Towards structured sharing of raw and derived neuroimaging data across existing resources

Data sharing efforts increasingly contribute to the acceleration of scientific discovery. Neuroimaging data is accumulating in distributed domain-specific databases and there is currently no integrated access mechanism nor an accepted format for the critically important meta-data that is necessary for making use of the combined, available neuroimaging data. In this manuscript, we present work from the Derived Data Working Group, an open-access group sponsored by the Biomedical Informatics Research Network (BIRN) and the International Neuroimaging Coordinating Facility (INCF) focused on practical tools for distributed access to neuroimaging data. The working group develops models and tools facilitating the structured interchange of neuroimaging meta-data and is making progress towards a unified set of tools for such data and meta-data exchange. We report on the key components required for integrated access to raw and derived neuroimaging data as well as associated meta-data and provenance across neuroimaging resources. The components include (1) a structured terminology that provides semantic context to data, (2) a formal data model for neuroimaging with robust tracking of data provenance, (3) a web service-based application programming interface (API) that provides a consistent mechanism to access and query the data model, and (4) a provenance library that can be used for the extraction of provenance data by image analysts and imaging software developers. We believe that the framework and set of tools outlined in this manuscript have great potential for solving many of the issues the neuroimaging community faces when sharing raw and derived neuroimaging data across the various existing database systems for the purpose of accelerating scientific discovery

Network and Seiberg Duality

We define and study a new class of 4d N=1 superconformal quiver gauge theories associated with a planar bipartite network. While UV description is not unique due to Seiberg duality, we can classify the IR fixed points of the theory by a permutation, or equivalently a cell of the totally non-negative Grassmannian. The story is similar to a bipartite network on the torus classified by a Newton polygon. We then generalize the network to a general bordered Riemann surface and define IR SCFT from the geometric data of a Riemann surface. We also comment on IR R-charges and superconformal indices of our theories.Comment: 28 pages, 28 figures; v2: minor correction

Localization of N=4 Superconformal Field Theory on S^1 x S^3 and Index

We provide the geometrical meaning of the ${\cal N}=4$ superconformal index. With this interpretation, the ${\cal N}=4$ superconformal index can be realized as the partition function on a Scherk-Schwarz deformed background. We apply the localization method in TQFT to compute the deformed partition function since the deformed action can be written as a $\delta_\epsilon$-exact form. The critical points of the deformed action turn out to be the space of flat connections which are, in fact, zero modes of the gauge field. The one-loop evaluation over the space of flat connections reduces to the matrix integral by which the ${\cal N}=4$ superconformal index is expressed.Comment: 42+1 pages, 2 figures, JHEP style: v1.2.3 minor corrections, v4 major revision, conclusions essentially unchanged, v5 published versio

Derived Data Storage and Exchange Workflow for Large-Scale Neuroimaging Analyses on the BIRN Grid

Organizing and annotating biomedical data in structured ways has gained much interest and focus in the last 30 years. Driven by decreases in digital storage costs and advances in genetics sequencing, imaging, electronic data collection, and microarray technologies, data is being collected at an ever increasing rate. The need to store and exchange data in meaningful ways in support of data analysis, hypothesis testing and future collaborative use is pervasive. Because trans-disciplinary projects rely on effective use of data from many domains, there is a genuine interest in informatics community on how best to store and combine this data while maintaining a high level of data quality and documentation. The difficulties in sharing and combining raw data become amplified after post-processing and/or data analysis in which the new dataset of interest is a function of the original data and may have been collected by multiple collaborating sites. Simple meta-data, documenting which subject and version of data were used for a particular analysis, becomes complicated by the heterogeneity of the collecting sites yet is critically important to the interpretation and reuse of derived results. This manuscript will present a case study of using the XML-Based Clinical Experiment Data Exchange (XCEDE) schema and the Human Imaging Database (HID) in the Biomedical Informatics Research Network's (BIRN) distributed environment to document and exchange derived data. The discussion includes an overview of the data structures used in both the XML and the database representations, insight into the design considerations, and the extensibility of the design to support additional analysis streams

More Three Dimensional Mirror Pairs

We found a lot of new three dimensional N = 4 mirror pairs generalizing previous considerations on three dimensional generalized quiver gauge theories. We recovered almost all previous discovered mirror pairs with these constructions. One side of these mirror pairs are always the conventional quiver gauge theories. One of our result can also be used to determine the matter content and weakly coupled gauge groups of four dimensional N = 2 generalized quiver gauge theories derived from six dimensional A_N and D_N theory, therefore we explicitly constructed four dimensional S-duality pairs.Comment: 33 pages, 18 figures version2 minor correction