- Metabolomics approaches
- General introduction
- Metabolic Fingerprinting
- Targeted Metabolomics
- Processing methods
- Quick Tutorial
- 1- Data preparation phase
- 2- View the spectra
- 3 - Interactive data processing
- 4 - Spectra Processing
- 5 - Bucketing
- 6 - Data Export
- 7 - Restore a session
- 8 - Batch mode execution
Thanks to the users who send us the encountered issues and bugs, NMProcFlow can thus be made more reliable. When an update is performed, it includes the online version, Docker containers as well as the Virtual Machine.
Version 1.3.08 - September 3, 2019
* Fixed an issue when exporting data matrix especially when the samples file is provided.
Macro-command files compatibility between versions 1.2.x and 1.3.x
* In the case where first-order phasing is necessary, you may need to add in the first line of the macro-command file the criterion: * either CRIT1=1; for "Absolute positives" or CRIT1=0; for "Negative values" (Use for that a simple text editor) * To know which one is better, test with your spectrum set without the macro-command file.
Version 1.3.02 - August 2, 2019
* NMR spectra of phosphorus (31P) is now supported * Now displays the full ppm range of spectra. This makes it possible to support the NMR spectra of phosphorus (31P). * Allows bucketing in ppm areas with negative values. (required for phosphorus). * Phase correction improvement
Version 1.2.30 - May 10, 2019
* Adds the possibility to make a first reset without having to reload the ZIP file and also to login again. This makes it easier to test several preprocessing settings.
Version 1.2.28 - March 5, 2018
* RS2D SPINIt format is now supported for both FID and 1r spectrum
Version 1.2.26 - October 29, 2018
* During the preprocessing phase, in case of failure on one or more spectra, these latter are not taken into account in order to avoid stopping at an error so that the process can continue with all the remaining spectra. * The visualization of the spectra has been made even more fluid by drastically improving its speed. This also results in a very slight loss of quality of the images produced. But it is possible to restore the previous quality (a button allows you to switch between SD - Small Definition and HD - High Definition). Thus sets of more than 300 spectra can be visualized with fluidity. * Added an animated logo during exports (which can take several seconds sometimes) serves to indicate that the current running process.
Version 1.2.24 - June 28, 2018
* In order to calibrate the ppm scale when a set of spectra has not been acquired with the same locking frequency, we have added a parameter in the preprocessing panel that allows to ignore the spectral region center parameter due to the fact it exhibes large differences between spectra ('O1' for Bruker,'tof' for Varian and'x_offset for Jeol). Instead, we choose an arbitrary zero at the third of the sweep width (i.e. SW in Hertz).
Version 1.2.22 - May 24, 2018
* To efficiently align some tricky ppm zones, the possibility to shift these zones on one or several spectra (corresponding to the same factor level) has been added. * More robust mouse management (movements and events) Now it is possible to move the mouse forward / backward to select ppm zones. Prevents the cursor loss * Fix some other minor bugs
Version 1.2.18 - March 1, 2018
* Jeol JDF format is now supported * Improvement of the Zero order phasing (needless in most time to proceed the First order phasing). * Improvement of the ppm scale calibration (usefull when no calibration with TSP/DSS) * Ease the preprocessing with differents parameters without need to upload again the ZIP file.
Version 1.2.12 - Oct 18, 2017
* Fixed bug when exporting the data matrix export (some bucket columns may be disappeared)
Version 1.2.10 - August 7, 2017
* Fixed bug when exporting the quantification workbook (column offsets could occured depending on the SNR value) * Implementation of the complete normalisation during the processing step (i.e. applied on the spectra based on selected ppm ranges).
Version 1.2.8 - June 15, 2017
* Fixed bug with FIDs coming from Bruker having a number of points not equal to a power of 2 * Fixed bug with FIDs coming from Agilent/Varian having intensities coded as float32 * Improved the algorithm for phase correction
Version 1.2.6 - March 27, 2017
* Fixed the bug when exporting the 'q-HNMR' WorkBook This occurred in the absence of factors.
Version 1.2.5 - Feb 15, 2017
* Improved the algorithm for phase correction (rewritten in C++)
Version 1.2.2 - Jan 20, 2017
* Added a spectra pre-processing module in order to support the FID (Free Induction Decay) directly as input. Two major vendors are supported, namely Bruker GmbH & Agilent Technologies (Varian), as well as the new nmrML format. * Added the airPLS baseline correction (implementation based on sparse matrices) * Added the "CluPA" alignment method (R package 'speaq'), slightly adapted to be more efficient * Added an alternative way to manage the capture mode using the "Ctrl Key"
Version 1.1.22 - Dec 10, 2016
* Added the "Time Warping" alignment method (R package 'ptw') * Added the data exportation within XLSX Workbooks, in particular for quantification (q-HNMR template) * Added the "Batch mode execution": similar subsets can be processed in batch mode (executed using the "rnmr1d" docker image, got from DockerHub)
Version 1.1.10 - July 11, 2016
* The first "official" release, available online: - as a web application - downloadable as a Virtual Machine (VMware & VirtualBox) - downloadable as a Docker image (DockerHub)