Task Descriptions

Topics:

Add Cores to Microarray Task

Once a microarray has been created additional cores can be added to the microarray. Users will be able to add new microarrays to the requisition in order to add cores to them.

Example: Several weeks after creating a microarray from several subjects from each stage of radiation poisoning, new radiation level tissue specimens from the previous subjects arrive in Mr. Richards’ lab. He would like to add these specimens to his previous microarray to compare the new specimens against the previous ones. He uses an Add cores to Microarray task to accomplish this by adding another column of specimen cores to the microarray to show the higher radiation level specimens.

To add cores to a microarray:

  1. Apply the Add Cores to Microarray Task to all desired parent specimens. The microarray with cores being added to it must be one of the specimens with the task applied  to it. Before this task can be Begun, the task property "Microarray ID" must be populated. After the task has been applied, the task properties can be edited by selecting the Edit Task button from the task column header menu.

  2. To create the cores, select Change Status > Add Cores from the task’s column header menu.  The Microarray Specification dialog opens.  The top pane contains the parent specimens, including all sample and specimen data. The bottom of this pane displays the row and column layout for the cores, showing any existing cores. There are two display options for this section:

    add_cores_to_a_microarray_task.jpg
      • From Layout view, users can drag and drop the parent vials into a table set up like a grid that represents the microarray. Click on any field of a specimen in the top pane, and drag it to a desired location in the grid on the bottom pane.  microarray_layout_view.png

      • The Contents tab shows a spreadsheet view of the microarray. From Contents view, the table is set up so that the users can manually enter data, use mass change, or import data into the row and column fields. Table data includes the microarray Row, Column, and the BSI ID of the sample in that particular space.

      • The dialog also has a View menu, which allows the user to save the field order of the dialog or revert to the default field order for the database. If fields are rearranged or hidden, then the user view is saved, the new arrangement of fields will be displayed by default every time that user views this dialog. From either view, once a core has been created it cannot be moved from its location in the microarray.

    • The first row and first column are reserved for planning purposes. Users can enter data to help guide organization of their microarray while they are adding cores to it. For example, you may wish to note Subject IDs in the planning column and dates in the planning row to ease the creation of a microarray capturing change over time. This data will be saved with the microarray and editable later.
  3. After all new core data has been added to the microarray, the user can Check Errors using the button on the right side of the dialog. Notification of errors will only occur if errors exist, otherwise nothing will happen.
  4. Press the Commit button. The dialog will be closed and the task will now have a status of Begun.
    • Right click the task's column header to display the menu, then select the Mark as Completed button. The Specify Core IDs dialog will open.
    • Enter the Starting Core Sequence. Select OK. The Complete Add Cores to Microarray task dialog will open.specify_core_ids_dialog_for_microarray_tasks.jpg
    • Add data and correct any errors using the Check Errors button. Users can Save, Save with Translation, and Reserve Locations from this dialog. Data can be added:
      • Manually
      • Using the Mass Change and Copy from Parent options. 
      • Importing data
      • Scanning Specimen or Scanning Specimen with Translations
    • Select Commit. The Parent Volume dialog will open. To verify that the volumes of all parent specimens have been updated, press Yes. To return to the previous dialog and update the volumes, press No.
    • A Commit Successful dialog will be displayed, if the batch was committed, to display the Parent and Child batch numbers. Press OK.

    Aliquot and Process Tasks

    Aliquot and Process tasks are completed in two phases in the Requisitions Editor.  First, BSI IDs for child specimens are requested and assigned in the Request Available Child BSI ID dialog.  If combining specimens, selected parent specimens can be combined into a single child specimen.  Once complete, child specimens are then listed in the editor and the task is marked as Begun but the specimens do not become 'real' until the task is completed.

    After an Aliquot or Process task is begun, the labels for the child specimens can be edited, if necessary, and printed. They can be printed via the Print Labels button in the “Request Available Child BSI Id(s)” dialog or via the toolbar button in the Requisition editor. See the section on the Current Label column menu for more information on editing and printing labels from the editor.

    When completing the task, the Child Completion dialog allows users to enter data for the children and change data for the parents.  When all the information has been entered and the changes have been committed, the task status for each of the parent specimens becomes Completed and the child specimens become 'real’ specimens.

     Example Aliquot Task: Professor Charles needs to test the effects of his new serum on whole blood. He uses an Aliquot task, creating a new "child" blood specimen from a "parent" blood specimen, to preserve his specimens’ integrity for future research, which allows him to perform the necessary tests. He creates 2 aliquoted "child" specimens from each "parent" specimen, then performs his tests on the new specimens.

    Example Process task: Professor Charles has finished testing his serum on whole blood with inconclusive results. He now wants to further test the whole blood components and subject tissue blocks. He uses a Process task in BSI to represent centrifuging the whole blood specimens into their component parts and another Process task for slicing tissue block specimens to examine under a microscope. After creating 2 child specimens from each tissue specimen and separating the whole blood, Dr. Charles tests his serum.

    To begin an Aliquot or Process task:

    1. Select Create Child Specimen from the task's column header menu. The Request Available Child IDs dialog will open, and the Specify Children dialog will open in front of it.Create_Child_Specimens_button.jpg
    2. From this menu, there are several options, such as generating children from the database, from a template, or generating different numbers of children per parent. BSI IDs assigned to child specimens will be unique, but not reserved. Select an option. See Generating Children below for more information.
    3. Press OK to create the children and view the Request Available Child BSI IDs dialog.
    4. From the Request Available Child BSI IDs dialog, users can also select the Combine button to combine parents into a single child specimen. Selected parent specimens are combined into a single child specimen.
      • The “Combination ID for Pooled Vials” standard report is available to report on the specific parent specimens combined into a child specimen.
    5. Users can Import data for children, edit Child Default Data, Scan Specimens and Check Errors. All errors must be resolved before the next step.
      • Some data for parent(s) and/or children can be edited, depending on the values set for that field in Customization.
    6. When all changes have been made, press OK.

    Generating children from the database or from a template

    Children can be generated either from the database or from a template. Generating from the database creates a set, user defined number of children for each parent specimen. To create children via this method, follow these steps:

    1. Enter a starting Sequence number.
    2. Select an option to assign sequence numbers:
      • Assign Same Starting Sequence for All Sample IDs - The system will look for the first unused sequential block of sequence numbers available to all of the parents’ Sample IDs. The size of the block is determined by the largest number of children created for a sample. Once a block of sequence numbers is found they are assigned to the children sequentially until all children have been assigned sequence numbers.
      • Assess Starting Sequence by Individual Sample ID - The system will look for the first unused continuous block of sequence numbers available for children belonging to each individual Sample ID. Once a block of sequence numbers is found they are assigned to the children sequentially until all children have been assigned sequence numbers.example_assigning_same_starting_sequence_to_all_samples_versus_by_individual_sample_id.png
    3. Specify the number of children to be created per parent:
      • Same Number of Children per Parent – Enter a number of children to be created. For each parent, this is the number of children BSI will create.
      • Different Number of Children per Parent – If this option is selected, the Specify different number of children per parent dialog will open after selecting OK. On this dialog, the Number of Children field may be manually updated or imported. When finished, select OK. For each parent, the specific number of children entered for that row will be added to the editor.

    Generating children from a template creates children according to the number of rows in the chosen template. If using a multiline template, the number of rows in the template will be the number of children created for each parent. Default values and commands set in the template will be applied to the new children. To create children via this method, follow these steps:

    • Select the Generate Children from a Template radial option.
    • Select Browse.
    • Choose a template.
    • Select OK.

    To Complete an Aliquot or Process task:

    1. Select Complete from the task's column header menu. The Child Completion dialog will open.
    2. Users can Import data for children, edit Child Default Data, Scan Specimens and Check Errors.  They can also select  Locations, Select Column View Template if it should be different than the template used in the requisition editor, Save and Save with Translation.
      • If saving with translation, the user will be prompted to specify whether they are exporting all rows or only the selected ones, then select the translation to be used. In either case the user will next select a location to save the file then press Save.
      • Users can right click the Volume column and select Subtract Child Values to subtract the total of all child volumes from the parent volume.
      • Users may also use the Delete Rows icon to remove child rows for specimens which were not created.
    3. When all errors have been resolved, the user can press Commit. The Committing Data dialog will open and notify the user that committing a batch will permanently alter the database. Press OK to continue or Cancel to return to the Child Completion dialog. 
    4. The Parent Volume dialog may open, prompting the user to verify that they have updated the parent specimen volumes. Select Yes to continue or No to return to the Child Completion dialog and edit volumes.
    5. A dialog will open to notify the user of a successful completion or of any errors encountered. Press OK.
    6. Once completed, the new specimen(s) will be displayed in the Requisitions Editor. They will be available to have tasks applied to them and completed.

    Blind Task

    The Blind task can be used to completely mask the origin of a specimen by creating a new record in BSI with a subset of the data of the original specimen.  There will be no visible links in BSI between the new specimen and the original until an Unblind task is completed on the original specimens.  This allows specimens to be blinded before transferring to another repository.

    The Blind task is completed in two stages.  In the first stage, new BSI IDs and Current Labels are reserved for the blinded specimens.  The second stage will create new records in BSI with a subset of the data from the first specimen.  Once complete, a new requisition is created containing the blinded specimens.  The blinded specimens in the new requisition can now be transferred to the destination repository without linking them to the original specimens.  

    The Unblind task can be added to reverse the Blind task, once the specimen no longer need to be blinded.  Completing the Unblind task merges the data from the original specimens into the blinded specimens.  In addition to merging data from the original specimens, the 'blinded' specimens will have the BSI ID of the original specimen set as the Parent ID.  The original specimens will remain with a Blinded Vial Status, the new records will be used for future tracking of the specimen in BSI.

     Example: Let’s say Repository A needs to send several specimens to Repository B for processing, but needs to redact sample information, such as the Study ID. If the researchers in Repository A complete a blind task, new BSI IDs will be reserved and assigned to the specimens and information may be redacted before the transfer. 

    To begin a Blind task and assign new IDs:

    This step is used to assign the new BSI IDs and Current Labels to the specimens that are to be blinded.  The new BSI IDs will be reserved once this step is completed.  If the new Current Labels assigned are in BSI ID format, these IDs will also be reserved.

    1. Add the Blind task and apply it to the desired specimens.
    2. Select Change Status > Assign Blinded IDs from the task's column header menu.  The Assign Blind Task IDs dialog will open.
    3. Press the Assign BSI IDs button on the task bar. Enter manually, Import, or Scan to add the Current Label and BSI ID values that are to be assigned to the blinded specimens.
      • If the Assign BSI IDs button is pressed, the Assign BSI IDs dialog will open. The user can specify which Sample ID and Sequence numbers to start assigning BSI IDs for the specimens with in the editable text fields. The user can also select criteria used to group specimens in the same sample. Press OK to assign the IDs or Cancel to exit the dialog without assigning the IDs.
    4. Select Check Errors and correct any errors.  Errors will be listed in the table at the bottom of the dialog.
    5. Select Commit. The new BSI IDs will be reserved for the blinded specimens.

    To complete an Blind task:

    1. Select the row or rows with a task status of Begun.
    2. Select Mark as Completed from the task's column header menu.  The Blind Completion dialog is displayed containing a subset of the data from the original specimens.  
    3. Modify any data as necessary.  New locations can be assigned to the blinded specimens at this time.
      • Manually enter location data - Location data can be entered directly into the editor.
      • Scan to assign locations - Press the Scan Specimens button and choose the Scan Specimens or Scanning with Translations option from the sub-menu.  See the appropriate section for instructions on scanning to assign locations.
      • Reserve Locations - Select the specimens that are to have locations assigned and press the Locations button.  Select the Reserve Locations option from the sub-menu to open the Location Reservation wizard.  Use the Location Reservation wizard to reserve and assign locations.
    4. Select Check Errors and correct any errors.  Errors will be listed in the table at the bottom of the dialog.
    5. Select Commit.  A batch confirmation dialog will be displayed.
    6. Select OK to commit the batch.  
      • The commit successful message will display the ID of the new requisition created and also any data entry batches created.
      • The specimens will have a Vial Status of Blinded.

    Box Return to Inventory Task

    A Box Return to Inventory task, similar to the Return to Inventory task, allows users to modify specimen data and returns the specimens to the repository’s inventory.  When this task is marked as “Completed”, these specimens are now available for inclusion in any other requisition.  The specimens' Include column status becomes “Returned”, and the Vial Statuses become “In”.  Since the vial is no longer included in the requisition it must be re-requested if a user wishes to do anything else to the vial.

    The completion of a Box Return to Inventory task requires an applied and finished Box Transfer task.

    Example: Let’s say Dr. Murray transferred all of box 10 to Dr. Nemo at Repository B using a Box Transfer task and Dr. Murrary has now completed DNA testing on them. Dr. Murrary will now need to place all of the specimens into his repository's inventory with a Box Return to Inventory task.

    When he completes this task, he specifies that Box 10 will now have an immediate parent container of “Freezer 221-B”. After completing the task, box 10 will be accessible in the sub-hierarchy of Freezer 221-B and all specimens which were originally contained box 10 will still be located in their original row/column within the box. The vial status of the specimen will be updated to "In" meaning that the specimens can be requisitioned again whenever necessary.

    To complete a Box Return to Inventory task:

    1. Add the task and apply it to the desired vials. Every vial in the box must be included in the requisition and have the task applied to it.

    2. Select the rows with the applied task.

    3. Select Mark as Completed from the Change Status menu on the task's column header menu.

    4. The Specify New Box Locations dialog will open. Select the code list button under the New Parent Container box.

      specify_new_box_locations_dialog.jpg
    5. The Locations Tree will open. Select the new parent container for the box. Press OK. After being returned to the Specify New Box Locations dialog, select OK.

    6. The Enter Data for Return to Inventory task dialog will open. Complete any modifications manually or by importing the data.
    7. To complete the task by scanning, select Scan Specimens. Either select Scan Specimen or Scan Specimen with Translation from the menu which opens. In the scan dialog that opens, the user can edit the specimen data.

    8. Select Check Errors and correct any errors.  Errors will be listed in the error table at the bottom of the dialog.
    9. Select Commit.  A batch confirmation dialog will be displayed.

      • Select OK to commit the batch.  A Communicating with Server message will be displayed while the batch is committing.  Once complete, a message showing the batch ID committed will be displayed.

      • Select Cancel to return to the Enter Data for Relabel Task dialog.

    Box Ship Task

    A Box Ship task is used when a box and all specimens inside it are shipped out. If the box/specimens are to be transferred to another repository for processing, a Box Transfer task should be used. The destination for a Box Ship task is assigned in the task properties. When completed, the task status is changed to Completed, the Vial Status for all specimens is changed to Out and the box is deleted from the locations tree. It may also be necessary to print task reports.

    A destination must be set in the Box Ship task’s properties before the task can be completed.

    Example: Repository A sends specimens to requesting researchers who are not part of any repository on their database. David wants to prepare the package ahead of time so that it can be shipped Monday morning. He completes a Package task on the specimens to assign them all to a shipping box in his freezer for the weekend. On Monday morning he completes the Box Ship task. All specimens in the box are required to be shipped via this task, so he can be sure none were mistakenly left behind.

    When he completes this task, he specifies that Box 10 will now have an immediate parent container of “Freezer 221-B”. After completing the task, box 10 will be accessible in the sub-hierarchy of Freezer 221-B and all specimens which were originally contained box 10 will still be located in their original row/column within the box. The vial status of the specimen will be updated to "In" meaning that the specimens can be requisitioned again whenever necessary.

    pBjpj4M9QlOuYS7zY9A6_temp-M.jpg

    To complete a Box Ship task:

    1. Add the task and apply it to the desired specimens. All specimens from the box must be included in the requisition and have this task applied to them before it can be completed.
    2. Select the rows with an Applied task that are to be completed.
    3. Select Mark as Completed or Scan to Complete from the Change Status menu on the task's column header menu:
      • Mark as Completed will change the task status to Completed for all selected rows that have the task applied.
      • Scan to Complete will open the Scan to Complete Task dialog.  From this dialog, the Scan option will open the standard scanning dialog that can be used to scan specimens with a barcode reader.  All specimens in this dialog that have a Yes in the Scanned column will have the task marked as Completed when OK is pressed.
    4. A Warning dialog will be displayed indicating the user is about to change the database.
      • Select Yes to complete the task. The task will be marked as Completed and the Vial Status will be Out.
      • Select Cancel to return to the Requisitions Editor without completing the task or changing the Vial Status of the selected specimen.

    Box Transfer Task

    The Box Transfer task is used to move an entire box and all the specimens located in it to another repository. The repository value of the specimens, and therefore ownership of the specimens, will changed when a Box Transfer task is completed. In order to complete the task, every specimen in the box must be included in the Requisition and have the Box transfer task applied to it. When completed, the box will be deleted from the original repository's location hierarchy.

    Example: Dr. Murray needs to send every specimen in box 10 from Repository A to a colleague at Repository B for DNA analysis. She can use a Box Transfer task.

    Let’s say Dr. Murray uses the Locations tree view to open box 10 from her freezers and highlights all the specimens inside and uses the right mouse button menu to create a requisition for the highlighted specimens. Dr. Murray can apply and complete a Box Transfer task on all of the specimens in the requisition, which will transfer the specimens and box 10 to Repository B, maintaining the box location data of the specimens. The box which the specimens are in will no longer exist on her repository's locations hierarchy.

    To complete a Box Transfer task:

    1. Add the task and apply it to the desired vials.
    2. Select the rows with an Applied task that are to be completed.
    3. Select Mark as Completed or Scan to Complete from the Change Status menu on the task's column header menu.
        • Mark as Completed will change the task status to Completed for all selected rows that have the task applied.
        • Scan to Complete will open the Scan to Complete Task dialog.
    4. After completing the task, a Warning dialog will be displayed indicating a user is about to change the database.
      • Select Yes to complete the task.  The task will be marked as Completed.
      • Select Cancel to return to the Requisitions Editor without completing the task.

    Broken/Destroyed, Destroy, Empty, and Lost Tasks

    The tasks Broken/Destroyed, Destroy, Empty and Lost will change a specimen's Vial Status when the task is completed.

    The Broken/Destroyed task changes the Vial Status to Broken/Destroyed. No other field values for the specimen are altered. This task cannot be applied to specimens stored in a multi-specimen container (MSC). For instance:

    Example Broken/Destroyed Task: Dr. Furter has recently realized that one of his underlings left Freezer 233 door open overnight and all the samples inside are no longer viable. He needs to remove these specimens and make notes about which underlings made the mistake.
    If he requisitions those specimens and completes the Broken/Destroyed task on them, the specimens will be assigned a Vial Status of “Broken/Destroyed” and their location values will be removed. Dr. Furter can detail the underling’s mistake in the task properties for future reference.

    The Destroy task also changes the Vial Status to Broken/Destroyed. As with the Broken/Destroyed task, no other specimen data is altered. This task cannot be applied to specimens stored in a multi-specimen container (MSC). For instance:

    Example Destroy Task: Dr. Furter has decided that the loss of all specimens in Freezer 233 makes his RHPS study impossible to complete, and would like to destroy all specimens from that study. After noting the reason for his decision in the task properties, Dr. Furter can complete the Destroy task. All specimens which were destroyed have the location value removed and the Vial Status set to “Broken/Destroyed”, which allows Dr. Furter to delete the associated locations.

    The Empty task changes the Vial Status to Empty. Other tasks and processes can be used to reduce the volume of a specimen to '0', but will not change the vial status of the specimen. To change the vial status to reflect the volume, use the Empty task. For instance:

    Example Empty Task: After pooling several specimens together to create a single specimen for his study RHPS, Dr. Furter needs to update the original specimen records so he knows that they are no longer available for his experiments. An Empty task completed in the same requisition can be used to change the Vial Status of the specimens to “Empty”. Once complete, the location data associated with the specimens will be removed and Dr. Furter can search BSI for specimens available to be requisitioned without returning these empty specimen records.

    The Lost task changes the Vial Status to Missing/Lost. This tracks information about specimens which are missing from the inventory. The task removes them from the pool of available specimens. If the specimen is stored in a multi-specimen container (MSC), then this task must be applied to all specimens in that MSC. For instance:

    Example Lost Task: Let’s say Dr. Nick opened his Freezer 001 this morning and noticed that several specimens he expected to find were missing. He needs to document the missing specimens in BSI then investigate to determine where they went. Dr. Nick uses a Lost task to modify the specimens’ Vial Status to “Lost/Missing”. Several weeks later, he realizes that a new intern mistakenly placed the specimens in Freezer 010. Dr. Nick uses a Return to Inventory task to move the specimens to the correct freezer and change their Vial Status back to “In”.

    To complete one of these tasks:

    1. Add the task and apply it to the desired specimen.

    2. Select the rows with an Applied task in the Requisitions Editor that are to be completed.

    3. Select Mark as Completed or Scan to Complete from the task's column header menu. If scanning to complete, the data will not be editable in the Scan to Complete dialog.

    4. A Warning dialog will be displayed indicating a user is about to change the database. Select Yes to complete the task or Cancel to return to the Requisitions Editor without completing the task or changing the Vial Status for the selected specimens. If Yes was selected, the task will be marked as Completed and the Vial Status will be changed.

    Create Child Specimens Task

    The Create Child Specimens task is a single step task that results in one or more children to be created for the selected parent(s).

    When completing the task, the Child Completion dialog allows users to enter data for the children and change data for the parents.  When all the information has been entered and the changes have been committed, the task status for each of the parent specimens becomes Completed and the child specimens become 'real’ specimens.

    Example: Professor Charles needs to test the effects of his new serum on whole blood. He uses a Create Child Specimens task, creating two new child blood specimens from a "parent" blood specimen.  Then he performs tests on the children specimens.

    To complete the task:

    1. Select Mark as Completed from the task's column header menu. The Specify Children dialog will open.
    2. From this menu, there are several options, such as generating children from the database, from a template, or generating different numbers of children per parent. BSI IDs assigned to child specimens will be unique, but not reserved. Select an option. See Generating Children below for more information.
    3. Press OK to create the children. The Create Child Specimens dialog will open.
    4. Users can Import data for children, edit Child Default Data, Scan Specimens and Check Errors.  They can also select Locations, Select Column View Template if it should be different than the template used in the requisition editor, Save and Save with Translation.
      1. If saving with translation, the user will be prompted to specify whether they are exporting all rows or only the selected ones, then select the translation to be used. In either case the user will next select a location to save the file then press Save.
      2. Users can right click the Volume column and select Subtract Child Values to subtract the total of all child volumes from the parent volume.
      3. Users may also use the Delete Rows icon to remove child rows for specimens which were not created.
    5. When all errors have been resolved, the user can press Commit. The Committing Data dialog will open and notify the user that committing a batch will permanently alter the database. Press OK to continue or Cancel to return to the Child Completion dialog.
    6. The Parent Volume dialog may open, prompting the user to verify that they have updated the parent specimen volumes. Select Yes to continue or No to return to the Child Completion dialog and edit volumes.
    7. A dialog will open to notify the user of a successful completion or of any errors encountered. Press OK.
    8. Once completed, the new specimen(s) will be displayed in the Requisitions Editor. They will be available to have tasks applied to them and completed.

    Generating children from the database or from a template

    Children can be generated either from the database or from a template. Generating from the database creates a set, user defined number of children for each parent specimen. To create children via this method, follow these steps:

    1. Enter a starting Sequence number.
    2. Select an option to assign sequence numbers:
      • Assign Same Starting Sequence for All Sample IDs - The system will look for the first unused sequential block of sequence numbers available to all of the parents’ Sample IDs. The size of the block is determined by the largest number of children created for a sample. Once a block of sequence numbers is found they are assigned to the children sequentially until all children have been assigned sequence numbers.
      • Assess Starting Sequence by Individual Sample ID - The system will look for the first unused continuous block of sequence numbers available for children belonging to each individual Sample ID. Once a block of sequence numbers is found they are assigned to the children sequentially until all children have been assigned sequence numbers.example_assigning_same_starting_sequence_to_all_samples_versus_by_individual_sample_id.png
    3. Specify the number of children to be created per parent:
      • Same Number of Children per Parent – Enter a number of children to be created. For each parent, this is the number of children BSI will create.
      • Different Number of Children per Parent – If this option is selected, the Specify different number of children per parent dialog will open after selecting OK. On this dialog, the Number of Children field may be manually updated or imported. When finished, select OK. For each parent, the specific number of children entered for that row will be added to the editor.

    Generating children from a template creates children according to the number of rows in the chosen template. If using a multiline template, the number of rows in the template will be the number of children created for each parent. Default values and commands set in the template will be applied to the new children. To create children via this method, follow these steps:

    • Select the Generate Children from a Template radial option.
    • Select Browse.
    • Choose a template.
    • Select OK.

    Create Microarray Task

    Microarray specimens are created from multiple cores (or aliquots) that have grid positions within the microarray. A Microarray Layout Map can be printed to display the grid position of cores in the microarray. BSI tracks the microarray specimen as a single specimen and, at the same time, tracks the specimens that make up the microarray to preserve lineage. Create Microarray tasks are completed in two phases in the Requisition Editor.  

    When the task is added to specimens, the Vial Type must be specified. In order for Task Properties dialog to list a Vial Type as a choice in the codes list associated with this field, the Vial Type must contain specifications for the row and column values. A valid Vial Type, if not already listed, can be created in the lkup_vial_type code list.

    After a microarray is created and the Create Microarray task is complete, users can apply the Create Microarray Tasks to add more cores to the microarray or Modify Microarray Task to edit the microarray.

    Example: Mr. Richards is experimenting on the effects of solar radiation on human tissue and blood. He has added several tissue specimens from different subjects, at various radiation levels to BSI. He would like to test them all at once, so Mr. Richards uses a requisition to place the specimens into a microarray. He arranges the smaller, aliquoted tissue specimens on the microarray in a grid pattern, with each row being from a different subject and the radiation level increasing from the left side to the right. Then he returns the larger parent specimens to the freezers and can begin comparing the microarray.

    He creates another microarray for the whole blood specimens and repeats the same tests on them.

    To begin a Create Microarray task:

    1. Add the Create Microarray task and apply it to all desired specimen.
    2. Upon applying the task, the Create Microarray Task Specification dialog opens. Specify a Vial Type with a row and column specification before creating a microarray. Select the OK button once the Vial Type has been chosen.  
    3. To create the microarray, select Change Status > Create Cores from the task’s column header menu.  The Microarray Specification dialog opens.  The top pane contains the parent specimen, including all sample and specimen data. The bottom of this pane displays the row and column layout for the cores. There are two display options for this section:
        • From Layout view users can drag and drop the parent specimens into a table set up like a grid that represents the microarray. Click on any field of a specimen in the top pane, and drag it to a desired location in the grid on the bottom pane. 
      microarray_layout_view.png
        • The Contents tab shows a spreadsheet view of the microarray. From Contents view, the table is set up so that the users can manually enter data, use mass change, or import data into the row and column fields. Table data includes the microarray Row & Column and the BSI ID of the sample in that particular space.microarray_contents_tab_view.jpg

        • The dialog also has a View menu, which allows the user to save the field order of the dialog or revert to the default field order for the database. If fields are rearranged or hidden, then the user view is saved, the new arrangement of fields will be displayed by default every time that user views this dialog.
    4. Add cores to the microarray grid using one of the two display options detailed above. Select Check Errors to identify if any errors were made. The errors will be highlighted in red and listed in a Note.
      • The first row and first column are reserved for planning purposes. Users can enter data to help guide organization of their microarray while they are adding cores to it. For example, you may wish to note Subject IDs in the planning column and dates in the planning row to ease the creation of a microarray capturing change over time. This data will be saved with the microarray.
    5. Select the OK button to save the microarray and return to the Requisition Editor. The task will be marked as Begun in the Requisition Editor for all specimens with the task applied.

    The next step is to complete the task.

    To complete a Create Microarray task:

    1. Select the Records with the begun task. Select Change Status > Mark as Completed to complete the task. The Specify Microarray and Core IDs dialog will open. mark_requisition_task_as_completed.jpg
    2. Add the Starting Microarray Sample ID & Sequence and the Starting Core Sequence. These values may be prepopulated by user preferences. Press OK.
    3. The Complete Microarray Task dialog appears.  The newly created microarray specimen shows up with purple as its background and the newly created array cores will show up with green backgrounds.
    4. Update the information for the microarray, array cores and the parent specimens. The Import button, Scan Specimens button, and the Save button are available to assist in completing the microarray task.  
    5. Assign locations for the microarray. Select the Locations button to open the Location Reservation wizard. Use the Location Reservation wizard to reserve and assign locations.
    6. Select Check Errors. If there are errors, they will be listed in a Note. If there are no errors when committing the batch, a dialog will be displayed listing the Batch IDs for the parent and child specimen batches. Select the OK button on this dialog to return to the Requisition Editor.  
      • If there are errors when committing the batch, a dialog will be displayed indicating that errors were encountered.  Select the OK button to return to the Microarray Task Completion dialog to save the work or correct the errors. Select the Save button on the Microarray Task Completion dialog to save the table as a comma-delimited file.
    7. When data entry is completed, select the Commit button. The Committing Data dialog will open. Select the OK button to commit the batch. The Parent Volume dialog will open, asking if the user has updated the volume of any parent specimens. Press Yes to continue or No to return to the Complete Microarray task dialog. 
    8. Committing the batch will:
      • Commit the data for the microarray specimen. This specimen will have an include status of Included and a Vial Status of Reserved. This record represents the actual microarray. 
      • Create new records for the cores. The Vial Status of core specimens will be “Array Core”. Array cores will not be listed in the Requisition Editor as they are now tracked with the microarray.
      • List the new microarray specimen in the Requisition Editor.
    9. If the task is successful, the Commit Successful dialog will open and display the parent batch and child batch numbers. If it is not successful, a dialog will open and allow the user to save the table for later editing or return to the Microarray Task Completion dialog.

    Discrepancy Task

    The Discrepancy task allows users to record information regarding discrepancies found while completing requisitions. Users can generate a Discrepancy Task Report containing information regarding the discrepancy and resolution data including the date the discrepancy report was sent and the date the resolution was received.

    Upon addition and resolution of a requisition discrepancy, the repository contact and the submitting user will receive an email notification. Submitting users can opt out of this notification via user preference.

    This task can be manually added but will also be automatically added if a discrepancy is added to a field via the RMB.

    Example: Dr. Carter has added several whole blood specimens to a new requisition. After walking to the freezer and removing the specimens, he realizes that two of them have handwritten labels, despite BSI noting that they have barcoded labels. He highlights these specimens, then from the “Label Status” right mouse button column header menu he selects Discrepancies > Add Discrepancy. Dr. Carter notes the difference and a Discrepancy task is applied to the specimens. He must then select Discrepancies > Resolve Discrepancy and note how the discrepancy was resolved. He chooses to copy the observed value of Handwritten to the specimen records. Dr. Carter Edits the Discrepancy task properties to include the required fields “Date Report Sent” and “Date Resolution Received”, then marks the task as complete.

    To complete a discrepancy task:

    1. Add the task and apply it to the desired vials.

      • Alternately, use the right mouse button to add a discrepancy to an appropriate specimen or sample field and a Discrepancy task will be automatically added to the selected specimen(s).

    2. Generate the Discrepancy Task Report from the task column header menu. Discrepancy_Task_Report_menu_option.jpg

    3. Select Edit Task… from the task column header menu and fill in the Date Report Sent and Date Resolution Received if you have not done so already.

      • Note that Date Report Sent and Date Resolution Received are not required to apply the task but are required to complete a Discrepancy Task.

    4. Select the rows with an applied task in the Requisitions Editor.

    5. The user could alternately select Scan to Complete from the task header menu.

      • Select Mark as Completed from the task's column header menu. The task will be marked as completed.

    Pull, Investigate, and Generic Tasks

    Generic tasks include the Pull task, Investigate task and Generic task.  These tasks are available for record keeping within the Requisitions Editor.  When completed, these tasks do not change any specimen data in the main database.

    Example: If the user needed to track an action that doesn’t change specimen data, which is not specifically captured by another task, they can use a Generic task. Let’s say particular researcher needs to track the physical receipt of specimens which were shipped to outside facilities via BSI.

    1. The user creates a new requisition, adds specimens, and applies a Ship task and a Generic task to them. The user changes the task label from “Generic” to “Receipt of Shipment” to make this generic type task name more informative.
    2. Once the Ship task is completed, the user could wait any length of time before completing the Generic task, noting that the task completion signifies.
    3. The Shipment has been received.

    Task reports can be printed for the Pull, Investigate, and Generic tasks.

    To Complete a Pull, Investigate or Generic task:

    Mark_Task_as_Completed.jpg
    1. Add the task and apply it to the desired specimens.

    2. Select the rows with an Applied task that are to be completed.

    3. Select Mark as Completed or Scan to Complete from the Change Status menu on the task's column header menu:

      • Mark as Completed will change the task status to Completed for all selected rows that have the task applied.

      • Scan to Complete will open the Scan to Complete Task dialog. When OK is pressed, all specimens in this dialog that have a Yes in the Scanned column will have the task marked as Completed

    The Generic task alters no data in BSI and serves to track an action taken with regard to the specimens. Similarly, The Investigate and Pull tasks also track specific actions performed on specimens without altering data. For Example:

    Investigate Task: Let’s say Dr. Jekyll suspected that several specimens were incorrectly labelled and needed to verify that before fixing the labels in BSI. He would first create a requisition then include those specimens in it. Next, he would apply and complete the Investigate task on all specimens, to track that he verified the label status of each specimen. In this case, if Dr. Jekyll were mistaken, and all specimens were labelled correctly, the Investigate task would still serve as a record that the user verified their status.

    Pull Task: In Repository A, several research aides are responsible for pulling specimens from freezers and delivering them to researchers. The research aids could create a requisition and apply a pull task to the specimens of interest.  Then the research aids could run a pull report from the pull task to print and bring with them to the freezer, in order to make sure they locate the correct specimens.  After pulling the correct specimens from the freezer, the research aid may scan to complete the task (which would provide another confirmation the correct specimen was pulled from the freezer) or mark the task as complete manually. 

    Hold Task

    The Hold task is used to change the Vial Status to On Hold when the task is completed.  This is done to reserve the specimens for a special use.

    Example: Dr. Watson needs to reserve several specific specimens, which an outside researcher will use to test brain tumors after she secures a grant. He uses a Hold task in BSI to locate the specimens the researcher needs to test and updates their Vial Status to “On Hold”. Other researchers will be unable to request these specific specimens while their status is “On Hold”.

    To complete a Hold task:

    Mark_Task_as_Completed.jpg
    1. Add the task and apply it to the desired specimens.
    2. Select the rows with an Applied task in the Requisitions Editor that are to be completed.
    3. Select Mark as Completed or Scan to Complete from the task's column header menu. If scanning to complete, the Scan to Complete Task dialog that opens will not be editable.
    4. A Warning dialog will be displayed indicating the user is about to change the database. Select Yes to complete the task or Cancel to return to the Requisitions Editor without completing the task or changing the Vial Status for the selected specimens. If Yes was selected, the task will be marked as Completed and the Vial Status will be changed to On Hold.

    Modify Task

    A Modify Task is a modification to specimens completed through a requisition. When completed, a modify batch is completed in the background and updated in the Requisition Editor.

    Example: Let’s say Mr. Lector tracks the liver toxins included in each of his liver specimens via a custom multi-choice field in BSI called “Liver Toxins”. After processing the specimens in a requisition, he would like to add the appropriate values for the specimens from several subjects to the "Liver Toxins" field. He doesn’t need to record each individual test result, so Mr. Lector uses a Modify task to change the value of the “Liver Toxins” field for each specimen then, in the requisition, uses a Returns to Inventory task to return the specimens to inventory.

    To complete a Modify Task:

    1. Add the Modify Task and apply it to the desired specimen.
    2. Select Mark as Completed from the task's column header menu. The Enter Data for Modify Task dialog will open.
    3. Enter any specimen data changed during the Modify Task.
    4. From this dialog, users can:
      • Check errors
      • Import specimen
      • Assign locations
      • Apply a task template to the specimen
    5. If the user is not scanning to complete, then once all changes have been made, select Commit.
    6. A Warning dialog will be displayed indicating the user is about to change the database.
      • Select Yes to complete the task.  The task will be marked as Completed. The changes made in the Modify Task will be shown as bold in the corresponding Data Entry Batch that was automatically created during task completion. The data entry batch number will be displayed in the Commit Successful dialog.
      • Select Cancel to return to the Requisitions Editor without completing the task .

    Modify Microarray Task

    After a microarray is created, it can be modified. Microarray grid data is editable via a Modify Microarray task. While modifying a microarray, users will not be able to add more specimens to the microarray. However, users can add more cores using the original microarray task. The following modifications can be performed with the Modify Microarray task:

    • Change row and column values. In Layout view, drag and drop the cores to the desired location or change the locations in Contents view.
    • Print a microarray map from this dialog. Select the Print icon. The Select Barcode Format dialog opens. Choose the correct format and select the OK button to generate the map.
    • Cancel the dialog by selecting the Cancel button.
    • Check errors with the Check Errors button. The errors will be listed in a Note.
    • Delete cores from the microarray. When the core is deleted and the changes committed, the cores associated specimen record is included in the current requisition with a Vial Status of reserved.
    • Edit grid planning rows.

    Example: After creating his microarray, Mr. Richards realizes that he mistakenly switched the grid locations of two tissue cores while entering data in BSI. He uses a Modify Microarray task to change the grid position of the two cores to their physical location.

    To modify a microarray:

    1. Add the Modify Microarray task and apply the task to an existing microarray.
    2. Select the specimen with the applied task, and then select Change Status > Mark as Completed and the Microarray Specification dialog appears.
    3. In the Microarray Specification dialog, make modifications to the microarray. The modifications that can be made are detailed in the list above.
    4. Select the Commit button. A communication with server message is displayed. In the Requisition Editor the task will be marked as Completed.

    Package Task

    A Package task is used to create a new box with the specimens inside it and to store that box temporarily in the repository’s location hierarchy. Users may subsequently want to ship/transfer the entire box to another facility.

    When completed, the task status is changed to Completed and the box is created in the locations tree. It may also be necessary to print task reports.

    Example: Repository A sends specimens to requesting researchers who are not part of any repository on their database. David wants to prepare the package ahead of time so that it can be shipped Monday morning. He completes a Package task on the specimens to assign them all to a shipping box in his freezer for the weekend. On Monday morning he completes the Box Ship task. All specimens in the box are required to be shipped via this task, so he can be sure none were mistakenly left behind.

    package_task_generating_boxes.pngTo begin a Package task:

    This step is used to create the box(es) which specimens will be put into for shipping or storage.

    1. Add the Package task and apply it to the desired specimens.
    2. Select Specify Package Box Data from the task's column header menu.  The Specify Box Data dialog will open.
    3. Highlight specimens and select Generate. The Box Data Generation dialog will open.
    4. Select the Parent Container inside which new boxes will be created.
      1. The code list button for this field will open the current repository’s location hierarchy.
      2. Expand the hierarchy and highlight the direct parent container for the new box(es).
      3. Select OK.
    5. Enter a Box Label, Box Layout, Box Label Increment, Starting Row, and Starting Col values, as desired.
    6. Select Assignment Pattern Options. By default, these options are selected based on user preference values.
    7. Select OK.
    8. Select Check Errors and correct any errors.  Errors will be listed in the table at the bottom of the dialog.
    9. Select Commit.

    To complete a Package task:

    1. Select the row or rows with a task status of Begun.
    2. Select Mark as Completed or Scan to Complete from the Change Status menu on the task's column header menu:
      • Mark as Completed will open the Complete Package Task dialog. Verify that box data is correct and select Commit.
      • Scan to Complete will open the Scan to Complete Task dialog. From this dialog, the Scan option will open the standard scanning dialog that can be used to scan specimens with a barcode reader. All specimens in this dialog that have a Yes in the Scanned column will have the task marked as Completed when OK is pressed.
    3. The box(es) will be created and specimens will be moved to them.

    If the new box’s label already exists in the selected parent container, BSI will rename the label to an unused value. A warning dialog will open displaying the requested label and the renamed label. If the selected parent container is reserved for a study, then the new box(es) will also be reserved for that study.

    Pool Task

    Pool tasks are similar to the Combine option available in an Aliquot task. They are used when combining material from multiple specimens into a single, new specimen. The “Complete Pool Task” role permission is required to begin or complete this task.

    The only way to report on the specific parent specimens combined into a child specimen is through the standard report “Combination ID for Pooled Vials”.

    Pool tasks are completed in two phases in the Requisitions Editor. First, BSI IDs for the child specimens are requested and assigned in the Request Available Child BSI ID dialog. A parent specimen cannot be selected for more than one combination in the same Pool task. Once complete, child specimens are then listed in the editor and the task is marked as Begun but the specimens do not become 'real' until the task is completed.

    After an Aliquot or Process task is begun, the following child specimen fields can be edited, if necessary: Sample ID, Sequence, Volume, Volume Unit, Study ID, Current Label and Material Type. The Current Label field can be printed. See the section on the Current Label column menu for more information on editing and printing labels from the Requisitions editor.

    When completing the task, the Child Completion dialog allows users to enter data for the children and change data for the parents. When all the information has been entered and the changes have been committed, the task status for each of the parent specimens becomes Completed and the child specimens become 'real’ specimens in BSI.

    Example: Doc Brown had five specimens but each only had a tiny amount of protein material needed for a particular lab test.  When the protein material was extracted and combined, Doc had enough for testing.  To combine specimens, Doc took an empty vial and placed one milliliter of extracted protein material from each specimen.  In BSI, this is referred to as a ‘Pool’ task and it reflects the process of placing all or a fraction of several specimens into an empty container.  Since Doc Brown likes to keep a copy of his work in a file, he printed a ‘Combination ID for Pooled Vials’ report.

    To begin a Pool task:

    1. After adding the task, select Specify Pooled Specimens from the task's column header menu.Begin Pool Task.jpg
    2. The Request Available Child IDs dialog will open, and the Specify Pooled Specimens dialog will open in front of it.
    3. From this dialog, there are several options which can be selected from:Specify Pooled Specimens dialog.png
      • Select a Parent Grouping Option – There are two radial options, one of which must be selected to continue in the dialog.
        • By Grouping Fields – You can select, from a code list, the fields which you wish to group specimens for pooling by.
        • By Current Sort and Number – This option allows you to pool specimens by the current sorted order into child specimen(s) in sets of a specified number.

    For example, you could select “Material Type” as a grouping field if you later wanted to combine 10 samples from the same subject’s Whole Blood into a child specimen and 10 samples of the same subject’s Plasma into a second child specimen.

      • The Pool Child Starting Sequence must be entered. This is the sequence number associated with the new child specimen, which will become the second half of its BSI ID.
      • Select one of the following radial button options:
        • Assign Same Starting Sequence for All Sample IDs - The system will look for the first unused sequential block of sequence numbers available to all of the parents’ Sample IDs. The size of the block is determined by the largest number of children created for a sample. Once a block of sequence numbers is found they are assigned to the children sequentially until all children have been assigned sequence numbers.
        • Assess Starting Sequence by Individual Sample ID - The system will look for the first unused continuous block of sequence numbers available for children belonging to each individual Sample ID. Once a block of sequence numbers is found they are assigned to the children sequentially until all children have been assigned sequence numbers

    option to assign by sample id.PNG

    1. To continue, select OK. The specimens are automatically grouped and combined into child specimens, which is denoted by the Parent specimens’ “Combination ID” value being the BSI ID of the child vial it was used to create. BSI IDs assigned to child specimens will be unique, but not reserved. The child specimen row will be highlighted in green.
      • Note – if Material Types, Volume Units, or Sample level data of the parent specimens do not match, a warning dialog will open asking if you really wish to pool the specimens. If this is purposeful, BSI will not automatically fill in a child specimen’s Material Type.
      • The Child volume will be the sum total of all combined specimens,  though those combined specimens will retain their volume value.Request Available Child BSI IDs.jpg

    5. If, instead, you don’t want to use any of those options, you can select Cancel to exit the dialog and use tools on the Request Available Child BSI ID(s) dialog to begin the task.
    6. Enter or edit any values necessary.
    7. Users can Scan Vials and Check Errors. All errors must be resolved before the next step. Users can Import data for children and edit Child Default Data only if they have added new child specimens via the Children button. The Combine option is used to combine parent specimens into a child specimen after using the Children button to create new specimens.
    8. When all changes have been made, press OK. The task status icon will be changed to “Begun” and the child will be added to the Requisition as a new row. The new row will be shown in green, with an Include status of “Reserved Child”.

    To Complete a Pool task:

    1. Select Mark as Completed from the task's column header menu. The Child Completion dialog will open.
    2. Edit any data which needs to be updated for the parent or child specimens. Vial and Sample level fields can be given certain properties with regard to editability in the Customization module, which apply to Pool tasks in Requisitions. Marking a box for the “Aliquot Process” row will apply the property to this task.
      • Most fields allow the user to select “Copy From Parent” from the right mouse button column header menu when selecting child specimens. This copies the parent specimen value for the selected field to the child.copy from parent.jpg
      • From the “Volume” right mouse button column header menu, the option to “Subtract Child Value” is also available. This automatically subtracts the Child specimen volume from the parent’s volume. The total child volume is divided by the number of parents contributing to it and that value is subtracted from each parent.subtract child value.jpg
    3. Users have all the same options from the Request Available Child IDs available for them in this dialog. Additionally, they can also select Locations, Select Column View Template (if it should be different than the template used in the requisition editor), Save, and Save with Translation.
      • If saving with translation, the user will be prompted to specify whether they are exporting all rows or only the selected ones, then select the translation to be used. In either case the user will next select a location to save the file then press Save.
    4. When all errors have been resolved, the user can press Commit. The Committing Data dialog will open and notify the user that committing a batch will permanently alter the database. Press OK to continue or Cancel to return to the Child Completion dialog.
    5. The Parent Volume dialog will open, unless the user preference to not display this dialog is selected, prompting the user to verify that they have updated the parent specimen volumes. Select Yes to continue or No to return to the Child Completion dialog and edit volumes.
    6. A dialog will open to notify the user of a successful completion or of any errors encountered. Press OK.

    Once completed, the new specimen(s) will be displayed in the Requisitions Editor with an Include status of Included. They will be available to have tasks applied to them and completed.

    Procedure Task

    The Procedure task is used to enter specimens’ results for a test or experiment via Requisitions.

    Example: Let’s say Dr. Hu has decided to begin using requisition tasks to track her specimens use. She already has a results batch recording her initial experiments on time travel with a group of specimens and would like to add another run of data to the first.

    1. After requisitioning her specimens, Dr. Hu can add the Procedure task. She will specify the procedure she will run and enter the batch ID where her previous results are recorded.
    2. She can then select Execute Assay to enter run properties and map her specimens.
    3. Dr. Hu uses the Add Results option to import her results data to the run.
    4. After importing all data, Dr. Hu can mark the procedure task as completed and return specimens to her inventory.

    To complete a Procedure task:

    1. In a requisition editor, highlight the specimens to which the procedure task will be applied.
    2. Click the Add Task icon from the toolbar. The Select a Task Type dialog will open. Highlight Procedure and click the OK button.
    3. The Procedure Task Specification dialog will open.  Fill in required and desired fields.   Procedure_Task_Properties.jpg
    4. By default, the Create New Results Batch checkbox is marked, which will create a new results batch for this task. If the user unmarks this checkbox, the Result Batch ID fields becomes required and the user must enter an existing results batch ID. The procedure task will then be associated with the entered batch ID when completed.
    5. When finished, click the OK button on the Procedure Task Specification dialog.
    6. In the requisition editor, the Procedure task will be applied to all previously highlighted specimen rows.
    7. To mark the Procedure task as begun, highlight specimens with the Procedure task applied.  Right click the Procedure column header and select Execute Assay. Right_mouse_button_Execute_Assay_option.jpg
    8. The Execute Assay wizard will open.
      • Depending on the Procedure Definition, there may be more pages in the wizard than listed here.
      • Anywhere the Copy button is available in the Wizard, pressing the Copy button copies data from the procedure definition into the Wizard.
    9. Fill in the Run Properties on the first page of the Wizard.  When finished, click the Next button. procedure_run_properties.jpg
    10. On the Specimen Mapping page, drag and drop specimens from the top panel into the cells of the bottom panel to show the mapping of the specimens. In the bottom panel, right click any cell to open a menu in which to mark that cell as a specific Standard or Characteristic defined for the procedure . This panel will automatically be set to view all mappings. The Remove Specimen from Mapping right mouse button and toolbar option will remove the mappings from all highlighted cells in the lower panel. When finished on the Specimen Mapping page, click the Execute button.Specimen_mapping_in_the_Execute_Assay_wizard.jpg
    11. In the requisition editor, the Procedure task will be marked as begun.
    12. Right click on the Procedure task column header again. From the menu, select Add Results.  This will open the Result Batch Editor. Add data and save. The user can also select Specify and Verify Specimen Order from the task header menu under the Specimen Order option.
    13. Back in the Requisition Editor, highlight the specimens and right click the Procedure column header one last time.  Select Mark as Completed from the menu.
    14. Now the requisition reflects that a procedure has been completed on these specimens.

    Relabel Task

    A Relabel task can be used when a user physically changes the current label for a specimen, such as when blinding specimens.  The BSI ID on a specimen does NOT change, only the current label.  Note: Users can change the Current Label field in a Data Entry Modify batch. This task is used to track work, not data correcting.

    Example: Dr. Stone requisitions 100 DNA specimens to map the appearance of a particular set of genetic markers. He realizes after pulling the specimens from his freezer that the labels are peeling away from the specimens’ containers. Dr. Stone uses a Relabel task to note his replacement of the labels. Since his lab uses the BSI ID to uniquely label each specimen, he uses the Copy BSI ID button to copy the BSI ID value to the new label column.

    To complete a Relabel task:

    1. Add the task and apply it to the desired specimens.
    2. Select the rows with an Applied task that are to be completed.
    3. Select Mark as Completed from the task column header menu.Mark_Relabel_Task_as_Completed.jpg
    4. The Enter Data for Relabel Task dialog shows the BSI ID, Current Label, Study ID, Repository, Label Status and New Label. On the dialog, users can:
        • Print, Print Errors and Print Labels
        • Import data
        • Scan Vials
        • Save to Disk - This option allows users to save the data in the dialog to their computer.
        • Check Errors
        • Use BSI ID - This option will copy the BSI ID of each specimen into the New Label field.
      Enter_Data_for_Relabel_task_dialog.jpg
    5. Press Commit. If the batch was sucessfully committed, a dialog will open displaying the batch number.

    There is a System Preference available which will split this task into two parts. 

    To begin a Relabel task:

    1. Add the task and apply it to the desired specimens.
    2. Select the rows with an Applied task that are to be completed.
    3. Select Specify New Labels from the task's column header menu. The Enter Data for Relabel Task dialog will open.
    4. The Enter Data for Relabel Task dialog will open displaying the BSI ID, Current Label, Study ID, Repository, Label Status and New Label columns.  The New Label columns is editable.  In addition to standard print options, users can:
        • Select the checkbox at the bottom of the dialog titled "Enforce BSI ID standards for new labels"  to prevent any new labels from being entered that do not conform to the standard BSI ID format.
        • Enter the New Label field manually.
        • Select the Check Errors button.
        • Select Scan Specimens or Scan Specimens with Translation.
        • Select the Import button to Import new labels, matching on either BSI ID or Current Label.
        • Select rows and click Use BSI ID to fill in the New Label field with the BSI ID.
        • Select Save to Disk to save a comma delimited file of the dialog.
        • Select rows and click Print Labels to select a label format, assign fields and open the Print Labels editor with the selected information.
      Enter_Data_for_Relabel_task_dialog_in_Begin_step_of_Relabel_task.jpg
    5. When all errors have been corrected, press OK to save before exiting the dialog and returning to the Requisition Editor. The task will have a status of Begun.

    To complete a Relabel task:

    1. Select the specimens with a task status of Begun.
    2. From the task header menu, under the Change Status option select either Scan to Complete or Mark as Complete. Both options allow the Label Status and New Label fields to be manually edited.
    3. If Mark as Completed from the task's column header menu is selected.  The Enter Data for Relabel Task dialog will open displaying the BSI ID, Current Label, Study ID, Repository, Label Status and New Label columns.  The New Label column is editable.  In addition to standard print options, users can:
      • Select the checkbox at the bottom of the dialog titled "Enforce BSI ID standards for new labels"  to prevent any new labels from being entered that do not conform to the standard BSI ID format.
      • Enter the New Label and Label Status fields manually.
      • Select the Check Errors button.
      • Select Scan Specimens or Scan Specimens with Translation.
      • Select the Import button to Import new labels, matching on either BSI ID or Current Label.
      • Select rows and click Use BSI ID to fill in the New Label field with the BSI ID.
      • Select Save to Disk to save a comma delimited file of the dialog.
      • Select rows and click Print Labels to select a label format, assign fields and open the Print Labels editor with the selected information.
    4. Enter values.
    5. Correct any errors, if necessary, and select Check Errors to verify there are no outstanding errors.  The Commit button will become enabled once all errors on the dialog have been resolved.
    6. Select Commit to complete the task.  A batch confirmation dialog will be displayed.
      • Select OK to commit the batch.  
      • Select Cancel to return to the Enter Data for Relabel Task dialog.
      • The batch number will be displayed in the Commit Successful dialog.

    Once a Relabel task has been completed, the Current Label field will be changed in the main database.  Changing the task status to Redo will not return the Current Label field to its previous value.

    Returned Task

    A Returned task tells the system the specimen has been returned to the repository after having been shipped out - this does NOT return the specimen to the repository’s inventory.  When the task is completed the Vial Status will change to Reserved and is available for further processing in the Requisitions Editor.  A Returned task can also be used to change the Vial Status back to Reserved after previously completing a task of Broken/Destroyed, Destroyed, Empty or Lost.

    A Returned task cannot be used to return a specimen to a Reserved status in a requisition after completing a Transfer Out or a Return to Inventory task.

    Example: A researcher, Ms. Katz, recently shipped a box of specimens to an outside research facility. The facility received the specimens but realized that they only needed 50 of them. After the facility sends the remaining specimens back to Dr. Katz, she uses the Returned task to receive the 50 shipped specimens. These specimens will have a Vial Status of “Reserved” and be given an Include column status of “Included” in the requisition. She can then return them to her inventory for further use via a Return to Inventory task, which will change the Vial Status to “In” and mark the specimens’ Include column status as “Returned”. Clarify the different between Return and Return to Inventory.  I think it has to do with vial status and if the specimens are still included in the req.

    To complete a Returned task:

    1. Add the task and apply it to the desired specimens.

    2. Select the rows, with an Applied task, that are to be completed.

    3. Select Mark as Completed or Scan to Complete from the task's column header menu.

      Mark_a_Returned_task_as_completed.jpg
    4. A Warning dialog will be displayed indicating you are about to change the database.

      • Select Yes to complete the task.  The task will be marked as Completed and the Vial Status will be Reserved.

      • Select Cancel to return to the Requisitions Editor without completing the task or changing the Vial Status of the selected specimens.

    Return to Inventory (RTI) Task

    A Return to Inventory task allows users to modify specimen data and returns the specimen to the repository’s inventory.  When this task is marked Completed, this specimen is now available for inclusion in any other requisition.  The specimen's include status becomes Returned, and the Vial Status becomes In.  Since the specimen is no longer included in the requisition it must be re-requested if a user wishes to do anything else to the specimen.

    If the specimen is stored in a multi-specimen container (MSC), then this task must be applied to all specimens in that MSC.

    Example: Dr. Ferdinand is studying bone marrow transplant recipients. She has requisitioned 10 newly created specimens and processed them to determine the rate of regrowth each subject has had since she last sampled them. She now uses a Return to Inventory task to place the specimens in her freezer and make them available for further testing.

    To complete a Return to Inventory task:

    1. Add the task and apply it to the desired specimens.
    2. Select the rows with an Applied task that are to be completed.
    3. Select Mark as Completed or Scan to Complete from the Change Status menu on the task's column header menu.  
      • Mark as Completed will open the Enter Data for Return to Inventory dialog which allows users to modify the specimen and sample data.  The task status will be changed to Completed for all selected rows that have the task applied.
      • Scan to Complete will open the Scan to Complete Task dialog.  From this dialog, the Scan option will open the standard scanning dialog that can be used to scan specimens with a barcode reader.  All specimens in this dialog that have a Yes in the Scanned column will have the task marked as Completed when OK is pressed.
    4. From the Enter Data for Return to Inventory dialog, users can complete any modifications manually or by importing the data.
    5. Assign locations to the batch, if necessary. Enter_Data_for_Return_to_Inventory_task.png
      • Manually enter location data - Location data can be entered directly into the editor.
      • Scan to assign locations - Press the Scan Specimen button and choose the Scan Specimen or Scanning with Translations option from the sub-menu.  See the appropriate section for instructions on scanning to assign locations.
      • Reserve Locations - Select the specimens that are to have locations assigned and press the Locations button.  Select the Reserve Locations option from the sub-menu to open the Location Reservation wizard.  Use the Location Reservation wizard to reserve and assign locations.
      • Select Column View Template to select the order the fields should be displayed in.
    6. Select Check Errors and correct any errors.  Errors will be listed in the error table at the bottom of the dialog.
    7. Select Commit.  A batch confirmation dialog will be displayed.
      • Select OK to commit the batch.  A Communicating with Server message will be displayed while the batch is committing.  Once complete, a message showing the batch ID committed will be displayed.
      • Select Cancel to return to the Enter Data for Return to Inventory Task dialog.

    Ship Task

    A ship task is used when a specimen is shipped out.  (If the specimen is to be transferred to another repository for processing, a Transfer Out task should be used.)  The destination for a ship task is assigned in the Task Properties.  When completed, the task status is changed to Completed and the Vial Status is changed to Out.  It may also be necessary to:

    • Set the task order
    • Print Ship task reports
    • Specify shipping box data

    If the specimen is stored in a multi-specimen container (MSC), then this task must be applied to all specimens in that MSC.

    Example: Repository A sends specimens to requesting researchers who are not part of any repository on their database. A technician at Repository A creates a new requisition and searches for specimens to include. The technician applies a Ship task to those specimens, then physically ships them to a requesting researcher and completes the Ship task in the requisition to remove the specimens from BSI’s available inventory.

    To complete a Ship task:

    1. Add the task and apply it to the desired specimens.
    2. Select the rows with an Applied task that are to be completed.
    3. Select Mark as Completed or Scan to Complete from the Change Status menu on the task's column header menu:
      • Mark as Completed will change the task status to Completed for all selected rows that have the task applied.
      • Scan to Complete will open the Scan to Complete Task dialog.  From this dialog, the Scan option will open the standard scanning dialog that can be used to scan specimens with a barcode reader.  All specimens in this dialog that have a Yes in the Scanned column will have the task marked as Completed when OK is pressed.Mark_a_ship_task_as_completed
    4. A Warning dialog will be displayed indicating the user is about to change the database.
      • Select Yes to complete the task.  The task will be marked as Completed and the Vial Status will be Out.
      • Select Cancel to return to the Requisitions Editor without completing the task or changing the Vial Status of the selected specimen.

    Shipment Received Task

    The Shipment Received task is used to track the receipt of existing specimens from within a requisition. The user is prompted to fill in properties of the received shipment when completing the task. It includes all of the standard task properties and the received properties that are seen in the Shipments module. This task will usually be applied after a Completed Transfer Out task.

    Example: Joanna Mertz manages the Central Storage Lab repository for her database. Other repositories accessing BSI send specimens to her site to be cryopreserved in long term freezers. Bryan uses a Transfer Out task to track sending 20 of his study’s specimens to long term storage. When the physical shipment arrives, Joanna applies and completes a Shipment Received task on the specimens to note that the shipment was actually received, as well as important properties of the receipt, such as the condition of the package.

    To complete a Shipment Received task:

    1. Add the task and apply it to the desired specimens.
    2. Select the rows, with an applied task, that are to be completed.
    3. Select Mark as Completed or Scan to Complete from the task's column header menu.
    4. The Shipment Received Task Specification dialog opens. The properties shown are the same as the properties displayed while receiving an Incoming Shipment. Select OK.

    Transfer Out Task

    A Transfer Out task is run when a specimen is being transferred to another repository.  The repository value of the specimen, and therefore ownership of the specimen, will changed when a Transfer Out task is completed.

    Shipping box data can be specified for a Transfer Out task.

    Example: Professor Porter, from Repository B, has requested that several hair samples be sent to him, from Repository A, to further his research. A technician at Repository A uses a Transfer Out task to send those specimens to Professor Porter’s repository so he can access their records in BSI and maintain accurate custody.  Repos A and B are both on the same BSI database, so they can transfer information back and forth and record all test results within the same database.

    To complete a Transfer Out task:

    1. Add the task and apply it to the desired specimens. A warning dialog will display if the Task Destination remains the default TBD in the task properties.
    2. Select the rows with an Applied task that are to be completed.
    3. From the task column header menu, users can:
      • Specify Shipping Box Data
      • Track the Package
      • Specify Specimen Order
      • Verify Specimen Order
    4. In some databases, before marking the task as complete, all selected specimens with the task applied to them must have a Specimen Order specified.
    5. Select Mark as Completed or Scan to Complete from the Change Status menu on the task's column header menu. Mark_a_transfer_out_task_as_completed.jpg
      • Mark as Completed will change the task status to Completed for all selected rows that have the task applied.
      • Scan to Complete will open the Scan to Complete Task dialog.  From this dialog, the Scan option will open the standard scanning dialog that can be used to scan specimens with a barcode reader.  All specimens in this dialog that have a Yes in the Scanned column will have the task marked as Completed when OK is pressed.
    6. A Warning dialog will be displayed indicating a user is about to change the database.
      • Select Yes to complete the task.  The task status is changed to Completed and the repository is changed to the repository that is specified by the task.
      • Select Cancel to return to the Requisitions Editor without completing the task or changing the Vial Status of the selected specimens.

    If there is a mistake in a Transfer Out task, the repository that now owns the specimen must be contacted so that they may complete a Transfer Out task to transfer it back to the first repository.

    Thaw Task

    A Thaw Task increments the Thaws field value by a specified integer when completed on specimens in a requisition. When completed, a modify batch is completed in the background and the Thaws field value is updated in the Requisition Editor.

    Example: Let’s say Dr. Curry pulls 50 specimens out of his freezer, aliquots them, and ships the newly created children to an external lab for processing. Each of the 50 parent specimens were thawed twice during this process: once when they were first pulled out of the freezer and a second time when they were aliquoted. Dr. Curry can use the Thaw task to increment the Thaw field value for each parent by 2.

    To complete a Thaw Task:

    1. Add the task and apply it to the desired specimens.
      • Enter a value for the Thaws Increment task property.
    2. Select Mark as Completed from the task's column header menu
      • Mark as Completed will change the task status to Completed for all selected rows that have the task applied.
      • Scan to Complete will open the Scan to Complete Task dialog. When OK is pressed, all specimens in this dialog that have a Yes in the Scanned column will have the task marked as Completed

    Mark_a_Thaw_task_as_completed

    Withdraw Task

    The Withdraw task is used to change the Vial Status to Out when the task is completed.

    Example: For a study on transfusion reaction factors, Dr. Cochrane collected several specimens from consenting subjects.  A few months into specimen collection, Dr. Cochrane found an antibody in some of the specimens that potentially disqualified them from the study.  Instead of destroying the specimens, Dr. Cochrane decided to store them in a non-designated BSI location since results from the investigation were not yet conclusive.   

    In BSI, Dr. Cochrane applied a ‘withdraw’ task to the questionable specimens which changed their vial status to ‘Out’ and removed their BSI location data.  The rest of their history was maintained and if needed, the specimens could be returned to the repository at a later time.

    To complete a Withdraw task:

    1. Add the task and apply it to the desired specimens.
    2. Select the rows with an Applied task that are to be completed.
    3. Select Mark as Completed or Scan to Complete from the Change Status menu on the task's column header menu. Mark_a_Withdraw_task_as_completed
    4. A Warning dialog will be displayed indicating the user is about to change the database.
      • Select Yes to complete the task.  The task will be marked as Completed and the Vial Status will be changed to Out.
      • Select Cancel to return to the Requisitions Editor without completing the task or changing the Vial Status for the selected specimens.

    Unblind Task

    The Unblind task is used to create a visible link in BSI between the original specimens and the blinded specimens.  It will also merge sample data from the original specimen back into the blinded specimens.  The Parent ID of the blinded specimen will be set as the BSI ID of the original specimen.  The original specimen will remain with a status of Blinded.  

    This task can be completed at any time, but keep in mind that completing the task will remove the blinding and the link will become visible in BSI.  An Unblind task can only be completed on specimens that have a completed Blind task in the same requisition.

    Example: Let’s say a researcher at Repository A has completed a Blind task, to redact information, and transferred specimens to Repository B, for processing. Once Repository B has transferred the specimens back to Repository A, with the results of their processing, the researcher can complete an Unblind task. This creates a link between the data collected from blinded specimens and data collected from the original specimens, so the researcher can use both sets of data to continue to process the specimens.

    To complete an Unblind task:

    1. Add the task and apply it to the desired specimens.
    2. Select the rows with an Applied task that are to be completed.
    3. Select Mark as Completed from the Change Status menu on the task's column header menu. Mark_an_Unblind_task_as_completed.jpg
    4. A dialog will remind the user that the database will be changed if the task is completed. Press OK to complete the task or Cancel to exit the dialog without completing the task.