Preparing for HL-LHC: Increasing the LHCb software publication rate to CVMFS by an order of magnitude

In the HEP community, software plays a central role in the operation of experiments’ facilities and for reconstruction jobs, with CVMFS being the service enabling the distribution of software at scale. In view of High Luminosity LHC, CVMFS developers investigated how to improve the publication workflow to support the most demanding use cases. This paper reports about recent CVMFS developments and infrastructural updates that enable faster publication into existing repositories. A new CVMFS component, the CVMFS Gateway, allows for concurrent transactions and the use of multiple publishers, increasing the overall publication rate on a single repository. Also, the repository data has been migrated to Ceph-based S3 object storage, which brings a relevant performance enhancement over the previously-used Cinder volumes. We demonstrate how recent improvements allow for faster publication of software releases in CVMFS repositories by focusing on the LHCb nightly builds use case, which is currently by far the most demanding one for the CVMFS infrastructure at CERN. The publication of nightly builds is characterized by a high churn rate, needs regular garbage collection, and requires the ability to ingest a huge amount of software files over a limited period of time.

Opening the Door to Registered Reports: Census of Journals Publishing Registered Reports (2013–2020)

Registered reports are a new publication workflow where the decision to publish is made prior to data collection and analysis and thus cannot be dependent on the outcome of the study. An increasing number of journals have adopted this new mechanism, but previous research suggests that submission rates are still relatively low. We conducted a census of journals publishing registered reports (N = 278) using independent coders to collect information from submission guidelines, with the goal of documenting journals’ early adoption of registered reports. Our results show that the majority of journals adopting registered reports are in psychology, and it typically takes about a year to publish the first registered report after adopting. Still, many journals have not published their first registered report. There is high variability in impact of journals adopting registered reports. Many journals do not include concrete information about policies that address concerns about registered reports (e.g., exploratory analysis); however, those that do typically allow these practices with some restrictions. Additionally, other open science practices are commonly encouraged or required as part of the registered report process, especially open data and materials. Overall, many journals did not include many of the fields coded by the research team, which could be a barrier to submission for some authors. Though the majority of journals allow authors to be anonymous during the review process, a sizable portion do not, which could also be a barrier to submission. We conclude with future directions and implications for authors of registered reports, journals that have already adopted registered reports, and journals that may consider adopting registered reports in the future.

Publication, Testing and Visualization with EFES: A tool for all stages of the EpiDoc XML editing process

"EpiDoc is a set of recommendations, schema and other tools for the encoding of ancient texts, especially inscriptions and papyri, in TEI XML, that is now used by upwards of a hundred projects around the world, and large numbers of scholars seek training in EpiDoc encoding every year. The EpiDoc Front-End Services tool (EFES) was designed to fill the important need for a publication solution for researchers and editors who have produced EpiDoc encoded texts but do not have access to digital humanities support or a well-funded IT service to produce a publication for them. This paper will discuss the use of EFES not only for final publication, but as a tool in the editing and publication workflow, by editors of inscriptions, papyri and similar texts including those on coins and seals. The edition visualisations, indexes and search interface produced by EFES are able to serve as part of the validation, correction and research apparatus for the author of an epigraphic corpus, iteratively improving the editions long before final publication. As we will argue, this research process is a key component of epigraphic and papyrological editing practice, and studying these needs will help us to further enhance the effectiveness of EFES as a tool. To this end we also plan to add three major functionalities to the EFES toolbox: (1) date visualisation and filter—building on the existing “date slider,” and inspired by partner projects such as Pelagios and Godot; (2) geographic visualization features, again building on Pelagios code, allowing the display of locations within a corpus or from a specific set of search results in a map; (3) export of information and metadata from the corpus as Linked Open Data, following the recommendations of projects such as the Linked Places format, SNAP, Chronontology and Epigraphy.info, to enable the semantic sharing of data within and beyond the field of classical and historical editions. Finally, we will discuss the kinds of collaboration that will be required to bring about desired enhancements to the EFES toolset, especially in this age of research-focussed, short-term funding. Embedding essential infrastructure work of this kind in research applications for specific research and publication projects will almost certainly need to be part of the solution. Keywords: Text Encoding, Ancient Texts, Epigraphy, Papyrology, Digital Publication, Linked Open Data, Extensible Stylesheet Language Transformations"

Modelo baseado em Frictionless Data aplicado aos dados abertos governamentais

O presente trabalho propõe um modelo baseado em Fricitionless Data (FD) para auxiliar na publicação de dados abertos governamentais (DAGs). FD é uma iniciativa da Open Knowledge Foundation, que pretende remover o "atrito" no trabalho com os dados, ou seja, quando se perde muito tempo e recursos para entender e trabalhar com o dado. No âmbito das instituições públicas, a ausência de padrões para publicação e processamento dos DAGs é problema comum quando se trata de abertura dos DAGs. O estudo procurou contribuir ao aplicar o modelo ao conjunto de dados com informações sobre as boas práticas executadas pelo Judiciário relacionadas aos Objetivos de Desenvolvimento Sustentável (ODS). Segundo a Portaria nº 133, a integração dos ODS com as boas práticas do Judiciário pode trazer diversos benefícios como: aperfeiçoamento dos mecanismos de busca nos Portais de Transparência dos Tribunais, de forma associada aos ODS; auxiliar na medição da eficiência do Poder Judiciário em atingir os ODS, entre outros. O modelo se baseou no Data Publication Workflow, um fluxo para publicação de dados disponível no site da iniciativa Frictionless Data e que aborda etapas como empacotamento, tratamento e publicação dos dados. A aplicação do modelo também utilizou ferramentas de código aberto baseados em Frictionless Data e os resultados mostraram a sua viabilidade para a abertura de um conjunto de dados abertos governamentais.

Census of Journal Policies for Registered Reports: The First Seven Years of Adoption

Registered reports are a new publication workflow where the decision to publish is based on the proposed methods before data is collected. Many journals have adopted this new mechanism; however, previous research suggests that submission rates are very low, suggesting author adoption may be lagging behind. We conducted a census of journals publishing registered reports (N = 243) using independent coders to collect information from submission guidelines, with the goal of documenting the early adoption of registered reports and providing useful information about common policies for registered reports. Common misconceptions about restrictive policies of registered reports are mostly disconfirmed: all journals allow exploratory analysis, and most journals allow multiple studies and secondary data analysis. Overall, missing data suggests that journal submission policies are incomplete, but as researchers learn more about registered reports, we may see increased adoption of this novel publication mechanism.

Open Access publication workflow for academic books

A draft (final version) of an media-neutral as well as both cost-effective and personnel-efficient publications workflow for Open Access (OA) monograph publishing at university presses is presented. The workflow has been developed as a result of the research project Open-Access-Hochschulverlag at the Leipzig University of Applied Sciences, Germany. The aim of the project is to develop a sustainable and adoptable workflow to enable universities to publish their publications as OA and printed books simultaneously in a state-of-the-art way and without any restrictions regarding the license, the variety of formats, print run etc. Up to now, we have defined 17 process groupswith up to 9processes,which a university press has to consider when publishing OA books state-of-the-art. These processes have been shown on the poster (it is the final version of the project, two preliminary versionswerealready published in April and June 2019). The arrangement and the arrows between the processes indicate in which order the processes should be ideally organised by the university presses. Since any university may adapt that workflow individually, it includes several possible ways by which an OA book can be published (see process group Ka or Qe at the poster). The visualisation of the publication workflow represents only a part of the results of our research project. In addition detailed descriptions for each process have been created, which explain a certain process in depth, e.g. who is responsible for it, what time it takes and what it may cost to complete the process. These detailed descriptions will be published elsewhere.

A checklist recipe: making species data open and FAIR

Species checklists are a crucial source of information for research and policy. Unfortunately, many traditional species checklists vary wildly in their content, format, availability and maintenance. The fact that these are not open, findable, accessible, interoperable and reusable (FAIR) severely hampers fast and efficient information flow to policy and decision-making that are required to tackle the current biodiversity crisis. Here, we propose a reproducible, semi-automated workflow to transform traditional checklist data into a FAIR and open species registry. We showcase our workflow by applying it to the publication of the Manual of Alien Plants, a species checklist specifically developed for the Tracking Invasive Alien Species (TrIAS) project. Our approach combines source data management, reproducible data transformation to Darwin Core using R, version control, data documentation and publication to the Global Biodiversity Information Facility (GBIF). This checklist publication workflow is openly available for data holders and applicable to species registries varying in thematic, taxonomic or geographical scope and could serve as an important tool to open up research and strengthen environmental decision-making.

DUnAS: primeiros passos na criação do Repositório de Dados de Investigação da Universidade de Aveiro

In June 2019, the University of Aveiro (UA), through the Library, Document Management and Museology Services and the Information Technology and Communication Services, in collaboration with the Research Support Office, took the first steps regarding the creation of the University of Aveiro Research Data Repository - DUnAs. The project aims to implement an open repository for the archive and publication of research data, promoting its visibility, impact and reproducibility. This work intends to highlight the strategy adopted while setting up the repository based on Dataverse, an open source platform, and the respective helpdesk service, addressing the initiatives and the phases for its implementation. The results obtained in the analysis of the Dataverse platform and the contact with researchers through the selection of pilot projects led to the definition of the deposit – curation – publication workflow and allowed the creation of a service adapted to the community.

Loose-leaf publishing using Antenna House and CSS

Loose-leaf publishing is the ability to typeset and print only the pages in a document that have changed since its last publication. This presents many interesting challenges. We developed a loose-leaf publication system using Antenna House Formatter, CSS for pagination, and XSLT for post processing the area tree into “change packages” which include only the changed pages. Both the CSS markup and the publication workflow warrant a closer look.

Towards an Open Access publication workflow for monographs for university presses

Adraft (second version) of an media-neutral as well as both cost-effective and personnel-efficient publications workflow for Open Access (OA) monograph publishing at university presses is presented. The workflow has been developed as a result of the research project Open-Access-Hochschulverlag at the Leipzig University of Applied Sciences, Germany. The aim of the project is to develop a sustainable and adoptable workflow to enable universities to publish their publications as OA and printed books simultaneously in a state-of-the-art way and without any restrictions regarding the license, the variety of formats, print run etc. Up to now, we have defined 18 main processes (in green) with up to 8 sub-processes (in orange) which a university press has to consider when publishing OA books state-of-the-art. These processes have been shown on the poster (it is the second veersion of the workflow draft - the first version was published on25th April 2019). The arrangement and the arrows between the processes indicate in which order the processes should be ideally organised by the university presses. Since any university may adapt that workflow individually, it includes several possible ways by which an OA book can be published (see process 1 or 3 at the poster). The visualisation of the publication workflow represents only a part of the results of our research project. In addition detailed descriptions for each process have been created, which explain a certain process in depth, e.g. who is responsible for it, what time it takes and what it may cost to complete the process. These detailed descriptions will be published elsewhere.