title: Extension of research data repository system to support direct compute access to biomedical datasets: enhancing Dataverse to support large datasets.
abstract: Access to experimental X-ray diffraction image data is important for validation and reproduction of macromolecular models and indispensable for the development of structural biology processing methods. In response to the evolving needs of the structural biology community, we recently established a diffraction data publication system, the Structural Biology Data Grid (SBDG, data.sbgrid.org), to preserve primary experimental datasets supporting scientific publications. All datasets published through the SBDG are freely available to the research community under a public domain dedication license, with metadata compliant with the DataCite Schema (schema.datacite.org). A proof-of-concept study demonstrated community interest and utility. Publication of large datasets is a challenge shared by several fields, and the SBDG has begun collaborating with the Institute for Quantitative Social Science at Harvard University to extend the Dataverse (dataverse.org) open-source data repository system to structural biology datasets. Several extensions are necessary to support the size and metadata requirements for structural biology datasets. In this paper, we describe one such extension-functionality supporting preservation of file system structure within Dataverse-which is essential for both in-place computation and supporting non-HTTP data transfers.
authors.affiliation: Department of Biochemistry and Molecular Pharmacology and SBGrid Initiative, Harvard Medical School, Boston, Massachusetts, and the Dataverse Project, Harvard University, Cambridge, Massachusetts.
authors.forename: Bill
authors.initials: B
authors.lastname: McKinney
authors.affiliation: Department of Biochemistry and Molecular Pharmacology and SBGrid Initiative, Harvard Medical School, Boston, Massachusetts, and the Dataverse Project, Harvard University, Cambridge, Massachusetts.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Meyer
authors.affiliation: Department of Biochemistry and Molecular Pharmacology and SBGrid Initiative, Harvard Medical School, Boston, Massachusetts, and the Dataverse Project, Harvard University, Cambridge, Massachusetts.
authors.forename: Mercè
authors.initials: M
authors.lastname: Crosas
authors.affiliation: Department of Biochemistry and Molecular Pharmacology and SBGrid Initiative, Harvard Medical School, Boston, Massachusetts, and the Dataverse Project, Harvard University, Cambridge, Massachusetts.
authors.forename: Piotr
authors.initials: P
authors.lastname: Sliz
mesh_terms: D022126:Access to Information; D000818:Animals; D035843:Biomedical Research / Q000639:trends; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods* / Q000639:trends; D003195:Computer Communication Networks / Q000295:instrumentation / Q000639:trends; D018360:Crystallography, X-Ray; D057225:Data Mining / Q000639:trends; D003628:Database Management Systems / Q000639:trends; D030562:Databases, Protein / Q000639:trends; D006801:Humans; D007090:Image Interpretation, Computer-Assisted; D020407:Internet; D010506:Periodicals as Topic; D011487:Protein Conformation; D012984:Software
keywords: Data Access Alliance; Dataverse; RDMS; SBGrid; X-ray diffraction; research data management system