Vinesch-Bioblitz
Overview
The idea would be to have a hands-on session so that all of us could observe, test and eventually modify and improve our current workflow - "from the plant to the graph". This would happen in two stages, the first one in the field, the second one in the lab.
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First session is a "bio-blitz" in the Vinesch vineyard (https://vinesch.ch/ and https://www.inaturalist.org/projects/vinesch). Simple rules : no taxonomical focus, maximize the coverage. This would allow to benchmark the current DBGI collection, labelling protocols, "real-life" and as a kind of transition from DBGI to EMI. Also possibility to test other sampling process (insects traps and similar with Donat) Of course this would also be a great occasion to gather and enjoy the Valais spring. Wine will be STRICTLY FORBIDDEN, obviously (apart for sampling purpose ... you'll define your sampling approach)
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Second part would be in the labs here. From Raw samples to a series of pertinent questions in the established Knowledge graph. Overview of the sample prep process, the metabolomics analysis, the data treatment, the enrichment process, the harmonization with external resource, graph creation and query.
This would allow all of us to have a clear overview + a hands on experience of the process ranging from the specimen collection in the field to the interrogation of its metabolome through SPARQL. It should allow us to benchmark all of the steps and see how things scale up and how the several tools can be used/misused/improved by the participants. We would also document as much as possible these days. This would be pushing the "bio-blitz" concept (https://www.inaturalist.org/pages/bioblitz+guide) a bit further than iNat observation or plain species monitoring.
We would like to fully document the two stages of our experiment here and issue a publication type "From the field to the graph: an open resource documenting the metabolome of XXX species established in XX days, by XX persons". Furthermore we might have a skilled and professional cameraman (Christian in cc.) to document the whole process and produce a short movie !
Organization
What should I do prior to the event ?
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Prepare my stuff (see checklist), and make sure to have all the necessary equipment for the field trip.
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Some software to fetch and account to create. See software.
https://github.com/orgs/digital-botanical-gardens-initiative/projects/2
Resources
Vinesch iNaturalist page
https://www.inaturalist.org/projects/vinesch
Vinesch web page
When ?
Saturday 8th June (day and night)
We'll meet all at 9:30 am at the Visp train station.
Where ?
How to get there ?
Note that in both cases, the vineyard is only accessible by foot. This is a 20-30 min walk from the parking lot. We will have stuff to carry up there, bring good shoes and a backpack !
For those who come by train
Join Visp train station https://maps.app.goo.gl/VVKXW2JpyNxmeWgc8 From there, we will organize a shuttle to the vineyard.
For those who come by car
If you drive directly to the vineyard, you can park at the bottom of the vineyard (P1) or at the top (P2).
Here the map Blue Full line walking from the car parking P2 Dotted line: walking from the parking at the bottom (P1) B Bus stop Stundhus (Bus Visp – Saas Fee)
Red Access by car. Access is through the gravel pit. The junction (J) branches off on the left side of the street!
Children