14 papers · ranked by Valyu relevance
Yasset Perez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg + 11 more
A ‘Ten Simple Rules’ guide to git and GitHub. We describe and provide examples on how to use these software to track projects, as users, teams and organizations. We document collaborative development using branching and forking, interaction between collaborators using issues and continuous integration and automation…
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…
Ziyao Li, Xuyang Liu, Weijie Chen, Fan Shen + 3 more
Recent breakthroughs on protein structure prediction, namely AlphaFold, have led to unprecedented new possibilities in related areas. However, the lack of training utilities in its current open-source code hinders the community from further developing or adapting the model. Here we present Uni-Fold as a thoroughly…
Dana E. Cobb-Lewis, Devin Synder, Sonya Dumanis, Robert Thibault + 6 more
The open science movement aims to transform the research landscape by promoting research transparency in order to enable reproducibility and replicability, lower the barriers for collaboration, and reduce unnecessary duplication. Recently, in recognition of the value of open science, funding agencies have begun to…
Nico Riedel, Miriam Kip, Evgeny Bobrov
Open research data are increasingly recognized as a quality indicator and an important resource to increase transparency, robustness and collaboration in science. However, no standardized way of reporting Open Data in publications exists, making it difficult to find shared datasets and assess the prevalence of Open…
Matthias Stangl, Jonathan Shine, Thomas Wolbers
Human fMRI studies examining the putative firing of grid cells (i.e., the grid code) suggest that this cellular mechanism supports not only spatial navigation, but also more abstract cognitive processes. This research area, however, remains relatively unexplored, perhaps us to the complexities of data analysis. To…
Pamela H Russell, Rachel L Johnson, Shreyas Ananthan, Benjamin Harnke + 1 more
In recent years, the explosion of genomic data and bioinformatic tools has been accompanied by a growing conversation around reproducibility of results and usability of software. However, the actual state of the body of bioinformatics software remains largely unknown. The purpose of this paper is to investigate the…
Eva Martín del Pico, Josep Lluis Gelpi, Salvador Capella-Gutiérrez
Software plays a crucial and growing role in research. Unfortunately, the computational component in Life Sciences research is challenging to reproduce and verify most of the time. It could be undocumented, opaque, may even contain unknown errors that affect the outcome, or be directly unavailable, and impossible to…
Yoshiharu Ikutani, Takatomi Kubo, Satoshi Nishida, Hideaki Hata + 3 more
Expertise enables humans to achieve outstanding performance on domain-specific tasks, and programming is no exception. Many have shown that expert programmers exhibit remarkable differences from novices in behavioral performance, knowledge structure, and selective attention. However, the underlying differences in the…
Jeremy Li, Alex Rubinsteyn, Sergey Feldman, Timothy O’Donnell + 18 more
Scientific computing has become a central component of modern scientific discovery. Yet many computational tools are developed by small, specialized teams under incentives that encourage the release of rapidly prototyped tooling without commensurate attention to engineering concerns, including performance and…
Christian B. Strømme, A. Kelly Lane, Aud H. Halbritter, Elizabeth Law + 7 more
Open Science (OS) comprises a variety of practices and principles that are broadly intended to improve the quality and transparency of research, and the concept is gaining traction. Since OS has multiple facets and still lacks a unifying definition, it may be interpreted quite differently among practitioners. Moreover…
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…
Mehrad Ansari, Andrew D. White
We present three deep learning sequence prediction models for hemolysis, solubility, and resistance to non-specific interactions of peptides that achieve comparable results to the state-of-the art models. These predictive models share a common architecture of bidirectional recurrent neural networks (LSTM). These models…
Serghei Mangul, Thiago Mosqueiro, Dat Duong, Keith Mitchell + 12 more
Developing new software tools for analysis of large-scale, biological data is a key component of advancing computational, data-enabled research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the…