December 7, 2001   NIH Bldg 31, Conference Room 10   6th Floor, C-Wing

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.

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	Download
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.	Download
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.	Download
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.	Download
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	Download
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.	Download
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.	Download
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