOTS FOR ONE MICROPLATE IN THE TEST DATA LIST 1 entire grid 1 MicroPlate one 8 x 12 well 1 well of that MicroPlate narrow vertical gridlines in wells markers of time thick vertical lines in wells end of day markers colored space
16. alue lag time and plateau time parameters click on the Average radio button in the Parameter groupbox the sum of all OmniLog values over all timepoints e the blue lines represent the same parametric plot described above click on the Area radio button in the Parameter groupbox Inflection e the time at which there is an equal area under the derivative curve on both sides e the blue line represents the first derivative plot e peaks indicate where the bacteria grew most rapidly click on the Inflection radio button in the Parameter groupbox 1 Click the radio button for the desired parameter Keep the following in mind e The Average Height and Area parameters are the most stable and well behaved parameters They have the disadvantage however of being sensitive to the accumulation of reads in excess of the Plateau Time Consequently it is advisable to adjust the Max Hour so that it is only slightly greater than the Plateau Time e The Inflection Time parameter is sensitive to anomalous upspikes in the plot When selecting this parameter you might want to reset the Max Hour designation for the experiment to a lower number This will get rid of any anomalies in the plots noise in the curves and allow you to look at only a proscribed time period of the study If for example the entry under Max Hour is 48 reducing it to 42 will eliminate any undesired noise during the period between 42 and 48
17. d be named according to new format which has the extension oka For example the data file search feature of the software only works on files named according to the new format FILE NAMING CONVENTIONS Old data files Four fields separated by underscores Fields are project code reader number date worksheet code File extension 01 25 A B these correspond to the position of the MicroPlate inside the OmniLog reader Reader number date and position uniquely identify each MicroPlate no two MicroPlates have identical values for these three fields Position example project code DPT_125_020321_A 16B reader number worksheet code New data files gt Eleven fields separated by underscores Fields are species strain gene compound other MicroPlate number temperature project code reader number date worksheet code position File extension oka OmniLog kinetic version A example species gene compound temp reader no worksheet code file extension ecol BW25115 runl 2 36 ZEC 138 Nov 20 2002 A 02A oka strain plate no project code position Page 5 OmniLog PM User Guide 1 November 03 Defining Setup tab Data Lists and Displaying Rinetic Plots Converting file name format Once you launch the File Management Kinetic Analysis program a Welcome page appears displaying name version and date information about the program WELCOME PAGE 1 Click the Setup tab on the menu bar 2
18. data captured 1 Make sure you are on the 20 Plate Data page 2 If you are satisfied with the thresholds you ve entered and with the white boxes the program outlined based on your selected parameters and thresholds click the Computer gt User button at the bottom of the 20 Plate Data page The white outlines will all turn black signifying that they are no longer tentative 3 If you are not fully satisfied with the computer s selections you can manually select or deselect individual wells as follows e Work on either the 1 Plate Data page or the 20 Plate Data page e Make sure the Outline Differences checkbox is checked e If you have NOT clicked Computer gt User you can select or deselect wells by clicking on them Wells that the computer has already outlined white will turn black signifying that you definitely want to select those wells If you click a black outlined well again it will turn back to white deselecting it e If you HAVE clicked Computer gt User saving the computer s selections you can deselect individual wells by clicking on them The black outlines will turn white e If you see wells that the computer did not select you can select them by clicking on them The outlines will turn gray These are called user picks If you want to display ONLY these not the computer s choices check the Just User checkbox All outlines will disappear except the gray ones you selected manually 4 If d
19. display that best serves your experimental purposes Retrieving test and reference data lists 1 Double click on the OL_PR_12 exe icon in the proper OmniLog PM folder A Welcome page appears displaying the program name version and date a CL PM Par 1 20 k Parametric Version Welcome Define Data List Export Setup Close Define Data List tab Welcome to OmniLog OL_PM_Par 1 20 A Parametric Version 18 07 02 WELCOME PAGE PARAMETRIC PROGRAM Page 20 OmniLog PM User Guide 1 November 03 Comparing Data Lists and Generating Reports 2 Click the Define Data Lists tab on the menu bar The page that appears has additional tabs you ll use during the process of comparing data lists and generating reports Welcome Define Data List Setep Expert Close Define Data Set 20 Piate Data 1 Piate Data Report Click here to load test data list Test list displays here Click here te bead Date List 1 Clear HRM Click here to tons Data List 2 CEN Set Click here to load reference data list DEFINE DATA LIST PAGE WITHOUT ENTRIES 3 Click in the Click here to load Data List 1 white box at the top of the page adjacent to the green box to load the test data list this will serve as the test list for this data set Reference list displays here 4 Navigate through the directories until you find the desired data list highlight the name and i
20. e p Define Data Set 28 Plate Dots 1 Plate Data Click here for visual aids that shovv differences in vvells 1 PLATE DATA PAGE WITH WELL DIFFERENCES HIGHLIGHED 9 Click the 20 Plate Data tab to view all 20 MicroPlates at once with the white outlines giving you a sweeping view of which wells might be interesting across the entire experiment Click here to make aia selections as well all computer and user eran r EE ram selections ui ps os 3 Q Esaa 8298048 aasa 2280 04 8 0 9072089 8 8 for ee EEEE a x LI 799999939 at dines js ettseenesses s ponies Click here to delete all RES sas a Pi ee on user selections mata aonar f L ji as img senis es z Click here to select all wells Check this box to remove display of all computer selections 20 PLATE DATA PAGE WITH WELL DIFFERENCES HIGHLIGHTED OmniLog PM User Guide 1 November 03 The reason for setting parameters thresholds and for carefully selecting and or deselecting wells is to create a useful set of data for display and for creating a report for exporting to Excel or Access x Page 31 Comparing Data Lists and Generating Reports Accepting or customizing selections The white boxes that outline the differences between wells are very useful markers The software enables you to either accept the program s automatic selections white boxes or manually change the boxed selections until you are satisfied with the
21. e File dialog pops up Name the data list and click OK to save it in the desired directory The program will automatically append a dlb file extension to the data list s file name OmniLog PM User Guide 1 November 03 Defining Data Lists and Displaying Rinetic Plots OMNILOG PM FILE EXTENSIONS oka new 1 1 field data file name dib data list w4c worksheet list 01 25 a b old 4 field data file name CVS comma delimited CSVfile Displaying Rinetic Plots A kinetic plot shows each well in a MicroPlate in a data list These plots are graphical representations of the data contained in a data list 1 kinetic plot 1 MicroPlate Kinetic plots 1 large black well 1 well of that MicroPlate represent a narrow vertical gridlines in wells markers of time change in thick vertical lines in wells end of day markers experimental colored curved plots data over time one color replicate Be horizontal lines i lis white light ti A i one n eii orizontal lines in wells white light absorption VV A over time This change reflects a combination of veh owth and 1 Before navigating to the kinetic plot page you can set up the colors respiration of the you want to appear for each column of data The color bars at the top LeSKCIRGH IST of each column in the data list dictate which colors will appear on the kinetic plot page If you want to change these colors click on the color bar at the top of each data list column A Color
22. e Type unique identifier assigned to each type of PM MicroPlate with a defined set of chemicals in all 96 wells This column lists a subset of the 40 possible PM MicroPlates types depending on the MicroPlates used in that experiment Expanding Columns These five expandable columns list the most common search criteria for the data files gt To view fully click on the edge of the header and drag the column to the right Data File Columns gt These wide column list the 11 field names of the data files found in your search Color of header row matches color of kinetic plot corresponding to that column of data color can be changed gt gt Each column corresponds to an additional replicate for each row that has an additional replicate Note that a particular row need not have the same number of replicates gt You can add 119 replicate plates when adding a replicate the program adds a column to the right of the applicable row in the data list so replicates line up laterally across columns x Page 10 OmniLog PM User Guide 1 November 03 Worksheet List j Add selected Plates am CECEE Data list x Page 11 Add all Plates Welcome Define Data List Kinetic Ptet Setup Export Close Worksheet List Click here te lead Worksheet Defining Data Lists and Displaying Kinetic Plots Click here to change kinetic plot colors DEFINE DATA LIST PAGE WITH WORKSHEET AND DATA LIST ENTRIES 3
23. e to a selected directory by clicking Save e To copy the displayed plot directly into the clipboard click Graph to Clipboard at the lower right corner of the page 99894 ions sills errereen Sr cer crs See Oren rnd RA RD RR CP acer 0 a uaanasasaua CREL 4 0 Rua seves aa wee vas ea amanmma snu a gt 0994 80 8 naD TET S aaasasasaas 9 9 aut Ree pores a 999149998 Clich here to save displayed plots 20 PLATE DATA PAGE x Page 32 OmniLog PM User Guide 1 November 03 x Page 33 Comparing Data Lists and Generating Reports 2 View a previously saved data set as follows e Click the Define Data Set tab on the menu bar Welcome Define Dats List Setup Export Close Define Data Set 20 Plate Data 1 Plate Data Report Select Data Lists Sie FATIGRVan Kathy KineticiireR DLE Click here to delete a data list DEFINE DATA SET PAGE e Click Clear 1 and Clear 2 to delete the test and reference data lists e Click on the white box containing the words Click here to load data list 1 and Click here to load data list 2 Retrieve the desired files from the Windows open file dialog The files will contain all your previous settings thresholds and selected wells e Alternatively you may save two data lists as a data set by clicking the Save Data Set button and using the pop up Save File Dialog The program will automatically append a dsb exte
24. end of the name Note You can use Windows Explorer to verify the new file names in the Destination directory folder It s easy to distinguish between the old and new naming formats the old file names are brief while the new ones are longer Populating a Worksheet List Worksheet lists serve two functions e to list data files found during a new search e to retrieve worksheet files created in the Data Collection program and to display them Conducting a new search 1 Click on the Define Data List tab on the menu bar den DL PM AMn 1 20 A Fle Mangement Kinetic Pist Version Welcome Define Data List Kinetic Ptet Setup Export Close Worksheet List Click here te bead Worksdeet Data File Search button Add Selected Platef s Add All Plates Chess All Files DEFINE DATA LIST PAGE OmniLog PM User Guide 1 November 03 Defining Data Lists and Displaying Rinetic Plots 2 To search for data files using specific criteria click on the Data File Search button at the far right corner of the page The Data File Search Dialog pops up Field filtering checkboxes Strain and Gene Compound are the two most frequent search delimiters Field drop down lists with available values for searching Click after completing selections DATA FILE SEARCH DIALOG 3 Use the directory tree on the right to locate the directory containing data files The window will momentarily flash white as the comput
25. er scans the directory for files with the oka extension The drop down lists on the left will be populated with all the values found for the 11 fields these are the same fields used for re naming the data files 4 Check the desired checkboxes to select the fields you want to filter the data files You can check as many checkboxes as desired this will narrow the search to only those data files that have matching values for all the selected fields If you don t check any check boxes the software will find all data files in the directory you selected Note If you narrow the search too much you may get a message saying that no files were found simply remove some of the checkmarks or select Consecutive searches are a different value for a field and the search may broaden cumulative in the 5 For each of the fields you ve checked select a value from the worksheet list corresponding drop down list on the left Click on the downward arrows to make each list drop down e You can only select one value from a given drop down list e Searches are cumulative you can search on one value then another thereby locating files that match either value e The results of subsequent searches are added to the bottom of the worksheet list x Page 8 OmniLog PM User Guide 1 November 03 If subsequent searches find a file that is already on the worksheet list the program will give you a warning message Ignore the message if yo
26. ers correspond to read times during the experiment This allows you to export OmniLog Signal values for specific time points including an end point reading Click the Up and Down arrows to select the desired time point Click the Max Hour button if you want to export only the last reading Observe the Data List 1 field If you ve saved the data list the name will appear here if not this field will be empty You can export the data whether you ve saved the data list or not To export data for the hour you selected in the upper right corner click Go Export Single Hour To export data for all hours in the displayed MicroPlate click Go Export All Hours The bottom section of the Export page Export All Plates from Data List 1 allows you to export data for all MicroPlates in the data list you are currently working with e Click Go Export Single Hour the one on the bottom of the page to export the data for the hour selected in the upper right corner but for all MicroPlates in the current data list e Click Go Export All Hours the one on the bottom of the page to export all values over the entire experiment for all MicroPlates in the current data list OmniLog PM User Guide 1 November 03 Defining Data Lists and Displaying Rinetic Plots 9 A progress bar and a message to Please Wait will appear while the data is exported 10 To locate the exported data open Excel and find the file as it is named in the Si
27. esired click Clear Picks on the 20 Plate Data page to go back to the original computer selections with no user selections outlined 5 If desired click Pick All on the 20 Plate Data page to select ALL wells for inclusion in your data set All wells will be outlined black or gray indicating selection OmniLog PM User Guide 1 November 03 Comparing Data Lists and Generating Reports WHAT DO DIFFERENT COLORED WELL OUTLINES INDICATE White Outlined Wells OmniLog PM software has performed calculations and selected these wells for inclusion in your data set They are tentative selections until you save them Black Outlined Wells You have indicated that the computer s selection is also one that you would make manually for definite inclusion in the data set Gray Outlined Wells You have selected wells that the software did not select They will be included in your data set Saving graphical displays and viewing saved files 1 Once you are satisfied with the parameters you ve selected the set thresholds and the wells selected for inclusion in the data set click one of the following e To save the displayed plot as a bitmap click Graph to BMP at the lower right corner of the 20 Plate Data page Name your file as desired and save to a selected directory by clicking Save e To save the displayed plot as a jpeg click Graph to JPEG at the lower right corner of the 20 Plate Data page Name your file as desired and sav
28. filling plots average data over time wiry black lines above and below curves SD horizontal lines in wells white light absorption W A x Page 24 2 All plots are displayed in default colors green for test plots red for reference plots and yellow for superimposed areas in common To change these colors click the Setup tab on the menu bar Go to the upper left corner of the page to change plot and background colors e In Display Options Colors click Plate 1 Test A color dialog pops up Click on the desired color for the test plots then click OK OmniLog PM User Guide 1 November 03 Comparing Data Lists and Generating Reports e In Display Options Colors click Plate 2 Ref A color The graphical dialog pops up Click on the desired color for the reference plots shown on the plots then click OK plas Daia page In Display Options Colors click Both A color dialog are AVERAGED i plots of replicates pops up Click on the desired color for the areas in common then click OK e In Display Options Colors click Background A color dialog pops up Click on the desired color for the grid areas behind the plots then click OK e In Display Options Colors click Default B W All plots will automatically revert to black white and gray this can be useful for black and white printing e In Display Options Colors click Default Colors All plots will automatically revert to green test red
29. hanges This occurs because of the elimination of some data points to increase speed Option What it does What to Click Show Every Nth Read this adjustment effects the speed at click the desired radio button for which the display changes the higher Show every Nth read Set to Different Colors allows you to display each replicate s plot in a different color check the Set to Different Color box standard deviation SD the average SD is displayed as shading on the upper edge of the curve while the average SD is displayed as shading on the lower edge of the curve Show Grid Lines allows you to add or remove the check the Show Grid Lines box horizontal and vertical grid lines within a well Outline Cells allows you to add or remove the dark check the Outline Cells box outline around each well Replicate Display Mode shows the kinetic plots for all the click on the Replicates radio button replicate plates Average Display Mode shows the average kinetic plot and the click on the Average radio button Averaging Data In order to perform parametric analysis on the data you ve collected you need to average the replicates in your data list The program does these averages automatically every time you save a data list You may want to experiment with various settings that the affect this averaging Page 15 To average replicates 1 Navigate to the Define Data List page by clicking on the pro
30. hese lists contains information about all the PM MicroPlates applicable to a given organism type or compound treatment and can handle replicate data runs of the same MicroPlate type Once a data list is defined you can view all the data on that list OmniLog values in a data list are exportable to an Excel spreadsheet Step 4 View parametric data and generate reports The Parametric program lets you take a data list as defined by the File Management Kinetic Analysis program and generate an assortment of parameters The program also allows you to compare parameters between two data lists These parameters can then be displayed in various formats output in reports or exported into external files for further analysis Page 3 OmniLog PM User Guide 1 November 03 Defining Data Lists and Displaying Rinetic Plots 2 Defining Data Lists and Displaying Rinetic Plots The File Management Rinetic Plot module of the OmniLog PM software In this section i gt Converting File lets you assemble several MicroPlates of data into a single data list Using Format this assembled data the program displays kinetic plots for every well of a gt Populating a MicroPlate The program can superimpose replicate plots thereby Worksheet List allowing you to observe the reproducibility of your data The data list also S serves as the organizational format for the Parametric program gt Displaying The data file search feature allows you to selec
31. icated PM s Suite of system for phenotype microarray testing and includes the following Programs components gt OmniLog Software Steps e Dedicated Windows based computer with preinstalled OmniLog PM software e OmniLog Incubator Reader OMNILOG PM SYSTEM OmniLog PM s Suite of Programs OmniLog PM Software contains a suite of four programs that work in conjunction with the OmniLog reader and Biolog s PM MicroPlates These programs allow you to generate kinetic PM MicroPlate data from the OmniLog reader manage and analyze the data export it in a variety of raw and processed forms and generate reports Program 1 Data Collection e Drives the OmniLog reader e Allows you to load read and unload MicroPlates from the reader e Creates a kinetic data file for each MicroPlate e Creates files for use in the other three programs x Page 1 OmniLog PM User Guide 1 November 03 Introducing the OmniLog PM System x Page 2 Program 2 Data Management e Allows you to view and edit individual MicroPlate data files Program 3 File Management Kinetic Analysis e Allows you to assemble MicroPlate data files into data lists e Displays kinetic plots of the data Program 4 Parametric Analysis e Takes data lists from the File Management Kinetic Analysis program and calculates parameters from the kinetic data e Allows you to compare two data lists OmniLog PM Software Steps Step 1 Step 2 optional View and
32. ific interest You may for example want to set the PM 1 8 limit at 100 and the PM 11 36 limit at 150 6 As soon as you start to adjust the numbers the boxes will flash red Press Enter once you reach the number you want in each box 7 Click the Define Data List on the menu bar then the 1 Plate Data sub tab Check the Outline Differences options under the Display Options group box OmniLog PM User Guide 1 November 03 Comparing Data Lists and Generating Reports VVells vvith vvhite outlines mark differences based on threshold settings Spindly blue lines appear when Plate Parameters option is enabled The white boxes that outline wells are tentative until you re completely satisfied with the thresholds and parameters you ve selected You then have to save your selections by using the functions at the bottom of the 20 Plate Data page x Page 30 The outlined wells will change based on the thresholds you set If necessary go back and forth between pages adjusting the thresholds until you are satisfied with the resulting outlined wells 8 On the 1 Plate Data page click Outline Differences in the Display Options groupbox This gives you a quick visual way to outline wells that are different Use the MicroPlate navigation tools across the bottom of the page to display other MicroPlates in that data set The same thresholds parameters and display option you selected will show for every MicroPlate sem Clos
33. ist Data lists organize the data files for subsequent analysis in the Parametric program Data lists allow you to x Page 9 e save a search e display kinetic plots e export files to external programs such as Excel e use the OmniLog parametric program OmniLog PM User Guide 1 November 03 Defining Data Lists and Displaying Rinetic Plots 1 If you are satisfied with the data files in the worksheet list on the upper half of the Define Data List page simply click the Add All Omni F an s Plates button The softvvare vvill copy all the listed data files into for organizing the data list on the lower half of the page data files Each data list represents an experiment that consists of a particular group will duplicate the data files in the data list however many times you click of compounds or strains in one set of media with a certain number of e The first few very narrow columns at the left of the data list replicates contain identifying information You can expand these columns by clicking on the edge of the colored header at the top of the data list and dragging the column to the right However the information in these columns is already displayed in the 11 field file name column Consequently you ll most likely only need to expand these columns to view data files named according to the old format WY Warning If you click Add Plates multiple times the software WHAT S ON A DATA LIST Left Column Plat
34. large quantities of data from kinetic plots to an external program such as Excel The raw data is exported in units of OmniLog Signal 1 Make sure the data you want to export is displayed on screen in the kinetic plot Check the MicroPlate navigation tool across the bottom of the page to make sure the desired MicroPlate is shown you ll see small carets on either side of the selected plate number such as lt 7 gt 2 Click the Export tab on the menu bar 3 The upper right side of the page contains three radio buttons that allow you to select a naming format for the export file This information is selected from the 11 field data file name for the first replicate of the selected MicroPlate Select the desired format by clicking on the proper radio button As you click each one you ll see changes in the export file name listed in the Single Hour File display box x Page 17 OmniLog PM User Guide 1 November 03 Defining Data Lists and Displaying Rinetic Plots Click here to export only one reading Click here to export all readings Click here to export a single reading for all MicroPlates on that data list x Page 18 Select the way you want to name the export file here Use arrows to select specific time point for exported data Click here to export last reading only EXPORT PAGE At the far right corner of the page you ll see a scrolling list of numbers entitled Single Hour These numb
35. ngle Hour File display box All OmniLog Signal values for the selected readings will appear on a spreadsheet 11 Click the Close tab on the menu bar when you ve finished Click Close again to exit the program Page 19 OmniLog PM User Guide 1 November 03 Comparing Data Lists and Generating Reports 3 Comparing Data Lists and Generating Reports Wa this section The Parametric portion of the OmniLog PM software displays a gt Comparing comparison of the data in two data lists The program superimposes Data Lists two kinetic plots allowing you to identify anomalous wells easily gt Saving This is useful for comparing a compound treated organism with a _Graphical reference organism You can also compare the mutant form of an Peas So ae organism with the wild type of that organism The contrasting colors Files used for the superimposed curves visually guide you in identifying gt Generating wells of interest ES En ave Once you ve displayed meaningful visual data you can save it and 3 Exporting generate reports These reports include graphical summaries of data Parameter Values kinetic plots exportable into Word or Power Point documents as well as non graphical data summaries you can export into Excel or Access Comparing Data Lists Once you ve created at least two data lists using the File Management Kinetic Plot portion of the software you will open the Parametric program and begin the process of creating a visual
36. nsion to the data set file Subsequently you can load the data set by clicking the Load Data Set box and using the pop up Open File Dialog The two data lists comprising that data set will automatically be loaded Generating non graphical reports The software allows you the option of displaying your parameter values in spreadsheet format for easy thorough review You can also save these spreadsheets as Excel csv files 1 Select a parameter on the 1 Plate Data page 2 Click the Report tab on the menu bar OmniLog PM User Guide 1 November 03 Comparing Data Lists and Generating Reports 3 The parameter values of the user selected wells on the 1 Plate Data and 20 Plate data pages will be transcribed into spreadsheet format 4 Review the spreadsheet for the following e Check the top of the report for organism strain name strain number and any other information you may have included for the first replicate of the test and reference data lists e Check the midsection of the list for phenotypes gained For these the test had a greater value than the reference for the parameter selected e Check the bottom of the report This displays phenotypes lost by the test strain These losses correspond to wells you selected that had a negative value for difference test list average height reference list average height In other words the reference had a greater value than the test for the parameter selected Note These values
37. orksheet MicroPlates 9 amp 10 listed as above Sensitivity Params worksheet MicroPlates 11 40 listed as above 8 x 12 format 8 rows and 12 columns wells Al H12 representing each parameter with MicroPlates arranged vertically and parameters arranged horizontally Page 36 OmniLog PM User Guide 1 November 03
38. per menu tab Click the Average Replicates button at the lower edge of the page If the averages have already been calculated by the program you will see a message indicating this Navigate to the Kinetic Plot page by clicking on the proper menu tab Click on the Average radio button on the right lower side of the page The averages will be displayed as a black line in each well OmniLog PM User Guide 1 November 03 Defining Data Lists and Displaying Rinetic Plots x Page 16 A1 zeroing the data PM MicroPlates 1 8 have a negative control vvell containing no chemical at the A 1 position If you have a plate that you suspect contains a background color in all wells you may want to subtract the color in A 1 from all wells This will clear the suspected background color from all wells In general you ll do this at the same time you average your data WY Warning Excessive growth in well Al prevents interpretation of the MicroPlate and the usefulness of the data Al zeroing is only for small corrections Navigate to the Setup page by clicking on the proper menu tab In the upper right corner you will see a red box Check the A1 Zero box Navigate to the Define Data List page by clicking on the proper menu tab Pe i 5 Click the Average Replicates button Note Even if your data list does not have more than one replicate you must click Average Replicates in order to Al Zero the data 6 The software will di
39. splay a message asking if you want to proceed with averaging replicates Click Yes or No as appropriate 7 Averaging will NOT automatically save your data Use Save to insure saving your data Click this to perform A 1 zeroing Click this to perform smoothing hitpiwww genome ad pi dget binrwww_bget epd OmniLog PM User Guide 1 November 03 Defining Data Lists and Displaying Rinetic Plots Smoothing the Data A Xinetic plot may have optical noise If desired you can smooth out the data to create a more even line The Smooth function of the software recalculates each OmniLog Signal value for each read as a weighted average of two consecutive reads This results in a smoother plot which makes plot comparison easier between replicates for example This selection is a matter of personal preference In general you ll do this at the same time you average your data Note Smoothing data influences parametric analysis results 1 On the Setup page click the Smooth radio button in the upper right corner of the page 2 Navigate to the Define Data List page by clicking the proper menu tab 3 Click the Average Replicates button Note Even if your data list does not have more than one replicate you must click Average Replicates in order to smooth the data 4 You will see a message reminding you that you have selected a non default option Exporting Data OmniLog PM software allows you to export
40. t data files according to R ean dera specific criteria such as organism strain gene compound plate type 3 Exporting Data temperature project code etc This offers a comprehensive streamlined search including the ability to evaluate data collected over long periods of time DEFINITIONS Data File A single file containing all information and data for one MicroPlate Contains plate number inoculum organism inoculum compound etc Worksheet List A worksheet list contains all the files that meet the criteria of your data file search Each row is a data file for one MicroPlate Each column corresponds to MicroPlate type gene compound organism strain and file name with an other column for comments Data List A way of organizing data files by relatedness or by membership in a single experiment Data files from any subset of 40 possible MicroPlates A data list includes averaged data over multiple replicates of a single MicroPlate Each row represents one MicroPlate type Each additional column shows an additional replicate for a particular MicroPlate type Data files in the same row are assumed to be replicates their data is averaged for reports x Page 4 OmniLog PM User Guide 1 November 03 Defining Data Lists and Displaying Rinetic Plots Converting File Format Data files may be named according to either an old or a nevv naming format In order to get the maximum use of the OmniLog PM software all files shoul
41. t will appear in the File Name box These files have a dlb extension 5 Click Open Note Check data file names carefully Make sure you retrieve the proper data files in the upper half of the page and the proper data files in the lower part of the page If you load a reference file on the top and a test file on the bottom the mathematical calculations will be incorrect 6 The program will automatically calculate the parameters and populate the upper half of the page with the retrieved data list Allow a few moments for this to occur 7 Click in the Click here to load Data List 2 white box in the middle of the page adjacent to the red box to load the reference data list this will serve as the reference list for this data set Navigate through the directories until you find the desired data list select the name and it will appear in the File Name box of the Open File Dialog These files have a dlb extension Page 21 OmniLog PM User Guide 1 November 03 Comparing Data Lists and Generating Reports 8 Click Open 9 The program will automatically calculate the parameters and populate the lower half of the page with the retrieved data list Allow a few moments for this to occur Note The columns that appear on the test and reference data lists are the same as those that appeared in the data list grid created using the Kinetic module of the program WHAT S ON THE DISPLAYED DATA LISTS Plate Type Left Column Pla
42. te Type unique identifier assigned to each kind of PM MicroPlate depending on the chemicals contained in all of the 96 wells This column lists a subset of the 40 possible PM MicroPlate types depending on the MicroPlates used in that experiment Color Bars Green Test bar in upper section denotes data list for test mutant form of organism Red Ref bar in upper section denotes data list for reference wild type form of organism Expanding Columns These five expandable columns list the most common search criteria for MicroPlates position sample number strain name strain number and other gt To view fully click on the edge of the header row and drag column to right Data File Columns gt These wide columns list the 11 field names of the files you created in the data list gt Each additional column represents an additional replicate if that plate has an additional replicate Test data files Reference data files ee bl Fixed Selection Modes MicroPlate Types display I E DEFINE DATA LISTS PAGE WITH TEST AND REFERENCE LISTS x Page 22 OmniLog PM User Guide 1 November 03 x Page 23 Comparing Data Lists and Generating Reports Narrovving dovvn the types of MicroPlates displayed l Once both data lists test and reference are displayed use the MicroPlate Types display tools at the bottom of the page to define the types of MicroPlates you want to compare In the Fixed Selection
43. u want to continue searching 6 Defining Data Lists and Displaying Kinetic Plots After you ve made the desired selections click the Find Data Files in Selected Directory button The window will momentarily turn white while the data files are added to the worksheet list Do not click anything until the original window color returns Once searching is complete you ll see the data files listed on the worksheet list Conduct as many searches as you like selecting different fields and or drop down values as desired Note You do not need to close and re open the Data File Search Dialog to perform subsequent searches 8 When you are satisfied with your search results as listed in the worksheet list close the Data File Search Dialog You ll return to the Define Data List page with the data files found according to the criteria you selected in the order you conducted the searches Retrieving an existing worksheet list 1 To view a worksheet list you ve previously created and saved click in the box containing the words Click here to load worksheet at the top of the Define Data List page A Windows Open File Dialog will pop up select the desired worksheet then click Open The data files will populate the worksheet list From here you can use them to assemble a data list as you would files from a new search Assembling a Data List Populating a worksheet list is an interim step in the process of compiling a data l

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