The Basis Set Exchange (BSE) has been a prominent fixture in the quantum chemistry community. First publicly available in 2007, it is recognized by both users and basis set creators as the de facto source for information related to basis sets. This popular resource has been rewritten, utilizing modern software design and best practices. The basis set data has been separated into a stand-alone library with an accessible API, and the Web site has been updated to use the current generation of web development libraries. The general layout and workflow of the Web site is preserved, while helpful features requested by the user community have been added. Overall, this design should increase adaptability and lend itself well into the future as a dependable resource for the computational chemistry community. This article will discuss the decision to rewrite the BSE, the new architecture and design, and the new features that have been added.
SUMMARYThe first Provenance Challenge was set up in order to provide a forum for the community to understand the capabilities of different provenance systems and the expressiveness of their provenance representations. To this end, a functional magnetic resonance imaging workflow was defined, which participants had to either simulate or run in order to produce some provenance representation, from which a set of identified queries had to be implemented and executed. Sixteen teams responded to the challenge, and submitted their inputs. In this paper, we present the challenge workflow and queries, and summarize the participants' contributions.
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SUMMARYWorkflows and data pipelines are becoming increasingly valuable to computational and experimental sciences. These automated systems are capable of generating significantly more data within the same amount of time compared to their manual counterparts. Automatically capturing and recording data provenance and annotation as part of these workflows are critical for data management, verification, and dissemination. We have been prototyping a workflow provenance system, targeted at biological workflows, that extends our content management technologies and other open source tools. We applied this prototype to the provenance challenge to demonstrate an end-to-end system that supports dynamic provenance capture, persistent content management, and dynamic searches of both provenance and metadata. We describe our prototype, which extends the Kepler system for the execution environment, the Scientific Annotation Middleware (SAM) content management software for data services, and an existing HTTPbased query protocol. Our implementation offers several unique capabilities, and through the use of standards, is able to provide access to the provenance record with a variety of commonly available client tools.
Systems biology research demands the availability of tools and technologies that span a comprehensive range of computational capabilities, including data management, transfer, processing, integration, and interpretation. To address these needs, we have created the Bioinformatics Resource Manager (BRM), a scalable, flexible, and easy to use tool for biologists to undertake complex analyses. This paper describes the underlying software architecture of the BRM that integrates multiple commodity platforms to provide a highly extensible and scalable software infrastructure for bioinformatics. The architecture integrates a J2EE 3-tier application with an archival Experimental Data Management System, the GAGGLE framework for desktop tool integration, and the MeDICi IntegrationFramework for high-throughput data analysis workflows. This architecture facilitates a systems biology software solution that enables the entire spectrum of scientific activities, from experimental data access to high throughput processing and analysis of data for biologists and experimental scientists.
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