Ochs / Casagrande / Davuluri Biomedical Informatics for Cancer Research

1. Auflage 2010
ISBN: 978-1-4419-5714-6
Verlag: Springer US
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 354 Seiten, eBook

view, showing that multiple molecular pathways must be affected for cancer to develop, but with different specific proteins in each pathway mutated or differentially expressed in a given tumor (The Cancer Genome Atlas Research Network 2008; Parsons et al. 2008). Different studies demonstrated that while widespread mutations exist in cancer, not all mutations drive cancer development (Lin et al. 2007). This suggests a need to target only a deleterious subset of aberrant proteins, since any tre- ment must aim to improve health to justify its potential side effects. Treatment for cancer must become highly individualized, focusing on the specific aberrant driver proteins in an individual. This drives a need for informatics in cancer far beyond the need in other diseases. For instance, routine treatment with statins has become widespread for minimizing heart disease, with most patients responding to standard doses (Wilt et al. 2004). In contrast, standard treatment for cancer must become tailored to the molecular phenotype of an individual tumor, with each patient receiving a different combination of therapeutics aimed at the specific aberrant proteins driving the cancer. Tracking the aberrations that drive cancers, identifying biomarkers unique to each individual for molecular-level di- nosis and treatment response, monitoring adverse events and complex dosing schedules, and providing annotated molecular data for ongoing research to improve treatments comprise a major biomedical informatics need.

Zielgruppe

Research

Autoren/Hrsg.

Ochs, Michael F.

Casagrande, John T.

Davuluri, Ramana V.

Inhaltsverzeichnis

Concepts, Issues, and Approaches.- Biomedical Informatics for Cancer Research: Introduction.- Clinical Research Systems and Integration with Medical Systems.- Data Management, Databases, and Warehousing.- Middleware Architecture Approaches for Collaborative Cancer Research.- Federated Authentication.- Genomics Data Analysis Pipelines.- Mathematical Modeling in Cancer.- Reproducible Research Concepts and Tools for Cancer Bioinformatics.- The Cancer Biomedical Informatics Grid (caBIG‚): An Evolving Community for Cancer Research.- Tools and Applications.- The caBIG‚ Clinical Trials Suite.- The CAISIS Research Data System.- A Common Application Framework that is Extensible: CAF-É.- Shared Resource Management.- The caBIG® Life Sciences Distribution.- MeV: MultiExperiment Viewer.- Authentication and Authorization in Cancer Research Systems.- Caching and Visualizing Statistical Analyses.- Familial Cancer Risk Assessment Using BayesMendel.- Interpreting and Comparing Clustering Experiments Through Graph Visualization and Ontology Statistical Enrichment with the ClutrFree Package.- Enhanced Dynamic Documents for Reproducible Research.

Leseproben

"Chapter 5 Federated Authentication (p. 91-92)

Frank J. Manion, William Weems, and James McNamee

Abstract Federated Authentication and Authorization is an emerging technology with the potential to facilitate seamless access to information from a variety of providers. Within this chapter we summarize the key concepts, technologies, protocols, and national and even international structures that are being developed to support federated security. We start with the environmental drivers that are stimulating this technology to develop. We then discuss two major approaches to federated security: those based on assertion-based identity and assurance and those based on public key infrastructure.

In the second part of the chapter, we discuss the three major components required for development of federated authentication systems: the representation of identity in cyberspace, the manner in which credentials or identity tokens are made available to users, and the required governance processes supporting these concepts. The chapter concludes with a brief overview of the emerging national-scale infrastructure in the form of identity federations, and we present a brief background on these initiatives and the tools and local infrastructure required for joining them.

5.1 Introduction

The topic explored in this chapter is federated authentication, which we define as the ability of a person or entity to rely on, at a particular level of trust, the identity and associated identity metadata asserted by a second entity. The situation is not limited to two-party arrangements; identity federations can be quite large, incorporating millions of individuals from hundreds of different companies and institutions. Although this chapter treats a topic in computer security, note that it is neither a general treatise on information security, nor is it intended as a primer for computer or network security in general.

There are a variety of reasons to use common, well-defined legal and technical architecture strategies to allow authentication and authorization practices and technology within and between academic medical center settings. Current models of authentication and authorization have been developed for specific use cases or narrow areas of focus that, almost exclusively, have been concerned with the security needs internal to one organization or corporate structure.

While these mechanisms have been reasonably effective within the domains in which they have been developed, to date a comprehensive consideration of an optimal security model to support collaboration across the broad academic medical community has not been done. Such an effort involves consideration of the scientific and clinical workflows that routinely occur between institutions and the development of structures – technical, legal, and procedural – to support these exchanges in a repeatable, scalable, and secure fashion.

Development of a multi-institutional common model of authentication and authorization structures would allow teams of clinicians and scientists working either between or within institutions to exchange data and research results easily and effectively in a secure and well-controlled fashion, with the potential to meet the needs of the research, patient, bench science, regulatory, and administrative communities (see Chap. 9 for a discussion of the caBIG® initiative as an example).

It would enable the development of workflows that cross institutional boundaries, resulting in increased laboratory throughput, particularly for teambased science initiatives such as those emerging from the NIH Clinical Translational Science Awards (CTSA) community. Development of a well-defined common model agreed upon by the academic medical community and one which is congruent with similar trends in broader academia and government will facilitate the use of national and even international scale shared resources, such as the TeraGrid [http://www.teragrid.org], at the local, state, and national scale. Taken together, these factors would facilitate clinical and basic research by providing an agreed infrastructure for securing clinical data exchanges with the research community."