Global software engineering requires supporting distributed collaboration for most software development activities. However, geographical distance challenges effective collaboration. Nowadays, we're ...witnessing significant advances in communication and collaboration technologies. So, researchers explored whether these advances enable effective remote collaboration. To that end, they studied the design activities of both colocated and distributed professional software designers. The findings are based on analysis of video recordings of design sessions and questionnaires. The researchers found that despite comprehensive technological improvements, distance still matters. To ensure effective distributed software design, designers must consider extra (nontechnical) details. This article is part of a theme issue on collaborative modeling.
Array programming with NumPy Harris, Charles R; Millman, K Jarrod; van der Walt, Stéfan J ...
Nature,
09/2020, Volume:
585, Issue:
7825
Journal Article
Peer reviewed
Open access
Array programming provides a powerful, compact and expressive syntax for accessing, manipulating and operating on data in vectors, matrices and higher-dimensional arrays. NumPy is the primary array ...programming library for the Python language. It has an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, materials science, engineering, finance and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves
and in the first imaging of a black hole
. Here we review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data. NumPy is the foundation upon which the scientific Python ecosystem is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Owing to its central position in the ecosystem, NumPy increasingly acts as an interoperability layer between such array computation libraries and, together with its application programming interface (API), provides a flexible framework to support the next decade of scientific and industrial analysis.
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FZAB, GEOZS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
deal.II is a state-of-the-art finite element library focused on generality, dimension-independent programming, parallelism, and extensibility. Herein, we outline its primary design considerations and ...its sophisticated features such as distributed meshes, hp-adaptivity, support for complex geometries, and matrix-free algorithms. But deal.II is more than just a software library: It is also a diverse and worldwide community of developers and users, as well as an educational platform. We therefore also discuss some of the technical and social challenges and lessons learned in running a large community software project over the course of two decades.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Despite lively debate over the past decade on the benefits and drawbacks of model-driven engineering (MDE), there have been few industry-wide studies of MDE in practice. A new study that surveyed 450 ...MDE practitioners and performed in-depth interviews with 22 more suggests that although MDE might be more widespread than commonly believed, developers rarely use it to generate whole systems. Rather, they apply MDE to develop key parts of a system.
Abstract
The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination of mass spectrometry proteomics data worldwide ...since 2012. In this paper, we describe the main developments since the previous update manuscript was published in Nucleic Acids Research in 2017. Since then, in addition to the four PX existing members at the time (PRIDE, PeptideAtlas including the PASSEL resource, MassIVE and jPOST), two new resources have joined PX: iProX (China) and Panorama Public (USA). We first describe the updated submission guidelines, now expanded to include six members. Next, with current data submission statistics, we demonstrate that the proteomics field is now actively embracing public open data policies. At the end of June 2019, more than 14 100 datasets had been submitted to PX resources since 2012, and from those, more than 9 500 in just the last three years. In parallel, an unprecedented increase of data re-use activities in the field, including ‘big data’ approaches, is enabling novel research and new data resources. At last, we also outline some of our future plans for the coming years.
Abstract
GenBank® (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for 420 000 formally described species. Most GenBank submissions ...are made using BankIt, the NCBI Submission Portal, or the tool tbl2asn, and are obtained from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Nucleotide database, which links to related information such as taxonomy, genomes, protein sequences and structures, and biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. Recent updates include an expansion of sequence identifier formats to accommodate expected database growth, submission wizards for ribosomal RNA, and the transfer of Expressed Sequence Tag (EST) and Genome Survey Sequence (GSS) data into the Nucleotide database.
The field of eHealth has a history of more than 20 years. During that time, many different eHealth services were developed. However, factors influencing the adoption of such services were seldom the ...main focus of analyses. For this reason, organizations adopting and implementing eHealth services seem not to be fully aware of the barriers and facilitators influencing the integration of eHealth services into routine care.
The objective of this work is to provide (1) a comprehensive list of relevant barriers to be considered and (2) a list of facilitators or success factors to help in planning and implementing successful eHealth services.
For this study, a twofold approach was applied. First, we gathered experts' current opinions on facilitators and barriers in implementing eHealth services via expert discussions at two health informatics conferences held in Europe. Second, we conducted a systematic literature analysis concerning the barriers and facilitators for the implementation of eHealth services. Finally, we merged the results of the expert discussions with those of the systematic literature analysis.
Both expert discussions (23 and 10 experts, respectively) identified 15 barriers and 31 facilitators, whereas 76 barriers and 268 facilitators were found in 38 of the initial 56 articles published from 12 different countries. For the analyzed publications, the count of distinct barriers reported ranged from 0 to 40 (mean 10.24, SD 8.87, median 8). Likewise, between 0 and 48 facilitators were mentioned in the literature (mean 9.18, SD 9.33, median 6). The combination of both sources resulted in 77 barriers and 292 facilitators for the adoption and implementation of eHealth services.
This work contributes a comprehensive list of barriers and facilitators for the implementation and adoption of eHealth services. Addressing barriers early, and leveraging facilitators during the implementation, can help create eHealth services that better meet the needs of users and provide higher benefits for patients and caregivers.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
U-Net is a generic deep-learning solution for frequently occurring quantification tasks such as cell detection and shape measurements in biomedical image data. We present an ImageJ plugin that ...enables non-machine-learning experts to analyze their data with U-Net on either a local computer or a remote server/cloud service. The plugin comes with pretrained models for single-cell segmentation and allows for U-Net to be adapted to new tasks on the basis of a few annotated samples.
Diffraction (X‐ray, neutron and electron) and electron cryo‐microscopy are powerful methods to determine three‐dimensional macromolecular structures, which are required to understand biological ...processes and to develop new therapeutics against diseases. The overall structure‐solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data‐quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time‐consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command‐line features of Phenix and streamlines the transition between programs, project tracking and re‐running of previous tasks.
Recent developments in the Phenix software package are described in the context of macromolecular structure determination using X‐rays, neutrons and electrons.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Abstract
MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression and play vital roles in various biological processes. It has been reported that aberrant regulation of ...miRNAs was associated with the development and progression of various diseases, but the underlying mechanisms are not fully deciphered. Here, we described our updated TransmiR v2.0 database for more comprehensive information about transcription factor (TF)-miRNA regulations. 3730 TF–miRNA regulations among 19 species from 1349 reports were manually curated by surveying >8000 publications, and more than 1.7 million tissue-specific TF–miRNA regulations were further incorporated based on ChIP-seq data. Besides, we constructed a ‘Predict’ module to query the predicted TF–miRNA regulations in human based on binding motifs of TFs. To facilitate the community, we provided a ‘Network’ module to visualize TF–miRNA regulations for each TF and miRNA, or for a specific disease. An ‘Enrichment analysis’ module was also included to predict TFs that are likely to regulate a miRNA list of interest. In conclusion, with improved data coverage and webserver functionalities, TransmiR v2.0 would be a useful resource for investigating the regulation of miRNAs. TransmiR v2.0 is freely accessible at http://www.cuilab.cn/transmir.
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