2004 Focus Sessions and Workshops
Practical Informatics
Wednesday, October 6, 2004, 8:00 AM - 12:00 PM
Practical Informatics is an intensive introduction to much of the basic knowledge and skills needed to effectively use information systems in the practice of pathology and oncology informatics. Recipients of CAP Informatics Awards are expected to attend; others interested in enhancing their foundation and knowledge of informatics are encouraged to attend.
Topics to be covered include:
8:00 AM - 9:00 AM |
Basic Architecture: from Bytes to Interfaces Dr. Sinard |
| 9:00 AM - 10:00 AM | Database Systems Dr. Sinard |
| 10:00 AM - 11:00 AM | Digital Image Acquisition and Processing Dr. Parwani |
| 11:00 AM - 12:00 PM | Digital Image Management and Utilization Dr. Parwani |
Microarray and Proteomics Data Analysis Workshop
James Lyons-Weiler, PhD
Wednesday, October 6, 2004, 8:00 AM - 12:00 PM
(Limited participation)
In this workshop, participants will learn how to use methods for assessing the data quality from microarray experiments, and how to evaluate methods for the analysis of data from microarray experiments, including: transformation, normalization, finding differentially expressed genes, performing class discovery and class prediction. They will enjoy hands-on experience with an online gene expression data analysis web application We will also explore challenges and solutions in the analysis of high-throughput proteomic peptide profiles. (http://bioinformatics.upmc.edu/GE2/GEDA.html).
API Working Group Session - Open Discussion of Pathology Digital Imaging Standards
Ulysses J. Balis, MD and Jules J. Berman, MD, PhD
Wednesday, October 6, 2004, 11:30 AM- 1:00 PM
This workshop follows discussions from last year's APIII session on Digital Imaging. At the prior workshop, pathologists, vendors and imaging specialists indicated that current imaging modalities for research and discovery in genomics and proteomics as well as widefield microscopy are complex, involving large binary objects (with gigabytes or more of data), multiplexed images (as in tiled images or multi-record tissue microarray images), and images representing data beyond the pictorial representation of a tissue section (e.g. spectral, Fourier-transformed, wavelet, or vector quantized data). DICOM (Digital Image Communications in Medicine) is the only medical imaging standard, and it has only been implemented in prototype fashion for pathology images. Currently, there is no commonly implemented data specification for the encapsulation of pathology images and associated annotative data (e.g. histopathologic description, clinical annotation, image analysis results, image capture parameters, security and authentication codes, and self-describing format details).
Recognizing the need for imaging standards, the API has included an image standard effort in its recently announced Laboratory Digital Imaging Project (LDIP). The purpose of the workshop is to provide a forum in which stakeholders can suggest the basic desired features of a pathology image standard. The results will be used to start development of an image specification within the LDIP initiative. Suggested topics of discussion include:
1. What are the needs of pathologists, vendors, and imaging specialists with regard to imaging standards?
2. What are the limitations of DICOM that have kept it from being implemented in pathology laboratories?
3. What are the most general features of a pathology imaging specification that must be considered when developing a new specification (e.g. DICOM compatibility, license statements, process for modifying the specification, etc.)?
4. What are possible collaborative directions that the pathology and associated research communities can jointly leverage to accelerate the pace of development and more importantly, adoption of this needed standard?
Moderators will include Drs. Ulysses Balis, Jules Berman and members of the LDIP Committee.
CAP TODAY / CAP FOCUS SESSION:
caBIG - Blueprint for Informatics in Cancer Centers
Wednesday, October 6, 2004, 1:00 PM - 5:00 PM
The Cancer Biomedical Informatics Grid Initiative (caBIG) is an innovative new program of the NCI, which aims to connect cancer research institutions with an interconnected set of open source, federated tools to be developed collaboratively. This program aims to serve the critical connectivity needs facing the cancer research community today. The program will initially focus on three domain workspaces (clinical trials, tissue banks/pathology tools and integrative cancer research) and two cross cutting workspaces (vocabularies/common data elements and architecture). This ambitious program will support the development and adoption of these tools in over 60 cancer centers and research institutes over the next three years.
Our speakers and panelists will focus on:
Understand the progress and future vision of the Cancer Biomedical Informatics Grid (caBIG) initiative
- ·Understand the major public policy issues for caBIG to address
- Understand the role and potential for caBIG in transforming cancer care and cancer research
- Recognize the strengths, weaknesses and opportunities of the program
- Address the challenges for integrating caBIG tools into NCI’s clinical and research programs
- Understanding the critical role of Pathology, Oncology and Bioinformatics in cancer research’s future
API) FOCUS SESSION:
Opportunities and Pitfalls in High-Throughput Genomic and Proteomic Based Medical Science: From Peptide Profiling to Pathways
Thursday, October 7, 2004, 1:00 PM – 5:00 PM
Good scientific practices beget good science. Development of integrated computational workspaces can help maximize the impact of that science by fostering re-examination and comparisons of existing data sets. It has become clear that translation of the patterns discovered into biological understanding can be enhanced by studying impacted pathways. Our speakers and panelists will focus on the following:
- How does one best insure that errors in the early stages of a discovery-oriented project do not threaten the possibility of discovery?
- How can one use highly integrated workspaces effectively to complement their own ongoing research projects?
- What are some of the best ways to study pathways and how pathways are impacted by differential expression and dysregulation?