Abstract
Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging ...integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/.
Graphical Abstract
Graphical Abstract
Overview of the large array of entities and systems that can be visualized and be manipulated with by the Mol* Viewer.
This paper considers the stationary distribution of the age of information (AoI) in information update systems. We first derive a general formula for the stationary distribution of the AoI, which ...holds for a wide class of information update systems. The formula indicates that the stationary distribution of the AoI is given in terms of the stationary distributions of the system delay and the peak AoI. To demonstrate its applicability and usefulness, we analyze the AoI in single-server queues with four different service disciplines: first-come first-served (FCFS), preemptive last-come first-served (LCFS), and two variants of non-preemptive LCFS service disciplines. For the FCFS and the preemptive LCFS service disciplines, the GI/GI/1, M/GI/1, and GI/M/1 queues are considered, and for the non-preemptive LCFS service disciplines, the M/GI/1 and GI/M/1 queues are considered. With these results, we further show comparison results for the mean AoI's in the M/GI/1 and GI/M/1 queues under those service disciplines.
In recent years, Internet of Things (IoT) as an essential infrastructure for industrial development, environmental protection and human life enhancement has attracted researchers' attention. ...Currently, there are four hot research topics in IoT fields, including sensor design, communication scheme, secure transmission, and data mining. The LoRaWAN, an unlicensed band based long range wide area network specification, is very suitable for the activities or operations in an IoT environment due to its low power and long range communication. In the LoRaWAN, star-of-stars topology, asynchronous communication, and three communication modes are used to reduce its power consumption. In order to enhance the security of network communication, the LoRaWAN adopts the 128-bit Advanced Encryption Standard (AES-128) and utilizes two session keys: network session key and application session key, for encrypting/decrypting data between end devices and network/application servers. However, according to the LoRaWAN Backend Interfaces 1.0 Specification announced by LoRa Alliance in 2017, the application layer communication securities between two arbitrary servers (including network servers, join server, and application servers) are out of the specification's scope. That is to say that the important data transmitted from one server to another may be attacked, falsified, or stolen easily. In this paper, a session key generation method is proposed to generate session keys with which two servers can securely communicate with each other, especially enhancing the application layer communication securities undefined in the LoRaWAN Specification. By integrating elliptic curve cryptography and AES-128, the session keys for different pairs of servers are created. The security discussion shows that the proposed method provides the features of mutual authentication, confidentiality and message integrity. Besides, it can also help to resist replay and eavesdropping attacks.
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.
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.
Power Management of Server Farms Pieroni, Alessandra; Iazeolla, Giuseppe
Applied Mechanics and Materials,
01/2014, Letnik:
492, Številka:
Power and Energy Systems III
Journal Article
Recenzirano
Odprti dostop
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
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 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/.
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 digitization of user services has increased, in line with the need for VPS and cloud computing services, which are rampant among application and platform developers. Quite a few companies that ...create applications or application users have servers to handle user needs. Testing is carried out using the ICMP Protocol to get real-time results and can be measured. From Scenario 1, carrying out 20 test requests, we get a packet loss of 5% with RTT Avarage of 195,838ms and Mdev 4,103ms. If you apply DNS failover in scenario 2, the client will likely access the web a little slower, as evidenced by the packet loss being 25% greater in value. Compared to scenario 1, having a high standard deviation (Mdev) of round-trip times is not desirable. This variation is also known as jitter. Increased jitter can cause a bad user experience, especially in real-time audio and video streaming applications. However, this is still understandable because it only has a 1-5 second effect on the service. Next, in scenario 3, we can see that private and public servers have relatively high gab with 0% packet loss, which has a small Mdev value of 0.309ms. Therefore, the DNS failover method is a solution for network administrators who have problems related to server migration between public servers and private servers so that services can run even if a server is maintaining or downlinking.
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