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| <h2><strong>What changed in ORIGAMI<sup>ANALYSE </sup>:</strong></h2> | ||
| <h2><strong>What changed in ORIGAMI<sup>ANALYSE</sup>:</strong></h2> | ||
| <p><strong>Note</strong> </p> | ||
| <p>This was meant to be a mini-update but it has spaned over several weeks and includes a fairly significant revamp of the <strong>Interactive output panel</strong> (with loads new features), addition of <strong>many</strong> new plot types, cleaner interface (in some places), bug fixes and more.</p> | ||
| <p>I have changed the way I compile ORIGAMI (switched from obsolete py2exe to pyinstaller) which increased the size of the directry (~2x) and made it less organised but it should result in better support. Overall, you should see similar performance and not notice the change.</p> | ||
| <p><strong>New in v1.1.2:</strong></p> | ||
| <ul> | ||
| <li>Added several new plotting methods: | ||
| <ul> | ||
| <li>Waterfall overlay</li> | ||
| <li>Violin</li> | ||
| <li>Scatter</li> | ||
| <li>Bar plot</li> | ||
| </ul> | ||
| </li> | ||
| <li>The document type (Type: Interactive) now supports addition of "Other..." data type. This is fairly versatile and can include any of the following: <em>line, multi-line, scatter, vertical-bar, horizontal-bar, grid-line, waterfall, grid-line and grid-scatter </em>and is mostly aimed at enabling exporting of more complex (and not necessarily MS related datasets) in an interactive format. To take advantage of its full potential I made a repository where you can see example files, but it basically requires specification of some meta-data (i.e. title, x/y-axis labels etc) and addition of data. You can learn more about it by going to <strong>Menu -> Help -> Help pages -> Learn more: Other datasets (shortcut F1+9)</strong>. Check out the example files <a href="https://github.com/lukasz-migas/ORIGAMI/tree/master/ORIGAMI_ANALYSE/other_datasets">here</a>. I've also included a couple example files in folder 'example_files/other_data'. </li> | ||
| <li>Added new "Annotation" panel that enables you add annotations to mass spectra (i.e. charge state, protein name, any description). To enable it, plot the mass spectrum and right-click in the Documents Tree and select -> Add/Show annotations (shown below). You can learn more about it going to <strong>Menu -> Help pages -> Learn more: Annotating mass spectra (shortcut F1+8)</strong></li> | ||
| <li>Added a proper version checker that will check whether new version of ORIGAMI is available online at each start of the program.</li> | ||
| <li>General changes to the Interactive Output panel: | ||
| <ul> | ||
| <li>Tried to reorganise several components to make it look less cluttered.</li> | ||
| <li>Added several new parameters that you can change</li> | ||
| <li>All generated plots can now benefit from using 'custom JavaScript' widgets and events. Events are currently limited to 'double-click in plot area will zoom-out' whereas widgets are much more versatile and include addition of buttons, sliders, toggles, radio buttons and few others. These can control the size of the labels, level of zoom, transparency or position of legend and many others. These are enabled by default and can be turned off in the <strong>Interactive Panel -> Annotations -> Add custom JS events/scripts when available</strong>. Addition of custom JS events/widgets slows down generation of interactive plots as these have to be compiled to JS. <strong>Note</strong>: First time you try this you will most likely be greeted with an error message. Follow the instructions there to solve it.</li> | ||
| <li>Expanded the list of available plots.</li> | ||
| <li>Interactive plots can be exprted in multi-threaded mode now, enabling you to do other tasks while they are being exported. <strong>Note: </strong>If you close the output window, the export process will stop.</li> | ||
| </ul> | ||
| </li> | ||
| <li>Overlay plots will not be added to overlay document by default. You first must toggle "Add overlay plots to document" in the menus of individual overlay panels.</li> | ||
| </ul> | ||
| <p><strong>Improvements in v1.1.2:</strong></p> | ||
| <ul> | ||
| <li>Loads of small improvements in the Interactive output pane</li> | ||
| <li>Improved and extended list of available labels</li> | ||
| <li>Reorganised the <strong>Plot parameters panel </strong></li> | ||
| <li>Some of the <strong>plot parameter</strong> options will take an immediate effected without the need to replot the data. Some will not!</li> | ||
| <li>General improvements to the Peak fitting/finding in the <strong>Processing panel</strong>.</li> | ||
| <li>General improvements to the Mass spectrum processing the <strong>Processing panel</strong>.</li> | ||
| <li>Usually at start of the program, ORIGAMI looks for Driftscope on your PC. If it doesn't find it, it usually notifies you of it. You can disable this behaviour now.</li> | ||
| <li>Configuration files are not saved automatically. You can disable this by going to <strong>Plot settings -> Extra -> Auto-save settings</strong> to off.</li> | ||
| <li>Added two new color palettes (cividis - colorblind friendly and winter)</li> | ||
| <li>Rearranged the UniDec panel and improved error messges.</li> | ||
| <li>Added label position optimisation (can be disabled if you don't like the results).</li> | ||
| </ul> | ||
| <p> <strong>Fixes in v1.1.2:</strong></p> | ||
| <ul> | ||
| <li>Many fixes that should improve the general usability and reliability of the analysis software</li> | ||
| <li>Fixed an issue where the colorbar wasn't displaying correct values</li> | ||
| <li>Fixed issues with the waterfall plots.</li> | ||
| <li>Fixed an issue which occurs when the size of the screen is not optimal. I've tested the software on screens with severan screen dimensions (1980x1080, 1680x1050, 1600x900, 1366x768, 1280x102 and 1280x800) and its looks pretty good. I would recommend using a decent sized screen for using ORIGAMI.</li> | ||
| </ul> | ||
| <p><strong>Planned features:</strong></p> | ||
| <ul style="list-style-type: square;"> | ||
| <li>Interactive panel: | ||
| <ul style="list-style-type: square;"> | ||
| <li>I don't like the current positiong of various settings and how they are actively enabled/disable upon selection in the list. I intend to add a separate window where when you double-click on an item it will open and you will only see relevant settings.</li> | ||
| <li>Widgets are awesome but still require a lot of work. A couple of really cool widgets I intend to add are toggles for colorblind mode, data selection dropdowns, comparison tools etc</li> | ||
| <li>I would like to add a number of neat plots, including circos-style plot for XL-MS, HDX-style grid plots etc</li> | ||
| </ul> | ||
| </li> | ||
| <li>Plots: | ||
| <ul style="list-style-type: square;"> | ||
| <li>I have a couple of ideas for new plot types, especially for RMSD-type plots</li> | ||
| </ul> | ||
| </li> | ||
| <li>Main program: | ||
| <ul style="list-style-type: square;"> | ||
| <li>Speed-up certain operations</li> | ||
| <li>Improve GUI</li> | ||
| <li>Add support for other vendor files. I intend to use <em>multiplierz </em>+ other open-source libraries</li> | ||
| </ul> | ||
| </li> | ||
| <li>Help pages: | ||
| <ul style="list-style-type: square;"> | ||
| <li>Improve the text + add more examples</li> | ||
| </ul> | ||
| </li> | ||
| <li>Videos: | ||
| <ul style="list-style-type: square;"> | ||
| <li>Record a couple of videos showing various features + usage</li> | ||
| </ul> | ||
| </li> | ||
| </ul> | ||
| <p><span style="color: #000000;">Again, this was meant to be a small-ish update but turned into a fairly significant revamp of ORIGAMI. Because of this, I have upgraded it to version 1.2.0.</span></p> | ||
| <p> </p> | ||
| <p><span style="text-decoration: underline;"><span style="color: #000000;"><strong>General:</strong></span></span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]:</strong> The underlying codebase of ORIGAMI has been improved to make it more readable and more responsive</span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]:</strong> Item font color will be automatically adjusted to ensure best contrast from the background color in various lists in the GUI</span></p> | ||
| <p><span style="color: #000000;"><strong>[CHANGED]</strong>: Modification of the table elements is now available by Right-clicking on the column name</span></p> | ||
| <p> </p> | ||
| <p><span style="text-decoration: underline;"><strong>Tandem MS [NEW]:</strong></span></p> | ||
| <p><span style="color: #000000;"><strong class="historyAdded">[NEW]:</strong></span> Added support to load .mgf and .mzIdentML file formats to visualise tandem mass spectrometry results. Menu -> Open open-source files... to load .mgf files. You can then annotate the tandem MS with peptide fragments. See Figure 1 for example.</p> | ||
| <p> </p> | ||
| <p><span style="text-decoration: underline;"><span style="color: #000000;"><strong>Interactive panel:</strong></span></span></p> | ||
| <p><span style="color: #000000;"><strong class="historyAdded">[NEW]: </strong>Started adding support for individual modification of parameters for interactive plots (double-clicking on an item in the list)</span></p> | ||
| <p><span style="color: #000000;"><strong class="historyAdded">[NEW]: </strong>Interactive documents can now be visualised without access to internet. Just check the "Add offline support" checkbox</span></p> | ||
| <p><span style="color: #000000;"><strong class="historyAdded">[NEW]:</strong> Annotated mass spectra will now include label + arrow (if available)</span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]</strong>: Legends now work with markers and shaded areas</span></p> | ||
| <p><strong>[FIXED]: </strong>Issue that prevent exporting interactive documents with legends has been removed</p> | ||
| <p><strong>[FIXED]:</strong> Issue that prevent proper showing of toolbar has been removed</p> | ||
| <p> </p> | ||
| <p><span style="text-decoration: underline;"><span style="color: #000000;"><strong>Peaklist panel:</strong></span></span></p> | ||
| <p><span style="color: #000000;"><strong class="historyAdded">[NEW]: </strong>Added 'Extract automatically' check tool (Peaklist -> Toolbar -> Extract...)</span></p> | ||
| <p><span style="color: #000000;"><strong class="historyAdded">[NEW]: </strong>Added 'Overlay automatically' check tool (Peaklist -> Toolbar -> Overlay...)</span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]:</strong> Added a lot of new shortcuts for easier plotting</span></p> | ||
| <p> </p> | ||
| <p><span style="text-decoration: underline;"><span style="color: #000000;"><strong>Text file panel:</strong></span></span></p> | ||
| <p><span style="color: #000000;"><strong class="historyAdded">[NEW]: </strong>Added 'Extract automatically' check tool (Peaklist -> Toolbar -> Extract...)</span></p> | ||
| <p><span style="color: #000000;"><strong class="historyAdded">[NEW]: </strong>Added 'Show chromatogram' and 'Show mobiligram' for each viewed file (Right-click -> Select appropriate)</span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]:</strong> Added a lot of new shortcuts for easier plotting</span></p> | ||
| <p><strong>[FIXED]:</strong> Removed an issue that prevented loading certain text files</p> | ||
| <p><strong>[FIXED]:</strong> Removed an issue that would incorrectly remove documents from the text file list</p> | ||
| <p> </p> | ||
| <p><span style="text-decoration: underline;"><span style="color: #000000;"><strong>Multiple MS files panel:</strong></span></span></p> | ||
| <p><span style="color: #000000;"><strong><strong class="historyAdded">[NEW]</strong>:</strong> The average mass spectrum can be re-binned/re-processed based on new parameters (Process -> Average mass spectra (current document))</span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]:</strong> Item font color will be automatically adjusted to ensure best contrast from the background color</span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]:</strong> Average mass spectrum will be automatically re-binned/re-processed when an item is added or deleted</span></p> | ||
| <p><strong>[FIXED]:</strong> Removed an issue that prevented typing-in numerical values in the 'variable' colument when using laptop keyboards. I have only ever encountered this issue once... Let me know if it still occurs!</p> | ||
| <p> </p> | ||
| <p><span style="text-decoration: underline;"><span style="color: #000000;"><strong>Document tree:</strong></span></span></p> | ||
| <p><span style="color: #000000;"><strong class="historyAdded">[NEW]: </strong>Double-clicking on the document header will now clear all plots and show the most basic plots for that document (e.g. MS, DT, RT, etc). You can also do this by Right-click -> Refresh document.</span></p> | ||
| <p><span style="color: #000000;"><strong class="historyAdded">[NEW]: </strong>You can now change the x-/y-axis labels for chromatograms and mobiligrams. Right-click on the item and slect 'Change x/y-axis to...'. These changes will be taken into account when extracting data from the chromatogram/mobiligram windows</span></p> | ||
| <p><span style="color: #000000;"><strong class="historyAdded"><strong>[IMPROVED]</strong>: </strong>Significant improvements to the right-click menus (most notably for UniDec/Annotations)</span></p> | ||
| <p> </p> | ||
| <p><span style="text-decoration: underline;"><span style="color: #000000;"><strong>Plots panel</strong></span></span></p> | ||
| <p><span style="color: #000000;"><strong><strong class="historyAdded">[NEW]:</strong></strong> Some images can now be rotated by 90 degrees (mainly 2D)</span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]</strong>: Significant improvements to the right-click menus.</span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]:</strong> Wheel-zoom in the X-dimensions has been improved (works like on maps now)</span></p> | ||
| <p> </p> | ||
| <p><span style="text-decoration: underline;"><span style="color: #000000;"><strong>Data extraction:</strong></span></span></p> | ||
| <p><span style="color: #000000;"><strong class="historyAdded">[NEW]:</strong> You can now extract mass spectra from the '2D' panel. Hold CTRL on your keyboard and drag the mouse in the plot area. Only works when standard plot is shown (e.g. Drift time (bins) vs Scans/Time)</span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]:</strong> Data extraction in the DT, RT, DT/MS panels now takes into account the plot labels/units.</span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]:</strong> Extracted mass spectra extracted in the DT and RT windows will be now shown in an area beneath the extraction plot (for convenience)</span></p> | ||
| <p> </p> | ||
| <p><span style="text-decoration: underline;"><span style="color: #000000;"><strong>MS annotations:</strong></span></span></p> | ||
| <p><span style="color: #000000;"><strong class="historyAdded">[NEW]:</strong> Peaks can now be annotated with an arrow (also available when exporting in an interactive format)</span></p> | ||
| <p><span style="color: #000000;"><strong class="historyAdded">[NEW]:</strong> Added new customisation parameters window where you can change your visualisation preferences. Action -> Customise other settings...</span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]:</strong> Selection of a peak in the MS window using the mouse (Annotating: On) will automatically try to determine the charge state based on the peaks isotopic distribution. You can change the error tolerance in Action -> Customise other settings -> Charge prediction value (default: 0.05).</span></p> | ||
| <p> </p> | ||
| <p><span style="text-decoration: underline;"><span style="color: #000000;"><strong>UniDec settings:</strong></span></span></p> | ||
| <p><span style="color: #000000;"><strong><strong class="historyAdded">[NEW]</strong>:</strong> Plots can now be customised using settings editor. (Settings: UniDec -> Customise plots...)</span></p> | ||
| <p><span style="color: #000000;"><strong><strong class="historyAdded">[NEW]</strong>:</strong> You can switch between tabbed view where each plot is in a separate tab OR continuous view where all plots are available on the same page (Customise plots... -> Panel view)</span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]:</strong> Deconvolution is now done in a multi-threaded mode. Should stop program from hanging</span></p> | ||
| <p> </p> | ||
| <p><span style="text-decoration: underline;"><span style="color: #000000;"><strong>MS comparison:</strong></span></span></p> | ||
| <p><span style="color: #000000;"><strong><strong class="historyAdded">[NEW]</strong>: </strong>You can now assign your own label to the plot.<br /></span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]:</strong> You can now compare ALL available mass spectra and not just those that were hidden under 'Mass Spectra' tag. (This includes: Mass Spectra, Mass Spectrum, Mass Spectrum (processed)). To open comparison panel: Menu -> View -> Open MS comparison panel...)</span></p> | ||
| <p> </p> | ||
| <p><span style="text-decoration: underline;"><span style="color: #000000;"><strong>Peak detection:</strong></span></span></p> | ||
| <p><span style="color: #000000;"><strong>[IMPROVED]:</strong> Works in multi-threaded mode. Should stop program from hanging.</span></p> | ||
| <p> </p> | ||
| <p><strong>ORIGAMI-MS:</strong></p> | ||
| <p>There have been no changes to ORIGAMI<sup>MS</sup>, so please download it from release 1.0.1.</p> | ||
| <p><strong>Video tutorials:</strong></p> | ||
| <p>A couple of videos is available on YouTube. Will try to add more in future.</p> | ||
| <p><a title="ORIGAMI-MS: Setup Guide" href="https://www.youtube.com/watch?v=XNfM6F_MSb0&list=PLrPB7zfH4WXMYa5CN9qDtl-G-Ax_L6AK8">ORIGAMI-MS: Setup Guide</a></p> | ||
| <p><a title="ORIGAMI-ANALYSE: Analysis of ORIGAMI-MS files" href="https://youtu.be/henWSN9tMgQ">ORIGAMI-ANALYSE: Analysis of ORIGAMI-MS files</a></p> | ||
| <p><strong>Mailing list</strong></p> | ||
| <p>If you would like to be added to a ORIGAMI mailing list where you will be notified of new releases, please contact <a href="mailto:lukasz.migas@manchester.ac.uk">lukasz.migas@manchester.ac.uk</a>. </p> | ||
| <p><strong>How to update</strong></p> | ||
| <p>Since the whole package was revamped, the only way to update ORIGAMI is to download the ORIGAMI_ANALYSE_v1.1.2.zip file, unpack it somewhere on your PC and it should work out of the box. :)</p> | ||
| <p>Since the whole package was revamped, the only way to update ORIGAMI is to download the ORIGAMI_ANALYSE_v1.2.0.zip file, unpack it somewhere on your PC and it should work out of the box. :)</p> | ||
| <p>As you might notice, the size of the directory increased quite a bit, it is about 1 Gb when unpacked.</p> | ||
| <p>Many thanks,</p> | ||
| <p>Lukasz</p> | ||
| <p>Lukasz</p> |