16 papers · ranked by Valyu relevance
Antica Culina, Ilona van den Berg, Simon Evans, Alfredo Sánchez-Tójar
'Alfredo Sánchez-Tójar'] Access to analytical code is essential for transparent and reproducible research. We review the state of code availability in ecology using a random sample of 346 nonmolecular articles published between 2015 and 2019 under mandatory or encouraged code-sharing policies. Our results call for…
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…
Michael John Grayling, Graham Mark Wheeler
design Authors: Michael John Grayling, Graham Mark Wheeler Our search yielded 4123 articles across the 31 considered journals ([Supplementary Table 1]()). Of these, 3875 were excluded on the following grounds: Non-adaptive design methodology (3817); Not a complete peer-reviewed article (40); Not directly applied to…
K. A. S. Mislan, Jeffrey M. Heer, Ethan P. White
Journals can promote the release of code used in ecological studies though a combination of increasing the visibility and discoverability of code and software and requiring code archiving. One way to increase visibility is to indicate code availability in the table of contents of all formats of the journal and have…
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…
Evan Russell, Andrew K. Hall, Conor McKaigney, Craig Goldie + 2 more
'Ingrid Harle' 'Marco L.A. Sivilotti'] Introduction Some patients with end-stage disease who may neither want nor benefit from aggressive resuscitation receive such treatment if they cannot communicate in an emergency. Timely access to patients’ current resuscitation wishes, or “code status,” should be a key metric of…
Stylianos Serghiou, Despina G. Contopoulos-Ioannidis, Kevin W. Boyack, Nico Riedel + 2 more
Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in…
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…
Adarsh Sivasankaran, Eric Williams, Mark Albrecht, Galen E. Switzer + 2 more
The success of Unrelated Donor stem-cell transplants depends not only on finding genetically matched donors but also on donor availability. On average 50% of potential donors in the NMDP database are unavailable for a variety of reasons, after initially matching a patient, with significant variations in availability…
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.…
Waqar Ahmed, Osman Hasan
Availability analysis is used to assess the possible failures and their restoration process for a given system. This analysis involves the calculation of instantaneous and steady-state availabilities of the individual system components and the usage of this information along with the commonly used availability modeling…
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…
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…