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2.
PLoS Comput Biol ; 16(5): e1007507, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32365137

RESUMO

Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished by researchers with domain expertise but without formal training in software engineering or computer science. This arrangement has led to underappreciation of sustainability and maintainability of scientific software tools developed in academic environments. Some software tools have avoided this fate, including the scientific library Rosetta. We use this software and its community as a case study to show how modern software development can be accomplished successfully, irrespective of subject area. Rosetta is one of the largest software suites for macromolecular modeling, with 3.1 million lines of code and many state-of-the-art applications. Since the mid 1990s, the software has been developed collaboratively by the RosettaCommons, a community of academics from over 60 institutions worldwide with diverse backgrounds including chemistry, biology, physiology, physics, engineering, mathematics, and computer science. Developing this software suite has provided us with more than two decades of experience in how to effectively develop advanced scientific software in a global community with hundreds of contributors. Here we illustrate the functioning of this development community by addressing technical aspects (like version control, testing, and maintenance), community-building strategies, diversity efforts, software dissemination, and user support. We demonstrate how modern computational research can thrive in a distributed collaborative community. The practices described here are independent of subject area and can be readily adopted by other software development communities.


Assuntos
Biologia Computacional/métodos , Pesquisa/tendências , Software/tendências , Comportamento Cooperativo , Análise de Dados , Engenharia , Biblioteca Gênica , Humanos , Modelos Moleculares , Pesquisadores , Comportamento Social , Interface Usuário-Computador
4.
J Med Syst ; 44(2): 41, 2019 Dec 23.
Artigo em Inglês | MEDLINE | ID: mdl-31872307

RESUMO

As a consequence of the epidemiological transition towards non-communicable diseases, integrated care approaches are required, not solely focused on medical purposes, but also on a range of essential activities for the maintenance of the individuals' quality of life. In order to allow the exchange of information, these integrated approaches might be supported by digital platforms, which need to provide trustful environments and to guarantee the integrity of the information exchanged. Therefore, together with mechanisms such as authentication, logging or auditing, the definition of access control policies assumes a paramount importance. This article focuses on the development of a parser as a component of a platform to support the care of community-dwelling older adults, the SOCIAL platform, to allow the definition of access control policies and rules using natural languages.


Assuntos
Troca de Informação em Saúde/tendências , Armazenamento e Recuperação da Informação/tendências , Processamento de Linguagem Natural , Qualidade de Vida , Software/tendências , Humanos , Sistemas de Informação/tendências , Linguística
5.
Anesthesiology ; 131(6): 1264-1275, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31730551

RESUMO

BACKGROUND: Perioperative controlled substance diversion and tracking have received increased regulatory focus throughout the United States. The authors' institution developed and implemented an automated web-based software application for perioperative controlled substance management. The authors hypothesized that implementation of such a system reduces errors as measured by missing controlled substance medications, missing controlled substance kits (a package of multiple controlled substance medications), and missing witness signatures during kit return. METHODS: From December 1, 2014 to March 31, 2017, the authors obtained missing controlled substance medication, controlled substance kit, and witness return signature data during the preimplementation, implementation, and study period of the controlled substance management application at a single university hospital. This before and after study was based on a QI project at the authors' institution. The authors included all cases requiring anesthesia services. The primary outcome of this study was the rate of missing controlled substance medications. Secondary outcomes included rates for kits not returned to pharmacy and missing kit return witness signatures. RESULTS: There were 54,302 cases during the preimplementation period, 57,670 cases during the implementation period, and 65,911 cases during the study period. The number of missing controlled substance medication (difference 0.7 per 1,000 cases; 95% CI, 0.38-1.02; P < 0.001) and kit return errors (difference 0.45 per 1,000 cases; 95% CI, 0.24-0.66, P < 0.001) declined after implementation of the application. There was no difference in the number of missing witness return signatures (difference 0.09 per 1,000 cases; 95% CI, -0.08 to 0.26, P = 0.350). A user survey with 206 of 485 (42%) response rate demonstrated that providers believed the new application managed controlled substances better than the previous system. CONCLUSIONS: A software application that tracks perioperative controlled substance kits with deep integration into the electronic health record and pharmacy systems is associated with a decrease in management errors.


Assuntos
Substâncias Controladas/normas , Pessoal de Saúde/normas , Assistência Perioperatória/normas , Desvio de Medicamentos sob Prescrição/prevenção & controle , Software/normas , Inquéritos e Questionários , Substâncias Controladas/efeitos adversos , Pessoal de Saúde/tendências , Humanos , Erros de Medicação/prevenção & controle , Erros de Medicação/tendências , Assistência Perioperatória/tendências , Desvio de Medicamentos sob Prescrição/tendências , Software/tendências
7.
IEEE Pulse ; 10(4): 25-27, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31395530

RESUMO

About this Series This is the sixth and last article in a series on the dramatic transformation taking place in health informatics in large part because of the new Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) standard. The first article provided background on health care, electronic health record systems for physicians, and the challenges they both face along with the potential of interoperability to help overcome them. The second introduced the basics of the FHIR standard and some suggested resources for those who are interested in its further exploration. The third introduced SMART on FHIR which, based on its wide adoption, has become the default standard FHIR app platform. The fourth looked at clinical decision support, arguably the single most important provider-facing use case for FHIR. The fifth introduced the personal health record and tools that can utilize the data stored in it as an important use case for FHIR in support of patients. This article looks at the future uses of FHIR with a particular emphasis on those that might impact on research uses of health data. The articles in this series are intended to introduce researchers from other fields to this one and assume no prior knowledge of healthcare or health informatics. They are abstracted from the author's recently published book, Health Informatics on FHIR: How HL7's New API is Transforming Healthcare (Springer International Publishing: https://www.springer.com/us/book/9783319934136).


Assuntos
Sistemas de Apoio a Decisões Clínicas/tendências , Assistência à Saúde/tendências , Registros Eletrônicos de Saúde/tendências , Nível Sete de Saúde/tendências , Software/tendências , Humanos
9.
Neural Netw ; 118: 43-53, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31228723

RESUMO

A novel statistical fault detection method, called the global-and-local-structure-based neural network (GLSNN), is proposed for fault detection. GLSNN is a nonlinear data-driven process monitoring technique through preserving both global and local structures of normal process data. GLSNN is characterized by adaptively training a neural network which takes both the global variance information and the local geometrical structure into consideration. GLSNN is designed to extract the meaningful low-dimensional features from original high-dimensional process data. After nonlinear feature extraction, Hotelling T2 statistic and the squared prediction error (SPE) statistic are adopted for online fault detection. The merits of the proposed GLSNN method are demonstrated by both theoretical analysis and case studies on the Tennessee Eastman (TE) benchmark process. Extensive experimental results show the superiority of GLSNN in terms of missed detection rate (MDR) and false alarm rate (FAR). The source code of GLSNN can be found in https://github.com/htzhaoecust/glsnn.


Assuntos
Redes Neurais de Computação , Software , Análise de Componente Principal , Software/tendências
10.
PLoS Biol ; 17(6): e3000333, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31220077

RESUMO

Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the installability and archival stability of computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee the continuing functionality of newly published tools. We have estimated the archival stability of computational biology software tools by performing an empirical analysis of the internet presence for 36,702 omics software resources published from 2005 to 2017. We found that almost 28% of all resources are currently not accessible through uniform resource locators (URLs) published in the paper they first appeared in. Among the 98 software tools selected for our installability test, 51% were deemed "easy to install," and 28% of the tools failed to be installed at all because of problems in the implementation. Moreover, for papers introducing new software, we found that the number of citations significantly increased when authors provided an easy installation process. We propose for incorporation into journal policy several practical solutions for increasing the widespread installability and archival stability of published bioinformatics software.


Assuntos
Biologia Computacional/métodos , Disseminação de Informação/métodos , Armazenamento e Recuperação da Informação/métodos , Pesquisa Biomédica , Bases de Dados Factuais , Humanos , Internet , Software/tendências
11.
12.
Neuroinformatics ; 17(4): 611-628, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-30972529

RESUMO

NengoDL is a software framework designed to combine the strengths of neuromorphic modelling and deep learning. NengoDL allows users to construct biologically detailed neural models, intermix those models with deep learning elements (such as convolutional networks), and then efficiently simulate those models in an easy-to-use, unified framework. In addition, NengoDL allows users to apply deep learning training methods to optimize the parameters of biological neural models. In this paper we present basic usage examples, benchmarking, and details on the key implementation elements of NengoDL. More details can be found at https://www.nengo.ai/nengo-dl.


Assuntos
Aprendizado Profundo , Redes Neurais de Computação , Software , Algoritmos , Aprendizado Profundo/tendências , Software/tendências
13.
Nat Biotechnol ; 37(5): 561-566, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30936564

RESUMO

Benchmark small variant calls are required for developing, optimizing and assessing the performance of sequencing and bioinformatics methods. Here, as part of the Genome in a Bottle (GIAB) Consortium, we apply a reproducible, cloud-based pipeline to integrate multiple short- and linked-read sequencing datasets and provide benchmark calls for human genomes. We generate benchmark calls for one previously analyzed GIAB sample, as well as six genomes from the Personal Genome Project. These new genomes have broad, open consent, making this a 'first of its kind' resource that is available to the community for multiple downstream applications. We produce 17% more benchmark single nucleotide variations, 176% more indels and 12% larger benchmark regions than previously published GIAB benchmarks. We demonstrate that this benchmark reliably identifies errors in existing callsets and highlight challenges in interpreting performance metrics when using benchmarks that are not perfect or comprehensive. Finally, we identify strengths and weaknesses of callsets by stratifying performance according to variant type and genome context.


Assuntos
Benchmarking , Biologia Computacional/tendências , Genoma Humano/genética , Genômica/tendências , Variação Genética/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Mutação INDEL/genética , Polimorfismo de Nucleotídeo Único , Software/tendências
14.
Adv Physiol Educ ; 43(2): 103-109, 2019 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-30835146

RESUMO

The use of computers as a pedagogical resource is currently on the rise. In the case of immunology, students present difficulties in visualizing molecular phenomena. Thus the use of animations and simulations available on the internet might facilitate the learning of complex immunological concepts. In this context, it is important to map and assess the currently available resources that may be used for educational purposes. This study comprises the search and analysis of educational immunology software freely available on the internet, which can aid students and health professionals in effective learning and continuing education scenarios. A detailed search in English on the existence of free software was carried out on websites and scientific databases. The results clearly indicate a lack of freely available and scientifically validated immunology educational software, despite the existence of several software programs that could be used as auxiliary teaching tools.


Assuntos
Alergia e Imunologia/educação , Instrução por Computador/métodos , Internet , Software , Alergia e Imunologia/tendências , Instrução por Computador/tendências , Humanos , Internet/tendências , Aprendizagem , Aplicativos Móveis/tendências , Software/tendências
15.
PLoS One ; 14(2): e0212476, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30779769

RESUMO

Test oracles are commonly used in software testing to determine the correctness of the execution results of test cases. However, the testing of many software systems faces the test oracle problem: a test oracle may not always be available, or it may be available but too expensive to apply. One such software system is a system involving abundant business processes. This paper focuses on the testing of business-process-based software systems and proposes a metamorphic testing approach for event sequences, called MTES, to alleviate the oracle problem. We utilized event sequences to represent business processes and then applied the technique of metamorphic testing to test the system without using test oracles. To apply metamorphic testing, we studied the general rules for identifying metamorphic relations for business processes and further demonstrated specific metamorphic relations for individual case studies. Three case studies were conducted to evaluate the effectiveness of our approach. The experimental results show that our approach is feasible and effective in testing the applications with rich business processes. In addition, this paper summarizes the experimental findings and proposes guidelines for selecting good metamorphic relations for business processes.


Assuntos
Validação de Programas de Computador , Software/normas , Software/tendências
16.
BMC Geriatr ; 19(1): 40, 2019 02 13.
Artigo em Inglês | MEDLINE | ID: mdl-30760204

RESUMO

BACKGROUND: The aim of this trial is to evaluate the effect of SENATOR software on incident, adverse drug reactions (ADRs) in older, multimorbid, hospitalized patients. The SENATOR software produces a report designed to optimize older patients' current prescriptions by applying the published STOPP and START criteria, highlighting drug-drug and drug-disease interactions and providing non-pharmacological recommendations aimed at reducing the risk of incident delirium. METHODS: We will conduct a multinational, pragmatic, parallel arm Prospective Randomized Open-label, Blinded Endpoint (PROBE) controlled trial. Patients with acute illnesses are screened for recruitment within 48 h of arrival to hospital and enrolled if they meet the relevant entry criteria. Participants' medical history, current prescriptions, select laboratory tests, electrocardiogram, cognitive status and functional status are collected and entered into a dedicated trial database. Patients are individually randomized with equal allocation ratio. Randomization is stratified by site and medical versus surgical admission, and uses random block sizes. Patients randomized to either arm receive standard routine pharmaceutical clinical care as it exists in each site. Additionally, in the intervention arm an individualized SENATOR-generated medication advice report based on the participant's clinical and medication data is placed in their medical record and a senior medical staff member is requested to review it and adopt any of its recommendations that they judge appropriate. The trial's primary outcome is the proportion of patients experiencing at least one adjudicated probable or certain, non-trivial ADR, during the index hospitalization, assessed at 14 days post-randomization or at index hospital discharge if it occurs earlier. Potential ADRs are identified retrospectively by the site researchers who complete a Potential Endpoint Form (one per type of event) that is adjudicated by a blinded, expert committee. All occurrences of 12 pre-specified events, which represent the majority of ADRs, are reported to the committee along with other suspected ADRs. Participants are followed up 12 (+/- 4) weeks post-index hospital discharge to assess medication quality and healthcare utilization. This is the first clinical trial to examine the effectiveness of a software intervention on incident ADRs and associated healthcare costs during hospitalization in older people with multi-morbidity and polypharmacy. TRIAL REGISTRATION NUMBER: Clinicaltrials.gov NCT02097654 , 27 March 2014.


Assuntos
Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos/epidemiologia , Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos/prevenção & controle , Hospitalização , Lista de Medicamentos Potencialmente Inapropriados/normas , Software/normas , Idoso , Idoso de 80 Anos ou mais , Estudos de Coortes , Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos/diagnóstico , Feminino , Hospitalização/tendências , Humanos , Incidência , Masculino , Alta do Paciente/tendências , Polimedicação , Lista de Medicamentos Potencialmente Inapropriados/tendências , Estudos Prospectivos , Estudos Retrospectivos , Fatores de Risco , Software/tendências , Resultado do Tratamento
17.
Clin Neuropsychol ; 33(2): 271-286, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30614374

RESUMO

OBJECTIVE: Digital devices are now broadly accessible and have the capacity to measure aspects of human behavior with high precision and accuracy, in a standardized manner. The purpose of this article is to characterize opportunities and barriers for modern digital neuropsychology, particularly those that are unique to digital assessment. METHODS: We provide a critical overview of the state-of-the-art in digital neuropsychology, focusing on personal digital devices. RESULTS: We identify three major barriers associated with digital neuropsychology, which affect both the interpretation of test scores and test norms: (1) variability in the perceptual, motor and cognitive demands of the same test across digital device classes (e.g. personal computer, tablet and smartphone); (2) hardware and software variability between devices within the same class that affect stimulus presentation and measurement and (3) rapid changes over time in hardware, software and device ownership, which can lead to rapid obsolescence of particular tests and test norms. We offer specific recommendations to address these barriers and outline new opportunities to understand and measure neuropsychological functioning over time and in everyday environments. CONCLUSIONS: Digital neuropsychology provides new approaches for measuring and monitoring neuropsychological functioning, informed by an understanding of the limitations and potential of digital technology.


Assuntos
Neuropsicologia/tendências , Smartphone/tendências , Software/tendências , Terapia Assistida por Computador/tendências , Humanos , Testes Neuropsicológicos/normas , Neuropsicologia/normas , Smartphone/normas , Software/normas , Telemedicina , Terapia Assistida por Computador/normas
18.
Methods Mol Biol ; 1897: 17-29, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30539431

RESUMO

Biobanks support medical research by facilitating access to biospecimens. Biospecimens that are linked to clinical and molecular information are particularly useful for translational biomedical research. Tracking and managing the biospecimens and their associated data are therefore crucial tasks in the functioning of a biobank. Adequate computing hardware, efficient and comprehensive biobanking software, and cost-effective data storage are needed for proper management of biospecimens. As biobanks build up extensive stores of specimens and patient data, ethical considerations also inevitably arise. Herein, we describe some basic considerations for establishing a biobanking information technology infrastructure that a beginning biobanker needs. Finally, we also discuss trends and future needs in biobanking informatics.


Assuntos
Bancos de Espécimes Biológicos/tendências , Pesquisa Biomédica , Tecnologia da Informação/tendências , Software/tendências , Computadores/tendências , Humanos
19.
Brief Bioinform ; 20(4): 1329-1336, 2019 07 19.
Artigo em Inglês | MEDLINE | ID: mdl-29351590

RESUMO

Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that 'ecosystem' of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and for informing initiatives aimed at its funding, long-term maintenance and improvement. In particular, the long-term maintenance of these tools is compromised because of their specific development model. Hundreds of published studies become irreproducible de facto, as the software tools used to conduct them become unavailable. In this study, we present a large-scale survey of >5400 publications describing Web servers within the two main bibliographic resources for disseminating new software developments in molecular biology. For all these servers, we studied their citation patterns, the subjects they address, their citation networks and the temporal evolution of these factors. We also analysed how these factors affect the availability of these servers (whether they are alive). Our results show that this ecosystem of tools is highly interconnected and adapts to the 'trendy' subjects in every moment. The servers present characteristic temporal patterns of citation/usage, and there is a worrying rate of server 'death', which is influenced by factors such as the server popularity and the institutions that hosts it. These results can inform initiatives aimed at the long-term maintenance of these resources.


Assuntos
Biologia Molecular/estatística & dados numéricos , Software , Biologia Computacional/métodos , Biologia Computacional/tendências , Internet , Biologia Molecular/tendências , Publicações Periódicas como Assunto/estatística & dados numéricos , Software/tendências
20.
Brief Bioinform ; 20(4): 1560-1567, 2019 07 19.
Artigo em Inglês | MEDLINE | ID: mdl-29028989

RESUMO

PHAST (PHAge Search Tool) and its successor PHASTER (PHAge Search Tool - Enhanced Release) have become two of the most widely used web servers for identifying putative prophages in bacterial genomes. Here we review the main capabilities of these web resources, provide some practical guidance regarding their use and discuss possible future improvements. PHAST, which was first described in 2011, made its debut just as whole bacterial genome sequencing and was becoming inexpensive and relatively routine. PHAST quickly gained popularity among bacterial genome researchers because of its web accessibility, its ease of use along with its enhanced accuracy and rapid processing times. PHASTER, which appeared in 2016, provided a number of much-needed enhancements to the PHAST server, including greater processing speed (to cope with very large submission volumes), increased database sizes, a more modern user interface, improved graphical displays and support for metagenomic submissions. Continuing developments in the field, along with increased interest in automated phage and prophage finding, have already led to several improvements to the PHASTER server and will soon lead to the development of a successor to PHASTER (to be called PHASTEST).


Assuntos
Genoma Bacteriano , Prófagos/genética , Software , Biologia Computacional , Mineração de Dados/tendências , Bases de Dados Genéticas , Internet , Metagenômica , Ferramenta de Busca/tendências , Software/tendências , Interface Usuário-Computador
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