01_basic_website_usage.md

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1. Basic Website Usage	doc_page

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1.1. Creating a User Account

Verifying first that you do not already have an account

Before creating an account, please verify first that you don’t already have an account. You can use “Search” menu to check if you already registered as a user.

In the "Search" menu, selecting the "People" tab and search your name. If nothing is found, proceed with the instructions below. Otherwise, clicking the “Login” button. If you have forgotten your password, you can retrieve it here.

Creating a user account

On the right of the toolbar, clicking on “Login.” It will take you to the login page. On the login page, clicking on the link “sign up for an account.” It will take you to the page below:

Filling in all of the information, then clicking "Create Account."

After you submit the information, an email will be sent to the provided email address. Checking your email and clicking on the link to activate your account.

1.2. Managing your Account

Login

To login, clicking the "Login" link in the toolbar on any page and enter your username and password.

If you have forgotten your password, you can retrieve it here.

Editing Account Settings

Account settings can be edited by clicking on the "my profile" link displayed as your user name, on the right of the toolbar. You must login, in order to access and change account settings.

You can add personal information to your account using the "View or update personal information" link.

To change your password, username, or your contact email, clicking on “Update account information” link. You must provide your old password before you can make any changes.

Changing Your Account Status: From “User” to “Submitter”

After you create an account, your account has a "user" status. This account has limited privileges.

Accounts with “user” status are able to:

• Change personal information
• Post comments on pages
• Post to the forum

To upgrade your account status to "submitter,” contact Cassavabase using the "contact" link provided at the footer of each page. Submitter accounts can add data, such as new plots, accessions, phenotype data and images. Click here to Contact Cassavabase.

Submitting Feedback on the Cassavabase Website and Wiki

We appreciate your feedback! Feel free to submit any questions or suggestions by using the "Feedback" link provided at the footer of each page.

1.3. Menu Layout

The Cassavabase website has a toolbar on the top of each page with a number of menus for convenient access of major functions. The menus, as pictured below, are “search,” “manage,” “analyze,” and “maps.” The toolbar also provides a quick search, a “log in” button, and a “new user” button.

Menu Options

Search

In the Search menu, the options are:

Tab	Description
Wizard	Search different accessions and plots by location, year, trial, and trait data. Can also be used to create lists of different types.
Accession and plots	Search accessions and plots using a variety of criteria
Trials	Search trials by name, description, breeding program, year, location, and trial type.
Markers	Search different markers
Images	Search images contained in the SGN database
People	Search Cassavabase users

Manage

In the Manage menu, the options are:

Tab	Description
Breeding Programs	View, add and delete breeding programs
Locations	View, add and delete locations
Accessions	Manage and search different accessions
Crosses	Create new crosses in the database
Field Trials	Manage field trials. Create trials using different field layouts.
Genotyping Trials	Manage genotyping trials. Create trials using different breeding programs, locations, and years.
Phenotyping	Upload phenotyping files from the Tablet Field Book application
Field Book App	Manage the field book app data (download files to tablet)
Barcodes	Refers to the old barcode system, mainly historical
Download	Download information in the database based on lists

Analyze

Clicking on the "Analyze" link will give a full menu of all analysis functions
In the Analyze menu, the options are:

Tab	Description
Breeder Tools
Breeder Home	Access breeding functionalities. Lists important and helpful links.
Barcode Tools	Manage, create, and download barcodes. Also access barcode tools.
Genomic Selection	Can search for traits, start building a GS model, and predict values based on genotypes
Sequence Analysis
BLAST	Sequence homology search for the cassava genome
Other
Ontology Browser	Browse all recorded ontologies

Maps

Tab	Description
Cassava 2011, 2013 and 2014 GBS Maps	Map of cassava genomes, has markers listed per chromosome
Genome
Cassava Genome Browser at JGI	Comprehensive genome browser provided by Joint Genome Browser

About

Tab	Description
About NextGen Cassava	Access home page of NextGen Cassava Project
Contact	CassavaBase contact form
Cite CassavaBase	cite CassavaBase in your publications
Manual	CassavaBase manual
Wiki	Access to NextGen Cassava wiki
FAQ	Cassavabase users frequently asked questions and useful answers
Forum	CassavaBase forum
Twitter	Sol Genomics twitter page
Facebook	Sol Genomics facebook page

1.4. Working with Lists

Lists are collections of identifiers that are stored in the database. Lists can be composed of accessions, plots, traits, locations, and trials. Lists are attached to the individual user's account, and can only be created and seen by the user while logged in. CassavaBase makes heavy use of lists in a number of tools on the website. For example, trials are created using lists of accessions.

Generating lists

IMPORTANT: You can add only items that are stored in the database into your lists.

Lists can be generated in various ways:

One way to create a list is by clicking on the "Lists" link located on the toolbar.

To create a new list, entering the name of your new list, then clicking on “New List” button.

You can find the list that you entered on the “Your Lists” page. To add items on your list, clicking on the view icon to open “List Contents” page.

On the “List Contents” page, entering items that you want to add to the list, then clicking on “Add” button.

The page will be updated and will display your items in a table at the bottom of the page.

Selecting the type of items in your list. To verify that the items that you added to your list are already stored in the database and that you selected a correct type for the items, clicking on the “Validate” button.

If those items are already in the database, a message will indicate that “This list passed validation”

Note that a list cannot contain duplicate elements. If a duplicate item is entered, the list manager will inform the user that the element is already in the list and will not add it again.

Another easy way to create a list is to use the Search Wizard, which can be accessed from the Search menu.

Viewing and editing lists

Lists can be viewed and edited using the "Lists" link on the toolbar. Clicking on the link will open a window that displays all of your lists, as well as an option to create new lists.

This page shows all lists that have been created, including those created by using the Search Wizard. You can view and edit your lists by using “Actions” buttons.

1. Clicking on the "view" icon will open a new window called "List Contents" that allows you to change the list name, the type of the list, add new items, or delete existing items.

2. Clicking on the “delete” icon will delete your list. Caution: this action cannot be undone.

3. Clicking on the “download” icon will download the contents of your list to your computer.

4. Clicking on the “make public” icon will make your list available for other users to view and use your list.