# ICR Workspace Teleconference

## Meeting Information

Date: October 22, 2008

Time: 2-4 PM ET\
Moderator: Elaine Freund

#### 

## Executive Summary

The ICR Workspace met to discuss the following:

-   All notes and other items created January 1, 2008 and on, will be
    transferred into new 508 compliance documents

-   caBIG^®^ is now registered by the U.S. Patent and Trademark Office

-   The new Support Service Providers were announced.

-   Upcoming Face to Face meetings were announced

-   Nanotech Working Group Updates

-   Workflow Working Group Updates

-   Molecular Analysis Tools Knowledge Center

-   ICR Outreach and Communication

-   TBPT WS Update

-   caDSR EA Plugin

## Key Outcomes and Decisions

N/A

## Action Items

Table 1: Meeting Action Item List

  ------------------------------------------------------------------------
  **Assigned To**   **Description**                         **Due Date**
  ----------------- --------------------------------------- --------------
  Team              Continue working on projects            

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

## Meeting Notes

Patti Kwong introduction/Li continue in ICR in a limited capacity
focused in ASBP.

### 508 Compliance and notes issue

-   Section 508 requires Federal agencies to make their Electronic and
    Information Technology (EIT) accessible to employees and customers
    with disabilities.

-   Visit <http://www.access-board.gov/sec508/guide/act.htm> to read the
    full Rehabilitation Act.

-   Under Section 508, EIT includes information technology and any
    equipment or interconnected system (or subsystem of equipment), that
    is used in the creation, conversion, or duplication of data or
    information, or used in the automatic acquisition, storage,
    manipulation, management, movement, control, display, switching,
    interchange, transmission, or reception of data or information.

-   The term EIT includes, but is not limited to:

    -   Web sites including those used externally and internally.

    -   Multimedia products such as on-line video, audio, animations,
        and simulations.

-   Community Web site has over 80,000 errors, including broken links
    and inaccessible information.

-   Anything in the public domain needs to comply, i.e. GForge and Wiki
    sites.

### Face-to-Face Announcements

-   TBPT F2F -TBPT Workspace\'s November 13th - 14th, 2008 Face-to-Face
    Meeting to be held in New Orleans, Louisiana. Accompanying this
    meeting will be a Pathology Imaging WG Working Session on November
    12th, to be held in the same conference facility as the Face-to-Face
    Meeting that will take place on November 13th & 14th. Registration
    available online

-   Pop Sci F2F - afternoon of Nov. 19th and end at noon on Nov. 21^st^
    at the University of Colorado Cancer Center. Registration available
    online.

### caBIG^®^ Registered by the U.S. Patent and Trademark Office

-   The cancer Biomedical Informatics Grid^®^ and caBIG^®^ are
    officially registered by the U.S. Patent and Trademark Office,
    effective September 2008. As such, the registered symbol (^®^)
    should replace the pending trademark symbol (™) in all instances of
    "cancer Biomedical Informatics Grid^®^" and "caBIG^®^"---including
    logos, graphics, and written references.

-   This change should be reflected on all materials that appear in
    print and on the Web. The caBIG^®^ Communications Team has been
    working to coordinate updates, and the NCI encourages all caBIG^®^
    participants to assist this effort by updating their working
    documents as soon as possible.

-   *Please note that you do not need to update dated materials (such as
    press releases, newsletter articles, or meeting minutes) created
    prior to September 1, 2008*. Otherwise, all new or updated documents
    must use the ^®^ symbol. If you need updated graphics, please
    contact
    [[caBIGinfo@cancer.gov]{.underline}](mailto:caBIGinfo@cancer.gov) to
    request new artwork with the registered symbol (^®^).

### Support Service Providers

The following list reflects the four categories of services offered by
caBIG^®^ Support Service Providers. Below each category is the list of
companies that have been licensed by NCI to market their services within
that category of the caBIG^®^ Support Service Providers Program.

-   Help Desk Support - This service category includes support for the
    end users and local IT administrators in institutions using the
    caBIG^®^ applications and tools contained within the three caBIG^®^
    Bundles (Life Sciences Distribution, Clinical Trials Compatibility
    Framework, and Data Sharing and Security Framework), as well as
    those wishing to adapt tools or connect their tools to the grid.

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-   Adaptation and Enhancement of caBIG^®^ -Compatible Software
    Applications - This service category supports caBIG^®^ -compatible
    software development and includes adaptation of existing systems for
    caBIG^®^ compatibility, custom enhancements to existing caBIG^®^
    tools that satisfy specific user-driven requirements while
    maintaining caBIG^®^ compatibility, and de novo development of
    caBIG^®^ -compatible applications and tools.

    -   <http://cabig.5amsolutions.com/>

    -   <http://www.ekagrasoft.com/Services.htm>

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-   Deployment Support for caBIG^®^ Software Applications - Includes
    onsite or offsite procurement and provisioning of hardware,
    operating systems and other software, such as application servers
    and databases, along with installation and configuration of caBIG^®^
    software, legacy data transformation and migration. Deployment
    support also includes integration of multiple caBIG^®^ tools and
    caBIG-compatible applications through open application programming
    interfaces (APIs). Possible services include data management,
    security services, hosting, performance tuning, network
    connectivity, grid enablement and maintenance of web server/database
    and application specific administrative IT tasks.

    -   <http://cabig.5amsolutions.com/>

    -   <http://www.akazaresearch.com/about_akaza/caBIG.html>

    -   <http://www.ekagrasoft.com/Services.htm>

    -   <http://www.sra.com/it/caBIG-SSPP>  

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-   Documentation and Training Materials and Services - This service
    category includes development of documentation and training
    materials and the provision of training services for
    caBIG^®^software applications, caBIG^®^ compatibility for existing
    systems, and use of caCORE infrastructure.

    -   <http://www.akazaresearch.com/about_akaza/caBIG.html>

 

Applicants for each service category are evaluated by committees against
four key criteria: Technical capabilities, Staffing and scalability,
Geographic coverage (when applicable), and Domain expertise in
biomedicine.  

### Access Announcements:  

-   NOW OPEN -- Due Tuesday, 18 November 2008:  caBIG is currently
    requesting applications for the caBIG Support Service Provider
    Program.  More information and the announcement can be downloaded
    from <https://cabig.nci.nih.gov/esn/ssp>.  

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-   Announcements for additional caBIG^®^ Support Service Providers will
    be issued on a recurring basis.

### Working Group Reports

#### Nanotech Working Group Update

#### [**https://gforge.nci.nih.gov/frs/download.php/4996/20081022_Nanotech_ICR_Update.ppt**](https://gforge.nci.nih.gov/frs/download.php/4996/20081022_Nanotech_ICR_Update.ppt)

-   Wrapping up white paper on Nanotech

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-   Recommendations for the field from first white paper reviewed

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-   Ontology white paper nearly done

-   Use cases underway

#### MATKC

<https://gforge.nci.nih.gov/frs/download.php/4998/20081022MATKC_ICR_WS_Meeting.ppt>

Update on wiki content and usage

-   Release updates for supported tools presented

-   Questions from the community gathered

-   Discussed how tools connect

#### IOC Working Group

<https://gforge.nci.nih.gov/frs/download.php/4985/ICR_IOC_Update_20081021.ppt>

-   Organizational items

-   Review of charter

#### Work Flow Working Group

#### White paper deliverable 

-   Service stability

-   Services on the grid

-   Grid version use

-   Need for Shims

-   Need for stats for data type re-use

#### Reference Workflow

-   On GForge

MyGrid services to the grid occurred today

#### TBPT WS Update

<https://gforge.nci.nih.gov/frs/download.php/4999/TBPT2ICR_2008-10-22.ppt>

-   Described TBPT and Tools

-   Dynamic extensions explored/explained in some detail due to coding
    fork -- caTissue Suite and Core

Questions:

-   What is the process of registration of dynamic extensions? Will it
    be done on an individual, institution or community basis? It appears
    that individual institutions submit objects to TBPT for vetting
    prior to going into the caDSR.

-   Lively discussion ensued.

    -   Noted that caLIMS is facing the same issue -- it calls for the
        ability to post your own information and leads to
        incompatibility.

    -   Registration of CDEs is not enough, they need to be put in the
        model

    -   There are different user groups of dynamic extensions. There are
        single institution idiosyncrasies on the one side but also
        potential dynamic extensions use across multiple institutions
        with the need to share annotations. There are arguments on both
        sides for "register all" or have "private objects"

    -   IPBS first used the dynamic extensions API to share and script
        exactly the same across 11 institutions.

-   Should dynamic extensions undergo same vetting process?

    -   Data model needs to share

    -   A fundamental question of caBIG -- how to deal with cases where
        you have specific implementations with common and specific
        parts. It is too burdensome to standardize it all.

    -   Bottleneck is centralized repository to enable sharing.

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-   Philosophical question on what to register

-   Technical question on how to register and for the grid -- how to
    keep schema up to date

-   Procedural question-- review and how to get applications versioned
    and how to monitor compatibility status, etc.

-   caTissue Suite 1.0 in pre-review. If there is an app not using
    dynamic extensions but are taking in data on the fly, how is that
    being handled? Ie.

-   Affy loaded via an caBIG app?

-   Tissue Microarray status? Is this being done? It has dropped of the
    radar

-   Pathology imaging status?

-   Biorepository?

-   Common model and vendors map to the common model...IPBS to query
    across multiple tools or solutions.

-   How does common model overlap with the LS DAM?

-   Common biorepository model to be simple and not as rich as the LS
    DAM and should map to it.

-   Do we have a contact with who is doing this work? ACTION ITEM:
    David...put in touch. Should info rep be in discussion with these
    people?

-   Brought back a focus one std and existing apps map to it.

### caDSR EA Plugin

<https://gforge.nci.nih.gov/frs/download.php/5003/cgmdr_DW_ICR.ppt>

## Next Steps

Continue working on projects and reporting to the Workspace.

## Next Meeting

November 12, 2008

November 26 meeting is cancelled.

## Attendees

Table 2: List of Meeting Attendees

  -----------------------------------------------------------------------
  **Affiliation**                     **Name**
  ----------------------------------- -----------------------------------
  3^rd^ Mill                          Elaine Freund

  BAH                                 Li Kramer

  BAH                                 Patti Kwong

  Baylor College of Medicine          David Steffen

  Broad Institute                     Ted Liefeld

  Broad Institute                     Jared Nedzel

  Columbia University                 Kiran Keshav

  Columbia University                 Zhong Li

  Dana Farber                         Deven Atnoor

  Fred Hutch                          Martin Morgan

  Jackson Laboratory                  Grace Stafford

  Mass General Hospital               Stanley Shaw

  Mayo Clinic                         Bob Freimuth

  NCI                                 Juli Klemm

  NCI                                 Sue Pan

  SAIC                                Donna Messersmith

  Stanford                            Samira Guccione

  Stanford                            David Paik

  University of North Carolina        Wei Wang

  Washington University               Nathan Baker

  Washington University               Rohit Pappu

  Washington University               J. Shaik

  Washington University               Mukesh Sharma

  NCI                                 Denise Warzel

  FKH                                 Trey White

  Princeton                           Gunter Schemmann

                                      Jim Sun

                                      Jenny Kelly

                                      Lalitha Viswanath

  IMS                                 Mary McAdams

  UCSD                                Hannes Neidner

  Nartech                             Tom Boals

  Duke                                Sal Mungal

                                      John Sandefuer
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