Commit 249a5ecb authored by jeremycherfas's avatar jeremycherfas
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Created /scripts and included drafts of wheat and rice

parent 6b1df892
Title: irri-script-draft-01
Author: Jeremy Cherfas
Date: 12 October 2016
Format: snippet
Welcome to Genesys, a one stop shop that lets you look at details of more than two and a half million samples of crop diversity. Through Genesys, you can not only find information about genebank accessions but also, in many cases, order samples directly from the genebank.
There are many, many ways to explore the diversity in Genesys. In this video, we're going to focus on one genebank, the International Rice Research Institute in the Philippines.
The easiest way to get there is through the list of countries. Click on P and then Philippines and you'll see IRRI at the top of the list, with code PHL001 and more than 127,000 accessions in Genesys.
The entry for IRRI takes you directly to some general information about the IRRI genebank's holdings, almost all of which, not surprisingly, are rice.
The Overview button tells you more about what's in the IRRI genebank, where it came from, what species it is and so on.
Domesticated Asian rice all belongs in the species Oryza sativa. But there is also African rice, domesticated independently. That belongs to the same genus Oryza, but a different species -- glaberrima. Let's take a look at IRRI's accessions of that species on a map.
Under the list of genera, on the left, click on Oryza. Now we can Refine search by category, selecting species. Start typing glaberrima into the search box, and pick the correct one. That gives us a list of more than 5000 accessions.
Note that if you want to share any list of acessions you've created with a colleague, for example, Genesys provides a special link -- here -- that you can use to get back quickly to a particular set of selections. You can also download your selections and see them on a map. Let's look at the map.
The green dots show where IRRI's accessions of Oryza glaberrima were collected -- mostly in West Africa. Zooming in, we can click on any collecting site to see the accession number and a link directly to information about that accession.
From the map, you can also download a shapefile to use in any geographic information system.
Let's do that again for a different species.
The back button takes you to the list for Oryza glaberrima. Click on the small x next to the label glaberrima in the filters at the top.
This takes you back to a list of all Oryza accessions. Let's look for Oryza nivara. This is a wild relative that is believed to be one of the ancestors of domesticated Asian rice.
If the Species row is still showing in the list of filters at the top, click anywhere in the row. If it isn't, you'll need to click on Refine search by category and select species again. Type niv in the search box, and you see a menu of possible species. Click on nivara and Apply.
Your list now contains just over 1,400 accessions. The overview shows you that they are kept at IRRI and in two genebanks in the United States. And that most of them were collected in Cambodia and India. You can again look at them on the map and zoom in to see details of each geo-referenced accession.
Of course, you can also use all the other functions of Genesys to search for accessions in the IRRI genebank with particular characteristics. The video tutorial on wheat will show you how to do that. Just apply the same principles after selecting all rice from IRRI.
One final note. You can do all this without logging into Genesys. But if you do create an account and log in, that gives you access to a few additional tools.
And if you come across any problems, or need support, the easiest way to contact Genesys is through Twitter, @genesyspgr. {==Not sure if you want anything like this, or if you feel you will be swamped. But maybe people need to know how to get support.==}
Title: wheat-script-draft-01
Author: Jeremy Cherfas
Date: 12 October 2016
Format: snippet
Welcome to Genesys, a one stop shop that lets you look at details of more than two and a half million samples of crop diversity. Through Genesys, you can not only find information about genebank accessions but also, in many cases, order samples directly from the genebank.
There are many, many ways to explore the diversity in Genesys. In this video, we're going to focus on wheat. But it could easily be any of the crops with data in Genesys.
There is a list of the most important crops in this box on the home page. If you don't see what you are looking for there. Try typing either the crop name or the scientific name into the big search box.
For now, though, lets use the list in the box of crops. Click on Wheat and you'll go straight to a list of almost 400,000 accessions.
The list shows you the accession number, which is, if you like, that accession's formal name. It also shows you the Latin name; the country of origin of the sample; the biological status -- is it a traditional farmers' variety, for example, or an advanced breeders' line; And the code of the institute holding that accession.
The accession number is a link to data about that accession. The more information Genesys has about an accession, the more you will find on this page.
And the holding institute's code is a link to information about that genebank, with easy access to more details about their accessions.
OK, back to our search for wheat.
One of the most powerful aspects of Genesys is that it allows you to refine your search in two different ways.
First, you can look for specific traits. Click on this link -- Refine search by trait -- and you get a list of all the characterisation data for wheat. So if you're looking for something specific, like purple wheat, you can click on kernel color and then Apply, down at the bottom. That shows you all the possible values of kernel color. Click on Purple and Apply, and that narrows down the list to 193 accessions.
Of course, you can combine several traits to narrow the list even further.
One thing to note, if you want to share your selections with a colleague, for example. Genesys provides a special link -- here -- that you can use to get back quickly to a particular set of selections. You can also download your selections, get a quick overview, and see them on a map. We'll explore those functions in a moment.
OK, let's look at the other way to narrow down your search, and that is to Refine search by category.
Category, in this case, is information about an accession that is not about the phenotype of the accession. Some of this information is called passport data. Things like where it was collected, whether it is safety duplicated, scientific name and so on.
One thing you might want to do is find wild relatives of wheat. To do that, you need to select Biological status of accession. That gives you a list of the various classifications that Genesys knows about.
First, note that this information is available for only about 64,000 of the accessions. Now, select Wild and click Apply.
That narrows the selection down even further, to 265 accessions.
Let's explore what we've found. The Overview button shows you which institutes hold wild relatives of wheat, the species names and other useful information. {==Why has number of accessions gone up to 38943?==}
The map shows you the collecting site of each accession that has geo-reference data. You'll probably need to zoom in, and then, when you click on a single site, a pop-up shows you the accession number and institute code with a direct link to that accession's data.
If you're looking for wild wheat from a specific country, that's easy too.
Refine search by category again, and now select Country of Origin. That creates a search box in which you can start typing a country name. I want to look for wild wheats from Libya. Genesys shows me 84 accessions. I want to see them on a map. Zooming right in, I can get the accession number and holding institute code and go straight to the data for that accession.
What about getting hold of samples?
On all lists of selections, there's a checkbox next to every accession. That's the key to obtaining samples. Once you have made some selections, you will see a number in the window next to My list, at the top. That's how many accessions you have selected. Click on My list, and you go to a page listing the accessions you selected. If they have geographical information, you can view their collecting sites on the map. And you can add and remove selections by hand.
When you're ready, click Send request for germplasm, and Genesys will check whether your selections are available. You'll then need to accept the terms and conditions and your request will be sent direct to the holding institute, with confirmation email to you.
That's it.
OK, so we've seen how to select a crop from the list on the home page. You can also use the big search box at the top of the page. Then we narrowed down the search using phenotypic traits and passport data, and we explored an overview of the filtered list and looked at some of them on a map. And we saw that Genesys provides a special link for every list you create. Finally, we saw how you can select just some of the accessions that you are interested in, and use that list to order samples.
One final note. You can do all this without logging into Genesys. But if you do create an account and log in, that gives you access to a few additional tools.
And if you come across any problems, or need support, the easiest way to contact Genesys is through Twitter, @genesyspgr. {==Not sure if you want anything like this, or if you feel you will be swamped. But maybe people need to know how to get support.==}
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