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We present an overview of best practices for publishing data in astronomy and astrophysics journals. These recommendations are intended as a reference for authors to help prepare and publish data in a way that will better represent and support science results, enable better data sharing, improve reproducibility, and enhance the reusability of data. Observance of these guidelines will also help to streamline the extraction, preservation, integration and cross-linking of valuable data from astrophysics literature into major astronomical databases, and consequently facilitate new modes of science discovery that will better exploit the vast quantities of panchromatic and multi-dimensional data associated with the literature. We encourage authors, journal editors, referees, and publishers to implement the best practices reviewed here, as well as related recommendations from international astronomical organizations such as the International Astronomical Union (IAU) and International Virtual Observatory Alliance (IVOA) for publication of nomenclature, data, and metadata. A convenient Checklist of Recommendations for Publishing Data in Literature is included for authors to consult before the submission of the final version of their journal articles and associated data files. We recommend that publishers of journals in astronomy and astrophysics incorporate a link to this document in their Instructions to Authors.
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Annotation is the labeling of data by human effort. Annotation is critical to modern machine learning, and Bloomberg has developed years of experience of annotation at scale. This report captures a wealth of wisdom for applied annotation projects, collected from more than 30 experienced annotation project managers in Bloombergs Global Data department.
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Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these methods is the use of bridging potential energy functions representing emph{alchemical} intermediate states that cannot exist as real chemical species. The data collected from these bridging alchemical thermodynamic states allows the efficient computation of transfer free energies (or differences in transfer free energies) with orders of magnitude less simulation time than simulating the transfer process directly. While these methods are highly flexible, care must be taken in avoiding common pitfalls to ensure that computed free energy differences can be robust and reproducible for the chosen force field, and that appropriate corrections are included to permit direct comparison with experimental data. In this paper, we review current best practices for several popular application domains of alchemical free energy calculations, including relative and absolute small molecule binding free energy calculations to biomolecular targets.
The U.S. Virtual Astronomical Observatory was a software infrastructure and development project designed both to begin the establishment of an operational Virtual Observatory (VO) and to provide the U.S. coordination with the international VO effort. The concept of the VO is to provide the means by which an astronomer is able to discover, access, and process data seamlessly, regardless of its physical location. This paper describes the origins of the VAO, including the predecessor efforts within the U.S. National Virtual Observatory, and summarizes its main accomplishments. These accomplishments include the development of both scripting toolkits that allow scientists to incorporate VO data directly into their reduction and analysis environments and high-level science applications for data discovery, integration, analysis, and catalog cross-comparison. Working with the international community, and based on the experience from the software development, the VAO was a major contributor to international standards within the International Virtual Observatory Alliance. The VAO also demonstrated how an operational virtual observatory could be deployed, providing a robust operational environment in which VO services worldwide were routinely checked for aliveness and compliance with international standards. Finally, the VAO engaged in community outreach, developing a comprehensive web site with on-line tutorials, announcements, links to both U.S. and internationally developed tools and services, and exhibits and hands-on training .... All digital products of the VAO Project, including software, documentation, and tutorials, are stored in a repository for community access. The enduring legacy of the VAO is an increasing expectation that new telescopes and facilities incorporate VO capabilities during the design of their data management systems.
Founded in 2010, the Taiwan Extragalactic Astronomical Data Center (TWEA-DC) has for goal to propose access to large amount of data for the Taiwanese and International community, focusing its efforts on Extragalactic science. In continuation with individual efforts in Taiwan over the past few years, this is the first steppingstone towards the building of a National Virtual Observatory. Taking advantage of our own fast indexing algorithm (BLINK), based on a octahedral meshing of the sky coupled with a very fast kd-tree and a clever parallelization amongst available resources, TWEA-DC will propose from spring 2013 a service of on-the-fly matching facility, between on-site and user-based catalogs. We will also offer access to public and private raw and reducible data available to the Taiwanese community. Finally, we are developing high-end on-line analysis tools, such as an automated photometric redshifts and SED fitting code (APz), and an automated groups and clusters finder (APFoF).
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