Document InformationAuthor:Jason Lucas/Gilberto Fragoso
Email:lucasjr@mail.nih.gov
Team:EVS
Contract:Contract number
Client:NCI CBIIT
National Institutes of Heath
US Department of Health and Human Services
Sign off |
Date |
Role |
CBIIT or Stakeholder Organization |
|---|---|---|---|
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|
|
|
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|
|
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The purpose of this document is to collect, analyze, and define high-level needs and features of the National Cancer Institute Center for Biomedical Informatics and Information Technology (NCI CBIIT) Protege Release 1.4.2. This document focuses on the functionalities proposed by the product stakeholders and target users in order to make it a better product. The use-case and supplementary specifications document will detail how the framework will fulfill these needs.
Vision and Needs
The objective of this release of Protege 1.4.2 is to provide bugs fixes found in previous Protege releases as well as validating functionality that had been developed in previous releases but never tested. Then fixing any defects that come out of that testing.
Current Solution
Protege 1.4.1.1 is currently in production.
Iteration 1
Feature Requests
GForge number |
Brief description of item |
(Approved or Proposed) |
|---|---|---|
16191 |
Export of inferred Ontology - Tweaks to output file |
|
18998 |
Load explanation server from the Protege KB using the OWL API converter in Protege 3.4 |
|
18999 |
Serialize state at explanation server shut-down so start-up can be incremental since previous run |
|
22785 |
Only exports the first page of results in LQT search |
|
23385 |
update protege/workflow and SWM to handle new XML Literal complex properties |
|
24359 |
Batch jobs performance improvements |
|
24360 |
Batch jobs robustness |
|
24461 |
Allow multiple domains and ranges |
|
26328 |
Report Writer outputs extra instances in 'Property value present' query |
|
26416 |
Unable to get filler values from roles in query export |
|
Bug Fixes
GForge number |
Brief description of item |
(Approved or Proposed) |
|---|---|---|
Rejection of changes to Retired Concept branch caused deletion of newly retired classes |
|
|
Time to delete the Change Ontology increases exponentially |
|
|
Error Message displays association error, yet performs edit |
|
|
Failure of Lucene to index at runtime |
|
|
Selection of display slot for individuals is not scrollable |
|
|
Changing a class from primitive to defined drops it to bottom of hierarchy level in Class Browser |
|
|
Hierarchy is not refreshing the D when retire concept |
|
|
search string appears empty when invoked from restriction dialog box |
|
|
Help > User's Guide goes to Protege 2000 page |
|
|
Enable the use of rdfs:comment |
|
Validation Tasks (Fixed in Previous Release but not Tested)
GForge number |
Brief description of item |
(Approved or Proposed) |
|---|---|---|
Duplicate Full Syn atom could not be deleted via NCI Editor Tab |
|
|
unable to find concept |
|
|
update protege/workflow and SWM to handle new XML Literal complex properties |
|
|
Legacy_Concept_Name should not transfer during merge |
|
|
Legacy_Concept_Name is ReadOnly but will be replicated in copy/split actions |
|
|
Conversion of windows characters to valid unicode |
|
|
Cannot change case of PT and PN |
|
|
Strange behavior on Preferred Name change |
|
|
Prompt - accept and reject icons in 'changed by' panel of 'table' view don't work |
|
|
SPCA contrib source |
|
|
properties set to protege:readOnly=true are still editable |
|
|
identificable ? |
|
|
Properties that have spaces cannot be edited in the Edit tab |
|
|
PROMPT Tree View reject gave null pointer exception |
|
|
Incorrect unretire functionality |
|
|
Lucene query tab default setting will not search PATO |
|
|
Allow multiple domains and ranges |
|
|
"Increase or Decrease Font Size" causes Edit Tab increment |
|
|
Search using contains is very slow |
|
|
Automated configuration of server project |
|
|
Remove hard-coding of LONG_DEFINITION and other deprecated complex properties |
|
|
Tool Tab compression and disappearance |
|
|
Protege incorrectly exporting names with quotes |
|
|
Report Writer outputs extra instances in 'Property value present' query |
|
|
Only exports the first page of results in LQT search |
|
|
Change of Focus after Retire |
|
|
Edit set as default instead of Load Please |
|
|
In all NCI Editor Tabs except the Edit tab concept name property is not displayed properly |
|
|
JavaScript window in the class Heirarchy |
|
|
Start or restart of the Explanation server has lost the time/date reference |
|
|
inheritance of role restrictions is no longer working correctly |
|
Iteration 2
Validation Tasks (Development from Previous Releases but not Tested)
GForge number |
Brief description of item |
(Approved or Proposed) |
|---|---|---|
Robustness/QC |
|
|
wiki collaboration |
|
|
"by code" (rdf:ID is meaningless) |
|
|
Runtime classification |
|
|
Internationalization |
|
|
Configurability |
|
General Support Activities
This section describes in detail all the related activities which must be performed for this release but do not add functionality. These activities are included in the scope and project plan due to level of effort or relative importance to the overall success of delivery of the release.
GForge number (hyperlinked) |
Brief description of general support activity |
Iteration |
|---|---|---|
|
Example, "Level 2 Support, integration of help and training to the user community." |
|
|
|
|
|
|
|
|
|
|
Stakeholder Summary
Customer Name |
Role |
Interest/Need |
|---|---|---|
NCI CBIIT EVS Content Editorial Team |
EVS Content Management |
Primary Users of Protege. Utilize Protege to edit EVS content |
|
|
|
|
|
|
CBIIT Staff/Contractor Name |
Role |
Responsibilities |
|---|---|---|
George Komatsoulis |
NCI CBIIT |
Oversees NCI CBIIT Application Infrastructure |
Avinash Shanbhag |
Director of CORE Engineering |
Oversees NCICB caCORE Software Engineering |
Frank Hartel |
EVS Product Manager |
Directs EVS Projects |
Sherri de Coronado |
Contract Project Officer |
Management/technical resource from Bioinformatics vertica. Contract management, coordinateion, testing, documentation |
Gilberto Fragoso |
Government Lead |
Technical resource from Bioinformatics vertical |
Technical Environment
This product uses the following technical components which have been derived from the current NCICB Technology Stack.
Client Application |
The Protege client is java based and provides a complete editing environment for Protege databases, call ontologies. It uses the same plugin architecture to support extensions, called Tabs. For example, the NCI Edit Tab, Workflow, Changes, and Prompt, are examples of plugin tabs. |
||
Application Server |
None |
||
Database Server |
MySQL |
||
Operating System |
Any that supports Java: Windows XP, Linux, OS X |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="105d1754-8f58-412a-a857-8f42d69377a8"><ac:plain-text-body><![CDATA[ |
[caCORE:Other] |
Portable ANSI-SQL compliant relational schemas |
]]></ac:plain-text-body></ac:structured-macro> |
Product Dependencies
This release is dependent on the caCORE components or products documented in the CORE Product Dependency Matrix.
[Provide additional explanation as applicable. For example, "The EVS vocabulary systems are used by the Java client to retrieve and validate concept information for naming and defining meanings."]
Out of Scope Items
Items that are out of scope were evaluated as part of the initial scoping activities for this release, and subsequently not included in the final approved scope. These items are also documented in the cumulative backlog of requirements found on the product GForge site. They include out-of-scope functional requirements (enhancements or new features), bug fixes, non-functional requirements, and general support activities.
GForge number (hyperlinked) |
Brief description of item moved from the in-scope section |
Iteration during which the item |
|---|---|---|
|
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|
|
|
|
|
|
|
|
|
|
Document History
Document Version: |
Click the Info tab. View the Recent Changes or click the link to view the page history. |
||
Last Modified: |
Refer to the first line displayed in the document window. |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="9e296cad-0b8c-499a-ae62-5611b8fd1d84"><ac:plain-text-body><![CDATA[ |
Project GForge site: |
[Project GForge site link] |
]]></ac:plain-text-body></ac:structured-macro> |
Most current version: |
Unless the display includes a notice that you are viewing a previous version, you are viewing the most current version of this Scope Document for the release indicated in the title. |
||
Revision history: |
Click the Info tab. In the Recent Changes area, click the link to view the page history. |
||
Review history: |
Click the Info tab. In the Recent Changes area, note the developer who made each change and the date and time. Refer to the Key People Directory for their roles. Click the link to view any page or to view the page history, and then click the link for a page. When the page opens, view the comments and changes made in that version. |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="94bf2802-266b-42ba-bfbe-53c8ecf358a8"><ac:plain-text-body><![CDATA[ |
Related documents: |
[Name and URL of each related document] |
]]></ac:plain-text-body></ac:structured-macro> |
Project Information
CBIIT Management |
Role |
Responsibilities |
|---|---|---|
Frank Hartel |
Product Manager |
Oversees development of the product: features, functions, definition of stakeholders, priorities within the scope, timeframe for release |
Avinash Shanbhag |
Engineering Manager |
Oversees NCICB caCORE software engineering practices, conducts design reviews, guides technical development |
Denise Warzel |
Product Line Manager |
Oversees NCICB caCORE product line. Responsible for overall product integration, major and minor release cycles. Supports Product Manager. |
Author: Jason Lucas/Gilberto Fragoso
Email: lucasjr@mail.nih.gov
Team: EVS
Contract: [Contract number]
Client: NCI CBIIT
National Institutes of Heath
US Department of Health and Human Services
Sign off |
Date |
Role |
CBIIT or Stakeholder Organization |
|---|---|---|---|
|
|
|
|
|
|
|
|
|
|
|
|
The purpose of this document is to collect, analyze, and define high-level needs and features of the National Cancer Institute Center for Biomedical Informatics and Information Technology (NCI CBIIT) Protege Release 1.4.2. This document focuses on the functionalities proposed by the product stakeholders and target users in order to make it a better product. The use-case and supplementary specifications document will detail how the framework will fulfill these needs.
Vision and Needs
The objective of this release of Protege 1.4.2 is to provide bugs fixes found in previous Protege releases as well as validating functionality that had been developed in previous releases but never tested. Then fixing any defects that come out of that testing.
Current Solution
Protege 1.4.1.1 is currently in production.
Iteration 1
Feature Requests
GForge number |
Brief description of item |
(Approved or Proposed) |
|---|---|---|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Bug Fixes
GForge number |
Brief description of item |
(Approved or Proposed) |
|---|---|---|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Validation Tasks (Fixed in Previous Release but not Tested)
GForge number |
Brief description of item |
(Approved or Proposed) |
|---|---|---|
Duplicate Full Syn atom could not be deleted via NCI Editor Tab |
|
|
unable to find concept |
|
|
update protege/workflow and SWM to handle new XML Literal complex properties |
|
|
Legacy_Concept_Name should not transfer during merge |
|
|
Legacy_Concept_Name is ReadOnly but will be replicated in copy/split actions |
|
|
Conversion of windows characters to valid unicode |
|
|
Cannot change case of PT and PN |
|
|
Strange behavior on Preferred Name change |
|
|
Prompt - accept and reject icons in 'changed by' panel of 'table' view don't work |
|
|
SPCA contrib source |
|
|
properties set to protege:readOnly=true are still editable |
|
|
identificable ? |
|
|
Properties that have spaces cannot be edited in the Edit tab |
|
|
PROMPT Tree View reject gave null pointer exception |
|
|
Incorrect unretire functionality |
|
|
Lucene query tab default setting will not search PATO |
|
|
Allow multiple domains and ranges |
|
|
"Increase or Decrease Font Size" causes Edit Tab increment |
|
|
Search using contains is very slow |
|
|
Automated configuration of server project |
|
|
Remove hard-coding of LONG_DEFINITION and other deprecated complex properties |
|
|
Tool Tab compression and disappearance |
|
|
Protege incorrectly exporting names with quotes |
|
|
|
|
|
|
|
|
Iteration 2
Validation Tasks (Development from Previous Releases but not Tested)
GForge number |
Brief description of item |
(Approved or Proposed) |
|---|---|---|
|
|
|
General Support Activities
This section describes in detail all the related activities which must be performed for this release but do not add functionality. These activities are included in the scope and project plan due to level of effort or relative importance to the overall success of delivery of the release.
GForge number (hyperlinked) |
Brief description of general support activity |
Iteration |
|---|---|---|
|
Example, "Level 2 Support, integration of help and training to the user community." |
|
|
|
|
|
|
|
|
|
|
Stakeholder Summary
Customer Name |
Role |
Interest/Need |
|---|---|---|
NCI CBIIT EVS Content Editorial Team |
EVS Content Management |
Primary Users of Protege. Utilize Protege to edit EVS content |
|
|
|
|
|
|
CBIIT Staff/Contractor Name |
Role |
Responsibilities |
|---|---|---|
George Komatsoulis |
NCI CBIIT |
Oversees NCI CBIIT Application Infrastructure |
Avinash Shanbhag |
Director of CORE Engineering |
Oversees NCICB caCORE Software Engineering |
Frank Hartel |
EVS Product Manager |
Directs EVS Projects |
Sherri de Coronado |
Contract Project Officer |
Management/technical resource from Bioinformatics vertica. Contract management, coordinateion, testing, documentation |
Gilberto Fragoso |
Government Lead |
Technical resource from Bioinformatics vertical |
Technical Environment
This product uses the following technical components which have been derived from the current NCICB Technology Stack.
Client Application |
The Protege client is java based and provides a complete editing environment for Protege databases, call ontologies. It uses the same plugin architecture to support extensions, called Tabs. For example, the NCI Edit Tab, Workflow, Changes, and Prompt, are examples of plugin tabs. |
||
Application Server |
None |
||
Database Server |
MySQL |
||
Operating System |
Any that supports Java: Windows XP, Linux, OS X |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="4813752b-1b61-4fc3-9f5e-3303477d4c95"><ac:plain-text-body><![CDATA[ |
[caCORE:Other] |
Portable ANSI-SQL compliant relational schemas |
]]></ac:plain-text-body></ac:structured-macro> |
Product Dependencies
This release is dependent on the caCORE components or products documented in the CORE Product Dependency Matrix.
[Provide additional explanation as applicable. For example, "The EVS vocabulary systems are used by the Java client to retrieve and validate concept information for naming and defining meanings."]
Out of Scope Items
Items that are out of scope were evaluated as part of the initial scoping activities for this release, and subsequently not included in the final approved scope. These items are also documented in the cumulative backlog of requirements found on the product GForge site. They include out-of-scope functional requirements (enhancements or new features), bug fixes, non-functional requirements, and general support activities.
GForge number (hyperlinked) |
Brief description of item moved from the in-scope section |
Iteration during which the item |
|---|---|---|
|
|
|
|
|
|
|
|
|
|
|
|
Document History
Document Version: |
Click the Info tab. View the Recent Changes or click the link to view the page history. |
||
Last Modified: |
Refer to the first line displayed in the document window. |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="594106ad-2214-4417-8aa8-0b3f1ce9b289"><ac:plain-text-body><![CDATA[ |
Project GForge site: |
[Project GForge site link] |
]]></ac:plain-text-body></ac:structured-macro> |
Most current version: |
Unless the display includes a notice that you are viewing a previous version, you are viewing the most current version of this Scope Document for the release indicated in the title. |
||
Revision history: |
Click the Info tab. In the Recent Changes area, click the link to view the page history. |
||
Review history: |
Click the Info tab. In the Recent Changes area, note the developer who made each change and the date and time. Refer to the Key People Directory for their roles. Click the link to view any page or to view the page history, and then click the link for a page. When the page opens, view the comments and changes made in that version. |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="4248b9c8-af23-4475-b6e3-fd95e54952b9"><ac:plain-text-body><![CDATA[ |
Related documents: |
[Name and URL of each related document] |
]]></ac:plain-text-body></ac:structured-macro> |
Project Information
CBIIT Management |
Role |
Responsibilities |
|---|---|---|
Frank Hartel |
Product Manager |
Oversees development of the product: features, functions, definition of stakeholders, priorities within the scope, timeframe for release |
Avinash Shanbhag |
Engineering Manager |
Oversees NCICB caCORE software engineering practices, conducts design reviews, guides technical development |
Denise Warzel |
Product Line Manager |
Oversees NCICB caCORE product line. Responsible for overall product integration, major and minor release cycles. Supports Product Manager. |
Author: Jason Lucas/Gilberto Fragoso
Email: lucasjr@mail.nih.gov
Team: EVS
Contract: [Contract number]
Client: NCI CBIIT
National Institutes of Heath
US Department of Health and Human Services
Sign off |
Date |
Role |
CBIIT or Stakeholder Organization |
|---|---|---|---|
|
|
|
|
|
|
|
|
|
|
|
|
The purpose of this document is to collect, analyze, and define high-level needs and features of the National Cancer Institute Center for Biomedical Informatics and Information Technology (NCI CBIIT) Protege Release 1.4.2. This document focuses on the functionalities proposed by the product stakeholders and target users in order to make it a better product. The use-case and supplementary specifications document will detail how the framework will fulfill these needs.
Vision and Needs
The objective of this release of Protege 1.4.2 is to provide bugs fixes found in previous Protege releases as well as validating functionality that had been developed in previous releases but never tested. Then fixing any defects that come out of that testing.
Current Solution
Protege 1.4.1.1 is currently in production.
Iteration 1
Feature Requests
GForge number |
Brief description of item |
(Approved or Proposed) |
|---|---|---|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Bug Fixes
GForge number |
Brief description of item |
(Approved or Proposed) |
|---|---|---|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Validation Tasks (Fixed in Previous Release but not Tested)
GForge number |
Brief description of item |
(Approved or Proposed) |
|---|---|---|
Duplicate Full Syn atom could not be deleted via NCI Editor Tab |
|
|
unable to find concept |
|
|
update protege/workflow and SWM to handle new XML Literal complex properties |
|
|
Legacy_Concept_Name should not transfer during merge |
|
|
Legacy_Concept_Name is ReadOnly but will be replicated in copy/split actions |
|
|
Conversion of windows characters to valid unicode |
|
|
Cannot change case of PT and PN |
|
|
Strange behavior on Preferred Name change |
|
|
Prompt - accept and reject icons in 'changed by' panel of 'table' view don't work |
|
|
SPCA contrib source |
|
|
properties set to protege:readOnly=true are still editable |
|
|
identificable ? |
|
|
Properties that have spaces cannot be edited in the Edit tab |
|
|
PROMPT Tree View reject gave null pointer exception |
|
|
Incorrect unretire functionality |
|
|
Lucene query tab default setting will not search PATO |
|
|
Allow multiple domains and ranges |
|
|
"Increase or Decrease Font Size" causes Edit Tab increment |
|
|
Search using contains is very slow |
|
|
Automated configuration of server project |
|
|
Remove hard-coding of LONG_DEFINITION and other deprecated complex properties |
|
|
Tool Tab compression and disappearance |
|
|
Protege incorrectly exporting names with quotes |
|
|
|
|
|
|
|
|
Iteration 2
Validation Tasks (Development from Previous Releases but not Tested)
GForge number |
Brief description of item |
(Approved or Proposed) |
|---|---|---|
|
|
|
General Support Activities
This section describes in detail all the related activities which must be performed for this release but do not add functionality. These activities are included in the scope and project plan due to level of effort or relative importance to the overall success of delivery of the release.
GForge number (hyperlinked) |
Brief description of general support activity |
Iteration |
|---|---|---|
|
Example, "Level 2 Support, integration of help and training to the user community." |
|
|
|
|
|
|
|
|
|
|
Stakeholder Summary
Customer Name |
Role |
Interest/Need |
|---|---|---|
NCI CBIIT EVS Content Editorial Team |
EVS Content Management |
Primary Users of Protege. Utilize Protege to edit EVS content |
|
|
|
|
|
|
CBIIT Staff/Contractor Name |
Role |
Responsibilities |
|---|---|---|
George Komatsoulis |
NCI CBIIT |
Oversees NCI CBIIT Application Infrastructure |
Avinash Shanbhag |
Director of CORE Engineering |
Oversees NCICB caCORE Software Engineering |
Frank Hartel |
EVS Product Manager |
Directs EVS Projects |
Sherri de Coronado |
Contract Project Officer |
Management/technical resource from Bioinformatics vertica. Contract management, coordinateion, testing, documentation |
Gilberto Fragoso |
Government Lead |
Technical resource from Bioinformatics vertical |
Technical Environment
This product uses the following technical components which have been derived from the current NCICB Technology Stack.
Client Application |
The Protege client is java based and provides a complete editing environment for Protege databases, call ontologies. It uses the same plugin architecture to support extensions, called Tabs. For example, the NCI Edit Tab, Workflow, Changes, and Prompt, are examples of plugin tabs. |
||
Application Server |
None |
||
Database Server |
MySQL |
||
Operating System |
Any that supports Java: Windows XP, Linux, OS X |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="b2ae075b-a385-43b3-9ff3-5b168614f3a9"><ac:plain-text-body><![CDATA[ |
[caCORE:Other] |
Portable ANSI-SQL compliant relational schemas |
]]></ac:plain-text-body></ac:structured-macro> |
Product Dependencies
This release is dependent on the caCORE components or products documented in the CORE Product Dependency Matrix.
[Provide additional explanation as applicable. For example, "The EVS vocabulary systems are used by the Java client to retrieve and validate concept information for naming and defining meanings."]
Out of Scope Items
Items that are out of scope were evaluated as part of the initial scoping activities for this release, and subsequently not included in the final approved scope. These items are also documented in the cumulative backlog of requirements found on the product GForge site. They include out-of-scope functional requirements (enhancements or new features), bug fixes, non-functional requirements, and general support activities.
GForge number (hyperlinked) |
Brief description of item moved from the in-scope section |
Iteration during which the item |
|---|---|---|
|
|
|
|
|
|
|
|
|
|
|
|
Document History
Document Version: |
Click the Info tab. View the Recent Changes or click the link to view the page history. |
||
Last Modified: |
Refer to the first line displayed in the document window. |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="6aa5dcff-bbc4-4348-b08e-a06835f81298"><ac:plain-text-body><![CDATA[ |
Project GForge site: |
[Project GForge site link] |
]]></ac:plain-text-body></ac:structured-macro> |
Most current version: |
Unless the display includes a notice that you are viewing a previous version, you are viewing the most current version of this Scope Document for the release indicated in the title. |
||
Revision history: |
Click the Info tab. In the Recent Changes area, click the link to view the page history. |
||
Review history: |
Click the Info tab. In the Recent Changes area, note the developer who made each change and the date and time. Refer to the Key People Directory for their roles. Click the link to view any page or to view the page history, and then click the link for a page. When the page opens, view the comments and changes made in that version. |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="e5fd6e85-2469-4953-a6ce-74628d280c6a"><ac:plain-text-body><![CDATA[ |
Related documents: |
[Name and URL of each related document] |
]]></ac:plain-text-body></ac:structured-macro> |
Project Information
CBIIT Management |
Role |
Responsibilities |
|---|---|---|
Frank Hartel |
Product Manager |
Oversees development of the product: features, functions, definition of stakeholders, priorities within the scope, timeframe for release |
Avinash Shanbhag |
Engineering Manager |
Oversees NCICB caCORE software engineering practices, conducts design reviews, guides technical development |
Denise Warzel |
Product Line Manager |
Oversees NCICB caCORE product line. Responsible for overall product integration, major and minor release cycles. Supports Product Manager. |
