MouseBIRN.2008AHMPlanOct20 (r1.1 vs. r1.23)
Diffs

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.23 - 20 Jun 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes
TOC: No TOC in "MouseBIRN.2008AHMPlanOct20"
Line: 21 to 21
    1. Add sort by column
    2. Add customizable columns (ie: right click table headers and select columns to display like Windows Explorer)
    3. Add resizable JPanel for table
Added:
>
>
    1. Thumbnail view

Do these concurrently or wait till framework is finished?

  1. Complete support for all query terms

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.22 - 17 Jun 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes
TOC: No TOC in "MouseBIRN.2008AHMPlanOct20"
Line: 11 to 11

Search Core

Added:
>
>
  1. Design client data source plugin framework [Daren,Queenie,Steve]
    1. will plugins work with current mbSearch core?
  2. Implement client data source plugin framework [Queenie]
  3. Migrate each datasource as plugin [Queenie]
    1. evaluate what info on metadata server is needed
  4. Query Results Table: [Steve]
    1. Add move/drag column (already exists)
    2. Add sort by column
    3. Add customizable columns (ie: right click table headers and select columns to display like Windows Explorer)
    4. Add resizable JPanel for table

Do these concurrently or wait till framework is finished?


  1. Complete support for all query terms
  2. Add CCDB datatypes (wait for plugins?)
    1. 3D images (returned as analyze images?)
    2. 3D reconstructed surfaces?
Changed:
<
<
  1. Design client data source plugin framework
    1. will plugins work with current mbSearch core?
  2. Migrate each datasource as plugin
    1. evaluate what info on metadata server is needed
>
>

Do we have time for this?


  1. Add keyword search functionality
    1. identify which datasources can have keyword functionality
    2. how does term source API integrate?
Changed:
<
<
  1. Add RDF query language functionality
    1. SPARQL (CCDB Cellular Knowledge Base: http://purl.oclc.org/ckb/)
>
>
    1. what will be result types and how to display in results table?
    2. design GUI (need clustering in the future)
  2. Add RDF query language functionality
    1. SPARQL (CCDB Cellular Knowledge Base: http://purl.oclc.org/ckb/)

Viewer Core

  1. CCDB Zoomify

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.21 - 10 Jun 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes
TOC: No TOC in "MouseBIRN.2008AHMPlanOct20"
Line: 21 to 21
    1. evaluate what info on metadata server is needed
  2. Add keyword search functionality
    1. identify which datasources can have keyword functionality
Changed:
<
<
    1. how does concept term mapping integrate?
>
>
    1. how does term source API integrate?

  1. Add RDF query language functionality
    1. SPARQL (CCDB Cellular Knowledge Base: http://purl.oclc.org/ckb/)
Line: 40 to 40
  1. ImageJ File Plugins

Open Issues

Added:
>
>
  1. ImageJ processing plugins

  1. Atlas interoperability
  2. Plugins Embedded?
    1. allow plugin to create JFrames vs. everything embedded in MBAT?

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.20 - 09 Jun 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes
TOC: No TOC in "MouseBIRN.2008AHMPlanOct20"
Line: 41 to 41

Open Issues

  1. Atlas interoperability
Changed:
<
<
  1. Plugin Embedded?
>
>
  1. Plugins Embedded?

    1. allow plugin to create JFrames vs. everything embedded in MBAT?
Added:
>
>
  1. Capture work
    1. XML save file

Collaborative Efforts

  1. CCDB/AIDB

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.19 - 09 Jun 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes
TOC: No TOC in "MouseBIRN.2008AHMPlanOct20"

Changed:
<
<

2008 AHM (Oct.20) MBAT Requirements

This document lists the required functionality for MBAT that will be delivered at the 2008 All-hands Meeting on October 20,2008.
>
>

2008 AHM (Oct.20) MBAT3.0 Requirements

This document lists the required functionality for MBAT that will be delivered at the 2008 All-hands Meeting on October 20,2008.

For each category, the collaborators are also listed.
Added:
>
>

Search Core

  1. Complete support for all query terms
  2. Add CCDB datatypes (wait for plugins?)
    1. 3D images (returned as analyze images?)
    2. 3D reconstructed surfaces?
  3. Design client data source plugin framework
    1. will plugins work with current mbSearch core?
  4. Migrate each datasource as plugin
    1. evaluate what info on metadata server is needed
  5. Add keyword search functionality
    1. identify which datasources can have keyword functionality
    2. how does concept term mapping integrate?
  6. Add RDF query language functionality
    1. SPARQL (CCDB Cellular Knowledge Base: http://purl.oclc.org/ckb/)

Viewer Core

  1. CCDB Zoomify
    1. annotation functionality
  2. Smart Atlas
    1. stereotaxic coordinates

Analysis Core

  1. Spatial Registration Plugins
    1. Landmark Based Warping (Davit)
    2. Jibber (Asif)

DocManager Core

  1. ImageJ File Plugins

Open Issues

  1. Atlas interoperability
  2. Plugin Embedded?
    1. allow plugin to create JFrames vs. everything embedded in MBAT?

Collaborative Efforts

  1. CCDB/AIDB
  2. Universal WebServices API


Task List

  1. Reevaluate AHM Requirements
Deleted:
<
<
    1. Determine current MBAT features to keep

    1. Determine new features to add by Fall AHM
      1. Keyword search
      2. Analysis component in viewer
Line: 29 to 70
    1. Shiva.IO classes to standalone module
    2. Data Source data in MetaData or XML
Added:
>
>

Existing MBAT Improvements

  1. Automatically sync to appropriate atlas slice for given slice
    • Also show a marker for location of smaller relative size datasets in atlas

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.18 - 21 May 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes
TOC: No TOC in "MouseBIRN.2008AHMPlanOct20"
Line: 24 to 24
      1. NeuroTerrain
  2. Redesign entire MBAT framework
    1. Code review for mbSearch core
Added:
>
>
    1. Merge old and new mbSearch datatypes (ie: ProbeNew?, etc)

    1. Refactor all icons to common/resources/icons. Check build scripts for unused or duplicate (nested) jar includes.
    2. Shiva.IO classes to standalone module
    3. Data Source data in MetaData or XML

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.17 - 09 May 2008 - SteveAnderson)

META TOPICPARENT LONIMBATTechnicalNotes
TOC: No TOC in "MouseBIRN.2008AHMPlanOct20"
Line: 24 to 24
      1. NeuroTerrain
  2. Redesign entire MBAT framework
    1. Code review for mbSearch core
Changed:
<
<
    1. Refactor all icons to common/resources/icons
>
>
    1. Refactor all icons to common/resources/icons. Check build scripts for unused or duplicate (nested) jar includes.

    1. Shiva.IO classes to standalone module
    2. Data Source data in MetaData or XML

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.16 - 09 May 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes
TOC: No TOC in "MouseBIRN.2008AHMPlanOct20"
Line: 7 to 7

2008 AHM (Oct.20) MBAT Requirements

This document lists the required functionality for MBAT that will be delivered at the 2008 All-hands Meeting on October 20,2008. For each category, the collaborators are also listed.
Added:
>
>

Task List

  1. Reevaluate AHM Requirements
    1. Determine current MBAT features to keep
    2. Determine new features to add by Fall AHM
      1. Keyword search
      2. Analysis component in viewer
      3. Framework for clients to add new Data Sources
      4. Access control module for client sources
      5. Public vs private databases
      6. Landmark Registration
    3. Determine collaborative efforts to support
      1. Uniform API (XCEDE, FUGE/MAGE, WebServices)
      2. AIDB / 3D Data sources
      3. Concept Mapper
      4. NeuroTerrain
  2. Redesign entire MBAT framework
    1. Code review for mbSearch core
    2. Refactor all icons to common/resources/icons
    3. Shiva.IO classes to standalone module
    4. Data Source data in MetaData or XML

Changed:
<
<

Existing MBAT Improvements

>
>

Existing MBAT Improvements


  1. Automatically sync to appropriate atlas slice for given slice
    • Also show a marker for location of smaller relative size datasets in atlas

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.15 - 02 Apr 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes
Changed:
<
<		 TOC: No TOC in "MouseBIRN.2008AHMPlanOct20"
>
>		 TOC: No TOC in "MouseBIRN.2008AHMPlanOct20"


 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.14 - 02 Apr 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes
Added:
>
>		 TOC: No TOC in "MouseBIRN.2008AHMPlanOct20"


2008 AHM (Oct.20) MBAT Requirements

This document lists the required functionality for MBAT that will be delivered at the 2008 All-hands Meeting on October 20,2008. For each category, the collaborators are also listed.
Line: 46 to 50
        1. BxD
        2. Development
        3. Reeler
Added:
>
>
        1. EAE

        1. Sex Differences/Dimorphism
Changed:
<
<
        1. Keyword (freetext)
>
>
        1. Keyword... (freetext)

      1. Investigator
        1. Any
Changed:
<
<
        1. Keyword (freetext)
>
>
        1. Keyword... (freetext)

    1. Gene/Molecule
Changed:
<
<
      1. add protein to dropdown
      2. add keyword to dropdown rather than the more specific gene function and we'll have to connect to a more powerful annotation DB-both Rob's and Paul Pavlidis'(?)
>
>
      1. Gene Attribute
        1. Gene Symbol (freetext)
        2. Gene Name (freetext)
        3. Protein (freetext)
        4. Keyword... (freetext)
      2. rather than the more specific gene function and we'll have to connect to a more powerful annotation DB-both Rob's and Paul Pavlidis'(?)

      1. Add way to list available gene symbols?
    2. Subject/Organism
Added:
>
>
      1. Species
        1. Mouse
      2. Strains
        1. C57BL
        2. 12956
        3. A/J
        4. B6D2F1
        5. BALB/c
        6. CBA
        7. C3H
        8. DBA
        9. FVB

      1. Developmental Stage
Line: 68 to 89
        1. Juvenile (24-60 postnatal days)
        2. Adult (60-300 postnatal days)
        3. days/weeks/months?
Changed:
<
<
    1. Disease Model
      1. Treatment
        1. default: Normal
        2. All/any
        3. Diseased/treated
          1. Alzheimer's
          2. Parkinson's
          3. Multiple Sclerosis
          4. Schizophrenia
>
>
      1. Gender
        1. any
        2. male
        3. female
        4. other

    1. Anatomical Area
      1. Any
      2. CNS hierarchy
Line: 84 to 101
      1. Cell
      2. Subcellular
      3. Other part (freetext)
Changed:
<
<
  1. Datatype -> Technique Dependencies [Jyl and Allan fill in]
    1. If Microarray selected, show Gene selection (required).
>
>
  1. Query Term Dependencies
    1. If Gene Expression selected --> show Gene/Molecule searchgroup
    2. If Gene/Molecule search group enabled --> grey MRI
    3. If MRI selected --> disable Gene/Molecule searchgroup

  1. Formulating query
    1. Integrate with Concept Term Mapping
    2. Integrate with Mediator
Line: 94 to 113
      1. Query terms?
      2. Steps required for MBAT to connect to AIDB?
Changed:
<
<		 <!-- 1. Datatype
>
>		 <!--
    1. Disease Model
      1. Treatment
        1. default: Normal
        2. All/any
        3. Diseased/treated
          1. Alzheimer's
          2. Parkinson's
          3. Multiple Sclerosis
          4. Schizophrenia 1. Datatype

      1. DataType/Content
        1. Any
          1. Cell Fills
Line: 148 to 177
    1. 2D - 2D
      1. manual
      2. default algo: Ryan and Craig's algorithm, taking advantage of Heng's UI for points (possibly contours)
Changed:
<
<
>
>

        • also take a look at Drexel's QA/registration JAVA tools
    1. Subimage - 2D
      1. default algo: manual

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.13 - 01 Apr 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes

2008 AHM (Oct.20) MBAT Requirements

This document lists the required functionality for MBAT that will be delivered at the 2008 All-hands Meeting on October 20,2008.

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.12 - 21 Mar 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes

2008 AHM (Oct.20) MBAT Requirements

This document lists the required functionality for MBAT that will be delivered at the 2008 All-hands Meeting on October 20,2008.
Line: 24 to 24
    • next steps are to use this framework to access MBL data using their atlas and Atlas Interoperability infrastructure

Query Engine [AIDB, all Mouse DBs, Brian, Vadim, and Bill]

Deleted:
<
<
  • this will be much easier if we can get things working through the Concept Term Mapping and possibly Mediator]

  1. Refactor
    1. Clean up v2.0
    2. Gene expression to mbSearch
      1. MBAT GUI code must change
Changed:
<
<
  1. Expand current terms
    1. CCDB datatypes?
      1. Brain mosaics
    2. Datatype -> Technique Dependencies [Jyl and Allan fill in]
      1. If Microarray selected, show Gene selection (required).
>
>
  1. Issues
    1. How to classify Brain mosaics in query terms
  2. Query Terms

    1. Experimental Info
      1. Experimental Type
        1. Any
Line: 87 to 84
      1. Cell
      2. Subcellular
      3. Other part (freetext)
Added:
>
>
  1. Datatype -> Technique Dependencies [Jyl and Allan fill in]
    1. If Microarray selected, show Gene selection (required).
  2. Formulating query
    1. Integrate with Concept Term Mapping
    2. Integrate with Mediator

  1. Expand current data sources
    1. AIDB
      1. Query terms?

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.11 - 20 Mar 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes

2008 AHM (Oct.20) MBAT Requirements

This document lists the required functionality for MBAT that will be delivered at the 2008 All-hands Meeting on October 20,2008.
Line: 34 to 34
      1. Brain mosaics
    2. Datatype -> Technique Dependencies [Jyl and Allan fill in]
      1. If Microarray selected, show Gene selection (required).
Changed:
<
<
    1. Datatype
      1. DataType/Content
>
>
    1. Experimental Info
      1. Experimental Type

        1. Any
Changed:
<
<
          1. Cell Fills
          2. Classical Histology
          3. Gene Expression (subsumes Protein Localization)
        2. Microarray
          1. Gene Expression (subsumes Protein Localization)
        3. Images: 2D
          1. Any
          2. Cell Fills
          3. Classical Histology
          4. Gene Expression (subsumes Protein Localization)
        4. Images: 3D
>
>
        1. Gene Expression
          1. Any
          2. Image based
          3. Microarray
        2. MRI
        3. Electron Microscopy
        4. Cell Fills
      2. Project

          1. Any
Changed:
<
<
          1. Cell Fills
      2. Technique
>
>
        1. BxD
        2. Development
        3. Reeler
        4. Sex Differences/Dimorphism
        5. Keyword (freetext)
      2. Investigator

        1. Any
Changed:
<
<
        1. Microscopy
          1. Any
          2. Light
          3. Confocal
          4. Fluorescence
          5. Multiphoton
        2. Electron
        3. MR
          1. Any
          2. T1
          3. T2
          4. DTI
        4. Electron Tomography
      • Possible to have the ability to "ADD" or "EXCLUDE" like in itunes?
>
>
        1. Keyword (freetext)

    1. Gene/Molecule
      1. add protein to dropdown
      2. add keyword to dropdown rather than the more specific gene function and we'll have to connect to a more powerful annotation DB-both Rob's and Paul Pavlidis'(?)
Line: 99 to 87
      1. Cell
      2. Subcellular
      3. Other part (freetext)
Deleted:
<
<
    1. Experimental Info (CCDB and AIDB)
      1. Project
        1. Any
        2. Project
          1. Any
          2. BxD
          3. Development
          4. Reeler
          5. Sex Differences/Dimorphism
          6. Keyword (freetext)
      2. Investigator
        1. Any
        2. Keyword (freetext)

  1. Expand current data sources
    1. AIDB
      1. Query terms?
      2. Steps required for MBAT to connect to AIDB?
Added:
>
>		 <!-- 1. Datatype
      1. DataType/Content
        1. Any
          1. Cell Fills
          2. Classical Histology
          3. Gene Expression (subsumes Protein Localization)
        2. Microarray
          1. Gene Expression (subsumes Protein Localization)
        3. Images: 2D
          1. Any
          2. Cell Fills
          3. Classical Histology
          4. Gene Expression (subsumes Protein Localization)
        4. Images: 3D
          1. Any
          2. Cell Fills
      2. Technique
        1. Any
        2. Microscopy
          1. Any
          2. Light
            1. Confocal
            2. Fluorescence
            3. Multiphoton
          3. Electron
        3. MR
          1. Any
          2. T1
          3. T2
          4. DTI
          5. PD
        4. Electron Tomography
      • Possible to have the ability to "ADD" or "EXCLUDE" like in itunes?
-->

Registration Workspace [UCSD, Drexel]

  1. Framework for loading data

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.10 - 28 Feb 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes

2008 AHM (Oct.20) MBAT Requirements

This document lists the required functionality for MBAT that will be delivered at the 2008 All-hands Meeting on October 20,2008.
Line: 31 to 31
      1. MBAT GUI code must change
  2. Expand current terms
    1. CCDB datatypes?
Deleted:
<
<
      1. Protein localization

      1. Brain mosaics
Added:
>
>
    1. Datatype -> Technique Dependencies [Jyl and Allan fill in]
      1. If Microarray selected, show Gene selection (required).

    1. Datatype
Changed:
<
<
      1. Redesign as DataType/Content
>
>
      1. DataType/Content

        1. Any
          1. Cell Fills
          2. Classical Histology
Changed:
<
<
          1. Gene Expression
          2. MRI
>
>
          1. Gene Expression (subsumes Protein Localization)

        1. Microarray
Changed:
<
<
          1. Gene Expression
>
>
          1. Gene Expression (subsumes Protein Localization)

        1. Images: 2D
          1. Any
          2. Cell Fills
          3. Classical Histology
Changed:
<
<
          1. Gene Expression
>
>
          1. Gene Expression (subsumes Protein Localization)

        1. Images: 3D
          1. Any
          2. Cell Fills
Changed:
<
<
      1. If Microarray selected, show Gene selection (required).
      • Possible to have the ability to "ADD" or "EXCLUDE" like in itunes?
    2. Collection technique
>
>
      1. Technique

      1. Any
      2. Microscopy
        1. Any
        2. Light
          1. Confocal
Changed:
<
<
          1. Flourescence
>
>
          1. Fluorescence

          1. Multiphoton
        2. Electron
      2. MR
Line: 67 to 65
        1. T2
        2. DTI
      2. Electron Tomography
Added:
>
>
      • Possible to have the ability to "ADD" or "EXCLUDE" like in itunes?

    1. Gene/Molecule
Changed:
<
<
      1. Protein (freetext)
      2. Keyword search rather than the more specific gene function and we'll have to connect to a more powerful annotation DB-both Rob's and Paul Pavlidis'(?)
>
>
      1. add protein to dropdown
      2. add keyword to dropdown rather than the more specific gene function and we'll have to connect to a more powerful annotation DB-both Rob's and Paul Pavlidis'(?)

      1. Add way to list available gene symbols?
    2. Subject/Organism
      1. Developmental Stage
Line: 86 to 85
        1. days/weeks/months?
    2. Disease Model
      1. Treatment
Changed:
<
<
        1. default: any
>
>
        1. default: Normal

        1. All/any
        2. Diseased/treated
Deleted:
<
<
          1. Normal??

          1. Alzheimer's
          2. Parkinson's
          3. Multiple Sclerosis
Line: 110 to 108
          1. Development
          2. Reeler
          3. Sex Differences/Dimorphism
Added:
>
>
          1. Keyword (freetext)

      1. Investigator
        1. Any
        2. Keyword (freetext)

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.9 - 27 Feb 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes

2008 AHM (Oct.20) MBAT Requirements

This document lists the required functionality for MBAT that will be delivered at the 2008 All-hands Meeting on October 20,2008.
Line: 34 to 34
      1. Protein localization
      2. Brain mosaics
    2. Datatype
Changed:
<
<
      1. Redesign as DataType/SubType
>
>
      1. Redesign as DataType/Content

        1. Any
          1. Cell Fills
          2. Classical Histology
Line: 50 to 50
        1. Images: 3D
          1. Any
          2. Cell Fills
Deleted:
<
<
          1. MRI

      1. If Microarray selected, show Gene selection (required).
      • Possible to have the ability to "ADD" or "EXCLUDE" like in itunes?
Added:
>
>
    1. Collection technique
      1. Any
      2. Microscopy
        1. Any
        2. Light
          1. Confocal
          2. Flourescence
          3. Multiphoton
        3. Electron
      3. MR
        1. Any
        2. T1
        3. T2
        4. DTI
      4. Electron Tomography

    1. Gene/Molecule
      1. Protein (freetext)
      2. Keyword search rather than the more specific gene function and we'll have to connect to a more powerful annotation DB-both Rob's and Paul Pavlidis'(?)
Line: 60 to 74
    1. Subject/Organism
      1. Developmental Stage
Added:
>
>
        • Embryonic and Postnatal days must be distinguished in DB

        1. default: adult
Changed:
<
<
        1. all/any
        2. embryo
        3. newborn
        4. infant
        5. juvenile
        6. elderly
>
>
        1. All/any
        2. Embryonic (0-11 embryonic days)
        3. Fetal (11-20(birth) embryonic days)
        4. Neonate/infant (0-12 postnatal days)
        5. Child/pup (12-24 postnatal days)
        6. Juvenile (24-60 postnatal days)
        7. Adult (60-300 postnatal days)

        1. days/weeks/months?
Added:
>
>
    1. Disease Model

      1. Treatment
Changed:
<
<
        1. default: normal
        2. all/any
        3. diseased
        4. prediseased
        5. treated
        6. mutant mouse strain
>
>
        1. default: any
        2. All/any
        3. Diseased/treated
          1. Normal??
          2. Alzheimer's
          3. Parkinson's
          4. Multiple Sclerosis
          5. Schizophrenia

    1. Anatomical Area
      1. Any
      2. CNS hierarchy
Line: 82 to 101
      1. Cell
      2. Subcellular
      3. Other part (freetext)
Deleted:
<
<
    1. Collection technique
      1. Any
      2. Microscopy
        1. Any
        2. Electron
        3. Confocal
        4. Light
        5. Flourescence
        6. Multiphoton
      3. MR
        1. Any
        2. T2
        3. T1
        4. DTI

    1. Experimental Info (CCDB and AIDB)
      1. Project
        1. Any
Line: 105 to 110
          1. Development
          2. Reeler
          3. Sex Differences/Dimorphism
Deleted:
<
<
        1. Disease Model
          1. Any
          2. Alzheimer's
          3. Parkinson's
          4. Multiple Sclerosis
          5. Schizophrenia

      1. Investigator
        1. Any
        2. Keyword (freetext)

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.8 - 20 Feb 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes

2008 AHM (Oct.20) MBAT Requirements

This document lists the required functionality for MBAT that will be delivered at the 2008 All-hands Meeting on October 20,2008.
Line: 30 to 30
    1. Gene expression to mbSearch
      1. MBAT GUI code must change
  2. Expand current terms
Added:
>
>
    1. CCDB datatypes?
      1. Protein localization
      2. Brain mosaics

    1. Datatype
      1. Redesign as DataType/SubType
        1. Any
Line: 51 to 54
      1. If Microarray selected, show Gene selection (required).
      • Possible to have the ability to "ADD" or "EXCLUDE" like in itunes?
    2. Gene/Molecule
Changed:
<
<
      1. Add Protein (freetext)
      2. Add a keyword search rather than the more specific gene function and we'll have to connect to a more powerful annotation DB-both Rob's and Paul Pavlidis'(?)
>
>
      1. Protein (freetext)
      2. Keyword search rather than the more specific gene function and we'll have to connect to a more powerful annotation DB-both Rob's and Paul Pavlidis'(?)

      1. Add way to list available gene symbols?
    2. Subject/Organism
Changed:
<
<
      1. Add Developmental Stage
>
>
      1. Developmental Stage

Line: 65 to 68
        1. juvenile
        2. elderly
        3. days/weeks/months?
Changed:
<
<
      1. Add Treatment
>
>
      1. Treatment

        1. default: normal
        2. all/any
        3. diseased
Line: 74 to 77
        1. mutant mouse strain
    2. Anatomical Area
      1. Any
Changed:
<
<
      1. Add CNS hierarchy
>
>
      1. CNS hierarchy

      1. Entire Organism
      2. Cell
      3. Subcellular
      4. Other part (freetext)
    2. Collection technique
Changed:
<
<
      1. Add Microscopy
>
>
      1. Any
      2. Microscopy

        1. Any
        2. Electron
        3. Confocal
        4. Light
        5. Flourescence
Changed:
<
<
      1. Add MR
>
>
        1. Multiphoton
      2. MR

        1. Any
        2. T2
        3. T1

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.7 - 14 Feb 2008 - DarenLee)

META TOPICPARENT LONIMBATTechnicalNotes

2008 AHM (Oct.20) MBAT Requirements

This document lists the required functionality for MBAT that will be delivered at the 2008 All-hands Meeting on October 20,2008.
Line: 31 to 31
      1. MBAT GUI code must change
  2. Expand current terms
    1. Datatype
Changed:
<
<
      1. Redesign DataType as "2d/3d" ... "subtype," i.e. Microarray/2D image/3D image/any, then the other selection would gene expression/classical histology/cell fills/MR/any
>
>
      1. Redesign as DataType/SubType
        1. Any
          1. Cell Fills
          2. Classical Histology
          3. Gene Expression
          4. MRI
        2. Microarray
          1. Gene Expression
        3. Images: 2D
          1. Any
          2. Cell Fills
          3. Classical Histology
          4. Gene Expression
        4. Images: 3D
          1. Any
          2. Cell Fills
          3. MRI

      1. If Microarray selected, show Gene selection (required).
Changed:
<
<
      1. Add "2D Images, Classical Histology" (CCDB)
      2. Add "3D Image Gene Expression" (CCDB) this is actually less of a gene expression and more of molecule/protein
      3. Add "3D Image Classical Histology" (CCDB)
      4. Add "3D Image Cell Fills" (CCDB)
      5. Add "3D Image MR" (AIDB)
      6. Add "3D Image connections" (?AIDB-Hongwei) this is not going to be on the table for awhile
      7. Add default "any" (is this feasible?) (duplicate records?)
      • Possible to have the ability to "ADD" or "EXCLUDE" like in itunes?
>
>
      • Possible to have the ability to "ADD" or "EXCLUDE" like in itunes?

    1. Gene/Molecule
Changed:
<
<
      1. Add way to list available gene symbols
>
>
      1. Add Protein (freetext)

      1. Add a keyword search rather than the more specific gene function and we'll have to connect to a more powerful annotation DB-both Rob's and Paul Pavlidis'(?)
Changed:
<
<
    1. Subject/Organism: Add Developmental Stage
>
>
      1. Add way to list available gene symbols?
    2. Subject/Organism
      1. Add Developmental Stage

      1. default: adult
      2. all/any
      3. embryo
Line: 52 to 64
      1. infant
      2. juvenile
      3. elderly
Changed:
<
<
      1. days/weeks/months?
        1. for above, set standard time (ie: newborn = 1-10 days), this was done by Rob Williams and is on the wiki somewhere...
    2. Subject/Organism: Add Treatment
>
>
        1. days/weeks/months?
      2. Add Treatment

      1. default: normal
      2. all/any
      3. diseased
      4. prediseased
      5. treated
      6. mutant mouse strain
Changed:
<
<
    1. Anatomical Area: Add CNS hierarchy
      1. cell
      2. subcellular
    2. Imaging Modality/ Collection technique: Add Microscopy if we have problems with this, we may wish to start with just two big categories, microscopy and MR
>
>
    1. Anatomical Area
      1. Any
      2. Add CNS hierarchy
      3. Entire Organism
      4. Cell
      5. Subcellular
      6. Other part (freetext)
    2. Collection technique
      1. Add Microscopy
        1. Any

      1. Electron
      2. Confocal
      3. Light
      4. Flourescence
Changed:
<
<
    1. Imaging Modality: MR
>
>
      1. Add MR
        1. Any

      1. T2
      2. T1
      3. DTI
Changed:
<
<
    1. Experimental Info (what DB supports this?) CCDB and AIDB should support this
      1. Project Priority at this point, but it encapsulates some of the Disease Group information below
>
>
    1. Experimental Info (CCDB and AIDB)
      1. Project
        1. Any
        2. Project
          1. Any
          2. BxD
          3. Development
          4. Reeler
          5. Sex Differences/Dimorphism
        3. Disease Model
          1. Any
          2. Alzheimer's
          3. Parkinson's
          4. Multiple Sclerosis
          5. Schizophrenia

      1. Investigator
Changed:
<
<
    1. Disease Group (what DB supports this?) may need to be tied to experimental information, it's possible this may not be explicit in some of the databases, but should be available in some way for CCDB and AIDB
      1. Parkinson's
      2. Alzheimer's
      3. Multiple Sclerosis
>
>
        1. Any
        2. Keyword (freetext)

  1. Expand current data sources
    1. AIDB
      1. Query terms?
Line: 96 to 126
      1. Infrastructure for remote binaries (Pipeline, UCSD Portal)
    2. Infrastructure for data types:
      1. subimage
Changed:
<
<
      1. 2D focus on this to start
      2. 3D
      3. 4D
      4. List here...
>
>
      1. 2D
      2. 3D
      3. 4D

    1. Infrastructure for landmark based algorithms
Changed:
<
<
    1. Infrastructure for intensity based algorithms? this may be where we can create a tie to Pipeline
>
>
    1. Infrastructure for intensity based algorithms? this may be where we can create a tie to Pipeline

  1. Supported Data types
    1. 2D - 2D
Added:
>
>
      1. manual

      1. default algo: Ryan and Craig's algorithm, taking advantage of Heng's UI for points (possibly contours)
Deleted:
<
<
    1. 2D - 3D
      1. default algo: ???: facilitate manual first-find close spot in atlas, then possible implementation of Erh-Fang's contour-based algorithms, although it may be too difficult to implement easily, then follow up with 2D - 2D using algorithm and interface developed above

    1. Subimage - 2D
      1. default algo: manual
    2. Subimage - 3D
      1. default algo: manual
Added:
>
>
    1. 2D - 3D
      1. default algo: ???: _facilitate manual first-find close spot in atlas, then possible implementation of Erh-Fang's contour-based algorithms, although it may be too difficult to implement easily, then follow up with 2D - 2D using algorithm and interface developed above_

Comparison Workspace


 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.6 - 07 Feb 2008 - JylBoline)

META TOPICPARENT LONIMBATTechnicalNotes

2008 AHM (Oct.20) MBAT Requirements

This document lists the required functionality for MBAT that will be delivered at the 2008 All-hands Meeting on October 20,2008.
Line: 18 to 18
    1. Needs more data in database
    2. Needs more metadata about data retrieved
Changed:
<
<

Atlasing [UCSD]

>
>

Atlasing [UCSD, Drexel]


  1. Infrastructure for Atlas Interoperability Server
Added:
>
>
  1. Importation of Drexel's NeuroTerrain Atlas into MBAT format
    • next steps are to use this framework to access MBL data using their atlas and Atlas Interoperability infrastructure

Query Engine [AIDB, all Mouse DBs, Brian, Vadim, and Bill]

  • this will be much easier if we can get things working through the Concept Term Mapping and possibly Mediator]
Line: 84 to 86
      1. Steps required for MBAT to connect to AIDB?

Changed:
<
<

Registration Workspace [UCSD]

>
>

Registration Workspace [UCSD, Drexel]


  1. Framework for loading data
    1. from Query workspace
    2. locally
Line: 104 to 106
    1. 2D - 2D
      1. default algo: Ryan and Craig's algorithm, taking advantage of Heng's UI for points (possibly contours)
Added:
>
>
        • also take a look at Drexel's QA/registration JAVA tools

    1. 2D - 3D
      1. default algo: ???: facilitate manual first-find close spot in atlas, then possible implementation of Erh-Fang's contour-based algorithms, although it may be too difficult to implement easily, then follow up with 2D - 2D using algorithm and interface developed above
    2. Subimage - 2D

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.5 - 07 Feb 2008 - JylBoline)

META TOPICPARENT LONIMBATTechnicalNotes

2008 AHM (Oct.20) MBAT Requirements

This document lists the required functionality for MBAT that will be delivered at the 2008 All-hands Meeting on October 20,2008.
Line: 29 to 29
      1. MBAT GUI code must change
  2. Expand current terms
    1. Datatype
Changed:
<
<
      1. Redesign DataType? as "2d/3d" ... "subtype," i.e. Microarray/2D image/3D image/any, then the other selection would gene expression/classical histology/cell fills/MR/any
>
>
      1. Redesign DataType as "2d/3d" ... "subtype," i.e. Microarray/2D image/3D image/any, then the other selection would gene expression/classical histology/cell fills/MR/any

      1. If Microarray selected, show Gene selection (required).
      2. Add "2D Images, Classical Histology" (CCDB)
      3. Add "3D Image Gene Expression" (CCDB) this is actually less of a gene expression and more of molecule/protein
Line: 103 to 103
  1. Supported Data types
    1. 2D - 2D
      1. default algo: Ryan and Craig's algorithm, taking advantage of Heng's UI for points (possibly contours)
Added:
>
>

    1. 2D - 3D
      1. default algo: ???: facilitate manual first-find close spot in atlas, then possible implementation of Erh-Fang's contour-based algorithms, although it may be too difficult to implement easily, then follow up with 2D - 2D using algorithm and interface developed above
    2. Subimage - 2D

 <<O>>  Difference Topic 2008AHMPlanOct20 (r1.4 - 06 Feb 2008 - JylBoline)

META TOPICPARENT LONIMBATTechnicalNotes

2008 AHM (Oct.20) MBAT Requirements

This document lists the required functionality for MBAT that will be delivered at the 2008 All-hands Meeting on October 20,2008.
Line: 21 to 21

Atlasing [UCSD]

  1. Infrastructure for Atlas Interoperability Server
Changed:
<
<

Query Engine [AIDB, all Mouse DBs, Brain, Vadim, and Bill-this will be much easier if we can get things working through the Concept Term Mapping and possibly Mediator]

>
>

Query Engine [AIDB, all Mouse DBs, Brian, Vadim, and Bill]

  • this will be much easier if we can get things working through the Concept Term Mapping and possibly Mediator]

  1. Refactor
    1. Clean up v2.0
    2. Gene expression to mbSearch
      1. MBAT GUI code must change
  2. Expand current terms
    1. Datatype
Changed:
<
<
      1. Redesign