AFT BioMS User Manual

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

 AFT BioMS User Manual

Supported Browsers and Versions

Windows

• FireFox version  v91.1
• Chrome version v102.0
• Microsoft Edge  v102.0

Note: Microsoft Internet Explorer is 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.

Site specific access

AFT BioMS also restricts user access to information based on the site and studies associated with the users log in ID and password. For example, a CRA from site 1 will only see patients registered to site 1 for the studies they have access to.

How to Log in

Please note that starting in 2017, AFT BioMS users would have to access the application through AFT Portal

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.

Login screen shot-1

Login screen shot-2

How to Log Out

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

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

1. Select Log Specimens from task menu.
2. Search for a patient based on the registration ID.
3. Choose your patient from drop down list & click Search.
   
4. Click on the patient initials. You will be taken to the specimen checklist for the patient.
5. Click on the Check box under the collected column. When the check box next to the specimen is clicked, AFT BioMS will populate the collection date with current date and time.
6. Click on the Calendar Icon to adjust the date and time.
7. Click Save. Status will now be changed to 'Collected' and the specimen is ready to add to a shipment.

Change specimen status from Collected to Pending

1. Click the check box to remove the check mark
2. Click Save. The specimen status will return to Pending. 

Mark a specimen as Not Collected

1. Select the Not Collected icon under the Actions column in the Specimen Checklist.
2. Select a reason why the specimen was unable to be collected from the drop down menu.
3. Enter a free text description of additional information  if needed
4. Click Save. AFT BioMS will update the specimen status to Not Collected.

Re-collect a specimen or Collect a specimen with a status of Not Collected

1. Click on the  Re-collect icon  under the Actions column of the Specimen Checklist. 
2. A pop up window will appear asking if the user would like to re-collect the specimen.
3. Click Yes. AFT BioMS will set the status of the specimen back to Pending.

Collecting the Alternate Specimen

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".  Click Save.
5. 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. 

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

Step 3: Select the appropriate reason from the drop down

Step 4: Click save button 

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

Adding a specimen Collection for a Recurrent Event

1. To add an additional specimen collection event, click on the 'Add More' button.
2. A message will be displayed asking the user to confirm the action.
3. Select Yes.
4. A new collection event will now be displayed that will be denoted by a [2].
5. Click on the "+" sign next to the collection event to access the specimen collection field for the added specimen. The specimen can now be logged as collected and set up for shipment.

Manage Shipments

To create a shipment for collected specimens, or to manage shipments already created with a status of "Not Shipped" or "In Transit",

Select Manage Shipments from the Task Menu.

The Manage Shipment Home Page default view will display all specimens that have been collected within the last 30 days that are pending shipment from your site.  All shipments that have a status of  "Not Shipped" or "In Transit" from your site will also be displayed.

To narrow the list of specimens viewed on the page, the user can select options from two different drop down menus located on the page.

To view specimens and shipments being shipped to a specific repository, a drop down menu located at the top of the page allows the user to select a specific Repository.  For example, if  the PCO Repository is selected,only those specimens pending shipment to the PCO Repository, and the shipments in transit and pending shipment to the the PCO Repository will be displayed.

To view specimens collected within a certain time frame, the user can select to view specimens collected from the current day, last 3, 7 or 30 days or all pending specimens from the drop down menu located at the top of the Specimens table.

On the left side of the Manage Shipments page a table is displayed that contains all specimens pending shipment from your site based on the options that were selected above, or if no options were selected, the default of all specimens pending shipment in the last 30 days will be displayed. The table has four columns.Under the "ID" column is the unique specimen identification number. The "Specimen" column displays the type of specimen.  The "Patient" column contains the patient registration identification number and initials, and under the "Study" column, the study protocol number is listed.

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

Shipment of samples in AFT BioMS is set up to accommodate multiple users at the same site.Since all specimens and shipments that are pending from the site are listed on the Manage Shipments page, CRAs can batch their samples with other CRAs from the same site that have samples shipping to the same repository by the same shipping method. 

Specimens can be added to a shipment using two different methods.

1. The Auto method is the default method. 
2. The Manual method gives the user more control over what shipment their specimen is added to.

Using the Auto Method: 

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:

Complete the steps below to place a specimen in a shipment using the Manual method:

1. Select the radio button next to a shipment that has a status of "Not Shipped" and matches the shipping requirements of the specimen(s) you wish to ship.
2. Select the radio button next to Manual in the floating window between Specimens and Shipments.
3. From the list of specimens pending shipment, locate the specimen or specimens you wish to manually add to a shipment and click the box next to the specimen ID.
4. Click the green arrow in the floating box between the Specimens and Shipments sections that is pointing right, towards the shipments
5. AFT BioMS will place your sample(s) into the designated shipment and the specimen will no longer appear on the table of specimens pending shipment.
   
   

How to create new shipments

A new shipment can be created by two different methods.

1.  Create a shipment from an existing shipment which will result in a shipment with the same exact ship to and ship method as the existing one the shipment was created from.
2.  Create a completely new shipment with user defined ship to and ship method.

  To create a new shipment from an existing shipment

1. Select the radio button next to the shipment you wish to create.The status of the existing shipment can be either "Not Shipped" or "In Transit". Make sure the shipment has the correct ship to and ship method that is required for the specimen.
2. Click on the Create button. Confirm the information in the pop up window and click Submit.
3. A new shipment will be created with the same ship to and ship method. The shipment will have a new unique shipment identification number.

  To create a New Shipment with user defined Ship to and Ship Method

1. Select the Create button.When the Confirm Shipment Details Window appears, select the location the shipment is to be shipped to from the drop down menu.
2. Select the desired Shipping Method from the drop down menu.
3. Click the submit button after you have selected the desired ship to and ship method information.
4. AFT BioMS will create a new shipment with the desired shipping criteria and unique shipment identification.

Sending a Shipment

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.

    
    

Edit or Delete a Shipment

To remove specimens from a shipment with a status of Not Shipped

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.

To edit a shipment with the status of "In Transit"

1. Set the status of the shipment back to "Not Shipped".
2. The shipment can be edited by following the steps above for editing a shipment with a status of "Not Shipped".

To change a status of a shipment that is In Transit back to Not Shipped

1. Click on the Radio button next to the shipment with the status of In Transit that you wish to edit.
2. Click the Edit button. AFT BioMS will display a pop up asking the user to confirm the edit of an In Transit Shipment.
3. The status of the shipment will be changed to Not Shipped. The shipment can not be edited utilizing the steps for editing a shipment with a status of "Not Shipped"

Search Feature

The AFT BioMS Search panel lets you search quickly for patients, specimens and shipments.  After selecting the desired patient, specimen or shipment, the user will be able to view study information and specimen details on the Specimen checklist.

 Search for a Patient

1.  Select Patients  in the Search panel on the left side of the screen. AFT BioMS will display the Patient Search home page.
2. From the Patient Search screen, initiate the search for the desired patient by choosing one of the three options listed in the pull down menu:
   
   1. Registration ID: Registration ID (also called Alliance ID) is assigned during patient study Pre-registration or Registration in OPEN. When you start typing the Registration ID, AFT BioMS suggests a list of Registration IDs that contain the letters or numbers entered. Select the desired Registration ID from the suggestions and select Search.
   2. Patient Initials: To search for a patient by initials, enter the first letter of the patient initials. AFT BioMS will display a list of patients that contain the entered letter. From the list of suggestions, select the desired patient and select Search.
   3. Study ID: Study ID is also called Study Number or Alliance Study number. Start typing the Study ID and AFT BioMS suggests a list of studies that contain the entered value. From the suggested studies, select the study to which the desired patient is registered.

Search for a specimen

From the Search panel select "Specimens". Search for a specimen to view details about the specimen on the Specimen checklist including collection status, shipment status, and patient information.

Search for specimens by choosing one of two methods from the drop down menu:

1. Specimen ID:  Begin by typing the Specimen ID. AFT BioMS will suggest a list of specimens that contain the values the entered. Select the desired specimen ID and click Search. AFT BioMS will display a table with information about specimens related to the selected specimen ID.

2. Patient ID:  Begin by typing the Patient ID. AFT BioMS will suggest a list of patients that contain the entered ID. From the suggestions, select the desired patient ID and click Search. AFT BioMS will display a table with information about specimens related to the selected patient ID.

Search for a Shipment

1. Click on Shipments in the Search panel on the left side of the screen. AFT BioMS will display the Shipment Search home page.
2. Search for shipments by selecting one of  the following options from the drop down menu:
   1. Shipment ID:  Enter the Shipment ID, AFT BioMS suggests a list of shipments that contain the entered values. From the suggestions, select the appropriate shipment ID and click Search. AFT BioMS will display a table that contains details related to selected shipment.
   2. Ship To:  Enter in the name of the Bio Repository the shipment was sent to. AFT BioMS will display a table that contains all shipments that have been sent from your site to the selected Bio Repository.
   3. Contains Specimen ID: If you know the Specimen ID, you can search for the shipment that contains that specimen. This option is useful if you are a Repository receiving specimens, have a specimen in hand with a Specimen ID, and want to look up the Packing Slip and shipment information regarding the specimen. Enter the Specimen ID and click Search. AFT BioMS will display a table with information about the shipment that contains that specimen.  The screen shot below is an example of searching for a shipment by using the specimen ID.

In addition to the methods described above, a general search can be done by selecting a search option, leaving the search field blank and clicking Search.  AFT BioMS will display a list of all shipments that are accessible from your specific site.

Viewing the Specimen Check List

The Specimen Checklist is a list of specimens that have been collected or may be collected for a patient registered to a study. Staff at collecting sites use the Specimen Checklist to "log" a specimen by recording that the specimen was collected on a certain date. For repository users, the Specimen Checklist displays in "view mode" only. Repository staff cannot log a specimen on behalf of a collecting site.

To view the Specimen Checklist for an individual patient

1. Initiate a search for the patient from the Patient Search home page.
2. When the Patient search results appears, select the Patient initials to open the Specimen checklist.

Adding, Editing & Deleting

 Add Study

1. Select Search/Manage Study located under the task menu of the AFT BioMS home page.
2. The Study details tab will be highlighted by default. 
   
3. Ensure the default tabs of Add and Study details are highlighted to begin building a new study.

4. Enter in all the required information in the designated fields of the Study details screen

5. Click on the submit button.

6. AFT BioMS will display a message indicating the the Study has been created successfully.

7. The newly created Study number will appear in the study details column to the left of where the original information is entered. 

Adding Epochs

Epochs are general groupings within the study. Within each Epoch there may be one or more Arms which contain Collection Events. Examples of Epoch names could include, but are not limited to Pre-Therapy, Therapy, and Post Therapy.

To add an Epoch,

1. Click on Add Epoch next to the Submit button.
2. AFT BioMS will display a page where Epochs can be added.
3. Enter the name of the epoch under the Label column.
4. The second column titled Sequence is a field to enter the order in which the epoch should appear in the study build tree.
5. More epochs can be added by selecting the Add more button at the top of the Add Epoch page.
6. Additional lines will appear to accommodate the names and sequence number of all the epochs required for the study.
7. Please note that no two epochs within the same study can have the same name. 
8. When finished with entering the names and sequences of the epochs, hit Submit. 
9. The information will populate in the Study details tree.
10. Click Save study.

 Add Study Arms

An Arm of a study is a group of collection events that occur under an Epoch. Each Epoch contains one or more Arms. For example, under the Therapy Epoch, there could be two different arms, each representing a different type of therapy the patient is on.The specimens collected would depend on which Arm of the study the patient is participating in.  If an Arm is represented as "ALL" it indicates that all arms of the study have the same collection events.  To add an Arm to a study Epoch,

1. Select the Epoch from the Study details tree.
2. Under Add Arm(s), a field is available to enter the name of the arm. Enter the name of the Arm.
3. If you have more than one Arm to add to the Epoch, click on the Add more button.
4. When finished adding Arms, click the submit key. 
5. A message will appear stating that the Arm(s) were added successfully and the created Arm(s) will appear in the Study details tree.

 Add Collection Event

1. Select the desired Arm from the Study details tree and select the Add Collection Event button.
2. Enter a name of the event in the Event label field.
   
3. Click the box next to Recurrent if it is a recurrent event.
4. From the Clinical status drop-down select a clinical status. If the clinical status is not known, select the default of Not Specified.
5. Enter the collection point in the study in days in the Calendar event point field. If the collection point is not known, enter a value of zero (0).
6. In Clinical diagnosis field, enter the same diagnosis that was entered when the study was created. Begin typing the clinical diagnosis and AFT BioMS will suggest a list of values that match the entered text. From the suggestions, select  the correct clinical diagnosis and click submit.
7. The Collection event will now appear in the Study Details tree. The Collection events will be displayed in the Edit Arm screen each time you click on the Arm in the study tree.
8. Repeat the steps above for each Collection event that is required for each arm of the study.

 Add Specimen Requirement

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. 

 Add Alternate Specimen

1. Select the desired specimen requirement from the tree structure and navigate to Alternate specimens section and click on the "+" icon.
2.  AFT BioMS will display the Add Alternate Specimen screen.Enter in all information about the alternate specimen using the same steps described above for adding Specimen Requirements.
3. Click on Submit.
4. You can add additional alternate specimens to a Specimen requirement by repeating the steps above.

 Adding an Associate (companion) study

1. Click on the Associated study(s) tab from the Build study page.
2. AFT BioMS will display a screen with a drop down menu from which you can select and add associate studies to the parent study.
3. Select the associate study from the list and click the "+" sign.
4. Click on the Study details tab. AFT BioMS will return to the main study build screen.
5. Click on the Submit icon.
6. Save the study.

 Add Coincident Events

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

   
   

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

Add Equivalent Specimens

Equivalent specimens can be added to a Specimen requirement if the Collection event of that Specimen requirement is also coincident event with an associated study. To add an equivalent specimen to a specimen requirement,

1. Select the specimen requirement from the Study details tree.
2. Click Add Equivalent specimens at the bottom of the Add Specimen Requirement page. AFT BioMS will display a pop up window with the study trees of both the main and associate studies. 
3. Expand the tree of the main study to view the specimen requirement that is to be linked as equivalent with the coincident event of the associate study.
4.  Expand the study tree of the associate study if necessary to view the sample requirement that is to be marked as equivalent.
5. Click the box next to the specimen.
6. A check mark will appear in the box indicating that it has been designated as an equivalent specimen to that of the same specimen in the main study.
7. Click on Save to close the pop up window and save the selection.
8.  Repeat the steps described to add additional equivalent specimens to other coincident event.
9. Click on Save study under the Study details tree when finished. 

Adding Specimen Requirement Groups

1. Click on the Collection event that contains the Specimens that are to be grouped together.
2. From the Add Collection Event screen,navigate to the center of the page and click Add next to Specimen Requirement Groups.
3. Under Group label, enter a name for the group.
4. From the drop down menu,choose the specimens to be included in the group and click the "+" sign to add them to the box below the menu.
5. Click submit when all required information has been entered.
6. To add additional Specimen requirement groups, repeat the steps above for each Collection event that a group is to be added.

Editing a Study

 Search for a Study

1. After log in, select Build Study from the Tasks menu.
2.  Click on the Edit tab.

3. BioMS displays the Search Study page. Search results are displayed in table form. The table displays the Study ID, Study Title, and the Study Status.

4. Regardless of the search method used, the study can be accessed by clicking on the Study ID displayed in the search table. A drop down menu provides the user with two different methods to search for a study. The methods are:

• Study ID: Study ID is also known as the Study Number or Alliance Study number. Begin by typing the desired Study ID into the search field. AFT BioMS will suggest a list of studies that contain the values entered. From the list of suggested studies, select the study to to be edited and click Search. When the Search table appears, click on the Study ID number.

• Study Title: Type the first few letters of study title in the search field. AFT BioMS will  suggest a list of studies that contain the entered text. From the list of suggestions, select the desired study and select Search.  When the Search table appears, click on the Study ID number.

An alternate method to use when Searching for a study is to click on the Search icon without entering any search criteria. AFT BioMS will display a list of all studies available in the search table. Locate the desired study and click on the Study ID.

Editing Study Information

The Title, Start date, Activity status, Principal Investigator and Clinical diagnosis information for a study can be edited.

1. After selecting the study to edit from the search table, navigate to the field that needs to be updated from the Study details page.
2. The Study title can be updated or corrected as needed by entering the information directly into the Title field.
3. The Start date of the study can be edited by selecting the correct date from the calendar icon, or typing in the date in correct format.
4. Update the Activity status by selecting the new status from the drop down menu.
5. Select the correct PI using the drop down menu.
6. Add or remove items from the clinical diagnosis field as needed.
7. Click on Submit when finished
8. Click on Save Study.

Editing an Epoch

1. After selecting the study to edit, click on the Epoch to be edited in the Study details tree.
2.  To edit the Name of the Epoch, update the Label field with the new information.
3.  Click on submit. The updated Epoch name will be saved, and the change will also be reflected in the study details tree.
4.  Click on Save study to save all updated information.

Adding or Deleting an Epoch

1. Select the study to be updated from the search table.
2. Under the Edit tab, add additional Epochs. New Epochs can be added to a study even after patients have been enrolled in the study.

To delete an Epoch

1. Select the study to be updated from the search table.
2. From the Study Details page click on Add Epoch.
3. Click on the box next to the Epoch to be deleted. A pop up will be displayed asking the user to confirm the action of deleting the Epoch and all arms collection events associated with it.
4. Click on yes to close the pop up. The Add Epoch(s) page will reflect the deleted Epoch.
5. Click Submit
6. Save Study.

Editing an Arm

1. Click on the Arm to be edited in the Study details tree.
2. To edit the Name of the Arm, update the Label field with the new information.
3. Click on submit. The updated Arm name will be saved, and the change will also be reflected in the study details tree.
4. Click on Save study to save all updated information.

Adding or Deleting an Arm

1.  Select the study to be updated from the search table.
2. Under the Edit tab, add additional Arms. New Arms can be added to a study even after patients have been enrolled in the study.

To delete an Arm

1. Select the study to be updated from the search table.
2. Click on the Epoch that contains the Arm to be deleted in the Study details tree.
3. From the Edit Epoch page navigate to the Add Arm(s) section and click on the box next to the Arm to be deleted.
4. Click on the Delete icon and then click Submit.
5. A pop up will be displayed asking the user to confirm the action of deleting the Arm and all collection events associated with it. Click on yes to close the pop up.
6. The Edit Epoch page will reflect the deleted Arm
7. Click Submit
8. Save Study.

Editing a Collection event

1. Click on the Collection event to be edited in the Study details tree. BioMS will display the Add a Collection event screen.
2. To edit the Name of the Collection event, update the Label field with the new information.
3. The Recurrent status of the event can be changed by clicking the box to remove or add a check mark.
4. The user can also edit the Clinical status, Calendar point event and the Clinical diagnosis fields if needed.
5. Click on submit when finished. The updated Collection event will be saved, and the change will also be reflected in the study details tree.
6. Click on Save study to save all updated information.

Adding or Deleting a Collection event

1. Select the study to be updated from the search table.
2. Under the Edit tab, add additional Collections events.
3. New Collection events can be added to a study even after patients have been enrolled in the study.

Delete a Collection event

1. Select the study to be updated from the search table.
2. Click on the Collection event to be deleted in the Study details tree.
3. From the Add a Collection Event page, click on the Delete icon located at the bottom of the screen under the section titled Specimen Requirement groups.
4. The Collection event will be deleted and the user will be taken back to the main Study details page.
5. Click Save study for the change to be saved.
   
   

Editing a Specimen requirement group

1. Select the study to edit,
2. Click on the Collection event that contains the Specimen requirement group to be edited in the Study details tree.
3. AFT BioMS will display the Add a Collection event screen.
4. To edit the Name of the Specimen Requirement group, navigate to the section on the screen titled Specimen Requirement Groups.
5. Update the Group Label field with the new information. The Specimen requirement(s) field can be edited by using the "+" or "-" and the drop down menu to add or remove specimens form the group.
6. Click Submit
7. Click Save Study. The changes will not be visible in the Study details tree, but will be displayed when you click on the Collection event associated with the Specimen requirement group.

Adding or Deleting a Specimen requirement group

1. Select the study to be updated from the search table.
2. Under the Edit tab, add additional Specimen requirement groups.

 To delete a Specimen requirement group

1. Select the study to be updated from the search table.
2. Click on the Collection event that contains the Specimen requirement group to be deleted in the Study details tree.
3. From the Add a Collection Event page, navigate to the Specimen requirements group section.
4. Place a check mark next to the Group label by clicking on the box.
5. Click on the Delete icon located in line with the title Specimen Requirement groups title. Please be aware that there will not be a pop up window asking for conformation as occurred when deleting an Epoch or Arm. The Specimen requirement group will be deleted and the user will be taken back to the main Study details page.
6. Click on Save Study. The changes will not be visible in the Study details tree, but will be displayed when you click on the Collection event associated with the Specimen requirement group.

Editing a Specimen requirement

1. Select the study to edit
2. Click on the Specimen requirement to be edited in the Study details tree. AFT BioMS will display the Add a Specimen Requirement screen.
3. To edit the Name of the Specimen requirement, navigate to the title field.
4. Update the Specimen name as required.
5. Update the Type, Anatomical site, Laterality of site, Pathological status, Quantity, and Tube type if needed.
6. All fields in the Shipping requirements section can also be edited
7. Click Submit
8. Save study.
   
   

Adding or Deleting a Specimen Requirement

1. Select the study to be updated from the search table.
2. Under the Edit tab, add additional Specimen requirements.

To delete a Specimen requirement

1. Select the study to be updated from the search table.
2.  Click on the Specimen requirement to be deleted in the Study details tree.
3. From the Add Specimen Requirement page navigate to the Shipping requirements section.
4. Click on the Delete icon located at the bottom of the page.

Editing an Alternate Specimen

Only the name of the Alternate specimen can be edited if patients are registered to the study.

1. Select the study to edit
2. Click on the Alternate specimen to be edited in the Study details tree. AFT BioMS will display the Add Alternate specimen screen.
3. To edit the Name of the Alternate specimen, navigate to the title field.
4. Update the Specimen name as required.
5. Update the Type, Anatomical site, Laterality of site, Pathological status, Quantity, and Tube type if needed.
6. Please note that the Class field cannot be edited once the study is built.
7. You can add a Specimen form if needed, and edit the preparation instructions.
8. All fields in the Shipping requirements section can also be edited.
9. After making changes, Click on Submit
10. Save study. The changes will  be visible in the Study details tree.

Adding or Deleting an Alternate specimen

To add an Alternate specimen

1. Select the study to be updated from the search table.
2. Under the Edit tab, add additional Alternate specimens.
   
   

To delete an Alternate specimen

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

Study sync

A study built in AFT BioMS will be synced to repositories by the Study Manager. When a study is completely built and is ready to be sent to repositories, the Study manger will initiate a sync action by clicking the 'Synchronize Study' from the Build study menu. All study data except the following will be synced. These attributes/relations can not be synced because they are not captured in the OpenSpecimen domain model.

• 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

To Sync a study

1. Ssearch for the desired study that is to be synched.
2. Ensure that the study has a status of Active
3. Click on Save Study, and then Synchronize Study.
4. AFT BioMS displays a success message indicating that the selected study is synchronized.
5. To view the study in OpenSpecimen, log into the desired OpenSpecimen.
6. From the OpenSpecimen home screen, click on the drop down menu located next to Search at the top of the screen.
7. From the drop down menu, select Simple.
8. OpenSpecimen displays a search page where you can search for the study that was just synchronized from AFT BioMS.

Study Registration Sync

After a participant is registered to a study in AFT BioMS, the Participant registration details are synced to the repository site OpenSpecimen instances. All the attributes (listed below) of the participant are synced to all repositories linked to AFT BioMS.

• First name
• Middle name
• Last name
• DOB
• Race
• Ethnicity
• Gender
• Genome type

Registration messages contains registrations of a participants to a Study and the participant is automatically registered to all Epochs and Arms of the study. Participant registration messages are synced to those repositories where the study was originally synced. The following attributes of Participant registration are synced

• Protocol Participant ID (PPID)
• Registration Date
• Participant
• Protocol

When a study registration is synced, all SCG and anticipated specimens for the participant study registration are created in the OpenSpecimen repository. In each repository, specimens shipped to that repository are mapped in the entity mapping table and all other anticipated specimens are marked 'Closed' and not mapped. The repository staff  does not modify the specimens marked closed. Any modifications to those closed unmapped specimens will not be synced back to OpenSpecimen.

Specimen Sync

Whenever a specimen status changes in  AFT BioMS, the updated specimen data is synced to the repository OpenSpecimen to which the specimen would be shipped to.

Specimen Collected: When a specimen is marked Collected by a CRA in AFT BioMS, the following attributes of the specimen will be synced to the corresponding Repository where the specimen is being shipped and received.

• Available Quantity
• Initial Quantity
• Collection Status (set to Collected)
• Created On Date

Specimen Collection Event Parameters will also be added to the specimen with the following information.

• Performed By ( set to CRA who collected the specimen)
• Time-stamp
• Container ( the Tube Type specified in the Specimen Requirement)
• Collection Procedure (set to Not Specified)

The specimen would put in a storage position created on the BMS_Site_Container. BMS_Site_Container will hold the specimen until the specimen is moved to a 'In Transit' container, which happens when the specimen is shipped by the collection site to a repository.

Specimen Pending: When the specimen is moved back to the Pending state from Collected in AFT BioMS, the following attributes of the specimen will be updated:

• Available Quantity (set to 0)
• Initial Quantity (set to 0)
• Collection Status (set to Pending)

All other attributes will remain same including the collection event parameter.

Specimen Not Collected: When a specimen is marked as Not Collected in AFT BioMS, the specimen status and the comment that captures the reason for not collected are synced to the Repository.

• Collection Status (set to Not Collected)
• Comment (capturing the reason why sample was not collected)

Shipment Sync

Shipments created in AFT BioMS are synced to the repository were the shipment is addressed to. The shipment is synced to Repository when the CRA sends the shipment in AFT BioMS. The following attributes of the shipment are synced.

• Label (set to BMS shipment ID)
• Send Date
• Sender Site
• Receiver Site
• Sender Contact Person
• Receiver Contact Person
• Specimens
• Activity Status (set to 'In Transit')

Specimen  Forms Sync

Whenever a CRA enters data on a specimen form in the checklist view, the form data is synced to the same Repository to which the specimen is synced. All attributes of the specimen form are synced and attached to the specimen via Specimen Record Entry. Once the form is synced from AFT BioMS, repository users will be able to see the form data in the Annotations tab for the specimen in OpenSpecimen.

User Sync

Whenever a CRA User is created/updated in AFT BioMS as part of Sync of user data from the Mayo DB, the user is synced to all the repositories. The user is synced to Repositories only for referential integrity. CRA users will not be able login to repository OpenSpecimen. The following attributes (all) of the User are synced:

• Log in Name
• Last Name
• First Name
• Email Address
• Institution
• Address
• Activity Status

Site Sync

When a new collection site is created/update in AFT BioMS as part of sync of Site data from the Mayo DB, the Site data is synced to all Repositories. All the sites from Mayo DB are created as a Collection Site in AFT BioMS and OpenSpecimen. The following  attributes of a new site are synced:

• Name
• Type
• Address
• Activity Status

Follow the steps below  to view Study Registrations and other Study details that are synced to Repository site OpenSpecimen
Log into the OpenSpecimen instance of the desired repository. From the top menu tabs select the drop down menu next to Bio specimens Data. Select Collection Protocol Based View.

Enter the Study number of the Study to be viewed in the Collection Protocol field.  As you enter the study number, OpenSpecimen will display a list of all possible matches. Select the desired study.

Click on the arrow located next to the Participant field. OpenSpecimen will display all the Participants that are registered to the study.  Select the desired participant by clicking on the Participant ID number. OpenSpecimen will display the Participant details page where you can view information about the Participant PHI and specimen collections.To view the details of any specimen requirement, select the desired specimen from Specimen Details section. OpenSpecimen will display a specimen details screen where information about the specimen can be found. 

To view shipments created in AFT BioMS and Synced to OpenSpecimen, log into OpenSpecimen. From the top menu tabs select the drop down menu next to Bio specimens Data. Select Shipping and Tracking.

OpenSpecimen will display the Shipments dashboard. Click on the down arrows next to Show Details in the Shipments field. The shipments synched to the Repository will be displayed in table form with information about the Sender site, Shipment label and Bar code label, Sender name, the date the shipment was shipped from the site, and the status of the shipment. Click on any of the underlined information in the table to be redirected to the Received shipment screen. Details about the shipment and the specimens in the shipment will be displayed. 

BioSpecimen Collection Kit Management

Biospecimen collection kit management feature enables

• AFT BioMS study manager to define specimen collection kit per study.
• CRAs to request for specimen collection kits defined in a study.
• Repository staff to process the submitted requests and mark them as sent once the collection kits are sent to the requesting site.

The Biospecimen collection kit management feature permits the AFT BioMS Administrator to create study specific specimen collection kit(s). Once the study is published, then AFT BioMS allows the CRAs to request the specimen collection kits defined by the AFT BioMS study which then sends the request to appropriate repository staff handling the collection kits. Request for collection kits can be placed only against active collection kit definitions in AFT BioMS. Then, repository staff can process submitted requests and mark them as sent once the collection kits are sent to the requesting site. CRAs and Biorepository staff are notified via email notifications when a request is placed or updated. Collection kit definition can be deleted only when there are no requests made for the kit already.

How to create specimen collection kit

Pre-Requisites: Administrative privileges

Steps:

1. Log into AFT BioMS as an Administrator
2. Navigate to a study's edit mode
3. Click on 'Specimen Collection Kit' tab.
   
4. Click on 'New Specimen Collection kit'.

        5. AFT BioMS displays a "Create Specimen Collection kit" pop up window. Please fill in the mandatory fields with the red asterisk ( 'Name', 'Kit Repository', 'Kit Contents' & 'Status')

    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

Pre-Requisites: CRA privileges

Steps:

1. Log into AFT BioMS as a CRA
2. Click on Kit Requests under Tasks menu, system displays the specimen kit request list
   
   
3. Click on 'Submit Kit Request'
   
   
4. Please fill in the mandatory fields of the kit request. The mandatory fields are 'Study', 'Specimen Collection Kit', 'Number of kits requested','Kit needed by', 'Requester site' and 'Site shipping address'.
    
   The Specimen Kit Request page contains several data elements:
      
   Study :The name of the Alliance study is displayed. Select the name of the study from the drop down menu.
   Specimen Collection Kit : Select one kit from the drop down menu. Only active specimen collection kits will be displayed.
   Repository : When the user selects the specimen collection kit, the name of the repository will be automatically populated.
   Kit Contents : When the user selects the specimen collection kit, the contents of the kit also will be automatically populated.
   Number of kits requested: Enter the exact number of kits needed.
   Kit needed by : Click on the calendar icon to record the requested date. A calendar will pop up, allowing you to select the date. This is only an information for the repository for prioritization and does not guarantee that the kit will be made available on the requested date. Please make sure to submit kit requests as early as possible to receive kits on time for patient visits.
   Patient ID: The unique identification number of the patient.
   Requester site: The associated site of the requester.
   Site shipping address : Shipping address of the requestor's site. Shipping address should not include PO Box numbers or other addresses to which couriers cannot deliver
   Requester's shipping account number: Shipping account number is mandatory for overnight shipping of specimen kit.
   Notes: Add any special instructions or notes.                                              
   
   
5. Click Submit. System will send the request to the appropriate repository staff handling the collection kits. A kit request placement email notification will be send to the CRA.

How to send a specimen collection kit

Pre-Requisites: Repository staff privileges

Steps:

1. Log into AFT BioMS as a Repository staff
2. Click on Kit Request under Tasks menu, system displays the specimen kit request lists
   
3. Click on send to send the specimen kit.      
   
4. AFT BioMS displays a "Send Specimen Collection kit" pop up window. Please fill in the mandatory fields with the red asterisk.   
   
5. Click Send. A kit request update email notification will be send to the Repository Staff.

SCG and Specimen Attachment Form

This feature enables CRAs to attach supporting documents like pathology reports and scan images to specimens and SCGs when they are marked as collected. The attached documents are uploaded and saved in BioMS and are also synced to the appropriate OpenSpecimen servers.

SCG Attachments

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 SCG form button to add attachments to the SCG
   
7. A SCG attachments window pops up
   
8. Add the necessary attachments and click save
9. The SCG attachments will be saved

Specimen Attachments

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 form button beside the specimen name's action section
   
7. A Specimen attachments window pops up
   
8. Add the necessary attachments and click save
9. The Specimen attachments will be saved

Mandatory Specimen Form

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.