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Informatics Shared Resource

Director: Okimoto, Gordon


The Informatics Shared Resource (ISR) of the Cancer Research Center of Hawaii (CRCH) was established as a core facility in 2004. Its goal is to promote multidisciplinary collaboration, and enhance the research excellence and productivity of CRCH by providing access to biomedical informatics expertise and computational support to all members of the Center. The prime objective of the ISR is to facilitate the management, sharing, and integration of diverse data types in cancer research, as well as the synthesis and analysis of more focused data sets from the basic, clinical, genomics and population sciences. The bioinformatics group of the ISR supports a dedicated scientific computing network for computational cancer biology,and leads the development and application of advanced algorithms and software tools that enable Center investigators to take a more integrative approach to cancer research for the purpose of accelerating the translation of basic research results into the clinic.






  • Cancer bioinformatics and systems biology service ( Data analysis service )

    The ISR provides expertise in the design and programming of bioinformatics tools and algorithms dedicated to the analysis, visualization and interpretation of high dimensional, genomic data sets. The ISR has also developed and maintains a web-based suite of analytical tools (CRCHXpress) that greatly accelerates the analysis, visualization and interpretation of microarray data of all kinds through the use of an intuitive, point-and-click graphical user interface. Other software tools that are available to investigators include Ingenuity Pathway Analysis for assessing the biological significance gene lists, Pathway Studio for inferring the up- and down-stream effects of a given set of molecules, and Geospiza/GeneSifter for the multi-way statistical analysis of microarray and next-generation sequence datasets. The ISR provides consultation and support on use of genomics and proteomics data repositories such as the Gene Expression Omnibus (GEO) which provides access to data for almost a billion expression measurements in over 4,000 experiments from over 1,000 organisms. The ISR also conducts research and development in new analytical tools and methods that ensure that Center investigators can quickly and effectively exploit the latest technology advances in cancer genomics, proteomics and systems biology.

  • Cancer biomedical informatics grid service ( Data analysis service )

    The CRCH has been a participating member of the NCI Cancer Biomedical Informatics Grid (caBIG) project (http://cabig.nci.nih.gov/) since the project was launched in February 2004. The caBIG project is a multi-centered initiative to build an informatics infrastructure for the development and sharing of tools and data in an open environment with common standards. In parallel with our participation in the caBIG project, the ISR is spearheading the effort to adopt the caBIG framework to build an integrative web-based system for all informatics needs at the CRCH. The ISR will be collaborating with other shared resources (e.g. the Biostatistics Shared Resource, Genotyping Shared Resource, Analytical Laboratory Shared Resource, Pathology Shared Resource, and the Clinical Protocol and Data Management Shared Resource) on this endeavor.

  • Computer software review and algorithm development service ( Support service )

    The ISR reviews commercial third-party software applications and provides investigators with software recommendations to meet their specific needs. The ISR also develops customized software tools and algorithms that address specific data management and analysis issues faced by investigators in a fast changing research environment. We have extensive experience in general programming languages such as HTML, JAVA, C, C++, Visual Basic, Matlab, R/Bioconductor and ASP.net and provide access to a number of specialized third-party software applications such as Ingenuity Pathway Analysis, Pathway Studio, and Geospiza/GeneSifter.

  • Data storage, extraction, sharing, integration and synthesis of data sets ( Data storage service )

    Consultation is provided on data management issues to ensure that the complex data from diverse sources can be integrated in appropriate ways prior to analysis. The ISR will aid researchers in publishing their data for use by others, if desired. In particular, the bioinformatics group of the ISR provides consultation to investigators on appropriate ways to structure, store, retrieve/extract high-dimensional genomics data sets for downstream normalization, visualization and analysis.

  • Database design and programming service ( Support service )

    The ISR provides consultation on design issues of complex relational as well as hierarchical information/database systems. Programmers within the ISR develop these systems in consultation with investigators and users and are also available for consultation to researchers developing database systems dedicated to a specific task or research project.


  • CRCHXpress ( Software )

    Bioinformatics Database and Analysis Toolkit. Web-based system.

  • Ingenuity IPA ( Software )

    "IPA is software that helps researchers model, analyze, and understand the complex biological and chemical systems at the core of life science research.

    IPA helps you understand biology at multiple levels by integrating data from a variety of experimental platforms and providing insight into the molecular and chemical interactions, cellular phenotypes, and disease processes of your system. Even if you don’t have experimental data, you can use IPA to intelligently search the Ingenuity®Knowledge Base for information on genes, proteins, chemicals, drugs, and molecular relationships to build biological models or get up to speed in a relevant area of research. IPA provides the right biological context to facilitate informed decision-making, advance research project design, and generate new testable hypotheses."

  • Mathematica ( Software )

    "Almost any workflow involves computing results, and that's what Mathematica does—from building a hedge fund trading website or publishing interactive engineering textbooks to developing embedded image recognition algorithms or teaching calculus.

    Mathematica is renowned as the world's ultimate application for computations. But it's much more—it's the only development platform fully integrating computation into complete workflows, moving you seamlessly from initial ideas all the way to deployed individual or enterprise solutions."

  • MATLAB ( Software )

    "MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran."

  • Partek Genomics Suite ( Software )

    "Partek Genomics Suite is a comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data. The software is unique in supporting all microarray and next generation sequencing technologies including gene expression and digital gene expression (DGE), exon/alternative splicing and RNA-Seq, copy number and association, ChIP-chip, ChIP-seq, and microRNA in a single software package, allowing for analysis of multiple applications in one complete solution."

  • Visual Studio ( Software )

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Last updated: 2011-04-20T19:03:36.793-05:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016