Abstract
caBIG® is a virtual network of organizations developing and adopting interoperable databases and analytical tools to facilitate translational cancer research (von Eschenbach and Buetow 2007). It is an open-source, open-access program, and all the tools and resources are freely available to the research community. The National Cancer Institute is developing resources to assist enterprise-wide adoption of the caBIG® tools. To this end, we have bundled mature software tools together to facilitate easy adoption and installation. The Life Sciences Distribution (LSD) is comprised of tools to support the continuum of translational research: caArray, for the management and annotation of microarray data; caTissue, to support the collection, annotation, and distribution of biospecimens; the Clinical Trials Object Data System, for the sharing of clinical trials information; the National Biomedical Imaging Archive, for annotation, storage, and sharing of in vivo images; cancer Genome Wide Association Studies, for publishing and mining data from GWAS studies; and geWorkbench, supporting the integrated analysis and annotation of expression and sequence data. All the LSD tools are connected to caGrid (Saltz et al. 2006), which makes it possible for the databases at multiple institutions to be interconnected to support data sharing and integration.
More information on the LSD suite of products, including installation packages, user and installation guides, and links to exemplar installations can be found at http://ncicb.nci.nih.gov/NCICB/tools/lsd.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Altschul SF, Gish W et al (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410
Ashburner M, Ball CA et al (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25(1):25–29
Brazma A, Hingamp P et al (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29(4):365–371
Foster I (2005) Globus toolkit version 4: software for service-oriented systems. Netw Parallel Comput, Proc 3779:2–13
Fridsma DB, Evans J et al (2008) The BRIDG project: a technical report. J Am Med Inform Assoc 15(2):130 –137
Komatsoulis GA, Warzel DB et al (2008) caCORE version 3: Implementation of a model driven, service-oriented architecture for semantic interoperability. J Biomed Inform 41(1):106–123
Lefebvre C, Lim WK, Basso K, Dalla Favera R, Califano A (2007) A context-specific network of protein-DNA and protein-protein interactions reveals new regulatory motifs in human B cells. Lect Notes Bioinform 4532:42–56
Margolin AA, Nemenman I et al (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinform 7(Suppl 1):S7
Rayner TF, Rocca-Serra P et al (2006) A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinform 7:489
Rzhetsky A, Iossifov I et al (2004) GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform 37(1):43–53
Saltz J, Oster S et al (2006) caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid. Bioinformatics 22(15):1910–1916
Shannon P, Markiel A et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504
von Eschenbach AC, Buetow K (2007) Cancer Informatics Vision: caBIG. Cancer Inform 2:22–24
Wang K, Alvarez MJ et al (2009) Dissecting the interface between signaling and transcriptional regulation in human B cells. Pac Symp Biocomput 20:264–275
Ward LD, Bussemaker HJ (2008) Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics 24(13):i165–i171
Waterhouse AM, Procter JB et al (2009) Jalview Version 2 – a multiple sequence alignment editor and analysis workbench. Bioinformatics 25(9):1189–1191
Whetzel PL, Parkinson H et al (2006) The MGED ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 22(7):866–873
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Klemm, J., Basu, A., Fore, I., Floratos, A., Komatsoulis, G. (2010). The caBIG® Life Sciences Distribution. In: Ochs, M., Casagrande, J., Davuluri, R. (eds) Biomedical Informatics for Cancer Research. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-5714-6_14
Download citation
DOI: https://doi.org/10.1007/978-1-4419-5714-6_14
Published:
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4419-5712-2
Online ISBN: 978-1-4419-5714-6
eBook Packages: MedicineMedicine (R0)