workflow4metabolomics · mtremblayfr · Jun 5, 2023 · Jul 3, 2023 · Jul 3, 2023 · Jul 3, 2023
diff --git a/topics/metabolomics/images/nmrpreprocessing_slides_1.png b/topics/metabolomics/images/nmrpreprocessing_slides_1.png
diff --git a/topics/metabolomics/images/nmrpreprocessing_slides_2.png b/topics/metabolomics/images/nmrpreprocessing_slides_2.png
diff --git a/topics/metabolomics/images/nmrpreprocessing_slides_3.1.png b/topics/metabolomics/images/nmrpreprocessing_slides_3.1.png
diff --git a/topics/metabolomics/images/nmrpreprocessing_slides_3.2.png b/topics/metabolomics/images/nmrpreprocessing_slides_3.2.png
diff --git a/topics/metabolomics/images/nmrpreprocessing_slides_4.1.png b/topics/metabolomics/images/nmrpreprocessing_slides_4.1.png
diff --git a/topics/metabolomics/images/nmrpreprocessing_slides_4.2.png b/topics/metabolomics/images/nmrpreprocessing_slides_4.2.png
diff --git a/topics/metabolomics/images/nmrpreprocessing_slides_4.3.png b/topics/metabolomics/images/nmrpreprocessing_slides_4.3.png
diff --git a/topics/metabolomics/images/nmrpreprocessing_slides_5.1.png b/topics/metabolomics/images/nmrpreprocessing_slides_5.1.png
diff --git a/topics/metabolomics/images/nmrpreprocessing_slides_5.2.png b/topics/metabolomics/images/nmrpreprocessing_slides_5.2.png
diff --git a/topics/metabolomics/images/nmrpreprocessing_slides_6.1.png b/topics/metabolomics/images/nmrpreprocessing_slides_6.1.png
diff --git a/topics/metabolomics/images/nmrpreprocessing_slides_6.2.png b/topics/metabolomics/images/nmrpreprocessing_slides_6.2.png
diff --git a/topics/metabolomics/images/nmrpreprocessing_slides_7.png b/topics/metabolomics/images/nmrpreprocessing_slides_7.png
diff --git a/topics/metabolomics/images/nmrpreprocessing_slides_8.png b/topics/metabolomics/images/nmrpreprocessing_slides_8.png
diff --git a/topics/metabolomics/images/nmrpreprocessing_slides_9.png b/topics/metabolomics/images/nmrpreprocessing_slides_9.png
diff --git a/topics/metabolomics/tutorials/nmr-preprocessing/faqs/index.md b/topics/metabolomics/tutorials/nmr-preprocessing/faqs/index.md
@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---
diff --git a/topics/metabolomics/tutorials/nmr-preprocessing/slides.html b/topics/metabolomics/tutorials/nmr-preprocessing/slides.html
@@ -0,0 +1,122 @@
+---
+layout: tutorial_slides
+logo: "GTN"
+
+title: "Nuclear Magnetic Resonance: preprocessing"
+contributors:
+  - mtremblayfranco
+  - ccanlet
+  - ManonMartin
+---
+name:nmrpreprocessing_workflow
+
+## The NMR preprocessing in W4M
+
+![Picture describing steps from the raw FID data to the preprocessed table included in the NMR_Preprocessing tool.](../../images/nmrpreprocessing_slides_1.png)
+
+---
+name:pepsnmr_rpackage
+
+## The PepsNMR R package
+
+![Picture describing steps from the raw FID data to the preprocessed table included in the NMR_Preprocessing tool.](../../images/nmrpreprocessing_slides_2.png)
+
+---
+name:nmr_read
+
+## The NMR_Read tool
+
+![Picture to show parameter values for the NMR_Read tool: the first one is the zip file including FID files; the 2nd one corresponds to the line in the title file to recover the FID names (usually in pdata/1/title); the 3rd one is a logical to indicate the Presence of subdirectories or not; the last parameter is a logical for the Use (sub)directories names as FID names or not.](../../images/nmrpreprocessing_slides_3.1.png)
+
+---
+name:files_organization
+
+## NMR_Read - directories organization
+
+![This figure illustrates how can be organized files generated by spectrometer. FID files can be organized into sub-directories, one per sample. Each sub-directory indludes the fid file and a 2nd level sub-directory with a 3rd level sub-directory inclunding a title file.](../../images/nmrpreprocessing_slides_3.2.png)
+
+---
+name:phase_shifts
+
+## Phase shifs
+
+![This slide explains reasons of phase shifts.](../../images/nmrpreprocessing_slides_4.1.png)
+
+---
+name:group_delay_correction
+
+## Group delay correction
+
+![This slide shows how phase is introduced in sprectra during aquisition and how to correct it.](../../images/nmrpreprocessing_slides_4.2.png)
+
+---
+name:group_delay_correction_illustration
+
+## Illustration of Group delay correction
+
+![This slide illustrates on an example the group delay introduced at the beginning of the FID and effect of correction or not on Fourier-transformed spectra.](../../images/nmrpreprocessing_slides_4.3.png)
+
+---
+name:solvent_suppression
+
+## Solvent suppression
+
+![This slide explains why solvent signals have to removend from preprocessed spectra and how solvent suppression is performed in the NMR_Preprocessing tool.](../../images/nmrpreprocessing_slides_5.1.png)
+
+---
+name:solvent_suppression_illustration
+
+## Illustration of Solvent suppression
+
+![This slide illustrates the effect of solvent suppression or not on FID and on Fourier-transformed spectra.](../../images/nmrpreprocessing_slides_5.2.png)
+
+---
+name:solvent_suppression
+
+## Solvent suppression
+
+![This slide explains why solvent signals have to removend from preprocessed spectra and how solvent suppression is performed in the NMR_Preprocessing tool.](../../images/nmrpreprocessing_slides_5.1.png)
+
+---
+name:solvent_suppression_illustration
+
+## Illustration of Solvent suppression
+
+![This slide illustrates the effect of solvent suppression or not on FID and on Fourier-transformed spectra.](../../images/nmrpreprocessing_slides_5.2.png)
+
+---
+name:apodization
+
+## Apodization
+
+![This slide explains the aim of apodization and how this is performed in the NMR_Preprocessing tool, with some weighing functions implemented in W4M.](../../images/nmrpreprocessing_slides_6.1.png)
+
+---
+name:apodization_illustration
+
+## Illustration of apodization
+
+![This slide illustrates the effect on Fourier-transformed spectra of apodization using the negative exponential for weighing function and different values of line broadening.](../../images/nmrpreprocessing_slides_6.2.png)
+
+---
+name:fourier_transform
+
+## Fourier tranform
+
+![This slide explains the conversion of the signal in the time domain into a spectrum in the frequency domain via the Fourier transform. It also explains where the ppm scale comes from.](../../images/nmrpreprocessing_slides_7.png)
+
+---
+name:zero_order_phase
+
+## Zero order phase correction
+
+![This slide explains the problem of zero order phase, how to correct it and algorithms available in the NMR_Preprocessing tool.](../../images/nmrpreprocessing_slides_8.png)
+
+---
+name:referencing_to_0_illustration
+
+## Illustration of Refrencing to 0
+
+![This slide illustrates the effect on preprocessed spectra of the Search zone parameter used to reference spectra to 0.](../../images/nmrpreprocessing_slides_9.png)
+
+---
diff --git a/topics/metabolomics/tutorials/nmr-preprocessing/tutorial-nmr-read-sub-true.png b/topics/metabolomics/tutorials/nmr-preprocessing/tutorial-nmr-read-sub-true.png
diff --git a/topics/metabolomics/tutorials/nmr-preprocessing/tutorial-nmr-read.png b/topics/metabolomics/tutorials/nmr-preprocessing/tutorial-nmr-read.png
diff --git a/...lomics/tutorials/nmr-preprocessing/tutorial-nmr-workflow-solventsuppression.png b/...lomics/tutorials/nmr-preprocessing/tutorial-nmr-workflow-solventsuppression.png
diff --git a/topics/metabolomics/tutorials/nmr-preprocessing/tutorial-nmr-workflow.png b/topics/metabolomics/tutorials/nmr-preprocessing/tutorial-nmr-workflow.png
diff --git a/topics/metabolomics/tutorials/nmr-preprocessing/tutorial.bib b/topics/metabolomics/tutorials/nmr-preprocessing/tutorial.bib
@@ -0,0 +1,72 @@
+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@article{Martin2018,
+  doi = {10.1016/j.aca.2018.02.067},
+  url = {https://doi.org/10.1016/j.aca.2018.02.067},
+  year = {2018},
+  month = aug,
+  publisher = {Elsevier {BV}},
+  volume = {1019},
+  number = {17},
+  pages = {1--13.e1},
+  author = {Manon Martin and Beno{\^{i}}t Legat and Justine Leenders and Julien Vanwinsberghe and R{\'{e}}jane Rousseau and Bruno Boulanger and Paul H. C. Eilers and Pascal De Tullio and Bernadette Govaerts},
+  title = {PepsNMR for 1H NMR metabolomic data pre-processing},
+  journal = {Anal Chim Acta}
+}
+
+@misc{EscribanoVasquez2018,
+  url = {https://www.theses.fr/2018SORUS348.pdf},
+  year = {2018},
+  month = dec,
+  author = {Unai Escribano Vazquez},
+  title = {Impact de souches commensales et probiotiques d'Escherichia coli
+sur la physiopathologie de l'h{\^{o}}te}
+}
+
+@article{Giacomoni2014,
+  doi = {10.1093/bioinformatics/btu813},
+  url = {https://doi.org/10.1093/bioinformatics/btu813},
+  year = {2014},
+  month = dec,
+  publisher = {Oxford University Press ({OUP})},
+  volume = {31},
+  number = {9},
+  pages = {1493--1495},
+  author = {F. Giacomoni and G. Le Corguille and M. Monsoor and M. Landi and P. Pericard and M. Petera and C. Duperier and M. Tremblay-Franco and J.-F. Martin and D. Jacob and S. Goulitquer and E. A. Thevenot and C. Caron},
+  title = {Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics},
+  journal = {Bioinformatics}
+}
+
+@article{Guitton2017,
+  doi = {10.1016/j.biocel.2017.07.002},
+  url = {https://doi.org/10.1016/j.biocel.2017.07.002},
+  year = {2017},
+  month = dec,
+  publisher = {Elsevier {BV}},
+  volume = {93},
+  pages = {89--101},
+  author = {Yann Guitton and Marie Tremblay-Franco and Gildas Le Corguill{\'{e}} and Jean-Fran{\c{c}}ois Martin and M{\'{e}}lanie P{\'{e}}t{\'{e}}ra and Pierrick Roger-Mele and Alexis Delabri{\`{e}}re and Sophie Goulitquer and Misharl Monsoor and Christophe Duperier and C{\'{e}}cile Canlet and R{\'{e}}mi Servien and Patrick Tardivel and Christophe Caron and Franck Giacomoni and Etienne A. Th{\'{e}}venot},
+  title = {Create,  run,  share,  publish,  and reference your {LC}{\textendash}{MS},  {FIA}{\textendash}{MS},  {GC}{\textendash}{MS},  and {NMR} data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics},
+  journal = {The International Journal of Biochemistry {\&} Cell Biology}
+}
+
+@online{gtn-website,
+  author = {GTN community},
+  title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
+  url = {https://training.galaxyproject.org},
+  urldate = {2021-03-24}
+}