Sharing Open Source License and Copyright Data with SPDX

Organizations across the globe are creating and distributing products that include open source software. To ensure compliance with the open source licenses, each company needs to evaluate exactly what open source licenses and copyrights are included - resulting in duplicated effort and redundancy. This talk will provide an overview of a new Software Package Data Exchange (SPDX) specification. This specification will provide a common format to share information about the open source licenses and copyrights that are included in any software package, with the goal of saving time and improving data accuracy. This talk will review the progress of the initiative; discuss the benefits to organizations using open source and share information on how you can contribute.

Beyond filtered backprojection: a reconstruction software package for ion beam microtomography data

A new version of the TomoRebuild data reduction software package is presented, for the reconstruction of scanning transmission ion microscopy tomography (STIMT) and particle induced X-ray emission tomography (PIXET) images. First, we present a state of the art of the reconstruction codes available for ion beam microtomography. The algorithm proposed here brings several advantages. It is a portable, multi-platform code, designed in C++ with well-separated classes for easier use and evolution. Data reduction is separated in different steps and the intermediate results may be checked if necessary. Although no additional graphic library or numerical tool is required to run the program as a command line, a user friendly interface was designed in Java, as an ImageJ plugin. All experimental and reconstruction parameters may be entered either through this plugin or directly in text format files. A simple standard format is proposed for the input of experimental data. Optional graphic applications using the ROOT interface may be used separately to display and fit energy spectra. Regarding the reconstruction process, the filtered backprojection (FBP) algorithm, already present in the previous version of the code, was optimized so that it is about 10 times as fast. In addition, Maximum Likelihood Expectation Maximization (MLEM) and its accelerated version Ordered Subsets Expectation Maximization (OSEM) algorithms were implemented. A detailed user guide in English is available. A reconstruction example of experimental data from a biological sample is given. It shows the capability of the code to reduce noise in the sinograms and to deal with incomplete data, which puts a new perspective on tomography using low number of projections or limited angle.

The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience.

The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online.

PaleoTools - extended software package for quantitative paleoenvironmental reconstructions

The Imbrie and Kipp transfer function method (IKM) and the modern analog technique (MAT) are accepted tools for quantitative paleoenvironmental reconstructions. However, no uncomplicated, flexible software has been available to apply these methods on modern computer devices. For this reason the software packages PaleoToolBox, MacTransfer, WinTransfer, MacMAT, and PanPlot have been developed. The PaleoToolBox package provides a flexible tool for the preprocessing of microfossil reference and downcore data as well as hydrographic reference parameters. It includes procedures to randomize the raw databases; to switch specific species in or out of the total species list; to establish individual ranking systems and their application on the reference and downcore databasessemi; and to convert the prepared databases into the file formats of IKM and MAT software for estimation of paleohydrographic parameters.

The New Software Package for Dynamic Hierarchical Clustering for Circles Types of Shapes

In data mining, efforts have focused on finding methods for efficient and effective cluster analysis in large databases. Active themes of research focus on the scalability of clustering methods, the effectiveness of methods for clustering complex shapes and types of data, high-dimensional clustering techniques, and methods for clustering mixed numerical and categorical data in large databases. One of the most accuracy approach based on dynamic modeling of cluster similarity is called Chameleon. In this paper we present a modified hierarchical clustering algorithm that used the main idea of Chameleon and the effectiveness of suggested approach will be demonstrated by the experimental results.

Expokit: A software package for computing matrix exponentials

Expokit provides a set of routines aimed at computing matrix exponentials. More precisely, it computes either a small matrix exponential in full, the action of a large sparse matrix exponential on an operand vector, or the solution of a system of linear ODEs with constant inhomogeneity. The backbone of the sparse routines consists of matrix-free Krylov subspace projection methods (Arnoldi and Lanczos processes), and that is why the toolkit is capable of coping with sparse matrices of large dimension. The software handles real and complex matrices and provides specific routines for symmetric and Hermitian matrices. The computation of matrix exponentials is a numerical issue of critical importance in the area of Markov chains and furthermore, the computed solution is subject to probabilistic constraints. In addition to addressing general matrix exponentials, a distinct attention is assigned to the computation of transient states of Markov chains.

Manual de uso del software Ocean Data View (ODV)

El presente manual de uso del software de visualización de datos “Ocean Data View” (ODV) describe la exploración, análisis y visualización de datos oceanográficos según el formato de la colección mundial de base de datos del océano “World Ocean Database” (WOD). El manual comprende 6 ejercicios prácticos donde se describe paso a paso la creación de las metavariables, la importación de los datos y su visualización mediante mapas de latitud, longitud y gráficos de dispersión, secciones verticales y series de tiempo. Se sugiere el uso extensivo del ODV para la visualización de datos oceanográficos por el personal científico del IMARPE.

Guidelines for CERIF-XML Data Exchange with CSUC’s Catalan Research Portal (PRC) (Version 2.2)

The Catalan Research Portal (Portal de la Recerca de Catalunya or PRC) is an initiative carried out by the Consortium for University Services in Catalonia (CSUC) in coordination with nearly all universities in Catalonia. The Portal will provide an online CERIF-compliant collection of all research outputs produced by Catalan HEIs together with an appropriate contextual information describing the specific environment where the output was generated (such as researchers, research group, research project, etc). The initial emphasis of the Catalan Research Portal approach to research outputs will be made on publications, but other outputs such as patents and eventually research data will eventually be addressed as well. These guidelines provide information for PRC data providers to expose and exchange their research information metadata in CERIFXML compatible structure, thus allowing them not just to exchange validated CERIF XML data with the PRC platform, but to improve their general interoperability by being able to deliver CERIFcompatible outputs.

Workflow data exchange semantics, object discovery & integration architecture for cross media production & distribution

There has been a clear lack of common data exchange semantics for inter-organisational workflow management systems where the research has mainly focused on technical issues rather than language constructs. This paper presents the neutral data exchanges semantics required for the workflow integration within the AXAEDIS framework and presents the mechanism for object discovery from the object repository where little or no knowledge about the object is available. The paper also presents workflow independent integration architecture with the AXAEDIS Framework.

From CAD to virtual reality: modelling approaches, data exchange and interactive 3D building design tools

Virtual reality has the potential to improve visualisation of building design and construction, but its implementation in the industry has yet to reach maturity. Present day translation of building data to virtual reality is often unidirectional and unsatisfactory. Three different approaches to the creation of models are identified and described in this paper. Consideration is given to the potential of both advances in computer-aided design and the emerging standards for data exchange to facilitate an integrated use of virtual reality. Commonalities and differences between computer-aided design and virtual reality packages are reviewed, and trials of current system, are described. The trials have been conducted to explore the technical issues related to the integrated use of CAD and virtual environments within the house building sector of the construction industry and to investigate the practical use of the new technology.

VRS: vital registration software package; information and operating manual

Manual que entrega instrucciones para el uso del programa computacional diseñado para el procesamiento ágil de las estadísticas vitales, escrito en Clipper y operado en microcomputador. Permite el ingreso relativamente simple de los datos y la posibilidad de obtener tabulaciones. Contiene tres secciones: a) entrada de datos; b) generación de tablas; c) apéndices. Entre éstos hay uno que incluye una lista de las variables para nacimientos y muertes.

Standard formats for weather data exchange among automated weather information systems /

"May 1990."

World rice study : a software package for analyzing international trade /

Issued Oct. 1975.

XML Presentation of Documents Used for Data Exchange in Management of Genetic Resources

In the global strategy for preservation genetic resources of farm animals the implementation of information technology is of great importance. In this regards platform independent information tools and approaches for data exchange are needed in order to obtain aggregate values for regions and countries of spreading a separate breed. The current paper presents a XML based solution for data exchange in management genetic resources of farm animals’ small populations. There are specific requirements to the exchanged documents that come from the goal of data analysis. Three main types of documents are distinguished and their XML formats are discussed. DTD and XML Schema for each type are suggested. Some examples of XML documents are given also.