Abstract:
:Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process.
journal_name
PeerJjournal_title
PeerJauthors
Mondelli ML,Magalhães T,Loss G,Wilde M,Foster I,Mattoso M,Katz D,Barbosa H,de Vasconcelos ATR,Ocaña K,Gadelha LMR Jrdoi
10.7717/peerj.5551subject
Has Abstractpub_date
2018-08-29 00:00:00pages
e5551issn
2167-8359pii
5551journal_volume
6pub_type
杂志文章相关文献
PeerJ文献大全abstract::Web-spinning spiders that inhabit stream channels are considered specialists of aquatic ecosystems and are major consumers of emerging aquatic insects, while other spider taxa are more commonly found in riparian forests and as a result may consume more terrestrial insects. To determine if there was a difference in spi...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.1324
更新日期:2015-10-15 00:00:00
abstract::Prior work in our lab has shown that an expanding image on a computer screen elicits a hiding response in the Caribbean terrestrial hermit crab (Coenobita clypeatus). We conducted two experiments to identify what properties of the expanding stimulus contribute to its effectiveness as a visual threat. First we found th...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.4058
更新日期:2017-11-30 00:00:00
abstract::Equine Herpesviruses (EHV) are common and often latent pathogens of equids which can cause fatalities when transmitted to non-equids. Stress and elevated glucocorticoids have been associated with EHV reactivation in domestic horses, but little is known about the correlation between stress and viral reactivation in wil...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.5422
更新日期:2018-08-22 00:00:00
abstract:Background:The coral genus Acropora contains more than 150 species with very high morphological diversity. This high diversity may have been caused by repeated hybridization via mass spawning. However, we have little information whether hybrids are formed in these corals. Identifying morphological differences between h...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6429
更新日期:2019-02-19 00:00:00
abstract::Limestone karsts of Southeast Asia can harbor high levels of endemism, but are highly fragmented, increasingly threatened, and their biodiversity is often poorly studied. This is true of the Padawan Limestone Area of Sarawak, Malaysia, home to the endemic Artocarpus annulatus, the closest known wild relative of two im...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.9897
更新日期:2020-09-21 00:00:00
abstract:Background:Extensive genome rearrangements, known as chromothripsis, have been recently identified in several cancer types. Chromothripsis leads to complex structural variants (cSVs) causing aberrant gene expression and the formation of de novo fusion genes, which can trigger cancer development, or worsen its clinical ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.7071
更新日期:2019-06-12 00:00:00
abstract::Herein, we identified the tomato SlMYB102 gene as a MYB family transcription factor of the R2R3-MYB subfamily. We additionally determined that the SlMYB102 promoter region contains photoresponsive, abiotic stress-responsive, and hormone-responsive regulatory elements, and we detected higher SlMYB102 expression in the ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.10059
更新日期:2020-10-07 00:00:00
abstract::The number of people suffering from eye fatigue induced by visual display terminal (VDT) viewing is expected to increase in the modern world. Eye dysfunction is suggested to induce a decrease in cognitive function, at least in the long term. Furthermore, considering other previous findings, it may be reasonable to thi...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.7978
更新日期:2019-10-29 00:00:00
abstract:Background:Cyclin A overexpression is found in a variety of human tumors and correlates with unfavorable outcome. We analyzed immunohistochemical expression of cyclin A in Wilms tumor (WT) in relation to clinicopathological characteristics, preoperative chemotherapy (PrOpChTh), and overall survival (OS). Methods:This ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6212
更新日期:2019-01-11 00:00:00
abstract:Background:The Aegean Sea coast of Turkey hosts one of the most important nesting grounds for loggerhead sea turtles (Caretta caretta) in the Mediterranean Sea. Previous studies have revealed that the sea turtle carapace provides favourable conditions for various epibiontic organisms. Epibionts occurring on the carapac...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.9406
更新日期:2020-07-17 00:00:00
abstract:Background:A virus-like particle (VLP) is an excellent tool for a compound delivery system due to its simple composition, symmetrical structure and self-assembly. Its surface modification both chemically and genetically is established, leading to the target-specific delivery and improved encapsulation efficiency. Howev...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6079
更新日期:2018-12-18 00:00:00
abstract::Koalas (Phascolarctos cinereus) are highly specialized herbivorous marsupials that feed almost exclusively on Eucalyptus leaves, which are known to contain varying concentrations of many different toxic chemical compounds. The literature suggests that Lonepinella koalarum, a bacterium in the Pasteurellaceae family, ca...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.10177
更新日期:2020-10-20 00:00:00
abstract:Background:Immunoglobulin superfamily member 10 (IGSF10) is a member of the immunoglobulin superfamily that is expressed at high levels in both the gallbladder and ovary. Currently, the role and possible mechanism of IGSF10 in breast cancer remain unclear. Method:By applying real-time quantitative polymerase chain rea...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.10128
更新日期:2020-10-21 00:00:00
abstract::Background. "Health is wealth" is a time tested adage. Health becomes more relevant when it comes to professionals whose job is to provide people with services that maintain an optimum state of mental, physical and social well-being. Healthcare professionals (HCP) differ from general population in regards to the natur...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.1250
更新日期:2015-09-17 00:00:00
abstract::Metabolic dysfunction in skeletal muscle is a major contributor to the development of type 2 diabetes. Endurance exercise training has long been established as an effective means to directly restore skeletal muscle glucose and lipid uptake and metabolism. However, in addition to the direct effects of skeletal muscle o...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.605
更新日期:2014-09-30 00:00:00
abstract::The octopus fauna from the southern Caribbean is an understudied field. However, recent taxonomic work in the Colombian Caribbean has led to the discovery of several new species in the family Octopodidae. To provide molecular evidence for recent descriptions in the area (i.e., Octopus taganga, O. tayrona and Macrotrit...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.7300
更新日期:2019-07-29 00:00:00
abstract::The study of vertebrate ontogenies has the potential to inform us of shared developmental patterns and processes among organisms. However, fossilised ontogenies of early vertebrates are extremely rare during the Palaeozoic Era. A growth series of the Late Devonian "acanthodian" Triazeugacanthus affinis, from the Migua...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.3969
更新日期:2017-10-27 00:00:00
abstract::Protein aggregation into highly-structured amyloid fibrils is linked to several neurodegenerative diseases. Such fibril formation by superoxide dismutase I (SOD1) is considered to be related to amyotrophic lateral sclerosis, a late-onset and fatal disorder. Despite much effort and the discovery of numerous anti-amyloi...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.9719
更新日期:2020-08-14 00:00:00
abstract::Ethylene response factors (ERFs) are plant-specific transcription factors (TFs) that play important roles in plant growth and stress defense and have received a great amount of attention in recent years. In this study, seven ERF genes related to abiotic stress tolerance and response were identified in plants of the Po...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.10206
更新日期:2020-10-20 00:00:00
abstract::Ephemeral rivers act as linear oases in drylands providing key resources to people and wildlife. However, not much is known about these rivers' sensitivities to human activities. We investigated the landscape-level determinants of riparian tree dieback along the Swakop River, a dammed ephemeral river in Namibia, focus...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.2622
更新日期:2016-10-27 00:00:00
abstract:Background:Bioactive peptides can prevent damage associated with oxidative stress in humans when consumed regularly. Recently, peptides have attracted immense interest because of their beneficial functional properties, safety and little or no side effects when used at high concentration. Most antioxidant peptides are s...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.5337
更新日期:2018-07-27 00:00:00
abstract::A period of starvation is regarded as a sound practice in aquaculture prior to handling, transportation and harvest, to minimise impacts on welfare and ensure proper hygiene after harvest. However, documentation of welfare issues such as stress following starvation and handling in adult Atlantic salmon are lacking. Th...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.3273
更新日期:2017-04-27 00:00:00
abstract:Background:Silkworm pupae is the main by-product of the sericulture industry with an interesting nutritional profile, especially in terms of proteins. In consideration of its possible use as a food or food ingredient in Western countries, a comparative proteomic experiment has been performed to investigate the differen...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6723
更新日期:2019-06-12 00:00:00
abstract::A strong argument can be made that the European Union has the most rigorous regulatory system for pesticides in the world, and that modern pesticide use poses fewer environmental threats than older regimes. Nevertheless, the impacts of pesticides on bees and other non-target organisms are much debated in Europe as els...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.5255
更新日期:2018-07-19 00:00:00
abstract:Introduction:Knowledge Translation (KT) is expected to be a critical learning outcome of a Continuing Professional Development (CPD) program. It continues to serve as an area of interest among educators and healthcare providers due to its importance to evidence-based practice. This study endeavored to develop a valid a...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.5323
更新日期:2018-08-13 00:00:00
abstract::We explored the genetic background of social interactions in two breeding metapopulations of the pied flycatcher (Ficedula hypoleuca) in Western Siberia. In 2005, we sampled blood from birds breeding in study areas located in the city of Tomsk and in a natural forest 13 km southward of Tomsk (Western Siberia, Russia)....
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6059
更新日期:2018-12-06 00:00:00
abstract::It has been reported that fermented products (FPs) prepared from sweet potato-shochu distillery by-product suppressed weight gain and decreased serum cholesterol levels in mice under normal dietary conditions. Furthermore, from the information gained from the above data regarding health benefits of the FPs, the aim of...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.7671
更新日期:2019-09-12 00:00:00
abstract::The spatial-temporal evolution of land use and land cover (LULC) and its multi-scale impact on the water environment is becoming highly significant in the LULC research field. The current research results show that the more significant scale impact on LULC and water quality in the whole basin and the riparian buffer s...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.7283
更新日期:2019-07-15 00:00:00
abstract::The emergence of herbicide-resistant weeds is a major threat facing modern agriculture. Over 470 weedy-plant populations have developed resistance to herbicides. Traditional evolutionary mechanisms are not always sufficient to explain the rapidity with which certain weed populations adapt in response to herbicide expo...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.3560
更新日期:2017-07-20 00:00:00
abstract::Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its a...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.1698
更新日期:2016-03-17 00:00:00