15 papers · ranked by Valyu relevance
Nitesh Kumar Sharma, Ram Ayyala, Dhrithi Deshpande, Yesha Patel + 13 more
'Viorel Munteanu' 'Dumitru Ciorba' 'Viorel Bostan' 'Andrada Fiscutean' 'Mohammad Vahed' 'Aditya Sarkar' 'Ruiwei Guo' 'Andrew Moore' 'Nicholas Darci-Maher' 'Nicole Nogoy' 'Malak Abedalthagafi' 'Serghei Mangul' 'Harry Hochheiser'] Data-driven computational analysis is becoming increasingly important in biomedical…
Nitesh Kumar Sharma, Ram Ayyala, Dhrithi Deshpande, Yesha M Patel + 11 more
Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are…
Lauren Cadwallader, Feilim Mac Gabhann, Jason Papin, Virginia E. Pitzer
On March 30, 2021, a new code sharing policy was introduced at PLOS Computational Biology . This policy requires any code supporting a publication to be shared unless there are ethical or legal restrictions that prevent sharing. The policy was introduced in response to community desire for a stronger position on code…
Tom Pollard, Thomas Sounack, Catherine A. Gao, Leo Anthony Celi + 5 more
Introduction The Transparent Reporting of a multivariable prediction model of Individual Prognosis Or Diagnosis (TRIPOD) statement was published to improve the reporting and critical appraisal of prediction model studies for diagnosis and prognosis. This paper describes the processes and methods that will be used to…
Authors not listed
Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms…
Taishi Kayano, Yura Ko, Kanako Otani, Tetsuro Kobayashi + 2 more
Correction to: Scientifc Reports 10.1038/s41598-023-44942-6, published online 18 October 2023 The original version of this Article contained errors in the Data availability section. The raw epidemiological data used in the study is not publicly available but can be accessed through an application to the National…
Kenneth F. Kellner, Jeffrey W. Doser, Jerrold L. Belant
Analytic reproducibility is important for scientific credibility in ecology, but the extent to which scientific literature meets this criterion is not well understood. We surveyed 497 papers published in 2018-2022 in 9 ecology-related journals. We focused on papers that used hierarchical models to estimate species…
Keith D. Harris, Guy Hadari, Gili Greenbaum
Modeling the dynamics of biological processes is ubiquitous across the ecological and evolutionary disciplines. However, the increasing complexity of these models poses a significant challenge to the dissemination of model-derived results. With the existing requirements of scientific publishing, most often only a small…
Daniel Krähmer, Laura Schächtele, Andreas Schneck, Simon Porcher
Transparency and peer control are cornerstones of good scientific practice and entail the replication and reproduction of findings. The feasibility of replications, however, hinges on the premise that original researchers make their data and research code publicly available. This applies in particular to large-N…
Gabriel Heckerman, Eileen Tzng, Arely Campos-Melendez, Chisomaga Ekwueme + 1 more
Several fields have described low reproducibility of scientific research and poor accessibility in research reporting practices. Although previous reports have investigated accessible reporting practices that lead to reproducible research in other fields, to date no study has explored the extent of accessible and…
Marc Dillmann, Julien Siebert, Adam Trendowicz
Result: Our results show that, controlling for the number of logical lines of codes (LLOC), cross-entropy computed by LLMs is indeed a predictor of maintainability on a class level (the higher the cross-entropy the lower the maintainability). However, this relation is reversed when one does not control for LLOC (e.g.…
Layan Bahaidarah, Ethan Hung, Andreas Francisco De Melo Oliveira, Jyotsna Penumaka + 2 more
'Jyotsna Penumaka' 'Lukas Rosario' 'A. Trisovic'] Abstract—An essential part of research and scientific communication is researchers' ability to reproduce the results of others. While there have been increasing standards for authors to make data and code available, many of these files are hard to reexecute in practice…
Authors not listed
Machine learning models are transforming data-driven research across scientific disciplines, yet their deployment as accessible and reliable web services remains a significant challenge. We introduce the NERDD framework, a scalable, maintainable, and secure microservices platform designed to support the sustainable…
Aaron M. Love, Nikhil U. Nair
As cellular engineering progresses from simply overexpressing proteins to imparting complex metabolic and regulatory phenotypes through multigene expression, judicious appropriation of cellular resources is essential. Since there is degeneracy in codons and their use is biased, codons may control cellular resources at…
Ruben Sanchez-Garcia, Dávid Havasi, Gergely Takács, Matthew C. Robinson + 3 more
Compound availability is a critical property for design prioritization across the drug discovery pipeline. Historically, and despite their multiple limitations, compound-oriented synthetic accessibility scores have been used as proxies for this problem. However, the size of the catalogues of commercially available…