23 papers · ranked by Valyu relevance
Andrew D Yates, Jeremy Adams, Somesh Chaturvedi, Robert M Davies + 7 more
Reference genome sequences are central to genomic interpretation and to defining a baseline of knowledge upon which our understanding of biological systems, phenotypes and variation are based. The ability to interpret such data is essential for the delivery of genomics into the clinic. As precision medicine becomes…
Andrew D Yates, Jeremy Adams, Somesh Chaturvedi, Robert M. Davies + 6 more
Reference sequences are essential in creating a baseline of knowledge for many common bioinformatics methods, especially those using genomic sequencing. We have created refget, a Global Alliance for Genomics and Health API specification to access reference sequences and sub-sequences using an identifier derived from…
Szymon Grabia, Ula Smyczynska, Konrad Pagacz, Wojciech Fendler
Multi-gene expression assays are an attractive tool in revealing complex regulatory mechanisms in living organisms. Normalization is an indispensable step of data analysis in all those studies, since it removes unwanted, non-biological variability from data. In targeted qPCR assays the normalization is typically…
Andres Munoz-Arcentales, Sonsoles López-Pernas, Javier Conde, Álvaro Alonso + 3 more
'Álvaro Alonso' 'Joaquín Salvachúa' 'Juan José Hierro' 'Rebeca P. Díaz Redondo'] In recent years, many proposals of context-aware systems applied to IoT-based smart environments have been presented in the literature. Most previous works provide a generic high-level structure of how a context-aware system can be…
Andrea Keyter, Sam Salek, Neil McAuslane, Shabir Banoo + 2 more
'Samvel Azatyan' 'Stuart Walker'] Background This study sought to identify criteria and current practices for implementing an abridged review process and understanding barriers and enablers in utilizing reliance models and to offer recommendations for the implementation of an abridged review process in South Africa…
Edward A. Lee, Ondřej Lhoták
Reference immutability is a type based technique for taming mutation that has long been studied in the context of object-oriented languages, like Java. Recently, though, languages like Scala have blurred the lines between functional programming languages and object oriented programming languages. We explore how…
Kirill Zinovjev, Lester Hedges, Rubén Montagud Andreu, Christopher Woods + 2 more
We present in this work the emle-engine package (https://github.com/chemle/emle-engine) – the implementation of a new machine learning embedding scheme for hybrid machine learning potential / molecular mechanics (ML/MM) dynamics simulations. The package is based on an embedding scheme that uses a physics-based model of…
Kérilin Stancine Santos Rocha, Sabrina Cerqueira-Santos, Genival Araújo dos Santos-Júnior, Lincoln Marques Cavalcante-Santos + 4 more
The implementation of clinical pharmacy services (CPS) has grown worldwide. However, few studies have used models and/or frameworks to facilitate the implementation process, especially in a low and middle-income countries. In addition, there are limitations in the ways that implementation frameworks are used.…
Victor Chen, Ayden Coughlin, Michael D. Bond
Automatically translating system software from C to Rust is an appealing but challenging problem, as it requires whole-program reasoning to satisfy Rust's ownership and borrowing discipline. A key enabling step in whole-program translation is interface translation, which produces Rust declarations for the C program's…
Shuvendu K. Lahiri, Chao Wang, Kartik Nagar, Prasita Mukherjee + 1 more
'Suresh Jagannathan'] Geo-replicated systems provide a number of desirable properties such as globally low latency, high availability, scalability, and built-in fault tolerance. Unfortunately, programming correct applications on top of such systems has proven to be very challenging, in large part because of the weak…
Richard Apodaca
Despite its widespread use, Simplified Molecular Input Line Entry System (SMILES) remains underspecified. The lack of a detailed specification encourages improvisation by software developers, complicates data standardization efforts, and undermines extension development. Balsa, a reformulation of SMILES, addresses…
Martin Šícho, Xuhan Liu, Daniel Svozil, Gerard van Westen
This manuscript describes the development and architecture of the GenUI software platform for integration of molecular generators. The source code for the components of the platform is available in the following repositories: https://github.com/martin-sicho/genui https://github.com/martin-sicho/genui-gui…
Duc Nguyen, Erin L. Rich, Joni D. Wallis, Kenway Louie + 1 more
The decisional reference point serves as a hidden benchmark for evaluating options in decision-making. Despite extensive behavioral evidence for the existence of the reference point, its neural instantiation remains unclear. To identify reference point encoding at both the single-neuron and population levels, we…
Josef Justa, Václav Šmídl, Aleš Hamáček
A new predictor-corrector filter for attitude and heading reference systems (AHRS) using data from an orthogonal sensor combination of three accelerometers, three magnetometers and three gyroscopes is proposed. The filter uses the predictor-corrector structure, with prediction based on gyroscopes and independent…
Ulysse Beaugnon, Basile Clément, Nicolas Tollenaere, Albert Cohen
Traditional optimizing compilers rely on rewrite rules to iteratively apply program transformations. This iterative approach hides optimization opportunities behind intermediate transformation steps. For instance, vectorization can only be applied to the innermost loop in a nest: one must first perform a loop…
George Dimitriadis, Ella Svahn, Andrew MacAskill, Athena Akrami
To realise a research project idea, an experimenter faces a series of conflicting design and implementation considerations, regarding both its hardware and software components. For instance, the ease of implementation, in time and expertise, should be balanced against the ease of future reconfigurability and number of…
Enola K. Proctor, Alicia C. Bunger, Rebecca Lengnick-Hall, Donald R. Gerke + 3 more
'Donald R. Gerke' 'Jared K. Martin' 'Rebecca J. Phillips' 'Julia C. Swanson'] Correction: Implementation Sci 18, 31 (2023) https://doi.org/10.1186/s13012-023-01286-z The original publication [1] of this article contained an incorrect citation and a missing reference. The incorrect citation appears in the section…
Hiun Kim
Modularity is the fundamental aspect of modern software engineering, however many advanced modularity techniques requires prospective technologies as part of development and operation process. In this paper, we present Refinable Function, an object-oriented approach to advanced languagebased, symmetric modularity…
A. Mark Payne, Haoyang Wu, Hao-Wei Pang, Colin A. Grambow + 4 more
To obtain accurate enthalpies of formation of a chemical species, Hf, one needs a procedure to quantitatively connect the results from quantum mechanical (QM) calculations with the experimental enthalpies of elements in their standard state, often along with additional empirical corrections. Although QM methods…
Viacheslav Bolnykh, Jógvan Magnus Haugaard Olsen, Simone Meloni, Martin P. Bircher + 3 more
We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computation of electrostatic QM/MM interactions is parallelized exploiting…
Gerald Baumgartner, Konstantin Läufer, Vincent F. Russo
Design patterns are distilled from many real systems to catalog common programming practice. However, some object-oriented design patterns are distorted or overly complicated because of the lack of supporting programming language constructs or mechanisms. For this paper, we have analyzed several published design…
Yegor Bugayenko
C++, Java, C#, Python, Ruby, JavaScript are the most powerful object-oriented programming languages, if language power would be defined as the number of features available for a programmer. EO, on the other hand, is an object-oriented programming language with a reduced set of features: it has nothing by objects and…
Semen Yesylevskyy
Transition to the memory safe natively compiled programming languages is a major software development trend in recent years, which eliminates memory-related security exploits, enables a fearless concurrency and parallelization, and drastically improves ergonomics and speed of software development. Modern memory-safe…