2024-03-28T12:51:23Z
https://zenodo.org/oai2d
oai:zenodo.org:8420393
2023-10-09T14:26:55Z
openaire
user-dbgi-zenodo-repository
user-commons-lab-repository
Maëlle Wannier
2023-10-09
<p>Presentation of MSc thesis</p>
https://doi.org/10.5281/zenodo.8420393
oai:zenodo.org:8420393
eng
Zenodo
https://zenodo.org/communities/dbgi-zenodo-repository
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.8420392
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
data visualization
JavaScript
Node.js
Dashboard
DBGI
Establishment of a data visualization interface for the Digital Botanical Gardens Initiative
info:eu-repo/semantics/lecture
oai:zenodo.org:7247943
2022-10-25T14:26:24Z
openaire
user-commons-lab-repository
Allard, Pierre-Marie
2022-10-25
<p>Presentation for the SGMS 2022 School.</p>
<p>https://www.sgms.ch/sgms/education/sgms-school-2022.php</p>
https://doi.org/10.5281/zenodo.7247943
oai:zenodo.org:7247943
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.7247932
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
computational mass spectrometry
metabolomics
knowledge graphs
MS/MS-based computational tools for large-scale metabolite annotation - SGMS School 2022
info:eu-repo/semantics/lecture
oai:zenodo.org:6379086
2022-05-26T10:14:52Z
user-commons-lab-repository
Allard, Pierre-Marie
2022-03-23
<p><strong>Introduction to metabolomics: data acquisition and processing (SBL.20004; 2 ECTS; lecture with practical). </strong></p>
<p> </p>
<p>This course is a theoretical and practical introduction to metabolomics (the large scale study of small molecules in complex mixtures). It will cover extraction methods, sample preparation, separation techniques and chromatography, detection procedures and data analysis (quantitative and qualitative). A particular focus will be given to mass spectrometry based metabolomics of specialized metabolomes and its applications in environmental biology and natural products research. The course includes a practical part on GC or LC-MS (Gas Chromatography or Liquid Chromatography coupled to Mass Spectrometry) and data processing.</p>
https://doi.org/10.5281/zenodo.6379086
oai:zenodo.org:6379086
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6379085
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
SBL.20004 material - Introduction to Metabolomics - UniFr
info:eu-repo/semantics/lecture
oai:zenodo.org:6515740
2022-05-26T10:14:52Z
user-commons-lab-repository
Allard, Pierre-Marie
2022-05-03
<p><strong>Introduction to metabolomics: data acquisition and processing (SBL.20004; 2 ECTS; lecture with practical). </strong></p>
<p> </p>
<p>This course is a theoretical and practical introduction to metabolomics (the large scale study of small molecules in complex mixtures). It will cover extraction methods, sample preparation, separation techniques and chromatography, detection procedures and data analysis (quantitative and qualitative). A particular focus will be given to mass spectrometry based metabolomics of specialized metabolomes and its applications in environmental biology and natural products research. The course includes a practical part on GC or LC-MS (Gas Chromatography or Liquid Chromatography coupled to Mass Spectrometry) and data processing.</p>
https://doi.org/10.5281/zenodo.6515740
oai:zenodo.org:6515740
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6379085
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
SBL.20004 material - Introduction to Metabolomics - UniFr
info:eu-repo/semantics/lecture
oai:zenodo.org:8344320
2023-09-14T14:26:52Z
openaire
user-earth-metabolome
user-dbgi-zenodo-repository
user-commons-lab-repository
Allard, Pierre-Marie
2023-09-14
<p>Slides of the talk given at CCCTA 2023 https://cccta.ch/journees-scientifiques-2023/</p>
<blockquote>
<p><strong>Les journées scientifiques 2023 auront lieu les 14 et 15 septembre. Le thème retenu cette année est : </strong></p>
<p><strong>” BIOLOGIE-CHIMIE, l’entre deux mondes ”</strong></p>
</blockquote>
https://doi.org/10.5281/zenodo.8344320
oai:zenodo.org:8344320
eng
Zenodo
https://zenodo.org/communities/dbgi-zenodo-repository
https://zenodo.org/communities/earth-metabolome
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.8344319
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
open science
semantic web
knowledge graphs
linked open data
metabolomics
DBGI
EMI
Les technologies du web sémantique pour l'exploration des données métabolomique.
info:eu-repo/semantics/lecture
oai:zenodo.org:6659855
2022-06-22T21:25:32Z
openaire
user-dbgi-zenodo-repository
user-commons-lab-repository
Allard, Pierre-Marie
2022-06-18
<p>Poster presenting the Digital Botanical Gardens Initiative and associated research subjects for a bioinformatics master research period in the COMMONS Lab. </p>
<p> </p>
https://doi.org/10.5281/zenodo.6659855
oai:zenodo.org:6659855
eng
Zenodo
https://zenodo.org/communities/dbgi-zenodo-repository
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6659854
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
open science
dbgi
biodiversity
computational metabolomics
The Digital Botanical Garden Initiative - BEFRI Genomics Day - 2022
info:eu-repo/semantics/conferencePoster
oai:zenodo.org:6390146
2023-03-20T07:25:21Z
user-commons-lab-repository
Allard, Pierre-Marie
2022-03-28
<p><strong>SBL.00123 Cellular and Genetic Networks [SS 22]</strong></p>
<p>Genes and cells function in complex genetic and cellular networks that form the basis of biological systems. Recent advances in genomic and high-throughput techniques allow us today to acquire a more “holistic” view of biological systems. In this course, we will discuss how experimental or theoretical approaches at the systems-level provide insights into cell-to-cell interactions, cell cycle and cell growth, transcriptional regulatory networks, neuronal networks, and interactions between the environment and cellular processes. Topics also include mathematical modeling and cutting-edge genomic technologies. The goal of this course is to learn how to approach biological questions at the systems-level by integrating different experimental methods.</p>
<p>No textbook is available. Recent papers related to the topics will be suggested by lecturers for further reading.</p>
<p>Within the SBL.000123 program this specific lecture will deal with <em><strong>Metabolomics, computational mass spectrometry and open science resources for the exploration of living systems metabolomes.</strong></em></p>
<p>It will be complemented by showcases of <a href="https://www.wikidata.org/">Wikidata</a> queries and <a href="https://scholia.toolforge.org/">Scholia</a> exploration.</p>
<p> </p>
<p> </p>
<ol>
</ol>
https://doi.org/10.5281/zenodo.6390146
oai:zenodo.org:6390146
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6390145
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
systems biology
metabolomics
natural products
SBL.000123 material - Cellular and Genetic Networks - Metabolomics - BEFRI
info:eu-repo/semantics/lecture
oai:zenodo.org:7886275
2023-05-02T12:29:24Z
user-commons-lab-repository
Pierre-Marie Allard
2023-05-02
<p>A set of required input files and expected output files for the Computational Metabolomics Workshop.</p>
<p>Before the workshop please:</p>
<ol>
<li>Read the README.pdf !</li>
<li>Download the workshop material (go to <a href="https://doi.org/10.5281/zenodo.6047248">https://doi.org/10.5281/zenodo.6047248</a> and make sure your are downloading the latest version as this link will probably have changed)</li>
<li>Get MZMine 2.53 (<a href="https://github.com/mzmine/mzmine2/releases">https://github.com/mzmine/mzmine2/releases</a>)</li>
<li>Creat an account on GNPS (<a href="https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp">https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp</a>)</li>
<li>Get Cytoscape (<a href="https://cytoscape.org/download.html">https://cytoscape.org/download.html</a></li>
</ol>
<p>Feedback & questions: <a href="https://github.com/commons-teaching/forum/discussion">https://github.com/commons-teaching/forum/discussion</a></p>
https://doi.org/10.5281/zenodo.7886275
oai:zenodo.org:7886275
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6045962
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
metabolite annotation
computational metabolomics
tutorial
Computational Metabolomics Workshop Material - BEFRI
info:eu-repo/semantics/lecture
oai:zenodo.org:6671155
2022-06-22T21:27:02Z
openaire
user-dbgi-zenodo-repository
user-commons-lab-repository
Allard, Pierre-Marie
2022-06-20
<p>Presentation of the Digital Botanical Garden Initiative at the Metabiodivex Summer school https://metabiodivex.sciencesconf.org/</p>
<p> </p>
https://doi.org/10.5281/zenodo.6671155
oai:zenodo.org:6671155
eng
Zenodo
https://zenodo.org/communities/dbgi-zenodo-repository
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6671129
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
dbgi
computational mass spectrometry
metabololomics
open science
The Digital Botanical Garden Initiative - Metabiodivex, Aussois, France - 2022
info:eu-repo/semantics/conferencePoster
oai:zenodo.org:6671130
2022-06-22T21:27:02Z
openaire
user-dbgi-zenodo-repository
user-commons-lab-repository
Allard, Pierre-Marie
2022-06-20
<p>Presentation of the Digital Botanical Garden Initiative at the Metabiodivex Summer school https://metabiodivex.sciencesconf.org/</p>
<p> </p>
https://doi.org/10.5281/zenodo.6671130
oai:zenodo.org:6671130
eng
Zenodo
https://zenodo.org/communities/dbgi-zenodo-repository
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6671129
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
dbgi
computational mass spectrometry
metabololomics
open science
The Digital Botanical Garden Initiative - Metabiodivex, Aussois, France - 2022
info:eu-repo/semantics/conferencePoster
oai:zenodo.org:7669184
2023-03-06T08:29:25Z
user-commons-lab-repository
Allard, Pierre-Marie
2023-02-23
<p><strong>Specialized metabolism (SBL.00073)</strong></p>
<p><em>In this class, we will define and explore the concept of specialized metabolome. We will study how metabolites are created (biosynthetic pathways) and we will see how important these small molecules are for humans (health and nutrition). More broadly, we will see how a better comprehension of specialized metabolism can be of interest in the field of ecology (chemical ecology).</em></p>
<p>Level: Bachelor</p>
<p>Credits: 1.5 ECTS</p>
<p>Frequency: annual. starting in Fall 2022</p>
<p>When: Thursdays, 08:15-10:00</p>
<p>Course coordinator: Pierre-Marie Allard (pierre-marie.allard@unifr.ch)</p>
<p><em><strong>Below you can find pdf files of the lecture slides and some additional materials for home study.</strong></em></p>
<p><em><strong>Slide contents licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/">CC-BY-SA 4.0</a> - feel free to share and/or modify.</strong></em></p>
<p> </p>
Each main course slides are followed by resumed slides which are reminded at the beginning of the following class (a week later).
You will find editable material (.pptx, .key and .mol used for structures) altough not necessarily completely up to date, in the previous versions of this Zenodo repo.
You will also find editable .key and .pptx slides in the zipped folder.
Most of the chemical structures used in the slides were drawn using using MarvinSketch form Chemaxon (https://chemaxon.com/) they are zipped in SBL.00060_structures.zip
https://doi.org/10.5281/zenodo.7669184
oai:zenodo.org:7669184
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6327280
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
specialized metabolism
natural products
biosynthesis
course material
SBL.00073 material - Specialized Metabolism - UniFr
info:eu-repo/semantics/lecture
oai:zenodo.org:7743854
2023-10-09T10:56:35Z
openaire
user-dbgi-zenodo-repository
user-commons-lab-repository
Brülhart, Edouard
2023-03-17
<p>Master work progress presentation for the course Research seminars in environmental biology (SBL.20081). Presentation of the DBGI and EMI project.</p>
https://doi.org/10.5281/zenodo.7743854
oai:zenodo.org:7743854
Zenodo
https://zenodo.org/communities/dbgi-zenodo-repository
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.7743853
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
DBGI
EMI
Sampling
Swiss Digital Botanical Gardens Initiative: Toward the characterization of chemodiversity in Swiss botanical collections
info:eu-repo/semantics/lecture
oai:zenodo.org:6604616
2022-06-01T21:14:06Z
user-commons-lab-repository
Defossez, Emmanuel
Glauser, Gaetan
Allard, Pierre-Marie
2022-06-01
<p><strong>Introduction to plant metabolomics</strong></p>
<p>CUSO - Molecular Plant Science doctoral program - 2022</p>
<p>This practical course intends to provide an overview of the different steps needed to perform mass spectrometry-based plant metabolomics.</p>
<p>After half a day of lectures on the topic, the course will take place in the laboratory and in computer rooms where participants will have the opportunity to become familiar with sample preparation, analysis by HPLC-MS, data processing, and compound identification.</p>
<p>Detailed program at https://biologie.cuso.ch/?id=2392&L=0&tx_displaycontroller[showUid]=6021</p>
<p> </p>
<p> </p>
https://doi.org/10.5281/zenodo.6604616
oai:zenodo.org:6604616
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6604615
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
computational mass spectrometry
plant science
Introduction to plant metabolomics - CUSO - Molecular Plant Science doctoral program - 2022
info:eu-repo/semantics/lecture
oai:zenodo.org:6386600
2022-03-27T01:49:24Z
openaire
user-commons-lab-repository
Allard, Pierre-Marie
2022-03-26
<p>Slides for the presentation given (remote) on the 25.03.2022 to students and researchers of Unifal (https://www.unifal-mg.edu.br/portal/). On invitation from Karen J. Nicácio and Claudio Viegas Junior.</p>
<p> </p>
<p> </p>
https://doi.org/10.5281/zenodo.6386600
oai:zenodo.org:6386600
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6386599
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
metabolite annotation
open science
[presentation] Slides Unifal Brazil - 25.03.2022
info:eu-repo/semantics/lecture
oai:zenodo.org:7431049
2022-12-13T14:26:38Z
openaire
user-dbgi-zenodo-repository
user-commons-lab-repository
The Digital Botanical Gardens Initiative Consortium
Allard, Pierre-Marie
2022-12-13
<p>Presentation given on the 13.12.2022 to the Pharmaceutical Biology group (https://pharma.unibas.ch/en/research/research-groups/pharmaceutical-biology/) of the University of Bâle, Switzerland.</p>
<p> </p>
https://doi.org/10.5281/zenodo.7431049
oai:zenodo.org:7431049
eng
Zenodo
https://zenodo.org/communities/dbgi-zenodo-repository
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.7431048
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
computational mass spectrometry
biodiversity
linked open data
Computational metabolomics & Large scale chemodiversity digitization initiatives - UniBasel - December 20222
info:eu-repo/semantics/lecture
oai:zenodo.org:7247933
2022-10-25T14:26:23Z
openaire
user-commons-lab-repository
Allard, Pierre-Marie
2022-10-25
<p>Presentation for the SGMS 2022 School.</p>
<p>https://www.sgms.ch/sgms/education/sgms-school-2022.php</p>
https://doi.org/10.5281/zenodo.7247933
oai:zenodo.org:7247933
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.7247932
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
computational mass spectrometry
metabolomics
knowledge graphs
MS/MS-based computational tools for large-scale metabolite annotation - SGMS School 2022
info:eu-repo/semantics/lecture
oai:zenodo.org:6045988
2023-05-02T12:29:23Z
openaire_data
user-commons-lab-repository
Pierre-Marie Allard
2022-02-11
<p>A set of required input files and expected output files for the Computational Metabolomics Workshop.</p>
https://doi.org/10.5281/zenodo.6045988
oai:zenodo.org:6045988
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6045962
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
metabolite annotation
Computational Metabolomics Workshop Material
info:eu-repo/semantics/other
oai:zenodo.org:6371926
2023-05-02T12:29:24Z
user-commons-lab-repository
Pierre-Marie Allard
2022-02-11
<p>A set of required input files and expected output files for the Computational Metabolomics Workshop.</p>
<p>Before the workshop please:</p>
<ol>
<li>Read the README.pdf !</li>
<li>Download the workshop material (go to <a href="https://doi.org/10.5281/zenodo.6047248">https://doi.org/10.5281/zenodo.6047248</a> and make sure your are downloading the latest version as this link will probably have changed)</li>
<li>Get MZMine 2.53 (<a href="https://github.com/mzmine/mzmine2/releases">https://github.com/mzmine/mzmine2/releases</a>)</li>
<li>Creat an account on GNPS (<a href="https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp">https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp</a>)</li>
<li>Get Cytoscape (<a href="https://cytoscape.org/download.html">https://cytoscape.org/download.html</a></li>
</ol>
<p>Feedback & questions: <a href="https://github.com/commons-teaching/forum/discussion">https://github.com/commons-teaching/forum/discussion</a></p>
https://doi.org/10.5281/zenodo.6371926
oai:zenodo.org:6371926
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6045962
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
metabolite annotation
computational metabolomics
tutorial
Computational Metabolomics Workshop Material - BEFRI
info:eu-repo/semantics/lecture
oai:zenodo.org:6047248
2023-05-02T12:29:23Z
openaire_data
user-commons-lab-repository
Pierre-Marie Allard
2022-02-11
<p>A set of required input files and expected output files for the Computational Metabolomics Workshop.</p>
https://doi.org/10.5281/zenodo.6047248
oai:zenodo.org:6047248
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6045962
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
metabolite annotation
computational metabolomics
tutorial
Computational Metabolomics Workshop Material
info:eu-repo/semantics/other
oai:zenodo.org:10842286
2024-03-20T07:50:51Z
user-commons-lab-repository
Allard, Pierre-Marie
2024-03-20
<p><strong>Introduction to metabolomics: data acquisition and processing (SBL.20004; 2 ECTS; lecture with practical). </strong></p>
<p> </p>
<p>This course is a theoretical and practical introduction to metabolomics (the large scale study of small molecules in complex mixtures). It will cover extraction methods, sample preparation, separation techniques and chromatography, detection procedures and data analysis (quantitative and qualitative). A particular focus will be given to mass spectrometry based metabolomics of specialized metabolomes and its applications in environmental biology and natural products research. The course includes a practical part on GC or LC-MS (Gas Chromatography or Liquid Chromatography coupled to Mass Spectrometry) and data processing.</p>
<p>The practicals consist of a pilot metabolomics project proposed by each group of students (2 to 3 per groups). In this pilot they will decide on a research axis they would like to explore. The samples are plants collected from the botanical garden of the University of Fribourg. After collection, sample preparation approach is proposed and realized by the students. The samples can be analyzed on a LC-HRMS (QE+) or a GC-QToF system. After data treatment and interpretation a report is returned on each groups github repositories. </p>
<p>The main repo is available here for more detailed instructions <a href="https://github.com/commons-teaching/SBL.20004.2024">https://github.com/commons-teaching/SBL.20004.2024</a></p>
<p>Course coordinator: Pierre-Marie Allard (pierre-marie.allard@unifr.ch)</p>
<p><em><strong>Below you can find pdf files of the lecture slides and some additional materials for home study.</strong></em></p>
<p><em><strong>Slide contents licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/">CC-BY-SA 4.0</a> - feel free to share and/or modify.</strong></em></p>
<p> </p>
<p>Each main course slides are followed by resumed slides. You will also find editable .key and .pptx slides in the zipped editable_slides.zip (see previous versions)</p>
https://doi.org/10.5281/zenodo.10842286
oai:zenodo.org:10842286
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6379085
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
SBL.20004 material - Introduction to Metabolomics - UniFr
info:eu-repo/semantics/lecture
oai:zenodo.org:6396850
2022-05-26T10:14:52Z
user-commons-lab-repository
Allard, Pierre-Marie
2022-03-23
<p><strong>Introduction to metabolomics: data acquisition and processing (SBL.20004; 2 ECTS; lecture with practical). </strong></p>
<p> </p>
<p>This course is a theoretical and practical introduction to metabolomics (the large scale study of small molecules in complex mixtures). It will cover extraction methods, sample preparation, separation techniques and chromatography, detection procedures and data analysis (quantitative and qualitative). A particular focus will be given to mass spectrometry based metabolomics of specialized metabolomes and its applications in environmental biology and natural products research. The course includes a practical part on GC or LC-MS (Gas Chromatography or Liquid Chromatography coupled to Mass Spectrometry) and data processing.</p>
https://doi.org/10.5281/zenodo.6396850
oai:zenodo.org:6396850
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6379085
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
SBL.20004 material - Introduction to Metabolomics - UniFr
info:eu-repo/semantics/lecture
oai:zenodo.org:10878404
2024-03-26T13:35:30Z
user-commons-lab-repository
Allard, Pierre-Marie
2023-03-26
<p><strong>Introduction to metabolomics: data acquisition and processing (SBL.20004; 2 ECTS; lecture with practical). </strong></p>
<p> </p>
<p>This course is a theoretical and practical introduction to metabolomics (the large scale study of small molecules in complex mixtures). It will cover extraction methods, sample preparation, separation techniques and chromatography, detection procedures and data analysis (quantitative and qualitative). A particular focus will be given to mass spectrometry based metabolomics of specialized metabolomes and its applications in environmental biology and natural products research. The course includes a practical part on GC or LC-MS (Gas Chromatography or Liquid Chromatography coupled to Mass Spectrometry) and data processing.</p>
<p>The practicals consist of a pilot metabolomics project proposed by each group of students (2 to 3 per groups). In this pilot they will decide on a research axis they would like to explore. The samples are plants collected from the botanical garden of the University of Fribourg. After collection, sample preparation approach is proposed and realized by the students. The samples can be analyzed on a LC-HRMS (QE+) or a GC-QToF system. After data treatment and interpretation a report is returned on each groups github repositories. </p>
<p>The main repo is available here for more detailed instructions <a href="https://github.com/commons-teaching/SBL.20004.2024">https://github.com/commons-teaching/SBL.20004.2024</a></p>
<p>Course coordinator: Pierre-Marie Allard (pierre-marie.allard@unifr.ch)</p>
<p><em><strong>Below you can find pdf files of the lecture slides and some additional materials for home study.</strong></em></p>
<p><em><strong>Slide contents licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/">CC-BY-SA 4.0</a> - feel free to share and/or modify.</strong></em></p>
<p> </p>
<p>Each main course slides are followed by resumed slides. You will also find editable .key and .pptx slides in the zipped editable_slides.zip (see previous versions)</p>
https://doi.org/10.5281/zenodo.10878404
oai:zenodo.org:10878404
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6379085
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
SBL.20004 material - Introduction to Metabolomics - UniFr
info:eu-repo/semantics/lecture
oai:zenodo.org:10203581
2023-11-24T11:19:28Z
openaire
user-commons-lab-repository
Allard, Pierre-Marie
2023-11-24
<p>Slides for Seminar series in Bioinformatics 2023 - UniFr.</p>
https://doi.org/10.5281/zenodo.10203581
oai:zenodo.org:10203581
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.10203580
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Mass-specs, computers and Linked Open Data for chemodiversity characterisation at the global scale.
info:eu-repo/semantics/lecture
oai:zenodo.org:6604633
2022-06-01T21:14:07Z
user-commons-lab-repository
Defossez, Emmanuel
Glauser, Gaetan
Allard, Pierre-Marie
2022-06-01
<p><strong>Introduction to plant metabolomics</strong></p>
<p>CUSO - Molecular Plant Science doctoral program - 2022</p>
<p>This practical course intends to provide an overview of the different steps needed to perform mass spectrometry-based plant metabolomics.</p>
<p>After half a day of lectures on the topic, the course will take place in the laboratory and in computer rooms where participants will have the opportunity to become familiar with sample preparation, analysis by HPLC-MS, data processing, and compound identification.</p>
<p>Detailed program at <a href="https://biologie.cuso.ch/?id=2392&L=0&tx_displaycontroller[showUid]=6021">https://biologie.cuso.ch/?id=2392&L=0&tx_displaycontroller[showUid]=6021</a></p>
<p> </p>
<p> </p>
https://doi.org/10.5281/zenodo.6604633
oai:zenodo.org:6604633
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6604615
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
computational mass spectrometry
plant science
Introduction to plant metabolomics - CUSO - Molecular Plant Science doctoral program - 2022
info:eu-repo/semantics/lecture
oai:zenodo.org:6687451
2022-06-23T13:51:00Z
openaire
user-commons-lab-repository
Brülhart, Edouard
2022-06-22
<p>DBGI pilot presentation realized for the Bachelor work presentation at the University of Fribourg</p>
https://doi.org/10.5281/zenodo.6687451
oai:zenodo.org:6687451
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6687450
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Presentation of the DBGI Pilot project, Bachelor work 2022
info:eu-repo/semantics/lecture
oai:zenodo.org:6327281
2023-03-06T08:29:24Z
user-commons-lab-repository
Allard, Pierre-Marie
2022-03-04
<p><strong>Specialized metabolism (SBL.00060)</strong></p>
<p><em>In this class, we will define and explore the concept of specialized metabolome. We will study how metabolites are created (biosynthetic pathways) and we will see how important these small molecules are for humans (health and nutrition). More broadly, we will see how a better comprehension of specialized metabolism can be of interest in the field of ecology (chemical ecology).</em></p>
<p>Level: Bachelor</p>
<p>Credits: 1.5 ECTS</p>
<p>Frequency: annual. starting in Fall 2021</p>
<p>When: Thursdays, 08:15-10:00</p>
<p>Course coordinator: Pierre-Marie Allard (pierre-marie.allard@unifr.ch)</p>
<p><em><strong>Below you can find pdf files of the lecture slides and some additional materials for home study.</strong></em></p>
<p><em><strong>Slide contents licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/">CC-BY-SA 4.0</a> - feel free to share and/or modify.</strong></em></p>
Each main course slides are followed by resumed slides which are reminded at the beginning of the following class (a week later).
https://doi.org/10.5281/zenodo.6327281
oai:zenodo.org:6327281
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6327280
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
specialized metabolism
natural products
biosynthesis
course material
SBL.00060 material - Specialized Metabolism - UniFr
info:eu-repo/semantics/lecture
oai:zenodo.org:7701068
2023-03-06T08:29:26Z
user-commons-lab-repository
Allard, Pierre-Marie
2023-02-23
<p><strong>Specialized metabolism (SBL.00073)</strong></p>
<p><em>In this class, we will define and explore the concept of specialized metabolome. We will study how metabolites are created (biosynthetic pathways) and we will see how important these small molecules are for humans (health and nutrition). More broadly, we will see how a better comprehension of specialized metabolism can be of interest in the field of ecology (chemical ecology).</em></p>
<p>Level: Bachelor</p>
<p>Credits: 1.5 ECTS</p>
<p>Frequency: annual. starting in Fall 2022</p>
<p>When: Thursdays, 08:15-10:00</p>
<p>Course coordinator: Pierre-Marie Allard (pierre-marie.allard@unifr.ch)</p>
<p><em><strong>Below you can find pdf files of the lecture slides and some additional materials for home study.</strong></em></p>
<p><em><strong>Slide contents licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/">CC-BY-SA 4.0</a> - feel free to share and/or modify.</strong></em></p>
<p> </p>
Each main course slides are followed by resumed slides which are reminded at the beginning of the following class (a week later).
You will find editable material (.pptx, .key and .mol used for structures) altough not necessarily completely up to date, in the previous versions of this Zenodo repo.
You will also find editable .key and .pptx slides in the zipped folder.
Most of the chemical structures used in the slides were drawn using using MarvinSketch form Chemaxon (https://chemaxon.com/) they are zipped in SBL.00060_structures.zip
https://doi.org/10.5281/zenodo.7701068
oai:zenodo.org:7701068
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6327280
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
specialized metabolism
natural products
biosynthesis
course material
SBL.00073 material - Specialized Metabolism - UniFr
info:eu-repo/semantics/lecture
oai:zenodo.org:6331500
2023-03-06T08:29:25Z
user-commons-lab-repository
Allard, Pierre-Marie
2022-03-04
<p><strong>Specialized metabolism (SBL.00060)</strong></p>
<p><em>In this class, we will define and explore the concept of specialized metabolome. We will study how metabolites are created (biosynthetic pathways) and we will see how important these small molecules are for humans (health and nutrition). More broadly, we will see how a better comprehension of specialized metabolism can be of interest in the field of ecology (chemical ecology).</em></p>
<p>Level: Bachelor</p>
<p>Credits: 1.5 ECTS</p>
<p>Frequency: annual. starting in Fall 2021</p>
<p>When: Thursdays, 08:15-10:00</p>
<p>Course coordinator: Pierre-Marie Allard (pierre-marie.allard@unifr.ch)</p>
<p><em><strong>Below you can find pdf files of the lecture slides and some additional materials for home study.</strong></em></p>
<p><em><strong>Slide contents licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/">CC-BY-SA 4.0</a> - feel free to share and/or modify.</strong></em></p>
Each main course slides are followed by resumed slides which are reminded at the beginning of the following class (a week later).
You will also find editable .key and .pptx slides in the zipped folder.
Most of the chemical structures used in the slides were drawn using using MarvinSketch form Chemaxon (https://chemaxon.com/) they are zipped in SBL.00060_structures.zip
https://doi.org/10.5281/zenodo.6331500
oai:zenodo.org:6331500
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6327280
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
specialized metabolism
natural products
biosynthesis
course material
SBL.00060 material - Specialized Metabolism - UniFr
info:eu-repo/semantics/lecture
oai:zenodo.org:6659892
2022-06-22T21:25:33Z
openaire
user-dbgi-zenodo-repository
user-commons-lab-repository
Allard, Pierre-Marie
2022-06-18
<p>Poster presenting the Digital Botanical Gardens Initiative and associated research subjects for a bioinformatics master research period in the COMMONS Lab. </p>
<p> </p>
https://doi.org/10.5281/zenodo.6659892
oai:zenodo.org:6659892
eng
Zenodo
https://zenodo.org/communities/dbgi-zenodo-repository
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6659854
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
open science
dbgi
biodiversity
computational metabolomics
The Digital Botanical Garden Initiative - BEFRI Genomics Day - 2022
info:eu-repo/semantics/conferencePoster
oai:zenodo.org:6671108
2022-06-22T21:25:33Z
openaire
user-dbgi-zenodo-repository
user-commons-lab-repository
Allard, Pierre-Marie
2022-06-18
<p>Poster presenting the Digital Botanical Gardens Initiative and associated research subjects for a bioinformatics master research period in the COMMONS Lab. </p>
<p> </p>
https://doi.org/10.5281/zenodo.6671108
oai:zenodo.org:6671108
eng
Zenodo
https://zenodo.org/communities/dbgi-zenodo-repository
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6659854
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
open science
dbgi
biodiversity
computational metabolomics
The Digital Botanical Garden Initiative - BEFRI Genomics Day - 2022
info:eu-repo/semantics/conferencePoster
oai:zenodo.org:6760189
2022-06-28T01:48:55Z
openaire
user-commons-lab-repository
Allard, Pierre-Marie
2022-06-27
<p>Slides presented at the MetaBioDivex 2022 summer school (https://metabiodivex.sciencesconf.org/). I describe here some knowledge management aspects which can be applied in natural products research and experience learned through the establishment of the LOTUS initiative. These slides are also meant to be a didactic material and summarize some of the multiple ways to interact with the LOTUS ressource (https://doi.org/10.7554/eLife.70780)</p>
<p>Not in the slides : we also used DataWarrior to view query results (https://openmolecules.org/datawarrior/)</p>
During this lecture we corrected a LOTUS entry in Wikidata see: https://www.wikidata.org/wiki/Talk:Q282629#modifying_an_erroneous_taxon
https://doi.org/10.5281/zenodo.6760189
oai:zenodo.org:6760189
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6760188
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
LOTUS
natural products
wikidata
computational metabolomics
knowledge management
linked open data
Strategies for knowledge management in natural products research - MetaBioDivex - Aussois, 2022
info:eu-repo/semantics/lecture
oai:zenodo.org:5726749
2022-06-22T21:23:54Z
openaire
user-dbgi-zenodo-repository
user-commons-lab-repository
Kozlowski, Gregor
Defossez, Emmanuel
Allard, Pierre-Marie
2021-11-24
<p>A poster for the bachelor project event. </p>
<p> </p>
<p>A pilot project aiming to establish a Molecular cartography of the Botanical Garden of the University of Fribourg.</p>
<p>This is a collaborative work between the <a href="https://www.unifr.ch/bio/en/groups/allard/">COMMONS Lab</a>, the <a href="https://www.unifr.ch/bio/en/groups/kozlowski/">Kozlowski Group</a> and the <a href="https://www3.unifr.ch/jardin-botanique/fr/">Botanical Garden of the University of Fribourg</a>.</p>
https://doi.org/10.5281/zenodo.5726749
oai:zenodo.org:5726749
Zenodo
https://zenodo.org/communities/dbgi-zenodo-repository
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.5726668
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
botanical gardens
mass spectrometry based digitization
university of fribourg
open science
Molecular cartography of the Botanical Garden of the University of Fribourg
info:eu-repo/semantics/conferencePoster
oai:zenodo.org:5726669
2022-06-22T21:23:53Z
openaire
user-dbgi-zenodo-repository
user-commons-lab-repository
Allard, Pierre-Marie
Defossez, Emmanuel
Kozlowski, Gregor
2021-11-24
<p>A poster for the bachelor project event. </p>
<p> </p>
<p>A pilot project aiming to establish a Molecular cartography of the Botanical Garden of the University of Fribourg.</p>
<p>This is a collaborative work between the <a href="https://www.unifr.ch/bio/en/groups/allard/">COMMONS Lab</a>, the <a href="https://www.unifr.ch/bio/en/groups/kozlowski/">Kozlowski Group</a> and the <a href="https://www3.unifr.ch/jardin-botanique/fr/">Botanical Garden of the University of Fribourg</a>.</p>
https://doi.org/10.5281/zenodo.5726669
oai:zenodo.org:5726669
Zenodo
https://zenodo.org/communities/dbgi-zenodo-repository
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.5726668
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
botanical gardens
mass spectrometry based digitization
university of fribourg
open science
Molecular cartography of the Botanical Garden of the University of Fribourg
info:eu-repo/semantics/conferencePoster
oai:zenodo.org:7751316
2024-03-18T07:36:24Z
user-commons-lab-repository
Allard, Pierre-Marie
2023-03-20
<p><strong>SBL.00123 Cellular and Genetic Networks [SS 23]</strong></p>
<p>Genes and cells function in complex genetic and cellular networks that form the basis of biological systems. Recent advances in genomic and high-throughput techniques allow us today to acquire a more “holistic” view of biological systems. In this course, we will discuss how experimental or theoretical approaches at the systems-level provide insights into cell-to-cell interactions, cell cycle and cell growth, transcriptional regulatory networks, neuronal networks, and interactions between the environment and cellular processes. Topics also include mathematical modeling and cutting-edge genomic technologies. The goal of this course is to learn how to approach biological questions at the systems-level by integrating different experimental methods.</p>
<p>No textbook is available. Recent papers related to the topics will be suggested by lecturers for further reading.</p>
<p>Within the SBL.00123 program this specific lecture will deal with <em><strong>Metabolomics, computational mass spectrometry and open science resources for the exploration of living systems metabolomes.</strong></em></p>
<p>If we have time, it will be complemented by showcases of <a href="https://www.wikidata.org/">Wikidata</a> queries and <a href="https://scholia.toolforge.org/">Scholia</a> exploration.</p>
<p> </p>
<p> </p>
<ol>
</ol>
https://doi.org/10.5281/zenodo.7751316
oai:zenodo.org:7751316
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6390145
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
systems biology
metabolomics
natural products
SBL.00123 material - Cellular and Genetic Networks - Metabolomics - BEFRI
info:eu-repo/semantics/lecture
oai:zenodo.org:10828849
2024-03-18T08:00:12Z
user-commons-lab-repository
Allard, Pierre-Marie
2024-03-18
<p><strong>SBL.00123 Cellular and Genetic Networks [SS 24]</strong></p>
<p>Genes and cells function in complex genetic and cellular networks that form the basis of biological systems. Recent advances in genomic and high-throughput techniques allow us today to acquire a more “holistic” view of biological systems. In this course, we will discuss how experimental or theoretical approaches at the systems-level provide insights into cell-to-cell interactions, cell cycle and cell growth, transcriptional regulatory networks, neuronal networks, and interactions between the environment and cellular processes. Topics also include mathematical modeling and cutting-edge genomic technologies. The goal of this course is to learn how to approach biological questions at the systems-level by integrating different experimental methods.</p>
<p>No textbook is available. Recent papers related to the topics will be suggested by lecturers for further reading.</p>
<p>Within the SBL.00123 program this specific lecture will deal with <em><strong>Metabolomics, computational mass spectrometry and open science resources for the exploration of living systems metabolomes.</strong></em></p>
<p>It will be complemented by showcases of <a href="https://www.wikidata.org/">Wikidata</a> queries and <a href="https://scholia.toolforge.org/">Scholia</a> exploration.</p>
<p> </p>
<p> </p>
https://doi.org/10.5281/zenodo.10828849
oai:zenodo.org:10828849
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6390145
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
systems biology
metabolomics
natural products
SBL.00123 material - Cellular and Genetic Networks - Metabolomics - BEFRI
info:eu-repo/semantics/lecture
oai:zenodo.org:6491368
2022-05-26T10:14:52Z
user-commons-lab-repository
Allard, Pierre-Marie
2022-04-26
<p><strong>Introduction to metabolomics: data acquisition and processing (SBL.20004; 2 ECTS; lecture with practical). </strong></p>
<p> </p>
<p>This course is a theoretical and practical introduction to metabolomics (the large scale study of small molecules in complex mixtures). It will cover extraction methods, sample preparation, separation techniques and chromatography, detection procedures and data analysis (quantitative and qualitative). A particular focus will be given to mass spectrometry based metabolomics of specialized metabolomes and its applications in environmental biology and natural products research. The course includes a practical part on GC or LC-MS (Gas Chromatography or Liquid Chromatography coupled to Mass Spectrometry) and data processing.</p>
https://doi.org/10.5281/zenodo.6491368
oai:zenodo.org:6491368
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6379085
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
SBL.20004 material - Introduction to Metabolomics - UniFr
info:eu-repo/semantics/lecture
oai:zenodo.org:6379449
2022-05-26T10:14:52Z
user-commons-lab-repository
Allard, Pierre-Marie
2022-03-23
<p><strong>Introduction to metabolomics: data acquisition and processing (SBL.20004; 2 ECTS; lecture with practical). </strong></p>
<p> </p>
<p>This course is a theoretical and practical introduction to metabolomics (the large scale study of small molecules in complex mixtures). It will cover extraction methods, sample preparation, separation techniques and chromatography, detection procedures and data analysis (quantitative and qualitative). A particular focus will be given to mass spectrometry based metabolomics of specialized metabolomes and its applications in environmental biology and natural products research. The course includes a practical part on GC or LC-MS (Gas Chromatography or Liquid Chromatography coupled to Mass Spectrometry) and data processing.</p>
https://doi.org/10.5281/zenodo.6379449
oai:zenodo.org:6379449
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6379085
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
SBL.20004 material - Introduction to Metabolomics - UniFr
info:eu-repo/semantics/lecture
oai:zenodo.org:6583450
2022-05-26T10:14:53Z
user-commons-lab-repository
Allard, Pierre-Marie
2022-05-03
<p><strong>Introduction to metabolomics: data acquisition and processing (SBL.20004; 2 ECTS; lecture with practical). </strong></p>
<p> </p>
<p>This course is a theoretical and practical introduction to metabolomics (the large scale study of small molecules in complex mixtures). It will cover extraction methods, sample preparation, separation techniques and chromatography, detection procedures and data analysis (quantitative and qualitative). A particular focus will be given to mass spectrometry based metabolomics of specialized metabolomes and its applications in environmental biology and natural products research. The course includes a practical part on GC or LC-MS (Gas Chromatography or Liquid Chromatography coupled to Mass Spectrometry) and data processing.</p>
<p>The practicals consist of a pilot metabolomics project proposed by each group of students (2 to 3 per groups). In this pilot they will decide on a research axis they would like to explore. The samples are plants collected from the botanical garden of the University of Fribourg. After collection, sample preparation approach is proposed and realized by the students. The samples can be analyzed on a LC-HRMS (QE+) or a GC-QToF system. After data treatment and interpretation a report is returned on each groups github repositories. </p>
<p>The main repo is available here for more detailed instructions <a href="https://github.com/commons-teaching/SBL.20004.2022">https://github.com/commons-teaching/SBL.20004.2022</a></p>
<p>Course coordinator: Pierre-Marie Allard (pierre-marie.allard@unifr.ch)</p>
<p><em><strong>Below you can find pdf files of the lecture slides and some additional materials for home study.</strong></em></p>
<p><em><strong>Slide contents licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/">CC-BY-SA 4.0</a> - feel free to share and/or modify.</strong></em></p>
<p> </p>
Each main course slides are followed by resumed slides. You will also find editable .key and .pptx slides in the zipped editable_slides.zip
https://doi.org/10.5281/zenodo.6583450
oai:zenodo.org:6583450
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6379085
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
SBL.20004 material - Introduction to Metabolomics - UniFr
info:eu-repo/semantics/lecture
oai:zenodo.org:6350485
2023-05-02T12:29:23Z
user-commons-lab-repository
Pierre-Marie Allard
2022-02-11
<p>A set of required input files and expected output files for the Computational Metabolomics Workshop.</p>
<p>Before the workshop please:</p>
<ol>
<li>Read the README.pdf !</li>
<li>Download the workshop material (go to <a href="https://doi.org/10.5281/zenodo.6047248">https://doi.org/10.5281/zenodo.6047248</a> and make sure your are downloading the latest version as this link will probably have changed)</li>
<li>Get MZMine 2.53 (<a href="https://github.com/mzmine/mzmine2/releases">https://github.com/mzmine/mzmine2/releases</a>)</li>
<li>Creat an account on GNPS (<a href="https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp">https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp</a>)</li>
<li>Get Cytoscape (<a href="https://cytoscape.org/download.html">https://cytoscape.org/download.html</a>)</li>
</ol>
https://doi.org/10.5281/zenodo.6350485
oai:zenodo.org:6350485
eng
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6045962
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
metabolite annotation
computational metabolomics
tutorial
Computational Metabolomics Workshop Material
info:eu-repo/semantics/lecture
oai:zenodo.org:6045963
2023-05-02T12:29:23Z
openaire_data
user-commons-lab-repository
Pierre-Marie Allard
2022-02-11
<p>A set of required input files and expected output files for the Computational Metabolomics Workshop.</p>
https://doi.org/10.5281/zenodo.6045963
oai:zenodo.org:6045963
Zenodo
https://zenodo.org/communities/commons-lab-repository
https://doi.org/10.5281/zenodo.6045962
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
metabolite annotation
Computational Metabolomics Workshop Material
info:eu-repo/semantics/other