#  Document control {#document-control .TOC-Title .unnumbered}

## Superseded documents {#superseded-documents .Doc-Control-Headings .unnumbered}

  ---------- -------- --------- -------- ------------ ------------ --------------
  Document   File     Version   Issue    Date         Replaced by  Reason
  Name       Name     Number    Date     with-drawn                

                                                                   

                                                                   
  ---------- -------- --------- -------- ------------ ------------ --------------

## Version history {#version-history .Doc-Control-Headings .unnumbered}

  --------- --------- -------- ------------------ ------------ -------------- -------------
  Version   Date      Author   **Comments**       **Sections   **Circulated   **Purpose**
                                                  affected**   to:**          

  0-02                                            All                         
  --------- --------- -------- ------------------ ------------ -------------- -------------

## Changes since last version {#changes-since-last-version .Doc-Control-Headings .unnumbered}

  ------------ ------------------------------------- ---------------------
  Section      Change                                Reason for change

                                                     
  ------------ ------------------------------------- ---------------------

## Outstanding issues and omissions {#outstanding-issues-and-omissions .Doc-Control-Headings .unnumbered}

  ------------ ----------------------------------------------------------
  Section      Issue or Ommission

               
  ------------ ----------------------------------------------------------

## Distribution control {#distribution-control .Doc-Control-Headings .unnumbered}

  --------------------- --------------------------- ---------------------
  Owner and approver    Shelley Tworoger            
  for distribution:                                 

  Signature:                                        Date:
  --------------------- --------------------------- ---------------------

## Distribution List {#distribution-list .Doc-Control-Headings .unnumbered}

  ------------- ------------------- ----------------- ---------------------
  **Company**   **Entity**          **Recipient       **Action**
                                    Name**            

                                    Shelley Tworoger  

                                    Mark Magid        

                                    Rakesh Kukatla    

                                    Helena            
                                    Judge-Ellis       

                                    Jeanne Sparrow    

                                    Eric Rimm         

                                    Sue Hankinson     
  ------------- ------------------- ----------------- ---------------------

#  Contents {#contents .TOC-Title .unnumbered}

1\. Introduction [4](#introduction)

1.1 Purpose of document [4](#purpose-of-document)

1.2 Background [4](#background)

1.3 Scope of the specification [4](#scope-of-the-specification)

1.4 Input [4](#input)

1.5 Output [4](#output)

1.6 Glossary of Terms and Definitions
[5](#glossary-of-terms-and-definitions)

1.7 Contacts [7](#contacts)

1.7.1 List of comments of final sign off
[7](#list-of-comments-of-final-sign-off)

2\. Functional Overview [8](#functional-overview)

2.1 Business Objectives
[8](#business-objectives-see-separate-expanded-flow-chart-for-sorting)

2.2 Functional Diagram [8](#functional-diagram)

2.3 Design Mock-up [9](#design-mock-up)

2.4 Requirements [9](#requirements)

2.4.1 Primary [9](#primary)

2.5 Non-Functional Requiremets [10](#non-functional-requiremets)

2.6 Outstanding Issues [10](#outstanding-issues)

# Introduction

## Purpose of document

The Aliquot Functionality will continue the process of sorting samples
pulled from the freezer and ultimately sending to a laboratory. This
functionality will build on the information generated in the Pull List
Functionality and Sort list functionality, specifically the location of
original vials into Original Sort Boxes. The purpose of this document is
to outline the specifications for the Aliquot functionality in
HealthTrack to create labels and box maps for the NHS, NHS2, PHS, and
HPFS cohorts.

## Background

Aliquoting original vials into smaller subvials is an integral part of
the blood laboratory operation. To reduce the number of times a sample
is thawed (and refrozen), when an original vial is pulled, it is often
aliquoted completely into subvials. The original vial is not put back in
the freezer. Occasionally (e.g. for buffy coat or cheek cells), only one
or two aliquots are made and then the original vial is put back in the
freezer and becomes a remainder vial. The aliquoting process requires
the sorting of original vials into case-control order. RAs will then
label potential new subvials, aliquot, and place subvials that are for a
specific lab code into aliquot boxes and subvials to be stored in the
repository into permanent storage boxes. The purpose of this project
will be to create a user interface for the research assistant to enter
the number of subvials to be created, make labels for the new subvials,
and to enter locations of new subvials into the database.

## Scope of the specification

The only concern of this application and specification are the aliquot
labels and lists to be used by the lab or analysts. A completed pull and
sort list is a requirement to any work within this application.

## Input

-   The Aliquot List functionality input data will be included on the
    Sorting Functionality form.

## Output

[Primary output -- Aliquotting Labels]{.underline}

> Generate labels for the Aliquot sort and store boxes and should have
> the format below:

Generate labels for subvials to be aliquoted and should have the format
below:

> The order of these labels will be: 1. Aliquots for the labcodes in the
> related pull list, sorted in priority order and 2. Other aliquots
> going to permanent storage in volume order.

Generate labels for boxes to go into permanent storage:

[Primary output -- Aliquot worksheet]{.underline}

> This is a list of IDs, in aliquot order (see Sorting Functionality
> Specifications), that are separated by original vial size. See
> Appendix A for more detail.

Box maps for all of the boxes generated will be created.

## Glossary of Terms and Definitions

  -----------------------------------------------------------------------
  Term              Definition
  ----------------- -----------------------------------------------------
  Assay             Any type of measurement done on a biological sample

  Translation Table A oracle view that combines fields from a normalized
                    structure of many fields to create one long but
                    shallow table of permutations that can be used in the
                    UI for user's ease

  Vial              A tube filled with biological specimen to be used in
                    an assay request or as part of a pull list.

  Pull List         General term for the functionality that generates the
                    all the vial lists including freezer locations, used
                    to pull biospecimens from freezers for a set of
                    labcodes.

  STAGES OF PULL    
  LIST              

  Initialization    Entering the initial data for a pull list, choosing
                    labcodes, setting parameters. Includes making
                    decisions about appropriate parameter settings and
                    changing those parameters to get the best list. Vials
                    are temporarily reserved until the parameters are
                    changed or approved.

  Active (Activate) Approved and finalized the pull list, all final
                    parameter settings selected. Vials are reserved in
                    the database. Pull list has been generated and blood
                    lab personnel are actively pulling samples out of the
                    freezer. Includes updating the freezer file when an
                    incorrect tube is found, getting new locations of
                    alternate vials, and noting what new subvials have
                    been created.

  Completed and\    After all vials have been pulled for a particular
  Updated           pull list, updates are made to the freezer file,
                    including marking of original vials (and subvials) as
                    removed. Also includes final update to the
                    sub-sending list that notes which vials were sent for
                    which assay requests.

  TYPES OF LISTS IN 
  PULL LIST         
  FUNCTIONALITY     

  Original vial     List of original vials, separated by vial type (i.e.
  list              vial size), with locations in the freezer and other
                    information (see appendix) to be used for pulling
                    vials for a Pull List. Generated by the pull list
                    functionality.

  Subvial list      List of subvials, separated by assay request, with
                    locations in the freezer and other information (see
                    appendix) to be used for pulling vials for a Pull
                    List. Generated by the pull list functionality.

  Index number      A sequential set of numbers, beginning at 1, assigned
                    to each vial in a pull list overall all original and
                    sub-vial lists. In other words, no number is repeated
                    and this acts as a unique identifier within pull
                    list.

  Unique Vial ID    ID number assigned by oracle for every vial handled
                    in a pull list or other project

  Participant ID    The ID number assigned to a participant when he or
                    she entered the study

  Pull list ID      ID number assigned by oracle for each Pull List
                    generated for a set of assay requests.

  Sub-sending list  A list of all potential IDs/vials in an assay
                    request. Notes what vial was sent for that
                    individual, whether a vial was sent for that
                    individual, and if not sent then why.

  Original Sort     A set of instructions, with list of original vials
  List              (separated by vial type/size), their locations in the
                    Freezer Pull Box and their new expected locations in
                    the Original Sort Box to prepare for aliquoting

  Sending Sort List A set of instructions, with a list of subvials
                    (separately by labcode and source of subvial) showing
                    their locations in a Freezer Pull OR an Aliquot Box,
                    and their new locations in the Final Sending box

  BOX CATEGORIES    

  Freezer Pull Box  A box that contains vials in freezer order, directly
                    pulled from the freezer repository. Separated by vial
                    type/size.

  Original Sort Box A box that contains original vials, separately by
                    vial size, that have been sorted into case-control
                    order.

  Aliquot Ship Box  A box that contains subvials that are newly aliquoted
                    from original vials in Original Sort Boxes (and are
                    therefore in caco order) for labcodes being sent out
                    to a lab. May include subvials from multiple lab
                    codes.

  Aliquot Store Box A box that contains subvials that are newly aliquoted
                    from original vials in Original Sort Boxes (and are
                    therefore in caco order) going back in to permanent
                    storage.

  Final Sending Box A box that contains subvials of a specified size for
                    a particular Assay Request/Labcode that is sorted
                    into case-control order, and has QCs

  Permanent\        A plastic 10X10 box in which subvials are placed to
  Storage box       be entered into permanent storage.
  -----------------------------------------------------------------------

## Contacts

+----------+---------------+------------+------------+---------------+
| Name     | Job Title/    | Signoff    | Telephone  | E-mail        |
|          | Position/     |            |            |               |
|          | Role          |            |            |               |
+----------+---------------+------------+------------+---------------+
| Shelley  | Project Lead  |            | 5-2087     | <n            |
| Tworoger |               |            |            | hsst@channing |
|          |               |            |            | .harvard.edu> |
+----------+---------------+------------+------------+---------------+
| Mark     | Project       |            | 5-0074     | mgmag         |
| Magid    | Development   |            |            | i@hotmail.com |
+----------+---------------+------------+------------+---------------+
| Rakesh   | Project       |            | 5-2575     | rkukatla@hsp  |
| Kukalta  | Development   |            |            | h.harvard.edu |
+----------+---------------+------------+------------+---------------+
| Helena   | Lab Manager   |            | 61         | <n            |
| Judge    |               |            | 7-732-5781 | hhje@channing |
| Ellis    | End User      |            |            | .harvard.edu> |
+----------+---------------+------------+------------+---------------+
| Jeanne   | Data Manager  |            | 5-4220     | nhjms@channin |
| Sparrow  |               |            |            | g.harvard.edu |
+----------+---------------+------------+------------+---------------+

####   {#section .unnumbered}

### List of comments of final sign off

# Functional Overview

## Business Objectives (See separate, expanded flow chart for sorting)

## Functional Diagram

Enter Assay Request Enter Assay Request Enter Assay Request

\*if replace/delete participants

\*\*if need to change parameters

Conduct tally to find cases/controls

that may need to be removed,

update sending lists.

Create Pull List Request

\* \*\*

See Intermediate Results (Put "hold" on potential vials)

Finalize Pull List

Generate Freezer Pull List(s)

\*\*\*if a vial is Generate Pull Box Labels

missing in

freezer, pull (Blood Lab RA Pulls Tubes\*\*\*)

alternate vial if

one exists, if Generate Sub-Sending List by Assay Request

not remove from to note which ID's will actually be set.

list + any matched

controls if a case Sorting Lists Information Defined (e.g. Box size,
aliquot volumes)

Sort Lists Generated

-Aliquot sort list, separated Final sort list, separate by assay

by original vial volume request , notes where subvials are

-Generates labels for newly placed into sending boxes. Make

aliquoted tubes QC labels

Actual aliquots recorded Add QCS w/ labels that have fake ID's

in healthtrack Put subvials into

sending box

New aliquots into Computer generates a box list/ASCII file

sending box Double check, give sub-sending list to programmer

## Design Mock-up

## Requirements

### Primary

The user will access the aliquot functionality from within the sort list
functionality as these two are inextricably linked. Below is the field
that is included in the Sort functionality that is particularly relevant
to the Aliquot user-interface:

Aliquot Preferences - multiple selection simple table (with columns Vial
Type, Volume, Number) is used to specify the number of aliquots (of a
specific volume) that need to be made for each vial type.

\*\*Htrack will automatically enter aliquots that are specifically for
the lab codes in the related pull list. The order of these aliquots will
be in the priority order of the lab codes noted in the pull list. The RA
will enter extra possible vials at various volumes to account for
variability in the original vial volumes.

[OTHER SPECIFICATIONS:]{.underline}

1\. Placement of aliquoted subvials for specific lab codes into the
aliquot send boxes

The location of subvials slated for a particularly lab code will be
noted by Htrack on the Aliquot Worksheet. They will be placed in the box
consecutively (in order of lab code priority) with no spaces between IDs
(note: vials for multiple lab codes will be in one box). These vials
will be scanned as they are made to make an accurate box list of the
aliquot send box (if a certain vial cannot be made this will be
recognized in Htrack). This information, along with the subvials pulled
from the freezer will be integrated to allow both vials types to be
sorted directly into the final sending boxes. (See sorting
specifications for more detail on this last aspect).

3\. Placement of aliquoted subvials for permanent storage\
The location for remaining subvials cannot be automatically assigned as
each ID may have a different number of subvials, depending on the volume
of the original vial. Vials will be placed in temporary aliquot store
boxes. Then the vials will be scanned as they are placed from the
aliquot store boxes into the permanent storage box. The RA will scan the
box label (which contains the unique box ID) and then will scan each
vial as it is placed into the box in order. The vial bar code contains
all the information needed to store it in the database, participant ID,
unique vial ID, and volume. When the box is filled (or all subvials are
placed), the RA will enter the data into the database. When the boxes
are put into their permanent freezer locations using existing
functionalities

4\. Placement of remainder original vials back into permanent storage\
Remainder vials (originals that have had at least one freeze-thaw cycle)
are to be placed back in their original locations. While the vial is
thawed, a new label, containing a barcode, will be placed on the label
so ease its placement back into the freezer. Using the original pull
list of original vials the RA will scan the vials individually and place
them back into the freezer. The database will be updated to reflect that
the vial is returned, add an additional freeze-thaw cycle and update the
expected volume. Vials that are not scanned will be considered as empty
and permanently removed.

## Non-Functional Requiremets

Research Assistants and Lab Technicians are not typically technically
advanced. The user interface of this and any part of Htrack needs to
accommodate for their skill set and ensure usability by making the
product as easy to use for non-technical people as possible.

## Outstanding Issues