An expanded and refined catalog of time patterns for workflows

Trabajos anteriores que definieron catálogos de patrones de control, recursos y datos para workflows tuvieron un rol fundamental en la evolución de esas dimensionesdentro de lenguajes y aplicaciones. Esos patrones han sido usados para evaluar la expresividad de los lenguajes, guiar su evolución, y para establecer una terminología básica que hoy en día es compartida por la mayoría de los desarrolladores de sistemas y lenguajes para workflows. Sin embargo, aún no se han obtenido resultados comparables en la dimensión de tiempo, a pesar de la gran importancia que esta tiene en muchos workflows y procesos de negocio. Aunque recientemente fueron propuestos algunos catálogos de patrones de tiempo, estas propuestas tienen variaslimitaciones en su alcance y en la precisión de las descripciones que los hacen inadecuados para tareas como evaluar lenguajes con respecto a su capacidad parasoportar esos patrones. En este artículo se presenta una aproximación para enfrentar este problema: por una parte, se presenta un catálogo extendido y refinado de patrones de tiempo para workflows; por otra parte, se presenta una formalización de dichos patrones basada en cálculo de eventos y en diagramas de estados, la cual permite hacer una evaluación de la expresividad de los lenguajes con respecto a los patrones y a la dimensión de tiempo

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain

The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.

Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for achieving
the goals. This report builds on the 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems (Boline et al., 2007, _Nature Preceedings_, doi:10.1038/npre.2007.1046.1) and includes a more detailed analysis of both the current state and desired state of digital atlasing along with specific recommendations for achieving these goals

Lexibank, a public repository of standardized wordlists with computed phonological and lexical features

The past decades have seen substantial growth in digital data on the world’s languages. At the same time, the demand for cross-linguistic datasets has been increasing, as witnessed by numerous studies devoted to diverse questions on human prehistory, cultural evolution, and human cognition. Unfortunately, most published datasets lack standardization which makes their comparison difficult. Here, we present a new approach to increase the comparability of cross-linguistic lexical data. We have designed workflows for the computer-assisted lifting of datasets to Cross-Linguistic Data Formats, a collection of standards that make these datasets more Findable, Accessible, Interoperable, and Reusable (FAIR). We test the Lexibank workflow on 100 lexical datasets from which we derive an aggregated database of wordlists in unified phonetic transcriptions covering more than 2000 language varieties. We illustrate the benefits of our approach by showing how phonological and lexical features can be automatically inferred, complementing and expanding existing cross-linguistic datasets

Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein-ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0

Reimagine Descriptive Workflows: A Community-Informed Agenda for Reparative and Inclusive Descriptive Practice

Executive Summary The Reimagine Descriptive Workflows project convened a group of experts, practitioners, and community members to determine ways of improving descriptive practices, tools, infrastructure, and workflows in libraries and archives. The result, this community agenda, is offered to the broad library and archives community of practice. The agenda draws together insights from the convening, related research, and operational work that is ongoing in the field. All institutions hold power to make meaningful changes in this space, and all share collective responsibility. The agenda is not a “how-to guide,” but it is constructed to instruct and chart a path toward reparative and inclusive description. The agenda is divided into two distinct parts. The first part provides contextual information regarding the project, the convening, and the methods used to create this agenda. It also frames the historical, local, and workflow challenges and tensions to consider when approaching inclusive and reparative metadata work. The second part, “A Framework of Guidance,” and the Appendix, suggest actions and exercises that can help frame local priorities and areas for change and also provides examples to inspire local work. Inclusive and reparative description work is highly dependent on local context, and therefore a specific course of action must be created that is unique to each institution’s readiness and position relative to communities. We have endeavored to be respectful and accurate with the terms that we have used, but we recognize that some words carry regional and community-based differences. Readers are advised that this report does contain a handful of illustrative examples of descriptive language that can and does inflict harm or offense. The urgency to address past harms and correct harmful behaviors and workflows must be tempered by proceeding at a speed that supports building trust, promotes continuous learning, and embraces iterative effort. The work of reparative and inclusive metadata will never be finished. Stewarding the data about library and archive collections for users today and into the future will require ongoing refinement to practice. OCLC, as an organization that plays a significant role in the stewardship of library metadata, is very pleased to be able to facilitate the production of this community agenda. The agenda and its recommendations will also be an important guide for OCLC as it charts its own way forward. The work of confronting and addressing harmful descriptive practices is not easy, and we are grateful for community contributions that have informed and shaped this project and publication

The Manhattan Research Library Initiative, Electronic Books, and the Scholarly Monograph at Risk

Describes the efforts of the Manhattan Research Libraries Initiative (MaRLI) to cooperative develop shared book collections consisting of print and electronic formats across North American commercial publishers, publishers from countries outslide of North America, and open access content

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.

As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing

DeWitt Wallace Library Annual Report 2014-2015

Summary of library and media services activities for 2014-201