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Support Email:bioms@alliancenctn.org

BioMS Application Link:https://bioms.wustl.edu/bioms/

Looking for help? Email bioms@alliancenctn.org
Or Phone 1(855)-55-BIOMS or 1(855)-552-4667

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Biospecimen Management System (BioMS) User Guide

Alliance • August 2012

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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Table of Contents
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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

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After your login is accepted, the Notifications screen appears. Your user ID will be displayed on the top right-hand corner of the screen at all times while you are logged into 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 CTEP ID. Logging out prevents unauthorized access.

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To log out of the application, select the Logout icon shown at the top of every screen.

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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.

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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 .

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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.

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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.

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  • 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.

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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. 

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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. 

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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.

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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.

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

Adding Specimens to a Shipment

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. 

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  • 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.

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  • 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.

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.  

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  • 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.  
  • 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. 
  • 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.
    • 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.  

Edit or Delete a Shipment

Shipments can be edited as long as the do not have a status of received at the repository.  BioMs will allow shipments with a status of "Not Shipped" as well as "In Transit" to be edited.  However, 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.

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  • 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.

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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:

Field name

Description

Alliance study number

A number that is used to uniquely identify a study in BioMs

Title

This field contains a Title/Description about the study that is being added. The text field accepts a long description about the study.  The title information should populate automatically when the Alliance study number is selected.

Start date

Click on the date icon to enter the start date of the study. BioMs will only accept patient registrations for a study after or on the start date.

Activity Status

Enter the Status of the study by selecting either Active, Closed or Disabled from the drop down menu.

Author

Select the name of the Principle Investigator and author of the study. BioMs displays the list of available Principle Investigators in a drop-down menu.

Clinical diagnosis

The clinical diagnosis is entered if known.  BioMs will display a list from which the correct clinical diagnosis can be selected. After selecting a diagnosis, click the Add button.  BioMs will add the selected clinical diagnosis. You can select and add multiple clinical diagnoses for a study

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.

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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.

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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.  

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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. 

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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.

Adding Specimen requirement groups

Similar specimens of a collection event can be grouped together into Specimen Requirement groups. To create a specimen requirement group, click on the Collection event that contains the Specimens that are to be grouped together.  From the Add Collection Event screen, navigate to the center of the page and click Add next to Specimen Requirement Groups.  A new area will be visible to enter details about the Specimen group.  Under Group label, enter a name for the group.  Form 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.  Click submit when all required information has been entered.  

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The added Specimen requirement group is displayed when the Collection event the group is associated it selected from the Study details tree. To add additional Specimen requirement groups, repeat the steps above for each Collection event that a group is to be added.  Please note that any number of specimen requirement groups can be added to a collection event, however, the same specimen requirement may be a part of only one specimen requirement group.

Editing a Study

BioMs allows users with administrative privileges to edit studies that have been previously built.  The information than can be edited will be dependent on participant registration in the study.  For example, if several patients are already registered to a particular Epoch and Arm of a study, that Epoch and Arm can not be deleted.  To edit a study, begin by initiating a search for the study to be edited. 

Search for a Study

Note: You must be logged in as an administrator to Edit a Study. After log in, select Build Study from the Tasks menu.  BioMs will display the Build Study page.  Two file tabs will be visible labeled Add and Edit.  Click on the Edit tab. 

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An alternate method to use when Searching for a study, is to click on the Search icon without entering any search criteria.  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. The Alliance study number can not be edited. After selecting the study to edit from the search table, navigate to the field that needs updated from the Study details page. The Study title can be updated or corrected as needed by entering the information directly into the Title field. 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. Update the Activity status by selecting the new status from the drop down menu.  Select the correct PI using the drop down menu.  Add or remove items from the clinical diagnosis field as needed.  Note: The Start date, Principal investigator, and Clinical diagnosis of a study can not be updated after a participant has been registered to the study. Click on Submit when finished, and then click on Save Study.

Editing a Epoch

The steps below describe how to change the name of, add or delete and Epoch.  BioMS will not allow the user to delete an Epoch if patients are registered to the study and have had specimens collected for the Epoch. 

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

Adding or Delete an epoch

Additional Epochs may be added to an existing study if required. To add Epochs, select the study to be updated from the search table.  Under the Edit tab, add additional Epochs by following steps described in the previous section titled Adding Epochs.  New Epochs can be added to a study even after patients have been enrolled in the study.

An epoch can be deleted from an existing study, but please note, all details (arms, collection events and specimen requirements) associated with the epoch are also deleted.  Epochs can not be deleted once patients are enrolled in the study and have had specimens collected for the Epoch. To delete an Epoch, select the study to be updated from the search table.  From the Study Details page click on Add Epoch. From the Add Epoch(s) page, 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. Click on yes to close the pop up.  The Add Epoch(s) page will reflect the deleted Epoch, however, the Study details tree and the update will not be saved until the user clicks Submit, and then Save Study. 

Editing an Arm

The steps below describe how to change the name of, add or delete a Arm. BioMS will not allow the user to delete a Arm if patients are registered to the study and have had specimens collected for the Arm.

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

Adding or Deleted an Arm

Additional Arms may be added to an existing study if required. To add Arms, select the study to be updated from the search table. Under the Edit tab, add additional Arms by following steps described in the previous section titled Adding Arms. New Arms can be added to a study even after patients have been enrolled in the study.

An Arm can be deleted from an existing study, but please note, all collection events and specimen requirements associated with the Arm are also deleted.  Arms can not be deleted once patients are enrolled in the study and have specimens collections associated with the Arm. To delete an Arm, select the study to be updated from the search table. Click on the Epoch that contains the Arm to be deleted in the Study details tree. From the Edit Epoch page navigate to the Add Arm(s) section and click on the box next to the Arm to be deleted.  Next click on the Delete icon and then click Submit. 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. The Edit Epoch page will reflect the deleted Arm, however, the Study details tree and the update will not be saved until the user clicks Submit, and then Save Study. 

 

Editing a Collection event

The steps below describe how to change the name of, add or delete a Collection event.  BioMS will not allow the user to delete a Collection if patients are registered to the study and have had specimens collected for the Collection event.

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

Adding or Deleting a Collection event

Additional Collection events may be added to an existing study if required.  To add Collection events, select the study to be updated from the search table.  Under the Edit tab, add additional Collections events by following steps described in the previous section titled Add collection event. New Collection events can be added to a study even after patients have been enrolled in the study.

A Collection event can be deleted from an existing study, but please note, all specimen requirements associated with the Collection event are also deleted.  Collection events can not be deleted once patients are enrolled in the study and have had specimen collections associated with the Collection event. To delete an Collection event, select the study to be updated from the search table. Click on the Collection event to be deleted in the Study details tree.  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. (Note: The delete key in line with the title Specimen Requirement groups is for add or deleting Specimen Requirement groups.) Please be aware that there will not be a pop up window asking for conformation as occurred when deleting an Epoch or Arm.  The Collection event will be deleted and the user will be taken back to the main Study details page. The deleted Collection event will be reflected in the study details tree, however, you must click Save study for the change to be saved. 

Editing a Specimen requirement group

The steps below describe how to change the name of, add or delete a Specimen requirement group.  BioMS will not allow the user to edit, add or delete an existing Specimen Requirement group if patients are registered to the study.

After selecting the study to edit, click on the Collection event that contains the Specimen requirement group to be edited in the Study details tree.  Bioms will display the Add a Collection event screen. To edit the Name of the Specimen Requirement group, navigate to the section on the screen titled Specimen Requirement Groups.  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.  When finished editing, click on submit, and then 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

Additional Specimen requirement groups may be added to an existing study if required, as long as no patients have been registered to the study.  To add a Specimen requirement group, select the study to be updated from the search table.  Under the Edit tab, add additional Specimen requirement groups by following steps described in the previous section titled Adding Specimen requirement groups.

A  Specimen requirement group can be deleted from an existing study, as long as no patients have been registered to the study.  To delete an Specimen requirement group, select the study to be updated from the search table. Click on the Collection event that contains the Specimen requirement group to be deleted in the Study details tree.  From the Add a Collection Event page, navigate to the Specimen requirements group section. Place a check mark next to the Group label by clicking on the box. 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 bake to the main Study details page. 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

The steps below describe how to change the name of, add or delete a Specimen requirement .  BioMS will not allow the user to delete an existing Specimen requirement if patients are registered to the study.  In addition, only the name of the Specimen requirement can be edited if patients are registered to the study.

After selecting the study to edit, click on the Specimen requirement to be edited in the Study details tree.  Bioms will display the Add a Specimen Requirement screen. To edit the Name of the Specimen requirement, navigate to the title field.  Update the Specimen name as required.  Update the Type, Anatomical site, Laterality of site, Pathological status, Quantity, and Tube type if needed.  Please Note that the Class field can not be edited once the study is built.  To update the class field would require deleting the specimen requirement.  You can add a Specimen form if needed, and edit the preparation instructions.  All fields in the Shipping requirements section can also be edited.  After making changes, click on Submit, and then Save study. 

Adding or Deleting a Specimen Requirement

Additional Specimen requirements may be added to an existing study if required. To add a Specimen requirement group, select the study to be updated from the search table. Under the Edit tab, add additional Specimen requirements by following steps described in the previous section titled Add specimen requirement.

A Specimen requirement can be deleted from an existing study, as long as no patients have been registered to the study. To delete a Specimen requirement, select the study to be updated from the search table. Click on the Specimen requirement to be deleted in the Study details tree.  From the Add Specimen Requirement page, navigate to the Shipping requirements section.  Click on the Delete icon located at the bottom of the page. Please be aware that there will not be a pop up window asking for conformation as occurrs when deleting an Epoch or Arm. Click on Save Study. The Specimen requirement will be deleted and the user will be taken bake to the main Study details page. The changes will  be visible in the Study details tree.

Editing an Alternate specimen

The steps below describe how to change the name of, add or delete an Alternate specimen. BioMS will not allow the user to delete an existing Alternate specimen or add a new Alternate specimen if patients are registered to the study. In addition, only the name of the Alternate specimen can be edited if patients are registered to the study.

After selecting the study to edit, click on the Alternate specimen to be edited in the Study details tree.  Bioms will display the Add Alternate specimen screen. To edit the Name of the Alternate specimen, navigate to the title field.  Update the Specimen name as required.  Update the Type, Anatomical site, Laterality of site, Pathological status, Quantity, and Tube type if needed.  Please Note that the Class field can not be edited once the study is built.  To update the class field would require deleting the Alternate specimen.  You can add a Specimen form if needed, and edit the preparation instructions. All fields in the Shipping requirements section can also be edited. After making changes, click on Submit, and then Save study. The changes will  be visible in the Study details tree.

Adding or Deleting an Alternate specimen

Additional Alternate specimens may be added to an existing study if no patients are registered to the study. To add an Alternate specimen, select the study to be updated from the search table.  Under the Edit tab, add additional Alternate specimens by following steps described in the previous section titled Add alternate specimen.

An Alternate specimen can be deleted from an existing study, as long as no patients have been registered to the study.  To delete an Alternate specimen, select the study to be updated from the search table. Click on the Specimen requirement for which the Alternate specimen to be deleted is associated in the Study details tree.  From the Add Specimen requirement page, navigate to the Alternate specimen(s) section. Highlight the Alternate specimen in the box that is to be remove.  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.   Click on the Submit icon located at the bottom of the page. Click on Save Study. The Alternate specimen will be deleted and the changes will  be visible in the Study details tree. Click on Save study.

 

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BioMs to caTissue Synchronization (forward sync)

A general rule applied on the sync of entities from BioMS to Catissue is that entities are only synced to the caTissue hosting those repositories where the entity would physically belong or is referenced by an entity that physically belongs. For example, specimen status updates are synced only to the repositories where the specimen will be shipped and received.

Study sync

A study built in 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 caTissue domain model.

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The Search result will be displayed in table form. 

Study Registration Sync

After a participant is registered to a study in BioMS, the Participant registration details are synced to the repository site caTissue instances.

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When a study registration is synced, all SCG and anticipated specimens for the participant study registration are created in the caTissue 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 BioMS.
Note: For testing, participant registrations can be created in BMS using the temporary Participant Registration page. The Participant Registration page can be accessed at <bioms- base-url>/participantRegistration.

Specimen Sync

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

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

Shipment Sync

Shipments created in 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 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 BioMS, repository users will be able to see the form data in the Annotations tab for the specimen in caTissue.

User Sync

Whenever a CRA User is created/updated in 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 caTissue. The following attributes (all) of the User are synced:

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

Site Sync

When a new collection site is created/update in 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 BioMs and caTissue. The following  attributes of a new  Site are synced:

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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 Kit Management

Biospecimen collection kit management feature enables

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The Biospecimen collection kit management feature permits the BioMS Administrator to create study specific specimen collection kit(s)Once the study is published, then BioMS allows the CRAs to request the specimen collection kits defined by the BioMS study which then sends the request to appropriate repository staff handling the collection kitsRequest for collection kits can be placed only against active collection kit definitions in BioMS. Thenrepository 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

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  1. Log into 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. 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

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  1. Log into BioMS as a CRA
  2. Click on Kit Requests under Tasks menu, system displays the specimen kit request lists
  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

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  1. Log into 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. 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

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