Use GOn Ramp to set up a collaborative

Use G-On. Ramp to set up a collaborative annotation environment on Apollo Yating Liu June 2018 G-On. Ramp workshop

Admin • Has system-wide administrative privileges • Create instructor accounts on Apollo for lab PIs / Faculty • Example: faculty who setup G-On. Ramp and Apollo Instructor • Can create organisms (Apollo instances), user groups and user accounts on Apollo • Administrative privilege on organisms, users and user groups that you have created • Example: faculty who manage a collaborative annotation project User • Can be granted administrative / write / read / export privileges on an organism by an instructor or an admin • Example: students involved in the collaborative annotation project Three types of user accounts on Apollo

General process of configuring the Apollo environment Get an Apollo instructor account which uses the same email address as your Galaxy account (created by administrator) Log into Galaxy Run the G-On. Ramp workflow for JBrowse to create a JBrowse instance for your interested genome Create accounts for collaborative annotators Apollo User Manager tool Create a user group Apollo User Manager tool Create an organism on Apollo with the JBrowse instance and grant permissions to the user group to access the organism on Apollo Create or Update Organism tool Add the annotators to the user group Apollo User Manager tool Log into Apollo Start genome annotation together

Galaxy tools to interface with Apollo • Requirements • Have an instructor or admin account on Apollo • Your Apollo account should use the same email address as your Galaxy account • Create or Update Organism tool • Adds an organism to the Apollo database • Grant write access to a selected user group • Apollo User Manager tool • • • Create Apollo users Delete Apollo users Create user groups Delete user groups Add Apollo users to a user group Remove Apollo users from a user group • Delete an Apollo record tool • Delete an organism from Apollo • Export all annotations on the organism

Get an Apollo instructor account • If you are the administrator of the G-On. Ramp instance • Should have an initial Apollo admin account • Log into Apollo and change the password • Update the password on supervisor configuration file at /etc/supervisor/conf. d/galaxy. conf, and restart the server • If you are not the administrator of the G-On. Ramp instance • Ask the administrator to create an Apollo instructor account for you with the same email address you used for your Galaxy account

Create users with the Apollo User Manager tool Click on “Insert New operation”. You can choose an operation from the dropdown menu: • Create a user • Delete a user • Create a user group • Delete a user group • Add a user to a group • Remove a user from a group Choose ”Create a user” from the drop-down menu

Create an instructor account with the Apollo User Manager Tool (system administrator) Create one account at a time Specify user email Specify user first name Specify user last name To create an instructor account, select the “instructor” option from drop-down menu

Create an instructor account with the Apollo User Manager Tool: output (system administrator) Operation First Name Create User galaxy_instructor Last Name demo Email New Password Role Group galaxy_instructor@apol lo. com mzgbkkgwrqxx instructor Add to Group Remove from Group

Create a user group Select “Create a user group” Create a user group at a time Specify the group name

Run the “G-On. Ramp workflow for JBrowse” to create a JBrowse instance Reference genome assembly Transcripts / proteins from informant genome RNA-Seq reads Sequence similarity Gene predictions RNA-Seq analysis Repeats JBrowse Archive Creator

Create an organism and grant permissions to the user group with the Create or Update Organism Tool Specify JBrowse Output from JBrowse Archive Creator If you want to create a new organism, select “Direct Entry” in the drop-down menu under the “Organism Common Name Source” field Optional: specify Genus and Species Specify the organism name that you would like to see on Apollo If set to public, this JBrowse instance is visible to all users on Apollo. Default is “No” Give a user group read/write/export permission to the organism

Update an existing organism with the Create Specify JBrowse Output from or Update Organism Tool JBrowse Archive Creator Choose the “Select” option in the drop-down menu for the “Organism Common Name Source” field, and then select the organism you want to update from the list Optional: specify Genus and Species If set public, this JBrowse is visible to all users on Apollo Give a user group read/write/export permission to the organism

Create accounts for collaborative annotators (create multiple user accounts at a time) Create a text file which include user information to create account. Then upload the text file to Galaxy. Open the Apollo User Manager tool and choose “Multiple users” under the “Manipulate a single user or multiple users” field Specify the text file format (support CSV and Tabular) Specify the text file

Create a text file to manage multiple users or user groups (examples) Text file for creating multiple users Text file for deleting multiple users Text file for creating or deleting multiple user groups Text file for • adding to multiple users to a user group • removing multiple users from a user group

Output of Apollo User Manager Operation First Name Create User Annotator 1 Create User Annotator 2 Create User Annotator 3 Create User Annotator 4 Create User Annotator 5 Last Name gonramp gonramp Email annotator 1@gonramp. com annotator 2@gonramp. com annotator 3@gonramp. com annotator 4@gonramp. com annotator 5@gonramp. com New Password xgckxbdnqhnk jjmvmchhjvtw qbdtqfjqglsx dvmcrjxdnvxw fqtqdmcgwmqh

Add a user to the user group Specify user email Select the group from the drop-down menu Note: if the group doesn’t show up in the list, refresh the browser

Add the annotators to the user group (add multiple users to the user group at the same time) Create a text file which include user information to create the accounts. Then upload the text file to Galaxy. Open the Apollo User Manager tool and choose “Multiple users” under the “Manipulate a single user or multiple users” field Specify the text file format Specify the text file

Genome annotation on Apollo A) The ‘Navigation Panel’ runs along the top of the main panel B) The ‘User-created Annotations’ panel contains the manual annotations C) The ‘Evidence’ panel includes all evidence tracks aligned to the reference genome assembly D) The ‘Annotator Panel’ allows curators to easily navigate the genome, and to display and export annotations See the “Use Apollo to do collaborative genome annotation” walkthrough for details

View annotation report Admin Tab: Click on “Report: : Instructor” to view the annotation report grouped by user groups. It includes: • Annotation record for each annotator within a user group • Detailed breakdown report for each annotator if you click on the username

View annotation report of the “D. miranda annotation” user group Select report for user group “D. miranda annotation” Export the report to a file in CSV / EXCEL / XML formats

Export the report to an Excel worksheet Username First Name Last Top Level Name User Group Organism Features Genes Transcripts Exons Transposab Repeat le Elements Regions Last Updated annotator 5 @gonramp. D. miranda Drosophila com Annotator 5 gonramp annotation miranda 6 6 6 32 0 0 5/21/18 annotator 2 @gonramp. D. miranda Drosophila com Annotator 2 gonramp annotation miranda 3 3 3 15 0 0 5/21/18 annotator 3 @gonramp. D. miranda Drosophila com Annotator 3 gonramp annotation miranda 1 0 1 5 0 0 5/21/18 annotator 1 @gonramp. D. miranda Drosophila com Annotator 1 gonramp annotation miranda 1 1 1 6 0 0 5/21/18 annotator 4 @gonramp. D. miranda Drosophila com Annotator 4 gonramp annotation miranda 2 2 2 12 0 0 5/21/18

Annotation details and organism breakdown for an individual annotator

Delete an Apollo organism • Delete an organism from Apollo • Export all the annotations for the organism

Summary • Three types of Apollo accounts • user, instructor, admin • General process of configuring an collaborative annotation environment on Apollo • Galaxy Apollo interaction tools • Create or Update Organism • Apollo User Manager • Delete an Apollo record

Practice: set up a collaborative annotation environment on Apollo for D. biarmipes • Create an instructor accounts for all participants (done by administrator) • Create an annotation user group: “D. biarmipes annotation” • Run G-On. Ramp workflow for JBrowse to create the D. biarmipes JBrowse instance • Create an organism on Apollo with D. biarmipes JBrowse and grant group “D. biarmipes annotation” access to Apollo organism “D. biarmipes ” • Create 10 fake accounts for the collaborative annotators • Add the annotators to the user group

Additional slides

General process of configuring the Apollo environment Get an Apollo instructor account which uses the same email address as your Galaxy account (created by administrator) Create a user group Log into Galaxy Apollo User Manager tool Run the G-On. Ramp workflow for JBrowse/Apollo to - Create a JBrowse instance for the genome of interests (JBrowse Archive Creator) - Create an organism on Apollo with the JBrowse instance and grant permissions to the user group to access the organism on Apollo (Create or Update Organism tool) Create accounts for collaborative annotators Apollo User Manager tool Add the annotators to the user group Apollo User Manager tool Log into Apollo Start genome annotation together

G-On. Ramp workflow for JBrowse/ Apollo Reference genome assembly Transcripts / proteins from informant genome RNA-Seq reads Sequence similarity Gene predictions RNA-Seq analysis Repeats JBrowse Archive Creator Create or Update Organism

Practice: set up a collaborative annotation environment on Apollo for D. biarmipes • Create an instructor accounts for all participants (by administrator) • Create an annotation user group: “D. biarmipes annotation” • Run G-On. Ramp workflow for JBrowse • Create D. biarmipes JBrowse instance • Create an organism on Apollo with D. biarmipes JBrowse • Grant group “D. biarmipes annotation” access to Apollo organism “D. biarmipes ” • Create fake 10 accounts for collaborative annotators • Add the annotators to the user group