DIVE: A Graph-Based Visual-Analytics Framework for Big Data

The need for data-centric scientific tools is growing; domains such as biology, chemistry, and physics are increasingly adopting computational approaches. So, scientists must deal with the challenges of big data. To address these challenges, researchers built a visual-analytics platform named DIVE (Data Intensive Visualization Engine). DIVE is a data-agnostic, ontologically expressive software framework that can stream large datasets at interactive speeds. In particular, DIVE makes novel contributions to structured-data-model manipulation and high-throughput streaming of large, structured datasets.

[1]  Rudesh D. Toofanny,et al.  Understanding protein unfolding from molecular simulations , 2012 .

[2]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[3]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[4]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[5]  Carole A. Goble,et al.  The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud , 2013, Nucleic Acids Res..

[6]  W. G. Hoover.  molecular dynamics , 1986, Catalysis from A to Z.

[7]  L. Guarente,et al.  Molecular Biology of Aging , 1999, Cell.

[8]  Eric Jones,et al.  SciPy: Open Source Scientific Tools for Python , 2001 .

[9]  V. Daggett,et al.  Structural consequences of mutations to the α-tocopherol transfer protein associated with the neurodegenerative disease ataxia with vitamin E deficiency. , 2013, Biochemistry.

[10]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[11]  Csongor Nyulas,et al.  BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications , 2011, Nucleic Acids Res..

[12]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[13]  Christopher G. Chute,et al.  The National Center for Biomedical Ontology , 2012, J. Am. Medical Informatics Assoc..

[14]  Bartek Wilczynski,et al.  Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..

[15]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[16]  Valerie Daggett,et al.  DIVE: a data intensive visualization engine , 2014, Bioinform..

[17]  William E. Lorensen,et al.  The visualization toolkit (2nd ed.): an object-oriented approach to 3D graphics , 1998 .

[18]  R Dustin Schaeffer,et al.  Dynameomics: a comprehensive database of protein dynamics. , 2010, Structure.

[19]  Ian Horrocks,et al.  Ontologies and the semantic web , 2008, CACM.