glyXalign GUI User Manual
Contents
1. lt 5 9 96 1 Run Alignment button e Prompts to select an output directory for the alignment result files and starts the processing using the specified parameters 2 Target data drop down list e Allows to choose to what data the alignment algorithm shall be applied to e Possible options include i all batches use all lanes of all batches default i selected lanes use only the currently selected lanes of the current batch 3 Initial conditions drop down list e Allows to choose how the initial power series parameters for the alignment algorithm are determined e Possible options include i default uses the central values specified in the power series parameter controls il current uses the currently determined parameters ob tained either from a previous automated alignment or from hand transforming ii random uses parameters picked randomly from the ranges specified in the power series parame ter controls default 4 Power series order spinner e Controls the power series order b Power series parameter bounds controls e Allow to specify value ranges for the power series coefficients e Consists of the following controls i Parameter drop down to select the coefficient il Central value spinner to specify the central value of the coefficient range iii Variation spinner to specify the maximum extent to which the coefficient may de viate from its central value 2 1 3 Plots Chapter 2 User Referenc2. 1 Load Files button e Opens the File Selection dialog see 2 2 2 Batch number spinner e Allows to select a specific batch to be displayed if input data is partitioned 3 Sort order drop down list e Allows to choose whether and how the input electrophero grams shall be sorted thereby specifying the order in which they will be aligned to each other e Possible options include i Original No re sorting default ii Total Intensity Sort w r t the total signal intensity iii Maximum Intensity Sort w r t the max signal intensity iv Number of Peaks Sort w rt the number of peaks identified 4 Honor boundaries checkbox e Controls whether only the signal intensities inside the interac tive migration time boundaries in the heat map shall be con sidered for determining the sort order 5 Crop to boundaries checkbox e Controls whether the heat map shall be cropped to the migra tion time range defined by the interactive boundaries inside it 6 Reset Data button e Resets the imported data to its original state reverting any alignment results in the process Chapter 2 User Reference Guide 2 1 2 Alignment Controls The middle horizontal panel contains controls for defining parameters per taining to the alignment algorithm as well as for starting the processing Alignment Controls Run Alignment i all batches Y using n z a conditions Power series order 2 Parameter bounds Py m
3. come any feedback so feel free to send your queries to info glyxera com
4. batches of electrophoretic data Further Reading The underlying algorithm of the glyXalign software is explained in detail in the following research paper 1 Behne A Muth T Borowiak M Reichl U amp Rapp E glyXalign High throughput migration time alignment preprocessing of electrophoretic data retrieved via multiplexed capillary gel electrophoresis with laser induced fluorescence detection based glycoprofiling Electrophoresis 2013 PMID 2367070 Chapter 1 Quick Start Guide Chapter 1 Quick Start Guide 1 1 Setting up the GUI Y Extract the downloaded archive containing the P file to a directory of your choice Y Launch the MATLAB software and change its Current Folder to the directory of the previous step e g using the Current Folder Browser Y Launch the glyXalign GUI either by selecting Run File after right clicking the P file in the Current Folder Browser or by typing alignGUI in the Command Window 1 2 Importing data Y In the main window of the glyXalign GUI press the Load Files button in the upper left corner Y In the File Selection dialog press the PickInput Directory button and then browse to the folder containing the electropherogram XML files you wish to process VY Select the electropherograms you wish to process from the list at the top and press the button to move them to the bottom list Y Select the electropherogram you wish to use as a reference by
5. 2 User Reference Guide 4 Crop to boundaries checkbox e Controls whether the reference preview plot shall be cropped to the migration time range defined by the interactive bounda ry rectangle inside it 5 Reference preview plot e Displays a signal intensity vs migration time plot of the refer ence electropherogram picked in the bottom input file list see 3 e Manipulate the interactive boundary rectangle by dragging its body or edges to specify a migration time range to which the display will be cropped if the Crop to boundaries checkbox is ticked see 4 6 Minimum peak height spinner e Allows to specify the minimum signal intensity below which local maxima of the signal time series of the imported electro pherograms will not be interpreted as peaks and will therefore not be taken into account for the automated alignment proc ess Press the OK button in the bottom right corner of the dialog to accept the specified settings or the Cancel button to discard them and return to the main window view of the GUI Chapter 3 Warranty and Support Chapter 3 Warranty and Support 3 1 Warranty The software is provided without warranty We do not take responsibility for any damage improper use of the application may do to your system or your files use at your own risk The application was developed primarily for internal use and therefore we can provide only limited support We are however open to suggestions and wel
6. double clicking its entry in the bottom list VY Press the button in the bottom right to accept the cho sen input 1 3 Processing data Y Back in the main window drag the two horizontal line objects in the heat map in the bottom left corner to define the migration time range of interest Y Adjust the other alignment parameters to your preference Y Press the Run Alignment button above the heat map and browse to a folder you wish the result files to appear in Chapter 2 User Reference Guide Chapter 2 User Reference Guide 2 1 The Main Window The main view of the application presents itself as follows o a Show Batch lpi Sort order Total Intensity x Honor boundaries Crop to Boundaries o 6 v using random v initial conditions Power series order 2 Parameter bounds Py vy 1 EX 01 4 k d J k d J L Reference 15 5500 6000 6500 7000 7500 28000 8500 9000 It is divided into three segments from top to bottom the Data Controls 1 the Alignment Controls 2 and the Plots 3 section Each of these is covered in detail in the following Chapter 2 User Reference Guide 2 1 1 Data Controls The topmost panel contains controls for setting up imported data files for processing Ge controls Load Files Files Show Batch 15 T Sort order Total Intensity V Honor boundaries V Crop to Boundaries ResetData
7. e Guide The bottom panel contains figures for visualizing electropherograms of the current batch as well as control elements to highlight and transform selected pieces of data Plots 5500 6000 6500 7000 7500 8000 8500 9000 00 5500 6000 6500 7000 7500 8000 8500 9000 1 Heat Map Displays a top down view of the signal intensities of the input data Each vertical lane represents a single electropherogram with the first lane always being the designated reference The vertical axis represents the migration time dimension and the horizontal axis marks the lane index Note that the lane index does not necessarily correspond to the individual indices of the electropherograms depending on the sort order chosen in the Data Controls section see 2 1 1 Contains two interactive horizontal line objects which can be dragged to specify the upper and lower bounds of the migration time region of interest if the Crop to Boundaries checkbox see 2 1 1 5 is ticked the line handles will be situated at the heat map axes top and bottom edges Selected lanes are highlighted with a red border in the heat map and are displayed side on in the electropherogram plot see 4 While the automated alignment is running the lane that is currently being processed is highlighted with a green border Use left click to select single lanes Use left click while holding down the Shift key to have lanes added to or re
8. ertical axis represents the signal intensity and the horizontal axis represents the migration time dimension Identified peaks of electropherograms are highlighted via circular markers If one or more items inside the transform selection list are selected the corresponding graphs are enveloped in a trans form rectangle which allows the following operations i Translate Shift data points along the migration time axis by dragging the body of the transform rectangle ii Scale Stretch or compress data points along the migration time axis by dragging the left or right edge of the transform rectangle 2 2 This window is dedicated to selecting and organizing input data as well as de The file selection dialog Chapter 2 User Reference Guide signating and previewing a reference electropherogram for the alignment 1 2 3 Batch Files References File Pick Input Directory Batch size 96 Crop to boundaries GlyAna 4AB 2012 01 601 48 27 07 ab1 xml VGhy amp na AB 2012 01 G02 AB 27 07 ab1 xml GhyA na 48 2012 01 H01 4 8 27 07 ab1 xml MGlhy Ana AB 2012 01 HO02 AB 27 07 ab1 xml Vhy amp na AB 2012 01 102 AB 27 07 ab1 xml olyAna 46 2012 01 J02 48 27 07 a1 xml GhyAna 4 8 2012 01 K01 4 8 27 07 ab1 xml GhyA na 4B 2012 01 K02 4 8 27 07 ab1 xml GlyAna 46 2012 01 B02 A48 27 07 ab1 xml GlyAna 4 6 2012 01 C01 A8 27 07 ab1 ml GlyAna AB 2012 01 D01 AB 27 07 ab1 xml GlyAna AB 2012 01 D02 AB 27 07 ab1
9. glyXalign GUI User Manual A high performance software tool for rapid alignment of electrophoretic glycan data Table of Contents Table of Contents direc E 2 Mew re MN 2 FUERO E JROACIEIO oiii nueces p a tuse t uec EE E M DE een ve 2 Chapter i QuickStart GUIE ssns ttam BM DEDE 3 1 1 Setting p th GUI NE 3 122 InioLF bescheid cnet ee UU A tI ee 3 1 5 Processing Gd cece reece cee eats fase neta tassels i ectetuer eterni trei iie 3 Chapier2 UserRelerence GUIE cc rescautareserareresrannessveatesneeateneeasnenannenen 4 DM oe Nato VII OM secas tette bo ni eee 4 2 I l Data Controls eeieesotietdi eie tius itetet e tees tib eceexcadecedeceseceecseusaics 5 2 1 2 Alignment Controls essen reete tnnt 6 zb PIO nee UU m 7 2 2 The file selection dialog 0 eee ssecssssssesssscssssseccssssecsssssscessssneseeneessecsesssecsees 9 Chapter 3 Warranty and Support 11 WU pg 11 s M U 9 M 11 Preface Migration time shifts are common distortions observed in data retrieved from capillary gel electrophoresis measurements They represent a significant im pediment to further analysis of the affected pieces of data To remove this bottleneck in day to day processing of large datasets the glyXera GmbH developed the glyXalign software tool in MATLAB to automatically align large
10. moved from the selection Use right click or alternatively left click while holding down the Control key to open a context menu containing the option to save the figure in MATLAB s fig format to a directory of your choice Chapter 2 User Reference Guide 2 Lane selection list Displays the lane indices in the sort order specified in the Data Controls section see 2 1 1 with the reference highlighted in bold red letters Mirrors the selection displayed in the heat map Selected in dices are highlighted with a darker background Use left click to select single lanes Use left click while holding down the Shift key to have lanes added to or removed from the selection 3 Transform controls Provides access to hand transforming lanes selected in either the heat map or the lane selection list see 1 2 Consists of the following controls i Transform checkbox enables disables the controls be low il Transform sel list displays the subset of lane in dices that are selected in the heat map or lane selection list il Save button Prompts to select an output di rectory to save the electrophero grams corresponding to the se lected indices in the transform selection list to files 4 Electropherogram plot Displays a side on view of the signal intensities of the lanes that are selected in the heat map or lane selection list see 1 2 Multiple electropherograms are distinguished using differ ent colors The v
11. xml GlyAna AB 2012 01 01 AB 27 07 ab1 xml GlyAna AB 2012 01 02 AB 27 07 ab1 xml 6000 7000 8000 9000 GlyAna AB 2012 01 F01 AB 27 07 ab1 xml double click list entry to select reference file Minimum peak height 20 07 Batch size spinner Allows to specify the number of electropherograms that are consolidated into batches after the dialog is closed via pressing the OK button in the bottom right corner Pick Input Directory button Prompts to select an input directory which will be searched for suitable input files to import also extends to sub folders Input file lists The top list displays all files that were found inside the direc tory specified using the Pick Input Directory button see 2 The bottom list displays all files that are selected for alignment once the dialog is closed via pressing the OK button Double click an item in the bottom list to designate the corre sponding electropherogram as the reference to be used for the automated alignment process and to preview it in the figure on the right hand side of the dialog see 5 To move items between the lists first select them by left click ing them multiple selections can be made while holding down the Shift key and then press the respective button between the lists The button with the downward pointing triangle icon moves items from the top list to the bottom list and the button with the upward pointing triangle icon does the opposite Chapter
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