Abstract
miRNet is an easy-to-use, web-based platform designed to help elucidate microRNA (miRNA) functions by integrating users' data with existing knowledge via network-based visual analytics. ...Since its first release in 2016, miRNet has been accessed by >20 000 researchers worldwide, with ∼100 users on a daily basis. While version 1.0 was focused primarily on miRNA-target gene interactions, it has become clear that in order to obtain a global view of miRNA functions, it is necessary to bring other important players into the context during analysis. Driven by this concept, in miRNet version 2.0, we have (i) added support for transcription factors (TFs) and single nucleotide polymorphisms (SNPs) that affect miRNAs, miRNA-binding sites or target genes, whilst also greatly increased (>5-fold) the underlying knowledgebases of miRNAs, ncRNAs and disease associations; (ii) implemented new functions to allow creation and visual exploration of multipartite networks, with enhanced support for in situ functional analysis and (iii) revamped the web interface, optimized the workflow, and introduced microservices and web application programming interface (API) to sustain high-performance, real-time data analysis. The underlying R package is also released in tandem with version 2.0 to allow more flexible data analysis for R programmers. The miRNet 2.0 website is freely available at https://www.mirnet.ca.
Power Management of Server Farms Pieroni, Alessandra; Iazeolla, Giuseppe
Applied Mechanics and Materials,
01/2014, Volume:
492, Issue:
Power and Energy Systems III
Journal Article
Peer reviewed
Open access
The power management of server farms (Sf) is becoming a relevant problem in economical terms. Server farms totalize millions of servers all over the world that need to be electrically powered. ...Research is thus expected to investigate into methods to reduce Sf power consumption. However, saving power may turn into waste of performance (high response_times), in other words, into waste of Sf Quality of Service (QoS). By use of a Sfmodel, this paper investigates Sf power management strategies that look at compromises between power-saving and QoS. Various optimizing Sf power management policies are studied combined with the effects of job queueing disciplines. The (policy, discipline) pairs, or strategies, that optimize the Sf power consumption (minimum absorbed Watts), the Sf performance (minimum response_time), and the Sf performance-per-Watt (minimum response_time-per-Watt) are identified.By use of the model, the work the server-manager has to do to direct hisSf is greatly simplified, since the universe of all possible (strategies he needs to choose from is drastically reduced to a very small set of most significant strategies.
Abstract
The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss) creates, maintains and disseminates a portfolio of reliable and state-of-the-art bioinformatics services and resources for ...the storage, analysis and interpretation of biological data. Through Expasy (https://www.expasy.org), the Swiss Bioinformatics Resource Portal, the scientific community worldwide, freely accesses more than 160 SIB resources supporting a wide range of life science and biomedical research areas. In 2020, Expasy was redesigned through a user-centric approach, known as User-Centred Design (UCD), whose aim is to create user interfaces that are easy-to-use, efficient and targeting the intended community. This approach, widely used in other fields such as marketing, e-commerce, and design of mobile applications, is still scarcely explored in bioinformatics. In total, around 50 people were actively involved, including internal stakeholders and end-users. In addition to an optimised interface that meets users' needs and expectations, the new version of Expasy provides an up-to-date and accurate description of high-quality resources based on a standardised ontology, allowing to connect functionally-related resources.
Graphical Abstract
Graphical Abstract
The illustration of Expasy's redesign through a user-centric approach: all the elements that contributed to the process (icons) and the main strengths (stars) of the new implementation.
Abstract
CRISPOR.org is a web tool for genome editing experiments with the CRISPR-Cas9 system. It finds guide RNAs in an input sequence and ranks them according to different scores that evaluate ...potential off-targets in the genome of interest and predict on-target activity. The list of genomes is continuously expanded, with more 150 genomes added in the last two years. CRISPOR tries to provide a comprehensive solution from selection, cloning and expression of guide RNA as well as providing primers needed for testing guide activity and potential off-targets. Recent developments include batch design for genome-wide CRISPR and saturation screens, creating custom oligonucleotides for guide cloning and the design of next generation sequencing primers to test for off-target mutations. CRISPOR is available from http://crispor.org, including the full source code of the website and a stand-alone, command-line version.
The combination of 5G and edge computing has been envisioned as a promising paradigm to empower pervasive and intensive computing for the Internet-of-Things (IoT). High deployment cost is one of the ...major obstacles for realizing 5G edge computing. Most existing works tried to deploy the minimum number of edge servers to cover a target area by avoiding coverage overlaps. However, following this framework, the resource requirement per server will be drastically increased by the peak requirement during workload variations. Even worse, most resources will be left under-utilized for most of the time. To address this problem, we propose CoopEdge, a cost-effective server deployment scheme for cooperative multi-access edge computing. The key idea of CoopEdge is to allow deploying overlapped servers to handle variable requested workloads in a cooperative manner. In this way, the peak demands can be dispersed into multiple servers, and the resource requirement for each server can be greatly reduced. We propose a Two-step Incremental Deployment (TID) algorithm to jointly decide the server deployment and cooperation policies. For the scenarios involving multiple network operators that are unwilling to cooperate with each other, we further extend the TID algorithm to a distributed TID algorithm based on the game theory. Extensive evaluation experiments are conducted based on the measurement results of seven real-world edge applications. The results show that compared with the state-of-the-art work, CoopEdge significantly reduces the deployment cost by 38.7% and improves resource utilization by 36.2%, and the proposed distributed algorithm can achieve a comparable deployment cost with CoopEdge, especially for small-coverage servers.
The blockage of the hERG K+ channels is closely associated with lethal cardiac arrhythmia. The notorious ligand promiscuity of this channel earmarked hERG as one of the most important antitargets to ...be considered in early stages of drug development process. Herein we report on the development of an innovative and freely accessible web server for early identification of putative hERG blockers and non‐blockers in chemical libraries. We have collected the largest publicly available curated hERG dataset of 5,984 compounds. We succeed in developing robust and externally predictive binary (CCR≈0.8) and multiclass models (accuracy≈0.7). These models are available as a web‐service freely available for public at http://labmol.farmacia.ufg.br/predherg/. Three following outcomes are available for the users: prediction by binary model, prediction by multi‐class model, and the probability maps of atomic contribution. The Pred‐hERG will be continuously updated and upgraded as new information became available.
The agriGO platform, which has been serving the scientific community for >10 years, specifically focuses on gene ontology (GO) enrichment analyses of plant and agricultural species. We continuously ...maintain and update the databases and accommodate the various requests of our global users. Here, we present our updated agriGO that has a largely expanded number of supporting species (394) and datatypes (865). In addition, a larger number of species have been classified into groups covering crops, vegetables, fish, birds and insects closely related to the agricultural community. We further improved the computational efficiency, including the batch analysis and P-value distribution (PVD), and the user-friendliness of the web pages. More visualization features were added to the platform, including SEACOMPARE (cross comparison of singular enrichment analysis), direct acyclic graph (DAG) and Scatter Plots, which can be merged by choosing any significant GO term. The updated platform agriGO v2.0 is now publicly accessible at http://systemsbiology.cau.edu.cn/agriGOv2/.
Abstract
GeneMANIA (http://genemania.org) is a flexible user-friendly web site for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given ...a query gene list, GeneMANIA finds functionally similar genes using a wealth of genomics and proteomics data. In this mode, it weights each functional genomic dataset according to its predictive value for the query. Another use of GeneMANIA is gene function prediction. Given a single query gene, GeneMANIA finds genes likely to share function with it based on their interactions with it. Enriched Gene Ontology categories among this set can point to the function of the gene. Nine organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Escherichia coli, Homo sapiens, Mus musculus, Rattus norvegicus and Saccharomyces cerevisiae). Hundreds of data sets and hundreds of millions of interactions have been collected from GEO, BioGRID, IRefIndex and I2D, as well as organism-specific functional genomics data sets. Users can customize their search by selecting specific data sets to query and by uploading their own data sets to analyze. We have recently updated the user interface to GeneMANIA to make it more intuitive and make more efficient use of visual space. GeneMANIA can now be used effectively on a variety of devices.
Abstract
This article discusses some use of cloud technology in mathematical calculations using Remote Desktop Ulteo OVD. To use such technologies, it is enough to have access to the Internet through ...a suitable browser to access an open virtual desktop on a powerful remote computer and then use the resources of the remote computer (server) to solve their problems in processing various information resources – solving mathematical problems, working out texts, translating from one language to another, help on the interpretation of different terms, their origin and more. You can organize access to Ulteo OVD from two servers (Application Server (Windows 2008R2) and Session Manager Server (Linux Ubuntu)), using the Proxmox web-based virtual environment. Gran1, Gran2D, Gran3D software can be installed on the application server. The article also examines in detail some examples of the use of the pedagogical software for educational purposes Gran1. In particular, the calculation of the approximate value of the double integral; graphical two-dimensional problem solving, the so-called linear programming problems; two-dimensional problems, including convex programming – finding the smallest value of a convex downward function (or the highest convexity of a function) on a convex set of inequalities (including linear ones). However, the use in the educational process of any technology, including modern information and communication, as well as the content of training, should be pedagogically balanced, which will allow to avoid any negative effects on the formation of personality of a future member of society, his mental and physical development.
Antibodies have become an indispensable tool for many biotechnological and clinical applications. They bind their molecular target (antigen) by recognizing a portion of its structure (epitope) in a ...highly specific manner. The ability to predict epitopes from antigen sequences alone is a complex task. Despite substantial effort, limited advancement has been achieved over the last decade in the accuracy of epitope prediction methods, especially for those that rely on the sequence of the antigen only. Here, we present BepiPred-2.0 (http://www.cbs.dtu.dk/services/BepiPred/), a web server for predicting B-cell epitopes from antigen sequences. BepiPred-2.0 is based on a random forest algorithm trained on epitopes annotated from antibody-antigen protein structures. This new method was found to outperform other available tools for sequence-based epitope prediction both on epitope data derived from solved 3D structures, and on a large collection of linear epitopes downloaded from the IEDB database. The method displays results in a user-friendly and informative way, both for computer-savvy and non-expert users. We believe that BepiPred-2.0 will be a valuable tool for the bioinformatics and immunology community.
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