Recognizing the widespread existence of intrinsically disordered regions in proteins spurred the development of computational techniques for their detection. All existing techniques can be classified ...into methods relying on single-sequence information and those relying on evolutionary sequence profiles generated from multiple-sequence alignments. The methods based on sequence profiles are, in general, more accurate because the presence or absence of conserved amino acid residues in a protein sequence provides important information on the structural and functional roles of the residues. However, the wide applicability of profile-based techniques is limited by time-consuming calculation of sequence profiles. Here we demonstrate that the performance gap between profile-based techniques and single-sequence methods can be reduced by using an ensemble of deep recurrent and convolutional neural networks that allow whole-sequence learning. In particular, the single-sequence method (called SPOT-Disorder-Single) is more accurate than SPOT-Disorder (a profile-based method) for proteins with few homologous sequences and comparable for proteins in predicting long-disordered regions. The method performance is robust across four independent test sets with different amounts of short- and long-disordered regions. SPOT-Disorder-Single is available as a Web server and as a standalone program at http://sparks-lab.org/jack/server/SPOT-Disorder-Single.
Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public ...Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO2 emissions generated by each Galaxy job.
Abstract
Here we present an update to MutationTaster, our DNA variant effect prediction tool. The new version uses a different prediction model and attains higher accuracy than its predecessor, ...especially for rare benign variants. In addition, we have integrated many sources of data that only became available after the last release (such as gnomAD and ExAC pLI scores) and changed the splice site prediction model. To more easily assess the relevance of detected known disease mutations to the clinical phenotype of the patient, MutationTaster now provides information on the diseases they cause. Further changes represent a major overhaul of the interfaces to increase user-friendliness whilst many changes under the hood have been designed to accelerate the processing of uploaded VCF files. We also offer an API for the rapid automated query of smaller numbers of variants from within other software. MutationTaster2021 integrates our disease mutation search engine, MutationDistiller, to prioritise variants from VCF files using the patient's clinical phenotype. The novel version is available at https://www.genecascade.org/MutationTaster2021/. This website is free and open to all users and there is no login requirement.
Graphical Abstract
Graphical Abstract
Identification of disease-causing variants with MutationTaster2021.
Abstract
The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI’s data resources and core bioinformatics analytical tools. EBI Search ...(https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.
Graphical Abstract
Graphical Abstract
Overview of the tools and data resources provided by EBI Search and Job Dispatcher services accessible via their webpage and programmatic interfaces.
Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R ...package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/.
At present, most of the university's conditions and teaching equipment have greater room for improvement, especially the management and teaching mechanism of computer laboratory need further ...improvement and breakthrough. Due to the rapid update speed of computer information technology related equipment, the update speed of university related equipment can not meet the needs of experimental education. Based on this, this paper first analyzes the application and development status of server virtualization technology, then studies the specific application of server virtualization technology in computer laboratory, and finally gives the application design strategy of server virtualization technology in computer laboratory.
IslandViewer (http://www.pathogenomics.sfu.ca/islandviewer/) is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal ...origin) in bacterial and archaeal genomes. GIs disproportionately encode factors that enhance the adaptability and competitiveness of the microbe within a niche, including virulence factors and other medically or environmentally important adaptations. We report here the release of IslandViewer 4, with novel features to accommodate the needs of larger-scale microbial genomics analysis, while expanding GI predictions and improving its flexible visualization interface. A user management web interface as well as an HTTP API for batch analyses are now provided with a secured authentication to facilitate the submission of larger numbers of genomes and the retrieval of results. In addition, IslandViewer's integrated GI predictions from multiple methods have been improved and expanded by integrating the precise Islander method for pre-computed genomes, as well as an updated IslandPath-DIMOB for both pre-computed and user-supplied custom genome analysis. Finally, pre-computed predictions including virulence factors and antimicrobial resistance are now available for 6193 complete bacterial and archaeal strains publicly available in RefSeq. IslandViewer 4 provides key enhancements to facilitate the analysis of GIs and better understand their role in the evolution of successful environmental microbes and pathogens.
With the development of the Internet, the company network architecture is also undergoing profound changes, and the boundaries between the original internal network and external network are becoming ...increasingly blurred with the emergence of cloud services. More and more company businesses are deployed on the cloud server, which increases the risk of data exchange between the cloud server and the intranet. An implementation method of zero-trust architecture is proposed in this paper to apply to this scenario. The method can ensure safe and reliable data exchange when the external application server accesses the internal network, effectively protect network communication and business access while not affecting the original internal network protection measures, and make the company network safer and controllable.
In recent years, with the development of our country, higher requirements are put forward for the power supply. Electric power enterprises want to improve their comprehensive strength, but also in ...order to adapt to the development of the times, it is necessary to carry out information construction. However, the traditional physical server has many shortcomings and shortcomings in the enterprise information construction. Therefore, this paper puts forward the application research of server virtualization technology in power information construction. This paper compares and analyzes the resources needed by physical server and virtual server, and points out that virtual server have obvious advantages of high information security, low energy consumption, high utilization rate and low maintenance cost. In order to make the virtual server successfully applied in the information construction of electric power enterprises, this paper puts forward the operation guidance standard of server virtualization implementation process, and emphasizes that the integration of server resources should be done well in the process of information construction. In order to ensure the security of server virtualization process, this paper lists the detailed security measures of server virtualization. According to the operation of the above steps, the power enterprise can complete the information construction work better through the virtualization of the server. It is considered that the use of virtual server in enterprise information construction is a big trend, which conforms to the development of the times and improves the utilization rate of resources.
Computing systems have been focused on performance improvements, driven by the demand of user applications in past few decades, particularly from 1990 to 2010. However, due to their ever-increasing ...energy demand which causes large energy bills and CO2 emissions, over the past six years the focus has shifted towards energy-performance aware. The average energy consumption of servers is increasing continuously; and several researchers suggest, if this trend continues further, the cost of energy consumed by a server during its lifetime will exceed the hardware costs. The energy consumption problem is even greater for large-scale infrastructures, such as clusters, grids and clouds, which consist of several thousand heterogeneous servers. Efforts are continuously made to minimize the energy consumption of these systems, but the interest of people in computational services and popularity of smart devices make it a difficult task. In this paper, we discuss the energy consumption of ICT equipment, and present a taxonomy of energy and performance efficient techniques for large computing systems covering clusters, grids and clouds (datacenters). We discuss both energy and performance efficiency, which makes this survey different from those already published in the literature. Key research papers are surveyed and mapped onto taxonomies to characterise and identify outstanding and key issues for further research. We discuss several state-of-the-art resource management techniques, reported in the literature, that claim significant improvement in the energy efficiency and performance of ICT equipment and large-scale computing systems such as datacenters, and identify a few open challenges.
•In clouds, energy aware scheduling techniques lead to significantly greater economies than consolidation techniques•In private clusters, switching off idle resources are more energy efficient than DPM methods, but, in clouds, performance is adversely affected due to fluctuated demand•In heterogeneous clouds, similar applications perform differently on similar CPU models, and, variations in runtime mean variations in cost and energy use•In clouds, due to resource heterogeneity, VM migrations affect energy use and the workload performance in terms of runtime (hence users cost)
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