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The document discusses CrossRef's plans to rebrand and simplify its identity. It aims to have a clearer identity through a new, simplified logo and revamped website. It also lists the many services that CrossRef enables, such as linking, discovery and delivery, evaluating, and collaborating of scholarly content through services like reference linking, metadata search, and linked data. Upcoming plans include relaunching the CrossRef website and rebranding other marketing materials within six months.

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The Environmental Data Initiative enables the environmental science community to maximize knowledge development through the reusability of FAIR environmental data by providing curation services, training, and a robust and modern data repository. Please cite as: Gries, Corinna. (2018, December). Introduction to the Environmental Data Initiative (EDI) (Version 1.0). Zenodo. http://doi.org/10.5281/zenodo.4672376

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ORCID, Inc

This document discusses updates from the American Geophysical Union (AGU) regarding ORCID identifiers. It notes that as of March 2016, ORCIDs are required for corresponding authors in AGU journals and encouraged for all other authors and reviewers. As of September 2016, over 18,000 ORCIDs were associated with AGU journal accounts. It also discusses recent alignment among publishers, repositories, and funders around data transparency and identifiers, as well as the Coalition on Publishing Data in the Earth and Space Sciences' efforts to link publishers and repositories to promote best practices around citations and identifiers.

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US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

The internet has opened up access to large amounts of chemistry related data that can be harvested and assembled into rich resources of value to chemists. The Royal Society of Chemistry’s ChemSpider database has assembled an electronic collection of over 28 million chemicals from over 400 data sources and some of the assembled data is certainly of value to those searching for chemical health and safety information. Since ChemSpider is a text and structure searchable database chemists are able to find relevant information using both of their general search approaches. This presentation will provide an overview of the types of chemical health and safety data and information made available via ChemSpider and discuss how the data are sourced, aggregated and validated. We will examine how the data can be made available via mobile devices and examine the issue of data quality and its potential impacts on such a database.

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This document summarizes new tools from CrossRef for small publishers. It describes a Web Deposit Form that allows small publishers to create metadata and DOIs without XML. It also introduces a Citation Depositor that extracts citations from article PDFs and matches them to DOIs. Additionally, it presents a References Widget that publishers can include on their pages to display references, and a CrossRef Metadata Search that allows faceted searching of metadata with options like OA status. Finally, it points to an open source pdf-extract tool that can pull references and identifiers from PDFs.

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Data in Brief, an Open Access journal published by Elsevier, exclusively publishes data articles wherein researchers describe their datasets. Data in Brief requires that all data be made publicly available either directly with the article as supplementary files or in a public repository. Data in Brief has teamed up with Dataverse to provide a venue for authors to archive and openly share their data.

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There is an increasing demand for approaches to integrate proteomics data with other ‘omics’ data types, especially genomics. In fact, current resources to integrate proteomics in a genome context are insufficient for large-scale studies. To bring the genomics and proteomics results into coherence, novel resources must be developed that provide simple links across previously acquired datasets with minimal preprocessing and hassle. PRIDE (http://www.ebi.ac.uk/pride) and Ensembl (http://www.ensembl.org) are world-leading resources for proteomics and genomics data. We have developed a new resource and framework to enable a systematic integration of mass spectrometry (MS) based proteomics evidences into genome browsers. We automatically integrate every high-quality MS-based peptidoform reported in the PRIDE database, into genome coordinates through Ensembl, and other genome browsers.

Biocontainers Hackathon Introduction

The document discusses the challenges of reproducibility in bioinformatics software and introduces BioContainers as a solution. BioContainers implements guidelines for versioning, testing, and dependency management to create reproducible Docker containers for bioinformatics software. It outlines current challenges related to findability, availability, and integration that BioContainers aims to address through developments like the BioContainers Registry 2.0 and improved documentation.

Do we need to make public our proteomics data?

The document discusses making proteomics data publicly available. It notes that one dataset that was made publicly available with no restrictions led to 4 papers and 3 new algorithms being developed. The document then summarizes the ProteomeXchange consortium, which aims to standardize data submission across several proteomics repositories including PRIDE, PeptideAtlas, and MassIVE. Current status of proteomics databases and ongoing/future work on quality assessment and integration of proteomics resources are also briefly discussed.

Design of an hexapeptide database for proteomics studies

Parallel conformational search of small molecules

The document discusses parallelizing the conformational search problem for small molecules. It presents the sequential nature of the problem and proposes a parallel computing solution using MPI. It describes a master-worker topology and shows results demonstrating speedup from using 4, 6, 8, and 10 processes on test cases of molecules with 5, 10, and 15 rotatable bonds. Speedup increases with more processes and rotatable bonds, with efficiencies generally between 50-80%.

PBS Web (Spanish)

Este documento describe un proyecto para implementar un servicio web que permita acceder al sistema de administración de trabajos OpenPBS de un cluster de computadoras a través de HTTP. El servicio brindará herramientas para que los usuarios envíen trabajos al cluster, revisen su estado y obtengan resultados de manera segura y confiable desde Internet. También llevará estadísticas del uso del cluster por parte de los diferentes usuarios.

Standarization in Proteomics: From raw data to metadata files

The document discusses various mass spectrometry file formats used in proteomics workflows, including the advantages of XML-based formats like mzML and mzIdentML that support metadata and can be read by different software. It also describes challenges with proprietary binary formats and efforts to develop common data standards and APIs through projects like ProteoWizard, PRIDE, and the ms-core-api library. Standard file formats are important for sharing and reusing proteomics data over time as instrumentation and software evolve.

PRIDE and ProteomeXchange – Making proteomics data accessible and reusable

The document discusses ProteomeXchange (PX), a consortium that aims to make proteomics data accessible and reusable. PX includes repositories like PRIDE, PeptideAtlas, and MassIVE. It allows standard data submission between repositories through a common identifier space. The document outlines the PX submission workflow, describes components like the PX submission tool and PRIDE Inspector. It also provides statistics on data available through PX, with over 1,300 datasets contributed primarily from human, mouse and yeast studies. Future plans include better integration of proteomics resources to facilitate data reuse.

Yasset perezriverol csi2011

This document summarizes an approach to protein identification using mass spectrometry that relies on in silico analysis of mass accuracy, isoelectric point, retention time, and N-terminal amino acid determination rather than relying solely on high-quality MS/MS spectra. The methodology was combined with selective isolation methods to increase the number of unique identified peptides and proteins. An OFFGEL-LC-MS/MS experiment demonstrated the feasibility of the approach, identifying 93% of proteins found through MS/MS alone with a low false positive rate.

Yasset iso point-cigb-2012

IPG (Immobilized pH Gradient) based separations are frequently used as the first step in shotgun proteomics methods; it yields an increase in both the dynamic range and resolution of peptide separation prior to the LC-MS analysis. Experimental isoelectric point (pI) values can improve peptide identifications in conjunction with MS/MS information. Our group has previously reported the possibility of identifying theoretically peptides and proteins based on different experimental properties. Thus, accurate estimation of the pI value based on the amino acid sequence becomes critical to perform these kinds of experiments. Nowadays, pI is commonly predicted using the charge-state model [3], and/or the co-factor algorithm. However, none of these methods is capable of calculating the pI value for basic peptides accurately. In this manuscript, we present an new approach that can significant improve the pI estimation, by using Support Vector Machines (SVM), an experimental amino acid descriptor taken from the AAIndex database and the isoelectric point predicted by the charge-state model.

SintCompound: A Small Compound Database for Virtual Screening