This book will review work from a number of researchers who have
produced open source software addressing the need for data
management, integration, analysis, and visualization to aid cancer
research. With the advent of high-throughput technologies in
biomedicine, the need for data management and appropriate data
analysis tools in genomics has increased dramatically, joining
clinical trials data as a major driver of informatics at cancer
research centers.
The gathering of this data requires careful encoding of
metadata, usually through the use of controlled vocabularies or
ontologies, as well as the linking of data from model organisms,
done at both a physiological level (e.g., anatomy) and at a
molecular level (e.g., orthology). This data will then find use
within computational and statistical models, which require data
pipelines and analysis systems, as well as algorithms,
visualization methods, and computational modeling systems. We will
introduce open source tools available for these aspects of the
problem.
The editors plan to divide the book into five sections,
beginning with a section containing high level overviews of the
field and key issues. This will include an introductory review of
informatics in cancer research, followed by five overviews
addressing issues in authentication and authorization, data
management, data pipelines and annotations, algorithms and models,
and the NCI caBIG initiative. This will be followed by sections
dedicated to data systems, data pipelines, algorithms for analysis
and visualization, and modeling systems. Each of these areas has
seen publication of open source tools, ranging from the widely
known R/Bioconductor package to little known but powerful systems
such as SImmune for biochemical modeling. The area of laboratory
information management systems has seen development of a number of
unpublished but powerful systems, which we would also include.
Three groups have agreed to provide chapters in this area
(USC/Norris CAFE extensible clinical trials system, St Jude Unified
LIMS, Fox Chase/British Columbia flow cytometry LIMS).
While there has been a great deal of development of informatics
tools that can be applied to problems in cancer research, there has
not been adequate dissemination of details on these tools to the
community. As such, there remains low adoption of all but a few
tools. This book aims to increase overall adoption of tools by
providing cancer center leaders and researchers with a single
volume detailing both issues that must be addressed and tools that
are ready for use.
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