1. 1 Using caArray to Share Pre- Publishing Data Fan Lin Ph.D. Molecular Analysis Tools Knowledge Center Columbia University and The Broad Institute of MIT and Harvard

2. 2 Introduction When manuscripts are submitted for publications, many journals require the microarray data associated with the manuscripts to be made available to reviewers in a MIAME compliant format. caArray can help users to meet this requirement by offering: Fast & easy MAGE-TAB compliant data upload to caArray server. Flexible access control: User can grant or revoke the reviewers’ access rights to user’s private experiments. Data can be stored in user’s local caArray server or in NCI’s public caArray server ( https://array.nci.nih.gov/caarray/home.action ).NCI’s public caArray server This presentation will show you how to use caArray to grant read/revoke access on an unpublished experiment to reviewers.

3. 3 User Account Prerequisite There are two previously created caArray user accounts used in this presentation: User Account – An account used to create & submit the experiment Caarrayuser (in this presentation) Reviewer’s account – An account to be used by reviewers to access user’s private data (a read only account) CU_reviewers (in this presentation)

4. 4 Permission at Group Level Since the permission on experiments can only be granted at the collaboration group level, We will first: 1. Create a new collaborator group, called “Reviewers”, under user account: “caarrayuser”. 2.Assign reviewers’ account, “CU_reviewers”, to be a member of this new collaboration group “Reviewers”.

5. 5 Create A New Collaborator Group To create a new collaborator group: 1.Click on “manage Collaborator Groups” 2.Click on “Add a New Collaboration Group” 3.Assign an unique name for the group. “Reviewers” is used in this presentation.

6. 6 Assign Member to a Collaborate Group To assign reviewer’s account: ” CU_Reviewers” to be the member of the group : Click on “Edit” button for collaborator group “Reviewers” as shown by arrow.

7. 7 Add New Members to a Group Find and add users to be member(s) of this new group: 1.Click on “Add a New Group Member” bottom. 2.Enter registered users last name, first name, or organization, click the “Filter” button to find the user 3.For each member to be added to the group, click the Add icon (+) in the far right column of the screen.

8. Different Views of A Private Experiment 8 A private experiment in “Draft” status (“user-00028”, Figure 1) is shown as “Not Available” to public (Figure 2).

9. 9 Draft Experiment Is Not Sharable. When the experiment is created, it is defaulted to be in “Draft” state, which is only accessible to its creator. To share this experiment with other users, this experiment must be submitted to a sharable area first. To share the private experiment “User-00028”, click on the name to open the experiment as shown by arrow.

10. 10 Submit Experiment Proposal Click on “Submit Experiment Proposal” button. The status of experiment “user-00028” will change from “Draft” to “In progress” status.

11. 11 Change Experiment’s Permission Experiment “User-00028” is now in sharable “In progress” state. To assign the read-only permission to a collaborator group, Click on permission icon under “Permissions” as shown by arrow.

12. Assign Collaborator Group to The Experiment Change collaborator group to be ‘Reviewers” as indicated by the arrow. 12

13. 13 Grant Access Role to A Collaborator Group To grant the access: 1.Click on “Edit Access Control” at the lower left corner. 2.Use drop down list at the right to assign permission to choose the access. 3.Assign “Read” to the collaborator group, “Reviewers”. 4.Click on “Save” button.

14. 14 Private Data is Sharable Re-login with reviewers’ account : “CU_reviewers”. Click on “Browse” at left menu to open the list of experiments. “CU_reviewers” can read annotation information and download array data from Experiment “user- 00028”.

15. 15 Revoke Access Role to A Collaborator Group To revoke the access, go back to permission access page: 1.Click on “Edit Access Control” at the lower left corner. 2.Use drop down list at the right to assign permission to choose the access. 3.Assign “None” to the collaborator group, “Reviewers”. 4.Click on “Save” button. You may also revoke the access by deleting the collaborator group.

16. 16 Need More Information? NCI is developing an extensive knowledge base to support various NCI molecular analysis tools. Visit the Molecular Analysis Tool Knowledge center: https://wiki.nci.nih.gov/x/R5GNAg For more information on MAGE-TAB format files, read MAGE-TAB Files at https://wiki.nci.nih.gov/x/zZCNAg A short video demo is available titled “Load MAGE-TAB Data into caArray” at https://wiki.nci.nih.gov/x/GZGNAg in the attachments https://wiki.nci.nih.gov/x/GZGNAg Have a caArray question? Find the answers in the caARRAY FAQ at https://wiki.nci.nih.gov/x/b5GNAg https://wiki.nci.nih.gov/x/b5GNAg New more help? Post in caArray Forum (https://cabig- kc.nci.nih.gov/Molecular/forums/viewforum.php?f=6).caArray Forum https://cabig- kc.nci.nih.gov/Molecular/forums/viewforum.php?f=6