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For Help with AFT BioMS, please call toll free number, 1-855-642-4667 OR email the AFT BioMS Help Desk Team at aftbiomshelp@bmiTeam aftbiomshelp@email.wustl.edu

 AFT BioMS User Manual

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The Alliance Foundation Trial (AFT) Biospecimen Management System (BioMS) is a web-based application that has been designed to support biospecimen tracking, inventory management and reporting for all Alliance Foundation sponsored clinical trials and companion correlative science studies.

Supported Browsers and Versions

Windows

• FireFox

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• version  v91.1
• Chrome version v102.0

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• Microsoft Edge  v102.0

Note: Microsoft Internet Explorer v11is no longer supported. 

Mac

• Safari 10.1
  

User Privileges

The AFT BioMS application allows access to certain functions based on the privileges assigned to the user log in ID and password. For example, only a user with administrative privileges can edit or build studies in AFT BioMS.

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1. Navigate to AFT Portal: https://alliancefoundationtrials.org/
2. Click on Research Staff Login at the top right side. Please see Login screen shot-1 below.
3. Enter your AFT Portal Login credentials. This will be your email address associated with your AFT ID and your corresponding password.
4. Once you are logged in, AFT Portal Home page would be displayed.
5. Please select the site from the top right menu option " My Sites" Please see Login screen shot-2 below
6. Once the site is selected, all applications applicable to that site will be displayed under the App Launcher
7. Select BioMS Application and that should launch the application with you logged in.
8. If you are a first time user of AFT BioMS, then you will be directed to complete a quick training. At the completion of the training, once you indicate that training has been completed, AFT BioMS application will be launched.

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Login screen shot-1

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Login screen shot-2

How to Log Out

1. Select the Logout icon shown at the top of every screen.
   
   

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Forgot Password

Just in case if you don't remember the password or your password has expired, you can reset the password by using the following link. https://alliancefoundationtrials.org/forgot-password

Once you enter your email address associated with your AFT ID and the text verification, you will be asked to answer one of the security questions. Once you successfully enter the required information, you will receive a password reset link through your email to reset your password.

User Account Issues

In case of unexpected issues related to login, please contact AFT BioMS Help Desk.

Logging a Specimen

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1.  Set the status of the Original sample to "Not Collected" in order to activate the Alternate sample.Click on the Not Collected icon in line with the original sample.
2. A pop up window titled "Mark Specimen as Not Collected" will appear. 
3. Select a reason from the drop down menu in the pop up window that best describes the reason.
4. You can free text additional information in the box provided next to "Describe".
5. Click Save.drop down menu in the pop up window that best describes the reason.
6. You can free text additional information in the box provided next to "Describe".  Click Save.
7. Now, the Alternate specimen will be enabled for Collection 

Please see the screen shots below explaining the same

Step-1

Mark the Primary specimen  as Not Collected by clicking on the icon as shown below. 

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Step 2: The below box will pop up. Click the below drop down to enter the reason for not collecting Primary specimen. 

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Step 3: Select the appropriate reason from the drop down

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Step 4: Click save button 

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Result:  You will now be able to select the Alternate item and include it on the shipping manifest.

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Adding a specimen Collection for a Recurrent Event

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On the right side of the Manage Shipments page, all the shipments that have status of "Not Shipped" or "In Transit" are displayed.  If a specific Repository was selected, only those shipments going to the selected Repository will be displayed, if not, the default view will display all shipments that are not shipped or in transit from your site.Menu buttons at the top of the list will allow users to Create, Send, Delete, Print or Edit shipments. Displayed next to each shipment is the unique shipment identifier, the ship to information, the shipping method, and the status.  A box icon that appears to be open denotes a shipment status of "Not Shipped". A box icon that appears to be closed denotes a shipment status of "In Transit".

Adding Specimens to a Shipment

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1.   Locate the specimen you wish to add to a shipment
2.  Click the box next to the specimen ID.
3.  Click the green arrow in the floating box between the Specimens and Shipments sections that is pointing right, towards the shipments
4. To verify the shipment that contains the specimen, click on the drop down arrow next to the shipment. AFT BioMS will display a list of all specimens contained in that shipment.  Once a specimen has been placed in a shipment, it will no longer appear on the table of specimens pending shipment.

Using the Manual Method: 

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1. Go to Manage Shipments page.
2. Select the radio button next to the the shipment to be shipped.
3. Click the Send button.
4. AFT BioMS displays the packing slip for the selected shipment. The Packing slip will have the unique shipment identification number at the top of the page along with basic instructions.
5. Fill in the required fields.
6. Click on the calendar icon to enter the date of shipment.

7. Review the packing slip for completeness.

8. Review the Contents of the shipment.

9. Click on the Send shipment button. A message will be displayed indicating the "Shipment has been Shipped Successfully."

10. Click on the Print button, print the packing slip, and place it in the shipping box with the specimens. 

    
    

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1. Click on the black down arrow located next to the the number of samples in the shipment. A list of the samples contained in the shipment will be displayed.
2. Click the box next to the sample to be removed from the shipment.
3. Click the green arrow that is pointing left towards the Specimens list.
4. The specimen will be removed from the shipment and placed back on the Specimens pending shipment list.

To delete shipment

1. Remove any specimens contained in the shipment.
2. Click on the radio button next to the shipment you wish to delete
3. Click Delete.

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 Add Specimen Requirement

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1. Select the desired Collection Event from Study details tree.
2. Select the Add Specimen Requirement button.
3. Several mandatory fields must be completed on the page.
   1. In the Title field, enter the name of the specimen.
   2. In the Class field, use the drop down menu to make a selection
   3. The drop down menu for the Type field will vary based on what Class was chosen
   4. Select the Anatomical site the specimen was collected from.
   5. Continue on to the Laterality of the collection site, and Pathological status fields and select the appropriate response from the drop down menus associated with these fields
   6. Enter the Quantity in the Quantity field, and choose a Tube type if applicable from the drop down menu.
   7. The Concentration field will be grayed out unless Molecular was selected for the Class of the sample
   8. If a Specimen form is required with the sample, select it from the drop down menu and click the plus sign next to the field under the drop down menu.
   9. Refer to the Study protocol and enter any special specimen Preparation Instructions.
   10. The Alternate specimen field is utilized to enter any alternate specimens that may be collected if the originally required specimen is not available
   11. In the shipping requirements section, choose the Shipment site you are shipping the specimen to from the drop down menu.
   12. Choose a Shipping method from the drop down menu. Refer to the study protocol and enter any special Shipping instructions in the designated field
4. Click on Submit.  
5. AFT BioMS adds the specimen requirement to the selected collection event.
6.  Select Save study to ensure that newly added specimen requirements are saved. 

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1. Navigate to the desired collection event that is coincident with the event of the associate study.

2. Begin by clicking on the Collection point event that is designated as a Coincident event from the Study details tree.
3. Click on "Co-incident event" next to the Event label field.
4. AFT BioMS will display a pop window with screen titled Co-incident Event Map
5. Click on the radio button next to the event to be designated at coincident
6. Click OK at the bottom of the pop up window to close and save the selection.
7. Click Submit
8. Save study to ensure the Coincident event was saved

    
   

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   Note: To add coincident events, the selected study must have at least one associated study

   
   

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1. Select the study to be updated from the search table.
2. Click on the Specimen requirement for which the Alternate specimen to be deleted in the Study details tree.
3. From the Add Specimen requirement page, navigate to the Alternate specimen(s) section.
4. Highlight the Alternate specimen in the box that is to be removed.
5. Click on the "-" icon next to the box. The Alternate specimen will be removed from the box. Please be aware that there will not be a pop up window asking for conformation as occurred when deleting an Epoch or Arm.
6. Click on the Submit icon located at the bottom of the page.
7. Click on Save Study. The Alternate specimen will be deleted and the changes will  be visible in the Study details tree.

 

AFT BioMS to OpenSpecimen Synchronization

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• Coincident Epoch
• Coincident CPE
• Alternate Specimen
• Equivalent Specimen
• Specimen Requirement - Tube Type
• Specimen Requirement - Repository
• Specimen Requirement - Shipping Type
• Specimen Requirement - Specimen Forms
• Specimen Requirement - Preparation Instruction
• Specimen Requirement - Shipping Instruction

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    6. Click Submit. System will display the newly created Specimen Collection kit under the specimen collection kit list. 

How to request a specimen collection kit

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1. Log into BioMS
2. Navigate to Log Specimens under Tasks
   
3. Search for a patient using Patient ID, patient initials or Study Id
4. Click on the patient Initials from the search results
5. System displays the specimen checklist for the patient
6. Click on the open form button with the red exclamation mark (!)
   
7. A Specimen attachments window pops up
   
8. Fill in the mandatory fields surgical pathology number and block Id
9. Add the necessary attachments and comments and click save
10. The Specimen attachments and the surgical pathology information will be saved.

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