Office of Human Research Affairs


Protocol Application & Tracking System (PATS)
Frequently Asked Questions (FAQ)

Below is a list of Frequently Asked Questions, divided into the following sections:

General | Submission | Applications | Conversion | Informed Consent Documents | Progress Reports | Amendments


AE = Adverse Event
CCI = Committee on Clinical Investigations
IRB = Institutional Review Board
KP = Key Personnel
MMC = Montefiore Medical Center
PR = Progress Report
PRC = Protocol Review Committee


I forgot my username and/or password - what should I do?
If you forgot your username, email Sathya.
If you forgot your password, click here to request a new one.
I want to let my secretary, research coordinator, or student have access to my protocols in PATS. What do I do?
Fax (718-430-8817) or email Sathya with a message naming the individual(s) whom you wish to authorize as your "PATS Delegate". NOTE: Only individuals who are trained in PATS may be assigned as delegate. For information on PATS training, click here.
Will the MMC IRB accept the printed forms from PATS?
What internet browser(s) can I use? I know I need to download Internet Explorer, but how do I do that?
Microsoft Internet Explorer (versions 6.0-8.0) is the only compatible browser.
(Download IE) As no compatible version of Internet Explorer is  available on the Mac, a PC is required.
After logging into PATS, it freezes - I can't expand any of the menu categories (e.g. "Applications," "Maintenance," or "Login/Logout").
The most likely cause of this problem is the use of a browser other than Internet Explorer 6.0-8.0. If you believe that this is not the problem, confirm that you are using Internet Explorer 6.0 or higher, then contact Sathya.
I'm unable to start a new Amendment/AE/Progress Report (or edit an existing one) even though I have an approved protocol. What's wrong with PATS?
There are two likely explanations:
  • The transaction you are trying to start was already started.  Solution: Try clicking on "Edit" instead of "New"
  • Your browser is caching (storing) outdated information.  Solution: Change the Internet Explorer settings to eliminate this problem.  Step-by-step directions for IE 8.0 are available.
How do I find out what my CCI # is?
As soon as you create a new application, a CCI # is assigned. It is displayed near the top of the application form, as well as on the printout. In PATS, CCI #s now have a 4-digit year, but retain the 3-digit serial number (04-123 is now 2004-123). Numbers that follow a second hyphen (e.g. the 001 in 2004-123-001) are sequence numbers specific to the transaction.
NOTE: If you submitted a grant to the CCI for a "Pending" signature, we will have assigned a CCI # for you. Look for the CCI # on the CCI Grant Application Form (or on the Internal Grant Approval form).


What do I need to submit, and how many copies?
Though PATS is an electronic, online system, signed printouts of all transactions are required. The specific requirements for each transaction are listed below:

New Applications: 

  1. The CCI's regularApplication Submission Requirements apply.


  1. The CCI's regularAmendment Submission Requirements apply.

Internal Adverse Events:  

  1. Adverse Event Form
  2. Copy of Report to Sponsor, if required

External/Group Adverse Events:  

  1. Adverse Event Form
  2. Backup documentation (e.g. Sponsor's Report)

Progress Reports (Submit Original and 3 Copies): 

  1. Signed Progress Report Form.
  2. Conflict of Interest Disclosure Forms. The PI and each of the Key Personnel must complete and sign a separate COI Form. Key Personnel include staff assigned to work on the protocol at any of the following institutions: AECOM, MMC, JMC, or NCB. (NOTE: On the Print page for the Progress Report form, there is a "COI" button which will produce a COI form for for the PI and each Key Personnel required to sign one.
  3. Full Review Protocols:
    1. Copy of the Summary, Risks, and Benefits.
    2. Adverse Event documentation.
    3. Summary of all protocol amendments since the study was first approved by the CCI.
    4. If an internal DSMC has been established, attach all DSMC reports.
  4. If an HHC facility is included, attach an updated HHC-641 with current budget and original signatures if the source or level of funding has been modified.
  5. For protocols that are being performed in collaboration with other sites/institutions/ individuals/laboratories, approval by the respective IRB is required. For this purpose, collaboration is defined as the (a) transfer of specimens to or from another institution; (b) inclusion of patients from another institution; or (c) transfer/subcontract of sponsor funds. In these cases, a copy of the current collaborating institutional IRB approval of this study must be included.
My protocol was converted to PATS (or the protocol was initially submitted using PATS), and now I need to submit a transaction (e.g. Adverse Event, Amendment, Progress Report, etc.). Can I send in the MS-Word form from the CCI website?
No. Once a protocol is in PATS, all transactions must be submitted electronically using PATS.
What are the deadlines for PATS submissions?
Full Review applications and amendments must be submitted by out deadlines, as outlined here. Exempt and Expedited applications may be submitted at any time. Progress reports are due by the due date specified in the Email Progress Report Notice.
I filled out an AE, but it doesn't show up in the list to submit/print/edit.&nbp; Where did it go?
This problem generally shows up on older computers. The only solution we have is to complete the AE in a single session. While still on the AE Form screen, complete the following steps:
  1. Save the AE. (Reminder: Do NOT leave the AE Form page.)
  2. Run the error check and fix any errors you may have.
  3. Click the "Submit" button on the AE Form screen. This will re-run the error check and, assuming you are error free, allow you to click the final "Submit" button to transfer the AE to us electronically.
  4. Return to the AE Form (by clicking the Return button on the Submission screen).
  5. Click the "Print" button to bring up the print-view of the AE. You should find the current date next to the "Date Submitted" text near the top of the page.
  6. Have the PI or other qualified individual sign the AE and send it to us.


I want to apply for a grant (on a new protocol) ... what do I do?
Follow our current procedure (which can be found here). In addition to the Grant Accounting face page, you must bring a completed CCI Grant Application Form to the CCI, and the grant will be signed "pending." A CCI # will be assigned. When the grant receives a "fundable score," an application (with the complete grant) must be submitted to the CCI for review. Use the application that was started by the CCI when you originally brought in your grant. (In PATS, for full/expedited review studies, go to "Applications | New/Edit Protocol," select the Investigator name and application type, click on "Edit Application," select the CCI # from the list on the right side of the screen, then click the "Continue" button at the bottom of the page.)
How do I submit a protocol, advertisement, etc.?
At this time PATS does not have an attachment feature, so all application components (except Informed Consent Documents and HIPAA forms) must be submitted on paper. For details, see the Submission section.
What is the procedure for submitting PRC studies?
Complete the CCI application using PATS. After completing the application, ensure that your application passes the Error Check, but do not submit electronically. Instead, use the PATS "Print" feature to print the application and submit it to the PRC. If the PRC requires changes, make them in PATS, then resubmit to the PRC. Once the PRC approves your protocol, electronically submit the application to the CCI.
Help! I started filling out one type of application (e.g. Chart Review), but now I realized I need a different type of application (e.g. Behavioral). How do I change the type?
The CCI has the ability to change your application type for you. This feature is only available before approval. If you encounter this problem, contact the CCI immediately.
I completed my application, but when I run the error check, it says "Informed Consent Documentation, Alteration or Waiver - When informed consent will be obtained, the protocol application can NOT be submitted until the ICD's are entered into PATS. To do so, return to the 'Applications' menu and click on the 'Assent/Consent Form' button." What does this mean?
This error message means that you have indicated in your application that you are obtaining Informed Consent. PATS produces this error when no ICDs have been included in the application. If you are completing a new applicaion, add the ICDs. If you have your ICD(s) in MS-Word (e.g. if you're converting or if you have a sponsor's ICD) click here.

NOTE: If you are obtaining Oral Informed Consent, you must include the script that you plan to use for obtaining consent.


How does conversion work?
There are several steps to conversion. On an approximately quarterly basis, the CCI selects investigators to be converted. As the conversion is prepared, the investigators are notified that they will be a part of the upcoming conversion and must signup for training. (Anyone who works on any CCI transactions for an investigator must be trained.)

The basic information in the applications (e.g. CCI #, title, funding sources, protocol sites, Internal Adverse Events, etc.) are converted through an automatic process. However, a lot of information cannot be automatically converted, and the responsibility for both auditing the automatically converted data as well as populating the missing fields rests with the researchers.
Where are my converted protocols?
After logging in, expand the "Applications" menu category (click on the plus [ ] sign) in the System Menu, then click on "New/Edit Protocol." In the main window, select the investigator's name from the "Investigator" drop-down menu, then select the type of Application. Next, click on the "Edit Application" button and a list of your protocols will appear in the "Application Selection" menu. Click on the CCI Number, then click the "Continue" button, located at the bottom left of the screen.
How do I get my Informed Consent Documents into PATS?
Follow the instructions for Converting ICDS from MS-Word to PATS.

Informed Consent Documents (ICDs)

Every time I try to access the ICD Editor, I either get errors or nothing loads at all. What am I doing wrong?
The most likely cause of this problem is the use of a browser other than Internet Explorer 6.0+. If you believe that this is not the problem, confirm that you are using Internet Explorer 6.0+, then contact Sathya.
How can I email my ICDs to other people/sites/etc.?
Currently, there is no built-in feature to email ICDs, however you can copy the entire text of the ICD. To do so, click the "Print Preview" icon, highlight the entire document (Ctrl-A), copy the document (Ctrl-C), then switch to another document editor (e.g. MS-Word) to paste into (Ctrl-V).
IMPORTANT NOTE: If you paste into MS-Word, the HTML code that allows the help text to disappear during printing will be changed. If you paste blue text (help text) from MS-Word to the ICD Editor, the text will appear blue, but will NOT disappear during printing.
How do I add a Spanish Consent?
Step 1: Start an Amendment in PATS, and enter the Spanish ICD. If it exists in MS-Word, you can paste the text into the ICD Editor, however you must follow the instructions for Converting ICDS from MS-Word to PATS. Submit the PATS Amendment.

Step 2a: If you had your English ICD translated by a translating service, print out the PATS Amendment and mail it with a copy of the PATS SpanishICD as well as the official translated copy.

Step 2b: If you are using the "back translation" method, print out the PATS Amendment and mail it with a copy of the PATS Spanish ICD as well as the back translation, names and credentials of the translators. NOTE: Do NOT input the "back translation" into PATS.
How do I insert special characters into my document?
You may copy special characters from this page.

Progress Reports (PRs)

I used to be able to include certain changes to my application (e.g. adding or removing Key Personnel) in my Progress Report. How do I do that now?
Any and all changes to the Application/Protocol must be done through an Amendment.
Last year's PR would be so helpful in completing this year's. Where can I get a copy of it?
If last year's PR was completed in PATS, you can use PATS to access it. Go to the PR section of PATS, then access your past PRs through the "Print Progress Report" button. If more than one of your CCI number appear (e.g. 2006-123-001 and 2006-123-002), choose the latest one (e.g. 2006-123-002). The lower numbered ones would be PRs from prior years.


How do I add KP to my approved protocol?
  1. Start an amendment. (If you have already started an amendment, access it, then continue below.)
  2. On the "New/Edit Amendments" screen, add the addition of Key Personnel to the "Amendment Justification/Explanation & Protocol Changes" box.
  3. Click on the "Application Amendments" button.
  4. In the application, scroll down to the orange "Key Personnel" button.
  5. On the KP page, make sure you are in "Add" mode (i.e. that the "Add" button is lit up).
  6. Select the name of the KP in the "Name" pull down menu. (NOTE: If the individual you wish to add is not listed, click the link to request an addition to the master list of KP. Wait for an email back indicating that the individual has been added. This may take up to 1 business day.)
  7. Verify the entries for the individual's Payroll, YU School, and Department are correct.
  8. Enter the KP's "Role in Study"
  9. Verify that the Individual completed the Training requirement.
  10. Click on the "Save" button.

Still have questions? Ask Sathya!

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