2023-06-20
This is Audrey's DBGI report
Context of the internship
The analytical team of the Institute of Organic and Analytical Chemistry (ICOA) of the University of Orléans is specialized in the characterization of plant extract and the determination of their bioactivity. Ornamental plants are highly produced in the Région Centre Val-de-Loire (France) being able to characterized and identify bioactive could lead to new way of valorisation of this large quantity of raw materials.
To discover the potential of ornamental plant, a metabolomic study is undertaken. In this study we are interested in 3 genera of ornamental plants. The CDHRC (Comité de Développement Horticol Région Centre) produce 2 Clematis spp, 1 Lonicera sp and 1 Euonymus sp and to extend our study to several species a collaboration with the DBGI (Digital Botanical Garden Initiative) had been established. The objective of this collaboration is to acquire news skills in metabolomic treatment, to access to several species of Clematis, Lonicera and Euonymus to the study and integrate this result to the DBGI dataset.
Methodology
Collaborative tools
The DBGI is an Open Science project, this ambition had lead the contributors to set up differents tools :
-
Visual Studio Code : Visual Studio Code is a source-code editor that can be used with a variety of programming languages.
-
Open notebook : An open daily notebook of each contributors of the project can be submitted to the DBGI dendron (http://www.dbgi.org/dendron-dbgi/).
-
Git Hub : GitHub, Inc. is an Internet hosting service for software development and version control using Git. Repositories, containing documents, scripts or tutorials can be easily shared thanks to Git (https://github.com/digital-botanical-gardens-initiative)
The used of this tools had required the learning of basics skills of navigating via a control terminal
| General command |
|---|
cd |
mkdir |
cd .. |
tree |
ls |
| Specific to git |
|---|
git clone + https url |
git pull |
git add |
git commit -m "exemple" |
git push |
| git status |
| Specific to the Open Notebook (in VS code) | use |
|---|---|
| ctrl+o+n | create a daily notebook |
Wetlab
A specific workflow for the organization of the wetlab part had been set up. The workflow required the used of the following software or application : directus, Avery, Qfield and Inaturalist. The global workflow is avaibable on the link
Metabolomics datatreatment
A specific workflow for the datatreatment of DBGI plant had been set up. The workflow required the used of the following software, application or git : MS convert, Inaturalist, GNPS, Mzmine 2.3, Sirius, Cytoscape, Met_annot_enhancer
The uses of the differents software required a higher calculation capacity than the personnal laptop used. An ssh connection had been establised between the servor and the computer in order to launch session, interfaced with Xpra, to run mzmine or sirius. The global workflow of datatreatment is available here
Results
Plant collections
DBGI collection : 16 Clematis, 16 Lonicera, and 4 Euonymus had been collected between Botanical Garden of Fribourg and Botanical Garden of Neuchatel. CDHRC collection : 2 Clematis, 1 Lonicera and 1_Euonymus had beed collected.