Sub Sending List Specs
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Pull List Specifications
Document control Previous documents Document Name
File Name
Version Number
Pullist specs
Pulllist_specs.doc
2
Missing vial update
Missing_vial_specs.doc
1
Reselection screen
Reselection_screen_specs.doc
1
Issue Date
Version history Version
Date
Author
0-01
Comments
Initial draft
Sections affected
Circulated to:
Purpose
All
Pull List Application: Sub-sending list management Design Specification Version: 1.1 Changes since last version Section
Change
Reason for change
Outstanding issues and omissions Section
Issue or Ommission
Distribution control Author:
Copyright of xxxx. All rights reserved.
Shelley Tworoger Signature:
Author: Shelly Tworoger
Date:
Page 1 of 11
Date: 24/12/2008
Pull List Specifications
Distribution List Company
Entity
Recipient Name
Action
Shelley Tworoger
Mark Magid Helena Judge Ellis Rachel DePasquale Jeanne Sparrow Eric Rimm Sue Hankinson
Author: Shelly Tworoger
Page 2 of 11
Date: 24/12/2008
Pull List Specifications
Contents 1. Introduction
4
1.1 Purpose of document................................................................................4 1.2 Background................................................................................................4 1.3 Scope of the specification.........................................................................4 1.4 Input
4
1.5 Output 4 1.6 Glossary of Terms and Definitions.............................................................6 1.7 Contacts8 2. Functional Overview.................................................................................9 2.1 Business Objectives..................................................................................9 2.2 Functional Diagram...................................................................................9 2.3 Design Mock-up.......................................................................................10 2.4 Requirements..........................................................................................10 2.5 Non-Functional Requiremets...................................................................11 2.6 Outstanding Issues..................................................................................11
Author: Shelly Tworoger
Page 3 of 11
Date: 24/12/2008
Document Title : [11632868.doc]
1.Introduction 1.1Purpose of document The purpose of this document is to outline the specifications and management of the sub-sending list. This is a list of all the IDs accessed for a particular assay request.
1.2Background It is important to track all of the changes that occur while preparing an assay request to send out to a laboratory. Changes can occur such that some participants cannot be sent and/or that new participants are added. The sub-sending list will keep a record of these changes and will ultimately provide the end-user with a final list of IDs/vials sent to the laboratory.
1.3Scope of the specification The concern of this specification is to define the parameters of the sub-sending list and note how it will be updated and accessed by the end-user.
1.4Input This is based on the sending list(s) that are entered for a specific assay request.
1.5Output The output will be a table accessible by the user that contains information about the vials/participants handled in the course of preparing an assay request to send to a laboratory. The table will have a number of fields (see example below): ID Caco status (if Match ID (if Sent to Reason not Reselected Date applicable) applicable) laboratory sent ID change # 1 or 2 # Yes or No See below #, if Date applicable Author: Shelly Tworoger /var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Page 4 of 11
Date: 24/12/2008
Document Title : [11632868.doc]
Description of fields: 1. ID: the participant ID of interest 2. Caco status: for a case-control study, note if it is a case (1) or control (2) 3. Match ID: The ID of the matched case for a case-control study 4. Sent to laboratory: Yes or no, will be updated throughout the process 5. Reason not sent: if an ID was not sent to the laboratory then a reason must be specified: a. Low volume b. Control of a case that was not sent c. Reselected d. OTHERS?? 6. Reselected ID: if a participant was reselected, note the ID that replaced it. 7. Date: Date of last change to that record.
Author: Shelly Tworoger /var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Page 5 of 11
Date: 24/12/2008
Document Title : [11632868.doc]
1.6Glossary of Terms and Definitions
Author: Shelly Tworoger /var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Page 6 of 11
Date: 24/12/2008
Document Title : [11632868.doc]
Term
Definition
Reselection
This occurs when for some reason a participant who was selected for a project (e.g. a control) needs to be excluded from the data set and a replacement added. The blood programmers will be responsible for choosing the new participant and uploading the relevant information to Healthtrack.
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 used to pull biospecimens from the freezer for a set of assay requests.
STAGES OF PULL LIST Initialization
Entering the initial data for a pull list, choosing assay requests, setting parameters. Includes making decisions about appropriate parameter settings and changing those parameters to get the best list.
Active
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 Updated
After all vials have been pulled for a particular pull list, finalized updates are made to the freezer file, including removal of original and subvials, addition of newly made subvials. 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 Author: Shelly Tworoger
List of original vials, separated by vial type (i.e. vial size), with locations in the freezer and other information (see appendix) to be used for pulling vials list24/12/2008 Page 7 offor 11 a Pull List. Generated by the pull Date:
/var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Document Title : [11632868.doc]
1.7Contacts Name
Job Title/ Position/ Role
Shelley Tworoger
Signoff
Telephone
E-mail
Project Lead
5-2087
[email protected] rvard.edu
Mark Magid
Project Development
5-0074
[email protected] om
Helena Judge Ellis
Lab Manager
617-732-5781
[email protected] rvard.edu
Rachel DePasquale
Lab Manager
Jeanne Sparrow
Data Manager
End User
[email protected] arvard.edu
End User 5-4220
[email protected] arvard.edu
Rakesh
Author: Shelly Tworoger /var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Page 8 of 11
Date: 24/12/2008
Document Title : [11632868.doc]
2.Functional Overview 2.1Business Objectives 2.2Functional 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 Finalize Pull List
***if a vial is missing in freezer, pull alternate vial if one exists, if not remove from list + any matched controls if a case
(Put “hold” on potential vials)
Generate Freezer Pull List(s) Generate Pull Box Labels (Blood Lab RA Pulls Tubes***) Generate Sub-Sending List by Assay Request to note which ID’s will actually be set. Sorting Lists Information Defined (e.g. Box size, aliquot volumes) Sort Lists Generated
Author: Shelly Tworoger /var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Page 9 of 11
Date: 24/12/2008
Document Title : [11632868.doc]
-Aliquot sort list, separated by original vial volume -Generates labels for newly aliquoted tubes Actual aliquots recorded in healthtrack
Final sort list, separate by assay request , notes where subvials are placed into sending boxes. Make QC labels Add QCS w/ labels that have fake ID’s
Put subvials into sending box
New aliquots into sending box
Computer generates a box list/ASCII file Double check, give sub-sending list to programmer
2.3Design Mock-up N/A
2.4Requirements The sub-sending list will be generated when a sending list is uploaded to an assay request. Changes to the sub-sending list will occur in the following situations: 1. A case or control is dropped during the pull list process because of low volume 2. A control(s) whose case was dropped due to low volume 3. A case or control was eliminated because no appropriate vial was located (in the missing vial update screen) 4. A control(s) whose case was dropped due to a missing vial 5. A control or ID was reselected, added, or deleted (in the reselection screen), in this situation removed ID(s) will be marked as not sent and new ID(s) will be added to the sub-sending list Author: Shelly Tworoger
Page 10 of 11
/var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Date: 24/12/2008
Document Title : [11632868.doc]
* Note that this list will be sent to the programmer the conducted the case –control selection before the samples are sent out the lab for final confirmation that everything looks correct. Also, the information about IDs not sent to the lab will be included in the README or fail file on the Unix system. * Another functionality that should be added is the ability of the end user to select a pull list ID and then healthtrack will merge the sub-sending lists from the assay requests in that pull list to form the following type of table: ID
Caco
Match ID
Participant ID
If applicable
If applicable
Sent assay request A Yes / No
Sent assay request B Yes / No
Sent assay request C… Yes / No
2.5Non-Functional Requiremets Research Assistants and Lab Technicians generally have not used oracle databases. 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.
2.6Outstanding Issues None.
Author: Shelly Tworoger
Page 11 of 11
/var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Date: 24/12/2008
Document control Previous documents Document Name
File Name
Version Number
Pullist specs
Pulllist_specs.doc
2
Missing vial update
Missing_vial_specs.doc
1
Reselection screen
Reselection_screen_specs.doc
1
Issue Date
Version history Version
Date
Author
0-01
Comments
Initial draft
Sections affected
Circulated to:
Purpose
All
Pull List Application: Sub-sending list management Design Specification Version: 1.1 Changes since last version Section
Change
Reason for change
Outstanding issues and omissions Section
Issue or Ommission
Distribution control Author:
Copyright of xxxx. All rights reserved.
Shelley Tworoger Signature:
Author: Shelly Tworoger
Date:
Page 1 of 11
Date: 24/12/2008
Pull List Specifications
Distribution List Company
Entity
Recipient Name
Action
Shelley Tworoger
Mark Magid Helena Judge Ellis Rachel DePasquale Jeanne Sparrow Eric Rimm Sue Hankinson
Author: Shelly Tworoger
Page 2 of 11
Date: 24/12/2008
Pull List Specifications
Contents 1. Introduction
4
1.1 Purpose of document................................................................................4 1.2 Background................................................................................................4 1.3 Scope of the specification.........................................................................4 1.4 Input
4
1.5 Output 4 1.6 Glossary of Terms and Definitions.............................................................6 1.7 Contacts8 2. Functional Overview.................................................................................9 2.1 Business Objectives..................................................................................9 2.2 Functional Diagram...................................................................................9 2.3 Design Mock-up.......................................................................................10 2.4 Requirements..........................................................................................10 2.5 Non-Functional Requiremets...................................................................11 2.6 Outstanding Issues..................................................................................11
Author: Shelly Tworoger
Page 3 of 11
Date: 24/12/2008
Document Title : [11632868.doc]
1.Introduction 1.1Purpose of document The purpose of this document is to outline the specifications and management of the sub-sending list. This is a list of all the IDs accessed for a particular assay request.
1.2Background It is important to track all of the changes that occur while preparing an assay request to send out to a laboratory. Changes can occur such that some participants cannot be sent and/or that new participants are added. The sub-sending list will keep a record of these changes and will ultimately provide the end-user with a final list of IDs/vials sent to the laboratory.
1.3Scope of the specification The concern of this specification is to define the parameters of the sub-sending list and note how it will be updated and accessed by the end-user.
1.4Input This is based on the sending list(s) that are entered for a specific assay request.
1.5Output The output will be a table accessible by the user that contains information about the vials/participants handled in the course of preparing an assay request to send to a laboratory. The table will have a number of fields (see example below): ID Caco status (if Match ID (if Sent to Reason not Reselected Date applicable) applicable) laboratory sent ID change # 1 or 2 # Yes or No See below #, if Date applicable Author: Shelly Tworoger /var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Page 4 of 11
Date: 24/12/2008
Document Title : [11632868.doc]
Description of fields: 1. ID: the participant ID of interest 2. Caco status: for a case-control study, note if it is a case (1) or control (2) 3. Match ID: The ID of the matched case for a case-control study 4. Sent to laboratory: Yes or no, will be updated throughout the process 5. Reason not sent: if an ID was not sent to the laboratory then a reason must be specified: a. Low volume b. Control of a case that was not sent c. Reselected d. OTHERS?? 6. Reselected ID: if a participant was reselected, note the ID that replaced it. 7. Date: Date of last change to that record.
Author: Shelly Tworoger /var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Page 5 of 11
Date: 24/12/2008
Document Title : [11632868.doc]
1.6Glossary of Terms and Definitions
Author: Shelly Tworoger /var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Page 6 of 11
Date: 24/12/2008
Document Title : [11632868.doc]
Term
Definition
Reselection
This occurs when for some reason a participant who was selected for a project (e.g. a control) needs to be excluded from the data set and a replacement added. The blood programmers will be responsible for choosing the new participant and uploading the relevant information to Healthtrack.
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 used to pull biospecimens from the freezer for a set of assay requests.
STAGES OF PULL LIST Initialization
Entering the initial data for a pull list, choosing assay requests, setting parameters. Includes making decisions about appropriate parameter settings and changing those parameters to get the best list.
Active
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 Updated
After all vials have been pulled for a particular pull list, finalized updates are made to the freezer file, including removal of original and subvials, addition of newly made subvials. 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 Author: Shelly Tworoger
List of original vials, separated by vial type (i.e. vial size), with locations in the freezer and other information (see appendix) to be used for pulling vials list24/12/2008 Page 7 offor 11 a Pull List. Generated by the pull Date:
/var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Document Title : [11632868.doc]
1.7Contacts Name
Job Title/ Position/ Role
Shelley Tworoger
Signoff
Telephone
Project Lead
5-2087
[email protected] rvard.edu
Mark Magid
Project Development
5-0074
[email protected] om
Helena Judge Ellis
Lab Manager
617-732-5781
[email protected] rvard.edu
Rachel DePasquale
Lab Manager
Jeanne Sparrow
Data Manager
End User
[email protected] arvard.edu
End User 5-4220
[email protected] arvard.edu
Rakesh
Author: Shelly Tworoger /var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Page 8 of 11
Date: 24/12/2008
Document Title : [11632868.doc]
2.Functional Overview 2.1Business Objectives 2.2Functional 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 Finalize Pull List
***if a vial is missing in freezer, pull alternate vial if one exists, if not remove from list + any matched controls if a case
(Put “hold” on potential vials)
Generate Freezer Pull List(s) Generate Pull Box Labels (Blood Lab RA Pulls Tubes***) Generate Sub-Sending List by Assay Request to note which ID’s will actually be set. Sorting Lists Information Defined (e.g. Box size, aliquot volumes) Sort Lists Generated
Author: Shelly Tworoger /var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Page 9 of 11
Date: 24/12/2008
Document Title : [11632868.doc]
-Aliquot sort list, separated by original vial volume -Generates labels for newly aliquoted tubes Actual aliquots recorded in healthtrack
Final sort list, separate by assay request , notes where subvials are placed into sending boxes. Make QC labels Add QCS w/ labels that have fake ID’s
Put subvials into sending box
New aliquots into sending box
Computer generates a box list/ASCII file Double check, give sub-sending list to programmer
2.3Design Mock-up N/A
2.4Requirements The sub-sending list will be generated when a sending list is uploaded to an assay request. Changes to the sub-sending list will occur in the following situations: 1. A case or control is dropped during the pull list process because of low volume 2. A control(s) whose case was dropped due to low volume 3. A case or control was eliminated because no appropriate vial was located (in the missing vial update screen) 4. A control(s) whose case was dropped due to a missing vial 5. A control or ID was reselected, added, or deleted (in the reselection screen), in this situation removed ID(s) will be marked as not sent and new ID(s) will be added to the sub-sending list Author: Shelly Tworoger
Page 10 of 11
/var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Date: 24/12/2008
Document Title : [11632868.doc]
* Note that this list will be sent to the programmer the conducted the case –control selection before the samples are sent out the lab for final confirmation that everything looks correct. Also, the information about IDs not sent to the lab will be included in the README or fail file on the Unix system. * Another functionality that should be added is the ability of the end user to select a pull list ID and then healthtrack will merge the sub-sending lists from the assay requests in that pull list to form the following type of table: ID
Caco
Match ID
Participant ID
If applicable
If applicable
Sent assay request A Yes / No
Sent assay request B Yes / No
Sent assay request C… Yes / No
2.5Non-Functional Requiremets Research Assistants and Lab Technicians generally have not used oracle databases. 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.
2.6Outstanding Issues None.
Author: Shelly Tworoger
Page 11 of 11
/var/www/apps/pdfcoke/pdfcoke/tmp/scratch2/11632868.doc
Date: 24/12/2008
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