title: Methods for visual mining of genomic and proteomic data atlases.
abstract: BACKGROUND
  As the volume, complexity and diversity of the information that scientists work with on a daily basis continues to rise, so too does the requirement for new analytic software. The analytic software must solve the dichotomy that exists between the need to allow for a high level of scientific reasoning, and the requirement to have an intuitive and easy to use tool which does not require specialist, and often arduous, training to use. Information visualization provides a solution to this problem, as it allows for direct manipulation and interaction with diverse and complex data. The challenge addressing bioinformatics researches is how to apply this knowledge to data sets that are continually growing in a field that is rapidly changing.
  
  
  RESULTS
  This paper discusses an approach to the development of visual mining tools capable of supporting the mining of massive data collections used in systems biology research, and also discusses lessons that have been learned providing tools for both local researchers and the wider community. Example tools were developed which are designed to enable the exploration and analyses of both proteomics and genomics based atlases. These atlases represent large repositories of raw and processed experiment data generated to support the identification of biomarkers through mass spectrometry (the PeptideAtlas) and the genomic characterization of cancer (The Cancer Genome Atlas). Specifically the tools are designed to allow for: the visual mining of thousands of mass spectrometry experiments, to assist in designing informed targeted protein assays; and the interactive analysis of hundreds of genomes, to explore the variations across different cancer genomes and cancer types.
  
  
  CONCLUSIONS
  The mining of massive repositories of biological data requires the development of new tools and techniques. Visual exploration of the large-scale atlas data sets allows researchers to mine data to find new meaning and make sense at scales from single samples to entire populations. Providing linked task specific views that allow a user to start from points of interest (from diseases to single genes) enables targeted exploration of thousands of spectra and genomes. As the composition of the atlases changes, and our understanding of the biology increase, new tasks will continually arise. It is therefore important to provide the means to make the data available in a suitable manner in as short a time as possible. We have done this through the use of common visualization workflows, into which we rapidly deploy visual tools. These visualizations follow common metaphors where possible to assist users in understanding the displayed data. Rapid development of tools and task specific views allows researchers to mine large-scale data almost as quickly as it is produced. Ultimately these visual tools enable new inferences, new analyses and further refinement of the large scale data being provided in atlases such as PeptideAtlas and The Cancer Genome Atlas.
authors.affiliation: Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98092, USA. john.boyle@systemsbiology.org
authors.forename: John
authors.initials: J
authors.lastname: Boyle
authors.forename: Richard
authors.initials: R
authors.lastname: Kreisberg
authors.forename: Ryan
authors.initials: R
authors.lastname: Bressler
authors.forename: Sarah
authors.initials: S
authors.lastname: Killcoyne
mesh_terms: D003110:Colonic Neoplasms / Q000235:genetics; D057225:Data Mining; D005260:Female; D023281:Genomics / Q000379:methods*; D005909:Glioblastoma / Q000235:genetics; D006801:Humans; D013058:Mass Spectrometry; D009369:Neoplasms / Q000235:genetics*; D010051:Ovarian Neoplasms / Q000235:genetics; D040901:Proteomics / Q000379:methods*; D012984:Software