Cluster Analysis of Open Research Data: A Case for Replication Metadata

Research data are often released upon journal publication to enable result verification and reproducibility. For that reason, research dissemination infrastructures typically support diverse datasets coming from numerous disciplines, from tabular data and program code to audio-visual files. Metadata, or data about data, is critical to making research outputs adequately documented and FAIR. Aiming to contribute to the discussions on the development of metadata for research outputs, I conducted an exploratory analysis to determine how research datasets cluster based on what researchers organically deposit together. I use the content of over 40,000 datasets from the Harvard Dataverse research data repository as my sample for the cluster analysis. I find that the majority of the clusters are formed by single-type datasets, while in the rest of the sample, no meaningful clusters can be identified. For the result interpretation, I use the metadata standard employed by DataCite, a leading organization for documenting a scholarly record, and map existing resource types to my results. About 65% of the sample can be described with a single-type metadata (such as Dataset, Software orReport), while the rest would require aggregate metadata types. Though DataCite supports an aggregate type such as a Collection, I argue that a significant number of datasets, in particular those containing both data and code files (about 20% of the sample), would be more accurately described as a Replication resource metadata type. Such resource type would be particularly useful in facilitating research reproducibility

Data preservation and reproducibility at the LHCb experiment at CERN

This dissertation presents the first study of data preservation and research reproducibility in data science at the Large Hadron Collider at CERN. In particular, provenance capture of the experimental data and the reproducibility of physics analyses at the LHCb experiment were studied. First, the preservation of the software and hardware dependencies of the LHCb experimental data and simulations was investigated. It was found that the links between the data processing information and the datasets themselves were obscure. In order to document these dependencies, a graph database was designed and implemented. The nodes in the graph represent the data with their processing information, software and computational environment, whilst the edges represent their dependence on the other nodes. The database provides a central place to preserve information that was previously scattered across the LHCb computing infrastructure. Using the developed database, a methodology to recreate the LHCb computational environment and to execute the data processing on the cloud was implemented with the use of virtual containers. It was found that the produced physics events were identical to the official LHCb data, meaning that the system can aid in data preservation. Furthermore, the developed method can be used for outreach purposes, providing a streamlined way for a person external to CERN to process and analyse the LHCb data. Following this, the reproducibility of data analyses was studied. A data provenance tracking service was implemented within the LHCb software framework \textsc{Gaudi}. The service allows analysts to capture their data processing configurations that can be used to reproduce a dataset within the dataset itself. Furthermore, to assess the current status of the reproducibility of LHCb physics analyses, the major parts of an analysis were reproduced by following methods described in publicly and internally available documentation. This study allowed the identification of barriers to reproducibility and specific points where documentation is lacking. With this knowledge, one can specifically target areas that need improvement and encourage practices that would improve reproducibility in the future. Finally, contributions were made to the CERN Analysis Preservation portal, which is a general knowledge preservation framework developed at CERN to be used across all the LHC experiments. In particular, the functionality to preserve source code from git repositories and Docker images in one central location was implemented.CERN Doctoral Student program, the Muir Wood studentship awarded by the Newnham College, the Dositeja award by the Fund for Young Talents in Serbi

Advancing Software Citation Implementation (Software Citation Workshop 2022)

Software is foundationally important to scientific and social progress, however, traditional acknowledgment of the use of others' work has not adapted in step with the rapid development and use of software in research. This report outlines a series of collaborative discussions that brought together an international group of stakeholders and experts representing many communities, forms of labor, and expertise. Participants addressed specific challenges about software citation that have so far gone unresolved. The discussions took place in summer 2022 both online and in-person and involved a total of 51 participants. The activities described in this paper were intended to identify and prioritize specific software citation problems, develop (potential) interventions, and lay out a series of mutually supporting approaches to address them. The outcomes of this report will be useful for the GLAM (Galleries, Libraries, Archives, Museums) community, repository managers and curators, research software developers, and publishers

If these data could talk

In the last few decades, data-driven methods have come to dominate many fields of scientific inquiry. Open data and open-source software have enabled the rapid implementation of novel methods to manage and analyze the growing flood of data. However, it has become apparent that many scientfic fields exhibit distressingly low rates of repeatability and reproducibility. Although there are many dimensions to this issue, we believe that there is a lack of formalism used when describing end-to-end published results, from the data source to the analysis to the final published results. Even when authors do their best to make their research and data accessible, this lack of formalism reduces the clarity and effciency of reporting, which contributes to issues of reproducibility. Data provenance aids both repeatability and reproducibility through systematic and formal records of the relationships among data sources, processes, datasets, publications and researchers.Engineering and Applied SciencesOrganismic and Evolutionary Biolog

Open is not enough

The solutions adopted by the high-energy physics community to foster reproducible research are examples of best practices that could be embraced more widely. This first experience suggests that reproducibility requires going beyond openness

Open is not enough

The solutions adopted by the high-energy physics community to foster reproducible research are examples of best practices that could be embraced more widely. This first experience suggests that reproducibility requires going beyond openness.Peer reviewe

Les droits disciplinaires des fonctions publiques : « unification », « harmonisation » ou « distanciation ». A propos de la loi du 26 avril 2016 relative à la déontologie et aux droits et obligations des fonctionnaires

The production of tt‾ , W+bb‾ and W+cc‾ is studied in the forward region of proton–proton collisions collected at a centre-of-mass energy of 8 TeV by the LHCb experiment, corresponding to an integrated luminosity of 1.98±0.02 fb−1 . The W bosons are reconstructed in the decays W→ℓν , where ℓ denotes muon or electron, while the b and c quarks are reconstructed as jets. All measured cross-sections are in agreement with next-to-leading-order Standard Model predictions.The production of $t\overline{t}$, $W+b\overline{b}$ and $W+c\overline{c}$ is studied in the forward region of proton-proton collisions collected at a centre-of-mass energy of 8 TeV by the LHCb experiment, corresponding to an integrated luminosity of 1.98 $\pm$ 0.02 \mbox{fb}^{-1}. The $W$ bosons are reconstructed in the decays $W\rightarrow\ell\nu$, where $\ell$ denotes muon or electron, while the $b$ and $c$ quarks are reconstructed as jets. All measured cross-sections are in agreement with next-to-leading-order Standard Model predictions

Observation of the B0 → ρ0ρ0 decay from an amplitude analysis of B0 → (π+π−)(π+π−) decays

Proton–proton collision data recorded in 2011 and 2012 by the LHCb experiment, corresponding to an integrated luminosity of 3.0 fb−1 , are analysed to search for the charmless B0→ρ0ρ0 decay. More than 600 B0→(π+π−)(π+π−) signal decays are selected and used to perform an amplitude analysis, under the assumption of no CP violation in the decay, from which the B0→ρ0ρ0 decay is observed for the first time with 7.1 standard deviations significance. The fraction of B0→ρ0ρ0 decays yielding a longitudinally polarised final state is measured to be fL=0.745−0.058+0.048(stat)±0.034(syst) . The B0→ρ0ρ0 branching fraction, using the B0→ϕK⁎(892)0 decay as reference, is also reported as B(B0→ρ0ρ0)=(0.94±0.17(stat)±0.09(syst)±0.06(BF))×10−6

Study of the rare B-s(0) and B-0 decays into the pi(+) pi(-) mu(+) mu(-) final state

A search for the rare decays $B_s^0 \to \pi^+\pi^-\mu^+\mu^-$ and $B^0 \to \pi^+\pi^-\mu^+\mu^-$ is performed in a data set corresponding to an integrated luminosity of 3.0 fb$^{-1}$ collected by the LHCb detector in proton-proton collisions at centre-of-mass energies of 7 and 8 TeV. Decay candidates with pion pairs that have invariant mass in the range 0.5-1.3 GeV/$c^2$ and with muon pairs that do not originate from a resonance are considered. The first observation of the decay $B_s^0 \to \pi^+\pi^-\mu^+\mu^-$ and the first evidence of the decay $B^0 \to \pi^+\pi^-\mu^+\mu^-$ are obtained and the branching fractions are measured to be $\mathcal{B}(B_s^0 \to \pi^+\pi^-\mu^+\mu^-)=(8.6\pm 1.5\,({\rm stat}) \pm 0.7\,({\rm syst})\pm 0.7\,({\rm norm}))\times 10^{-8}$ and $\mathcal{B}(B^0 \to \pi^+\pi^-\mu^+\mu^-)=(2.11\pm 0.51\,({\rm stat}) \pm 0.15\,({\rm syst})\pm 0.16\,({\rm norm}) )\times 10^{-8}$, where the third uncertainty is due to the branching fraction of the decay $B^0\to J/\psi(\to \mu^+\mu^-)K^*(890)^0(\to K^+\pi^-)$, used as a normalisation.A search for the rare decays Bs0→π+π−μ+μ− and B0→π+π−μ+μ− is performed in a data set corresponding to an integrated luminosity of 3.0 fb−1 collected by the LHCb detector in proton–proton collisions at centre-of-mass energies of 7 and 8 TeV . Decay candidates with pion pairs that have invariant mass in the range 0.5–1.3 GeV/c2 and with muon pairs that do not originate from a resonance are considered. The first observation of the decay Bs0→π+π−μ+μ− and the first evidence of the decay B0→π+π−μ+μ− are obtained and the branching fractions, restricted to the dipion-mass range considered, are measured to be B(Bs0→π+π−μ+μ−)=(8.6±1.5 (stat)±0.7 (syst)±0.7(norm))×10−8 and B(B0→π+π−μ+μ−)=(2.11±0.51(stat)±0.15(syst)±0.16(norm))×10−8 , where the third uncertainty is due to the branching fraction of the decay B0→J/ψ(→μ+μ−)K⁎(892)0(→K+π−) , used as a normalisation.A search for the rare decays Bs0→π+π−μ+μ− and B0→π+π−μ+μ− is performed in a data set corresponding to an integrated luminosity of 3.0 fb−1 collected by the LHCb detector in proton–proton collisions at centre-of-mass energies of 7 and 8 TeV . Decay candidates with pion pairs that have invariant mass in the range 0.5–1.3 GeV/c2 and with muon pairs that do not originate from a resonance are considered. The first observation of the decay Bs0→π+π−μ+μ− and the first evidence of the decay B0→π+π−μ+μ− are obtained and the branching fractions, restricted to the dipion-mass range considered, are measured to be B(Bs0→π+π−μ+μ−)=(8.6±1.5 (stat)±0.7 (syst)±0.7(norm))×10−8 and B(B0→π+π−μ+μ−)=(2.11±0.51(stat)±0.15(syst)±0.16(norm))×10−8 , where the third uncertainty is due to the branching fraction of the decay B0→J/ψ(→μ+μ−)K⁎(892)0(→K+π−) , used as a normalisation.A search for the rare decays $B_s^0 \to \pi^+\pi^-\mu^+\mu^-$ and $B^0 \to \pi^+\pi^-\mu^+\mu^-$ is performed in a data set corresponding to an integrated luminosity of 3.0 fb$^{-1}$ collected by the LHCb detector in proton-proton collisions at centre-of-mass energies of 7 and 8 TeV. Decay candidates with pion pairs that have invariant mass in the range 0.5-1.3 GeV/$c^2$ and with muon pairs that do not originate from a resonance are considered. The first observation of the decay $B_s^0 \to \pi^+\pi^-\mu^+\mu^-$ and the first evidence of the decay $B^0 \to \pi^+\pi^-\mu^+\mu^-$ are obtained and the branching fractions, restricted to the dipion-mass range considered, are measured to be $\mathcal{B}(B_s^0 \to \pi^+\pi^-\mu^+\mu^-)=(8.6\pm 1.5\,({\rm stat}) \pm 0.7\,({\rm syst})\pm 0.7\,({\rm norm}))\times 10^{-8}$ and $\mathcal{B}(B^0 \to \pi^+\pi^-\mu^+\mu^-)=(2.11\pm 0.51\,({\rm stat}) \pm 0.15\,({\rm syst})\pm 0.16\,({\rm norm}) )\times 10^{-8}$, where the third uncertainty is due to the branching fraction of the decay $B^0\to J/\psi(\to \mu^+\mu^-)K^*(890)^0(\to K^+\pi^-)$, used as a normalisation