Notice of Rights - CALGB members and participants may print, photocopy, distribute, and introduce this publication into an electronic retrieval system provided that such use constitutes "fair use" under copyright law, or is otherwise permitted by applicable law.

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Introduction

The Alliance Biospecimen Management System (BioMS) is a web-based application that has been designed to support biospecimen tracking, inventory management, and reporting for all Alliance clinical trials and companion correlative science studies. BioMS is based on the functionality and user interface of the CALGB Specimen Tracking System (STS), but incorporates many new usability enhancements and capabilities to support the operations of the Alliance biorepository network.

 User Privileges

The 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 BioMs.

 Site specific access

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. 

Logging into Biospecimen Management System (BioMS)

Use the following URL to access the Biospecimen Management System login screen: http://bioms.allianceforclinicaltrialsinoncology.org
 The Alliance BioMS login screen appears as shown below.

 

Enter your ID.me User ID and password in the designated fields, read the information regarding login access, and click "Sign in with ID.me”.   If you do not have a ID.me user ID or have forgotten your user ID or password, please click on the Id.me links on the Login screen for addtional help. If you have the correct Id.me user ID and password but still cannot log into BioMS, please contact the BioMS Help Desk at  1-855-55-BIOMS (1-855-552-4667) or email at BioMS Help

After your login is accepted, the Notifications screen appears. Your user name will be displayed on the top right-hand corner of the screen at all times while you are logged into BioMS.  

Also, the landing page shown below includes the details about the functions within BioMS and you can come back to this page by clicking on the Home page icon on the top right side while you are on any page within BioMS.

 

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Logging out of BioMS

It is important to log out of BioMS when you leave your computer workstation or finish using the application. Although the system automatically "times out" and returns to the login screen after 30 minutes of being idle, the recommended security procedure is to log out even if you leave your computer workstation for only a few minutes. While you are logged into the system, all tasks performed are associated with your name and User Id. Logging out prevents unauthorized access. To log out of the application, select the Logout icon shown at the top of every screen and once you are successfully logged out of the BioMS application, the following page is displayed.

 

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Using the Search feature

The  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

To search for a specific patient, select "Patients" from the Search panel.  Search for a patient to view details about the patient on the Specimen checklist including: Patient initials and Registration ID, any studies the patient is registered to, and specimen collection and shipment information for the patient.

 

To search for a patient, select Patients  in the Search panel on the left side of the screen. BioMS will display the Patient Search home page.
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, 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.  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 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.

 In the following  example, the user is searching for patients in Study 80702. As the user begins typing the study ID number, BioMS suggests a list of Studies that contain the letters and or numbers entered.

 

  
From the list of suggestions, select the desired Study ID and click the Search button.  A table will be generated showing patients that  are registered to the selected study.

 

  
The Patient Search Results table shows Patient Initials, Registration ID , and the Study IDs for studies the patient is registered. Click on the desired patient initials to open the Specimen checklist home page, where the user can log patient specimens. To read more about logging specimens, see the section titled Logging a specimen.

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.  BioMs will display a list of all patients and studies that are accessible from your specific site.

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 .

To search for a specimen, select Specimens from the Search panel on left side of the screen.  BioMs will display the Specimen search home page.  From the Specimen Search home page, search for specimens by choosing one of two methods from the drop down menu:

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

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

The following example shows how to search for a specimen by using the Specimen ID, in this case the ID is 35801.  Begin by typing the first few letters of the specimen ID into the field.  Select the desired specimen ID from the list of suggestions displayed by BioMS and click the Search button.
 

BioMS will display a table that contains the Specimen ID, a description of the specimen, Patient registration ID and Initials, Study ID, and the Status of the specimen.

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.  BioMs will display a list of all specimens that are accessible from your specific site.

Search for a Shipment

Search for a shipment to view the Packing slip created for the shipment. The Collection site reviews the Packing slip before placing it in the shipping box to ensure the specimens listed are included in the shipment, and that all other required information on the Packing slip has been filled out correctly. Repository staff will review the Packing slip for accuracy when specimens are received from the collection sites.

 

To search for a Shipment, click on Shipments in the Search panel on the left side of the screen. BioMs will display the Shipment Search home page.

 
Search for shipments by selecting one of  the following options from the drop down menu:

1. Shipment ID:  Enter the Shipment ID, BioMS suggests a list of shipments that contain the entered values . From the suggestions, select the appropriate shipment ID and click Search.  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.  BoiMs 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.  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.

Select the Shipment ID in the table to view packing slip of that shipment.  To learn more about shipments and viewing the packing slip, see the section titled Send a shipment.

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.  BioMS will display a list of all shipments that are accessible from your specific site.

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Viewing the specimen checklist

The Specimen Checklist is a listing 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, initiate a search for the patient from the Patient Search home page. For instructions on searching for a patient, see the previous section titled Search for a Patient.

 When the Patient search results appears, select the Patient initials to open the Specimen checklist.

 The Patient Registration ID and initials are shown at the top of the screen, along with the Study ID. Tabs across the top of screen show Epochs in chronological order - for example, Pre-Therapy, On Therapy, Post-Therapy, and Progression. Epochs are general groupings. Within each Epoch there may be one or more Arms which contain Collection Events. Collection events show the specimens to be collected during a single patient visit.

 The Specimen Checklist contains several columns:

Collected: This column contains a check box used to indicate when a specimen has been collected.  When the user clicks on the check box, a check mark will appear, the Collection Date will automatically populate to the current date and time.

Study:  The Alliance study number is displayed.

Specimen expected:  A description of the specimen to be collected is displayed. The description may include:

• Amount of specimen expected (e.g. 20 ml)

• Type of specimen (e.g.Whole Blood)

• Number of specimen containers (e.g.1)

• Type of specimen container (e.g.Green Top Tube) Note:  The Specimen Expected column shows the total amount of specimen required and the number of containers that should be used. For example, if the Specimen Checklist shows "20 ml Whole Blood (4 x 6 ml Green Top Tubes)" this translates to:  a total of 20 ml of blood should be collected into the four green top tubes, with approximately 5 ml blood collected into each tube.

• Clicking on the specimen description opens a pop up window titled "Specimen preparation and shipping instructions".  The window will display specific information about the sample type, volume, tube type that should be collected, the repository site the specimen is shipping to, and the shipping method.  The user can also find any specific sample preparation or shipping instructions related to the specimen. The preparation and shipping instructions displayed in pop up widow for a specimen are referenced directly from the Study Protocol.  Below is an example of a Specimen Preparation and Shipping instructions Window.  There are three sections:
  
  

  • Type of Specimen and an abbreviated list of information about the sample and shipment.

  • Specimen preparation instructions describe any special preparation instructions related to the sample. Information may include the type of specimen container to use, label instructions, and whether to freeze, refrigerate, or store the specimen at room temperature.

  • Shipping instructions describe the type of shipping container to use, when to send the specimen (e.g., within two weeks), and additional instructions as needed. Clicking on the 'X" on the right hand corner of the screen will close the window.

Quantity:  The volume or quantity of the specimen expected.  This field can be edited.

Collection date: Click on the calendar icon to record the date and time a specimen was collected.  A calendar will pop up, allowing you to select the date. After selecting the date, the time of collection can also be adjusted by sliding the button next to the hour and minute to select the desired time.  Click "Done" to close the calendar when finished. The date and time can also be entered directly into the collection date field using the mm/dd/yyyy format for the date and hh:mm for the time.  

 Status:  The current status of the specimen is displayed. The following are examples of possible sample statuses:

• Pending

• Collected

• Uncollected

• In transit

• Received

Actions:  Under this column, a group of icons are displayed which represent specific functions related to specimen collection.

• The Clip Board - By clicking this icon, the user can enter any comments they may have about the specimen.  (ie.. unable to collect full tube of blood).  Comments can be added at any time, even after the specimen has been received by the repository.  Please Note:  If a comment is added to a specimen after it has been received by the repository, no notification is generated by BioMs to the receiving repository.  If you have a comment to add to a specimen that has already been received by the repository that could affect how the sample is processed by the repository staff, please call the repository and inform them of any new information you have about the specimen.

• Red Exclamation Point - A red exclamation point (not shown in example) indicates that there is a mandatory form that needs to be completed.  Clicking on the Red exclamation point icon will display the form in a pop up window for completion.

• Mark as Not Collected (Tube in red circle with line) - Selecting this icon allows the user to set the specimen status to "Not Collected".  A pop up window will appear when the icon is clicked that allows users to select reason why the sample is not going to be collected from a drop down menu. (ie.. Patient Missed Appointment).  There is also an area where more detailed information can be entered.

• Recollect (Tube surrounded by green arrows) - Samples that have had a previous status such as "Uncollected" can be updated to Collected by selecting the Recollect icon. A pop window will appear that alerts the user that asks the user to confirm the action.
  
  

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Specimen checklist Task bar

Two buttons appear on the menu bar across the top and bottom of the screen.

• Save: Click the Save button to save the collection information entered for a specimen. BioMs will save the information and remain on the current Specimen Checklist so the user can continue to log addition specimens for the patient if needed. Once the Save button has been selected, the specimen status will be updated. (ie..from "Pending" to "Collected" under the status column.)

• Add to shipments: Click the Add to shipments button to save the specimen collection information and advance to the Manage Shipments home page where the specimen can be added to a shipment.  Selecting Add to shipments also updates the specimen status, but the user is taken from the specimen checklist page to the Manage shipments page. Note:  Selecting Add to shipments when logging in a specimen does not actually add the specimen to a shipment. Please see the section titled Manage shipments for detailed instructions on shipping specimens.

Logging a specimen

Please Note: Specimens identified in Alliance protocols that are not received, processed, stored or returned to Alliance Biorepositories will not be logged or tracked using BioMS.  An example of a specimen that falls into this category is a cytogenetics specimen that will  only render results and will never be queried in a distribution protocol by researchers.

Logging a specimen refers to recording that you have collected a specimen for a particular patient. Select Log specimens from the Tasks panel or Patients from the Search panel to display the Patient search screen.

As instructed in the section titled Search for a Patient, select the Registration ID, Patient initials or Study ID option to search for a patient.

When BioMs displays the Patient Search screen, click on the patient initials.

The user can record collection of specimens by simply clicking on the Check box under the collected column.

When the check box next to the specimen is clicked, BioMs will populate the collection date with current date and time. The date and time can be adjusted by clicking on the Calendar Icon.  

Specimen Collection can also be recorded  by clicking on the Calendar icon and selecting the date and time of collection.  After the date and time has been selected, click Done to close the Calendar icon.  A check will appear in the Collected box. 

The status of the specimen will still be Pending until you select Save located on top/bottom right corner to mark the specimen as collected.  If the specimen is ready for shipment, click the Add to Shipments button to be taken directly to the Manage Shipments home page.  Shipment of samples is covered under the section titled Manage shipments.

Change specimen status from Collected back to Pending

If a specimen was marked as collected in error, simply click the check box to remove the check mark and click Save.  The specimen status will return to Pending.  

Mark a specimen as Not Collected

If a specimen is not able to be collected, click on the Not Collected icon.  Using this feature will change the specimen status to Not Collected, and will give the user a method to record the reason why the specimen was not collected.  Select the Not Collected icon under the Actions column in the Specimen Checklist.  A pop up window will appear.

Select a reason why the specimen was unable to be collected from the drop down menu. Enter a free text description of additional information  if needed, and click save.  BioMS will update the specimen status to Not Collected.

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

Specimens with the status of Not Collected, or that were received in unacceptable condition at the Repository can be Re-collected by utilizing the Re-collect icon . To re-collect a specimen with a status of  Not Collected, click on the  Re-collect icon  under the Actions column of the Specimen Checklist.  A pop up window will appear asking if the user would like to re-collect the specimen. 

After clicking Yes, the window will close and BioMs will set the status of the specimen back to Pending.
 

An additional use for the Re-collect option would be in a situation where the sample was received broken or damaged at the Repository, or if for some reason, the specimen was not received by the Repository at all.   For example, the specimen status would indicate that the specimen had been Received, but was unacceptable, or that the specimen had not been received in the shipment. 

In these cases, the Repository staff will mark the the specimen as Not in Shipment, or Unacceptable, and enter the quantity received as zero.  A message will be sent to BioMS and an email will be generated and sent to the CRA at the collection site.  The email will contain details about the specimen in question, and a URL associated with the specimen ID.  The CRA will then click the URL associated with the specimen in the email and log into BioMS, if necessary, to be taken directly the Specimen Checklist. Note:  For the URL to work, the user must be at a computer that has access to the BioMS application.  In this situation, since the sample has already been collected, the pop up window will display the message shown below.

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After selecting Yes, BioMS will display a new sample beneath the first sample with a green circular arrow next to the specimen to indicate it is a recollection.  The new sample can now be logged as collected and shipped to the Repository.  The Clip Board icon could be utilized in this case to indicate that the sample is a recollection of a previous sample.

Collecting the Alternate Specimen

The steps below describe how to collect an Alternate specimen. Examples of Alternate samples might be sending tissue slides instead of a Paraffin block, or a whole blood tube instead of serum or plasma.  Before collecting the Alternate sample in BioMS, you must first set the status of the Original sample to "Not Collected" in order to activate the Alternate sample.  You will not be able to select and collect the Alternate sample until this step has been completed.  To set the status of the Original sample to "Not Collected",  Click on the Not Collected icon in line with the original sample. A pop up window titled "Mark Specimen as Not Collected" will appear.  Select a reason from the drop down menu in the pop up window that best describes the reason you are not collected this sample.  In the example below, we are selecting "Cannot Release Block", if you don't see a appropriate response in the drop down, choose "Other".  You can free text additional information in the box provided next to "Describe".  When finished entering information in the pop up, select Save. 

The Status of the original sample will update to "Not Collected" and the Alternate sample will now be active.  You will now be able to collect the alternate sample and add it to a shipment.  See section titled Logging a specimen for more information if needed. 

Adding a Specimen Collection for a Recurrent Event

It is sometimes necessary to add additional specimen collection events for patients who are to have specimen collections at designated time points during a particular phase of the study.  For example, if a patient is to have specimens collected every 6 months while they are in remission, and it is unknown how long the patient will be in remission, the CRA can add collection events as needed.  When the Epoch for the time point is selected, the CRA will see two additional buttons that will allow a collection event to be added or deleted if necessary. The time point must have been designated as a Recurrent event when the study was created to allow for this function.

To add an additional specimen collection event, click on the Add More button.  A message will be displayed asking the user to confirm the action.  Select Yes. 

A new collection event will now be displayed that will be denoted by a [2].

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

Using the Auto Method:  The Auto method is the default method and is indicated by a filled in radio button next to Auto in the floating box that displays the Auto or Manual choice.  The Manual mode can not be selected unless the user is utilizing the manual ship method which will be covered next.  Complete the following steps to add a specimen to a shipment using the Auto Method:

• From the list of specimens pending shipment, locate the specimen you wish to add to a shipment and click the box next to the specimen ID.

• Click the green arrow in the floating box between the Specimens and Shipments sections that is pointing right, towards the shipments.

• BioMS knows the required shipping requirements of the specimen and will automatically add the specimen to a shipment that meets the shipment requirements for the specimen.  If a shipment does not exist that is going to the required Repository by the required ship method, (ie..dry ice, ambient, cold pack),  a new shipment will be created.

• To verify the shipment that contains the specimen, click on the drop down arrow next to the shipment.  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.
  
  

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Using the Manual Method:  The manual method of placing a specimen into a shipment allows the user to control which shipment the specimen is placed in.  As long as the shipment matches the specimen ship to and ship method requirements, the user can manually place specimens into the shipment of their choice.  Note:  BioMs will not allow specimens to be placed into shipments that do not match the shipping requirements for that specimen.  For example, if a user attempts to manually place a specimen in a shipment going to the PCO repository with a shipping method of dry ice, and the specimen is required to be shipped on a cold pack, Bioms will not place the specimen in the box, even when utilizing the manual ship method.  Complete the steps below to place a specimen in a shipment using the Manual method:

• 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. If a shipment does not exist that matches the required shipping criteria for the sample(s), one can be created.  See the section below titled Creating a Shipment for more details.

• Select the radio button next to Manual in the floating window between Specimens and Shipments.

• 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.

• Click the green arrow in the floating box between the Specimens and Shipments sections that is pointing right, towards the shipments.

• BioMS will place your sample(s) into the designated shipment and the specimen will no longer appear on the table of specimens pending shipment.

• To verify the shipment that contains the specimen(s), click on the drop down arrow next to the shipment.  BioMS will display a list of all specimens contained in that shipment.

Create new shipment

BioMs allows users to manually create new shipments.  It may be necessary to create a new shipment if you wish to place samples in a shipment using the manual method, and a shipment does not exits that matches the shipping requirements of the specimen you wish to ship. A new shipment can be created by two different methods.  You can 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, or you can create a completely new shipment with user defined ship to and ship method.

To create a new shipment from an existing shipment, follow these steps:

• 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.

• Click on the Create button.  Confirm the information in the pop up window and click Submit.

• 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 follow the steps below:

• 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.

• Next select the desired Shipping Method from the drop down menu.

• Once you have the desired ship to and ship method information selected, click the submit button.

• BioMs will create a new shipment with the desired shipping criteria and unique shipment identification.

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Sending a shipment

Sending a shipment is accomplished from the Manage Shipments page that was used to add specimens to shipments and create shipments.  When finished adding specimens to a shipment, the shipment can be prepared for shipment.  BioMs will generate a packing slip to be placed with the specimens.  The packing slip will contain necessary information that will be helpful to the staff at the Repository receiving the shipment.  

• To begin the shipping process, select the radio button next to the the shipment to be shipped and click the Send button.

• 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.
  
  

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• The body of the packing slip contains some basic information that the CRA will need to complete. Fields marked with a red asterisk are required.  

• In the first column of the body of the packing slip, sender information is entered.  Information contained in the drop down menu next to Sender Site will be site specific.  When a site is selected, the "From" field will automatically populate with the site specific address. The information contained in the drop down menu next to Sender Contact will also be site specific.  However, user will be required to manually enter phone number and email information.

• The middle column contains information about the site receiving the shipment. The Receiver site and ship to address will automatically populate.

• The user will choose a Receiver Contact from the drop down menu, and will be required to enter a phone number for the receiving site.  A field is provided for an email contact for the receiver, but it is not required. 

• In the last column, a drop down menu is used to select the intended carrier.  A field is provided to enter the tracking number of the shipping air bill if desired, but the information is not required.  Please Note:  BioMs does not generate air bills!

• Click on the calendar icon to enter the date of shipment. 

• After all required information has been entered, review the packing slip for completeness. 

• Review the Contents of the shipment.  The specimens contained in the shipment will be displayed at the bottom of the packing slip.  Each specimen will be listed in table form with columns identifying the specimen identification number, the type of specimen, the patient registration identification number and initials, the study ID, and the epoch, arm and CPE of the study the specimen was collected for.  
  
  

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• After the review is complete, click on the Send shipment button.  A message will be displayed indicating the "Shipment has been Shipped Successfully."  The option to print the packing slip is now available.  Click on the Print button, print the pacing slip, and place it in the shipping box with the specimens.  Note: The packing slip must accompany the specimens.  It is required by the receiving repository. 
  
  

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• If necessary, a packing slip can be reprinted.  There are two ways to reprint: 
  
  

  •  Click on the radio button next to the shipment associated with the packing slip that needs to be reprinted.  The Shipment will have a status of "In Transit".  Next click on the Print button.  The packing slip will be displayed along with the option to print.
    
    

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  • A packing slip can also be printed by using the Search for a Shipment option.  For information on searching for a shipment, see the section titled Search for a Shipment.  When the shipment search results appear, click on the Shipment ID. The packing slip will be displayed along with the option to print.  
    
    

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Edit or Delete a Shipment

Shipments can be edited by site users only within 24 hours after a shipment has been sent. Site users are prevented from making any changes 24 hours after a shipment has been sent to eliminate unexpected issues as a repository staff might be receiving the shipment at the same time. BioMs will allow shipments with a status of "Not Shipped" to be edited. If you need to edit a shipment 24 hours after you send it, please reach out to BioMS Help Desk and they can assist you to make the necessary changes after checking with the repository. Once a shipment has a status of received by the repository in BioMs, the shipment will not appear in the Manage Shipment home page, and can not be edited.

The following steps will show how to edit a shipment with a status of "Not Shipped" to remove specimens, or delete the shipment.

• To remove specimens from a shipment with a status of Not Shipped, 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. Click the box next to the sample
  to be removed from the shipment.  Next click the green arrow that is pointing left towards the Specimens list.  The specimen will be removed from the shipment and placed back on the Specimens pending shipment list.

• To delete shipment, first remove any specimens contained in the shipment by the utilizing the previous step.  Then click on the radio button next to the shipment you wish to delete and click the Delete key.
  
  

  Open

  

To edit a shipment with the status of "In Transit" you must first set the status of the shipment back to "Not Shipped".  Once the status has been changed, 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:

• Click on the Radio button next to the shipment with the status of In Transit that you wish to edit.

• Click the Edit button.  BioMs will display a pop up asking the user to confirm the edit of an In Transit Shipment.

• 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"

Build Alliance Study Protocols in BioMs

Protocols for Alliance clinical trials and companion correlative science studies are approved and sent to the BioMs development team for review.  After the protocol has been through the designated review process, the components of the study are built in BioMS.  The building of new studies  and the management of existing studies in BioMs is limited to users with system administrator access.

 Add study

To build/add a new study begin by selecting Build Study located under the task menu of the BioMs home page. Four file tabs will be visible.  The larger tabs at the top of the page are titled Add and Edit. The Add tab will be highlighted by default.  The smaller tabs located under the first two are titled Study details and Associated Studies.  The Study details tab will be highlighted by default.  Ensure the default tabs of Add and Study details are highlighted to begin building a new study.

Only studies that have been previously approved can be built in BioMs.  The Alliance study number and Title will be available to select only if the study has been approved.  If it is not available, BioMs will not accept your entry into the Alliance Study number field.  If a study you wish to build has already been entered into BioMs an error message indicating that the Alliance Study number already exists will be displayed.  If the Alliance number of the study you wish to build does not exist in BioMs, contact the BioMs support team. The required information to enter into the Study details section to begin building a study includes:

After entering in all the required information in the designated fields of the Study details screen, click on the submit button.

After clicking submit, BioMs will display a message indicating the the Study has been created successfully.  The newly created Study number will appear in the study details column to the left of where the original information is entered.  This column is where the study "tree" will be visible.  As new Epochs, Arms and Collection events are created for the study, they will appear in this section in outline form. Note: Click on Save study before proceeding to the next step of adding an Epoch.  Clicking on Save Study periodically while building a study is recommended to ensure all the details of the new study are saved.  If you exit the study before saving it, anything created since the last save will be lost, including the creation details of the study itself.

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 a Epoch, click on Add epoch next to the Submit button. BioMs will display a page where Epochs can be added.  The Epoch screen has two columns. Enter the name of the epoch under the Label column.  The second column titled Sequence is a field to enter the order in which the epoch should appear in the study build tree.  More epochs can be added by selection the Add more button at the top of the Add Epoch page. Additional lines will appear to accommodate the names and sequence number of all the epochs required for the study. If the study only has one Epoch, click submit to continue. If more are required, click Add more until the desired number of spaces are available for the epochs required for the study. Please note that no two epochs within the same study can have the same name.  When finished with entering the names and sequences of the epochs, hit submit.  The information will populate in the Study details tree. Before proceeding to the next step of adding study arms, 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, select the Epoch from the Study details tree. BioMs will display a screen that has two sections. The first section is Edit Epoch, the second is Add Arm(s).  Under Add Arm(s), a field is available to enter the name of the arm.  Enter the name of the Arm.  If you have more than one Arm to add to the Epoch, click on the Add more button. This will provide more fields to enter additional Arms.  When finished adding Arms, click the submit key.  A message will appear stating that the Arm(s) were added successfully and the created Arm(s) will appear in the Study details tree.  It is a good idea to click on Save study before continuing.

Add collection event

After Arms are added to Epochs, next step is to add Collection events to an arm.  Collection events are a group of specimens that are collected under a specific arm of a study. To add a collection event, select the desired Arm from the Study details tree and select the Add collection event button.

BioMs will display the Add Collection Event screen. Enter a name of the event in the Event label field.  Click the box next to Recurrent if this is to be a recurrent event.  An example of a Recurrent event would be if the patient was a on specified schedule for a blood draw until they are out of remission.  This could be several weeks to several months. Selecting Recurrent will allow the CRA to add Collection events from the Patient Specimen Check list view as needed.  Next, from the Clinical status drop-down select a clinical status.  In the example shown, the Epoch is labeled Pre-Therapy, therefore Pre-therapy has been selected for the clinical status.  It the clinical status is not known, select the default of Not Specified. 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).  In Clinical diagnosis field, enter the same diagnosis that was entered when the study was created. Begin typing the clinical diagnosis and BioMs will suggest a list of values that match the entered text. From the suggestions, select  the correct clinical diagnosis and click submit.  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. Repeat the steps above for each Collection even that is required for each arm of the study.

Add specimen requirement

After adding Collection Events to study Arms, the next step is to add Specimen Requirements to Collection Events.  Specimen requirements will inform the CRA exactly what specimen is to be collected, the quantity of the specimen, and detail how to process and ship the specimen. 
To add a Specimen Requirement to a Collection Event, select the desired Collection Event from Study details tree.  When BioMs displays the Add a Collection Event screen, select the Add Specimen Requirement button.

BioMs will display the Add Specimen Requirement page.  Several mandatory fields must be completed on the page.  In the Title field, enter the name of the specimen.  In the Class field, use the drop down menu to make a selection. The drop down menu for the Type field will vary based on what Class was chosen.  For example, if Fluid was chosen in the Class field, you will see choices such as whole blood, serum, plasma, saliva appear in the drop down.  If tissue was chosen in the Class field, choices such as Fixed tissue, frozen tissue, or fresh tissue will appear in the drop down menu.  After selecting a sample Type, Select the Anatomical site the specimen was collected from, if known.  If unknown, select Not Specified.  Continue on the 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.  If the information is not know, select Not specified. Enter the Quantity in the Quantity field, and choose a Tube type if applicable from the drop down menu.  The Concentration field will be grayed out unless Molecular was selected for the Class of the sample.  If that is the case, the Concentration can be entered here.  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.  The required form will appear here.  Refer to the Study protocol and enter any special specimen Preparation Instructions. The Alternate specimen field is utilized to enter any alternate specimens that may be collected if the originally required specimen is not available. The Alternate specimen field will be covered later. In the shipping requirements section, choose the Shipment site you are shipping the specimen to from the drop down menu.  Next choose a Shipping method from the drop down menu. Refer to the study protocol and enter any special Shipping instructions in the designated field.  When all information has been entered, click on Submit. 

BioMs adds the specimen requirement to the selected collection event,  The study details tree is updated to reflect the newly added specimen requirement. Select Save study to ensure that newly added specimen requirements are saved. 

Add alternate specimen

The Alternate specimen field is utilized to enter any alternate specimens that may be collected if the originally requested specimen is not available. To add an alternate specimen to a specimen requirement, select the desired specimen requirement from the tree structure and navigate to Alternate specimens section and click on the "+" icon. BioMs will display the Add Alternate Specimen screen.

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.  When finished, click on Submit. 

 

BioMs will  add the alternate specimen to the selected Specimen requirement and the Study Details tree structure will be updated to display the alternate specimen. The alternate specimen will also be displayed in the Alternate specimen(s) box when the Specimen requirement page for the original sample is displayed. You can add additional alternate specimens to a Specimen requirement by repeating the steps above.

 

Adding an Associate (companion) study

Many Main Study protocols may have one or more Companion studies associated with them.  Patients are usually consented to participate in any Companion studies associated with the Main study at the time time they are registered and give consent for the main study.  BioMs allows for linking of the Main,(often referred to as the Parent) with companion studies so that collectors can view all specimen collection events from one patient check list.  If collection events happen to be the same for one or more of the associated studies, the specimens can be collected at the same time, or shared between studies.  To add Associate studies to a parent(main) study, click on the Associated study(s) tab from the Build study page.  BioMs will display a screen with a drop down menu from which you can select and add associate studies to the parent study.  Select the associate study from the list and click the "+" sign.  

Click on the Study details tab. BioMs will return to the main study build screen.  It is very important that after clicking on the Study detail tab, that the user clicks on the Submit icon.  After clicking Submit, Save the study.  The associate study will now be linked to the parent (main) study.  When the Associate study(s) tab is selected, the associate study number will appear in the box.  Multiple associate (companion) studies can be associated to the main(parent) study.

Add Coincident Events

A coincident event is when  two specimen collection events occur at the same time for studies that are associated. Up to two events in associated studies can be linked as coincident. To add a coincident event to a study, navigate to the desired collection event that is coincident with the event of the associate study. Note: to add coincident events, the selected study must have at least one associated study.  In the example below, the Week one collection point event of a 10ml EDTA from the parent study of SG0009 is going to be linked as a coincident event with the Week one collection point event of a 10mL EDTA from associate study SG0008.  Begin by clicking on the Collection point event that is do designated as a Coincident even from the Study details tree.  Then click on "Co-incident event" next to the Event label field. BioMs will display a pop window with at screen titled Co-incident Event Map. From the study tree display of the associate study, (in this example it is SG0008), click on the radio button next to the event to be designated at coincident.  Next click OK at the bottom of the pop up window to close and save the selection. 

After the pop up window closes, Click Submit, and then Save study to ensure the Coincident event was saved.  The Coincident event tree with the selected event will be displayed when the user clicks on "Co-incident event" next to the Event label field of the Add a Collection Event Screen.  Coincident events can be designated for additional associated studies if applicable.  Please note that only one collection event from each of the associated studies can be selected as a coincident event with the selected collection event from the main 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, select the specimen requirement from the Study details tree.  Click Add Equilvalent specimens at the bottom of the Add Specimen Requirement page.  BioMs will display a pop up window with the study trees of both the main and associate studies.  Expand the tree of the main study (in the example shown, the main study is SG0009) to view the specimen requirement that is to be linked as equivalent with the coincident event of the associate study (in the example below, the associate study is SG0008).  A check mark will already be present next to the specimen requirement in the tree of the main study.  Expand the study tree of the associate study if necessary to view the sample requirement that is to marked as equivalent.  Click the box next to the specimen. 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. Click on Save to close the pop up window and save the selection.  Repeat the steps described to add additional equivalent specimens to other coincident event.  Click on Save study under the Study details tree when finished. Please note that one specimen requirement from main study may have any number of equivalent specimens. However, from one associated study, only one specimen requirement may be made equivalent to a specimen requirement from main study.