NCI has established the Center for Bioinformatics (NCICB) to provide bioinformatics
support and integration of its diverse research initiatives. To achieve this goal the
NCICB has been constituted as a network of Initiative-Specific Modules. These modules
are connected through intelligent interfaces, coordinated through an NCI Core Module
and deployed through open source tools and systems. The NCICB also serves as the locus
for strategic planning to address the NCI's expanding research initiative's informatics
needs. The NCICB communicates, coordinates, or establishes information exchange standards
within the NCI research community.
Download the Jamboree intro here:
AM Session: NCICB Core Technologies |
Technology |
Time |
Presenters |
Description |
Download |
caBIO |
9:00-9:45 |
Himanso Sahni Scott Gustafson |
Provide an overview of the cancer Bioinformatics Infrastructure
Objects (caBIO), the caBIO Architecture (RMI,SOAP,RDF), the caBIO API,
Usage (bean and Web Services), and future services (LDAP and EVS I/F) |
Download |
EVS |
9:45-10:30 |
Sherri DeCoronado Frank Hartel |
Discuss the Enterprise Vocabulary System (EVS) Metaphrase API, EVS DTS Ontylog
API, EVS Concept Based Indexing tool, and Least Upper Bound Servlet prototype |
Download |
Break | 10:30-10:45 | | | |
SBR/CDE |
10:45-11:30 |
J.J. Maurer Dr. John Silva |
Provide an overview of some of the architectural aspects of the Standards Based
Repository (SBR) for Common Data Elements (CDE), how the SBR is being extended for
clinical trials, the API that facilitates access to the SBR, how to use the SBR as
a content manager or user, how to use the SBR as a development team, and the next
steps in the development effort |
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DCP DESK/PIMS |
11:30-12:15 |
Lisa Chatterjee Christina Schrivera |
Discuss the major components and architecture of the DESK/PIMS (Desktop Enterprise
System Knowledgebase/Protocol Information Management System) systems developed for the
Division of Cancer Prevention (DCP) including the technical architecture, technology
stack, highlights of the data model, highlights of the functional components, and how
it is built and maintained (machine generated code). Also, discuss the functional
components of the DCP, (what it does) and the relationships to the other NCI CT models. |
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Lunch | 11:30-12:15 | | | |
PM Session: NCICB Projects |
CGAP |
1:00-1:30 |
Carl Schaefer |
The goal of the Cancer Genome Anatomy Project (CGAP) is to correlate gene expression,
genetic polymorphism, and chromosome abnormalities with cell morphology and topography. The
CGAP database and web site has tools for browsing cDNA and SAGE libraries, analyzing gene
expression by tissue and histology, querying gene function, and finding recurrent chromosome
aberrations in cancer. |
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GAI |
1:30-2:00 |
Michael Edmonson Bob Clifford |
The CGAP Genetic Annotation Initiative (GAI) identifies single nucleotide polymorphisms from
publicly available EST sequencing traces. The GAI provides a variety of web-based tools for viewing
information about SNPs. These include: search engines for selecting SNPs by gene name, keyword,
or chromosomal location; a viewer for displaying SNPs in the context of sequence assemblies; and
tools for viewing SNPs in the context of transcripts, open reading frames and protein motifs. |
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CMAP |
2:00-2:30 |
Carl Schaefer |
The goal of the Cancer Molecular Analysis Project (CMAP) is to integrate data on molecular
profiles of cancers, molecular targets, therapeutic and diagnostic targets, and clinical trials.
The prototype CMAP database and web site have only limited data at present; however, the data
model and software infrastructure are available to store, analyze and display additional data. |
Download |
Break | 2:30-2:45 | | | |
MMHCC |
2:45-3:15 |
Himanso Sahni Dana Zhang |
Provide an overview of the mouse models cancer database that was designed for the Mouse Models of
Human Cancer Consortium (MMHCC) including the UI, EVS interface, existing application and database
schema, and the object model |
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DC |
3:15-3:45 |
John Yost Jennifer Long |
Provide an overview of the Director's Challenge (DC) microarray (gene expression) database,
existing standards (MAGE ML), the architecture and API, and data upload and browsing tools. |
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caLIMS |
3:45-4:15 |
Bill Havanki Denny Chan |
Provide an overview of the cancer Laboratory Information Management System (caLIMS), the
LIMS architecture, API (LDAP I/F), and instructions for creating adapters. |
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Web/Portal Development |
4:15-4:45 |
Clint Malone Ryan Landy |
Provide an overview of the Zope site structure and security model. Discuss the
Apache JetSpeed NCICB portal ("My NCICB"). |
Download |