Changelog

06/06/2017 (MetaboLab 0.99.8.2)

General functionality

- MetaboLab is now distributed as a compiled software for the Apple OSX, Linux and Microsoft Windows platforms.

- A new licensing system is in place, which requires users to obtain node locked licenses prior being able to use the software

- Our new combination of NMR and MS data for the modelfree determination of isotopomers is integrated now. Please check out our publication in Angewandte Chemie.

- New versions will be continually available via the new integrated software update functionality.

03/04/2014 (NMRLab 3.5.0.0)

General functionality

 - Fixed bug in getdecim for data from older Bruker spectrometers

 - Fixed expiry date bug

 - Fixed bug for nmrlab directory pathnames containing spaces

 - Fixed Load and Save button in main figure. Both commands now load and save all necessary variables.:w

 - Save button in main figure now saves all opened figures

 - Load button in main figure now restores all previously opened figures and closes current figures if saved with new Save function

 - The load function (load_workspace) now allows to add spectra to existing spectra as well as replacing existing spectra


MetaboLab GUI

 - Fixed bug for PLS dataset export, when not all spectra are exported

 - Fixed bug to restore all previously selected options when re-opening MetabolabGUI

 - Added Load/Save buttons to load/save the global workspace


1D Spectra Display

 - Added Load/Save buttons to load/save the global workspace

 - Changed how phase correction is performed for 1D spectra. Phase correction is now done in the same window and not using sliders anymore. Overlaid spectra are still displayed during phase correction

 - expup/expdown handles the display of multiple spectra now. It keeps track of which spectra were displayed already


2D Spectra Display

 - Added Load/Save buttons to load/save the global workspace


Assignment Tool

 - Added Load/Save buttons to load/save the global workspace


Metabolite Library

 - Fixed anserine

 - Added SMPDB and KEGG entries for new metabolites

 - Fixed HMDB entry for Sucrose

 - Fixed semi-colons in all metabolite files

 - Fixed metabolite names in glycolysis pathway file

 - Fixed metabolite names in TCA cycle pathway file

 - Fixed metabolite names in Glucose Alanine cycle pathway file

 - Fixed metabolite names in Alanine metabolism pathway file

 - Fixed metabolite names in Glutamate metabolism pathway file

 - Fixed metabolite names in ketone body metabolism pathway file

 - Fixed metabolite names in Malate Aspartate shuttle pathway file

 - Fixed metabolite names in pentose phosphate pathway file

 - Fixed metabolite names in Pyruvate metabolism pathway file

 - Fixed metabolite names in Urea cycle pathway file


Time Series Analysis Tool

 - Added automatic time vector calculation for Bruker spectra

 - Added CSV export of experimental data, fitted curves and fit function

 - Added button to exclude spectra automatically which were de-selected in MetaboLab GUI

 - Added Load/Save buttons to load/save the global workspace

 - Added standard fit functions for 13C label incorporation

 - Fixed plot function for 13C label incorporation plots

General functionality

 - Fixed bug in getdecim for data from older Bruker spectrometers

 - Fixed expiry date bug

08/02/2013 (NMRLab 3.3.1.0)

General functionality

 - Fixed bug in getdecim for data from older Bruker spectrometers

 - Fixed expiry date bug

MetaboLab GUI

 - Fixed bug for PLS dataset export, when not all spectra are exported

 - Fixed bug to restore all previously selected options when re-opening MetabolabGUI

Metabolite Library

 - Fixed anserine

 - Added SMPDB and KEGG entries for new metabolites

 - Fixed HMDB entry for Sucrose

 - Fixed semi-colons in all metabolite files

 - Fixed metabolite names in glycolysis pathway file

 - Fixed metabolite names in TCA cycle pathway file

 - Fixed metabolite names in Glucose Alanine cycle pathway file

 - Fixed metabolite names in Alanine metabolism pathway file

 - Fixed metabolite names in Glutamate metabolism pathway file

 - Fixed metabolite names in ketone body metabolism pathway file

 - Fixed metabolite names in Malate Aspartate shuttle pathway file

 - Fixed metabolite names in pentose phosphate pathway file

 - Fixed metabolite names in Pyruvate metabolism pathway file

 - Fixed metabolite names in Urea cycle pathway file

 - fixed bug in peak transfer for manual integration


11/09/2012 (NMRLab 3.3.0.4)

1D spectra display

 - fixed bug in peak transfer for manual integration

 - added initial reporting tool for picked peaks (chemical shift and peak height are reported for time series)

 - added improved algorithm for transfer of picked peaks between different spectra

      the new algorithm copes with signals shifting through other signals during the time series

      it's selected with the Alg2 checkbox

 - added independend phase correction for the left/right half spectra (comboPhase) to the interactive phase correction tool (uiphase2)


2D spectra display

 - fixed bug in library reference tool

 - added interactive zoom capability to 2D phase correction during row/column selection

      - pressing 'z' will switch into zoom mode

      - in zoom mode, a left mouse click will zoom in, pressing the middle mous button (or any key but 'q') will reset the zoom status

      - pressing 'q' or the right mouse button will switch back to row/column selection mode

 - added "untilt" functionality to extract true proton chemical shifts from TILT-TOCSY spectra after selecting the diagonal signal of a spin system. This button overrides the "Callc. Projection" button, but is only displayed for TILT spectra

 - changed behaviour when changing from one data set to another, the zoom now stays the same


Assignment Tool

 - fixed set_metlib_path2 bug

 - fixed bug in create_local_metlib

 - added increase/decrease plot levels to the assign4 GUI

 - fixed select spectra dialog for TILT spectra

 - fixed add/delete peak bug for TILT spectra

 - fixed Filter library for TILT spectra

 - added a HSQC report function which automatically calculates label incorporations for metabolites

     - added consistency check for HSQC report functionality

     - added graphical user interface for HSQC functionality from within the AssignmentTool

 - added consistency check for spreadsheet export

 - fixed bug in spreadsheet export

 - added tool to create mean spectra from technical replicates on which assignments can be prepared

 - added a tool to load/save assignments. This tool also takes care of class assignments. Several classes can be saved/loaded at a time

 - assignments can be transfered between normal and TILT-HSQC spectra

    - inter HSQC transfer retains multiplet structures

    - if assignments are transfered between normal and TILT spectra, multiplet shifts are replaced by the mean of shifts

 - added search functionality to the picked metabolites searchtool

 - when setup is closed the last picked metabolite is displayed

 - more than 230 metabolites have been added to the spectral library (most originating from HMDB)

 - metabolite files now contain a reference to their HMDB metabocard

 - references to the pathways involved have been added to the metabolite files for SMPDB and KEGG

 - added the option to display picked peaks from other spectra in overlay mode

 - fixed bug in Add/Delete peak which prevented the last peak to be deleted

 - reference spectra in hsqc_report can now have more peaks assigned than the labeled data set

 - added maximum number of spins to be dealt with in each screen for TILT spectra

 - fixed class assignment transfer bug when loading in previously saved mean spectra

 - fixed bug when loading in mean spectra from multiple separate .mat files

 - added interactive switch between local optimum picking and picking exactly where the cursor is during adding/deleting peaks (by pressing 'l')

 - added export to the new time series analysis tool

 - changed peak picking behaviour for TILT-TOCSY spectra: When one or more diagonal signals are picked, all cross peaks are predicted

 - added "untilt" functionality for TILT-TOCSY spectra to extract true proton chemical shifts after selecting the diagonal signal of a spin system


TSA tool (NEW)

 - a new GUI for the analysis of NMR spectra time series has been added, the main focus is real time metabolomics, relaxation and titration data

 - the tool can be started either from the manual integration tool for 1D spectra or from the assign4 GUI for 2D spectra

 - it offers to fit intensities as well as chemical shift values for as many peaks and samples as needed

 - added selection of specific colours for either different samples (data sets) and/org different peaks

 - added a "Plot spectra" tool to display the local region of the selected peak for all spectra including the picked peak maximum (1D spectra only)


General functionality

 - added a new improved automatic phase correction algorithm. The new algorithm replaces the prvious algorithm using the apk4 command. The old algorithm is still available as apk3

 - A small bug in the automatic phase correction routine (apk4) that could lead to an infinite loop execution was fixed

 - The number of distributed metabolite assignment files has been increased from 15 to >150. All assignments were obtained from HMDB.

 - fixed bug in automatic referencing routine that prevented automatic nucleus recognition when both dimension were the same nucleus but slightly differen transmitter offset

 - fixed bug when reading in Bruker 1D NMR spectra with empty title files

 - fixed bug in browse2 when loading in previously saved .mat files. The NE (number of experiments) variable now reflects the true number of experiments in the data set


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06/02/2012 (NMRLab 3.2.6.0)

General functionality

 - added plotmetlib function which selects a metabolite and overlays with current J-resolved spectrum (source spectra of BML required, currently internal use only)

 - added search functionality to the 2D-HSQC reference dialog

 - introduced nmrlab_setpaths function to set non-default locations for MATLABPATH, swap paths etc

 - added nmr2wavelab for individual editing of wavelab paths

 - added a graphical user interface to configure the most important global variables for NMRLab setup

 - a pushbutton for the NMRLabConfig utility is now included as part of the main NMRLab figure


MetaboLab GUI

 - added "export to NMRLab" functionality. Now spectra can be bulk edited in the MetaboLab GUI and the results will be exported to the NMRLab data structure.

 - segmental alignment now provides a graphical interface to the icoshift software (which has to be obtained separatly)

 - added a noise filtering option for improved classification after statistical data analysis

 - glog auto optimize (to be executed on technical replicates) is now working


AssignmentTool

 - added search tool for metabolite list

 - added metabolic pathway tool for metabolite list

 - added button to open selected metabolic pathway from small molecule pathway database (SMPDB) in web browser

 - added save/load functionality to store/restore previously assigned metabolites (select spectra menu)

 - added dialog to assign classes/colours to different spectra, a colour gradient is used in overlay mode when no classes are defined


2D spectra display

 - Calc proj now creates a new 1D data set at Set+1,Exp


1D spectra display

 - If baseline correction is carried out on a projected data set, baseline correction will be carried out for the 2D spectrum and a new projection will be calculated (sum, columns) (Note: the behaviour in MetaboLabGUI is different, there a "normal" baseline correction of the pJres spectrum will be calculated)

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05/01/2012 (NMRLab 3.2.5.1, internal release only)

1D spectra display (dr2)

 - fixed bug originating from inconsistent NMRDAT(s,e).MANINT data structures for manual integration

 - fixed bug in manual peak integration routine (using real part of the spectrum, rather than absolute maximum)

 - fixed bug for colour gradient selection, now first spectrum can be of arbitrary colour


2D spectra display (uicont2)

 - fixed bug for library assignment when using the search tool


MetaboLab GUI

 - Fixed Bruker spectra export for Windows based systems

 - Fixed referencing bug for Bruker spectra export


ScriptBuilder

 - fixed bug concerning whitespaces in pathnames when creating a script

 - fixed bug concerning script names starting with a number or containing spaces

 - fixed directory selection for directories containing no acqus/procpar or fid/ser files (function test_dirs), returned error code now indicates whether the fid file (errorCode = 1), the acqu*s/procpar (errorCode = 2) or the directory (errorCode = 3) was not found

 - fixed bug related to not recognising pulse program names


AssignmentTool

 - fixed referencing bug for assignment transfer

 - fixed pushbuttons not disappearing after assignment transfer

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04/11/2011 (NMRLab 3.2.5.0)

1D spectra display / 2D spectra display: Buttons have been reorganised. They are now in a more logical order (pretty much reading in data --> processing data --> analysing data etc. from top to bottom). The order is now also consistent between 1D and 2D display.

1D spectra display: Manual integration has been improved, it now detects peak maxima in selected regions, which can be transferred to other spectra in the series optimising the peak position sequentially for each spectrum. Colour selection (selspc) has been improved and now enables an easy way to generate colour gradients e.g. for time series analysis.

MetaboLab GUI: The segmental alignment algorithm has been substantially improved. Changes that were made to the NMR spectra (alignment etc) can now be exported back into the NMRDAT data structure.

HSQC assignment tool: There is now an easy way to generate a separate local HSQC library which can be used either in conjunction with or without the NMRLab standard HSQC library (type helpwin create_local_metlib at the MATLAB command prompt) which also makes it useful to use the HSQC assignment tool for 15N-HSQC spectra (e.g. for titration analysis).

There is now a way to store user defined global settings (nmrlab_globals.m). Several small bug have been fixed.

© Christian Ludwig 2017