scholarly journals MMseqs2 desktop and local web server app for fast, interactive sequence searches

2018 ◽  
Author(s):  
Milot Mirdita ◽  
Martin Steinegger ◽  
Johannes Söding
Keyword(s):  
Protein Sequence ◽  
Response Times ◽  
Source Code ◽  
Web Server ◽  
Link Type ◽  
Server Application ◽  
The Web

SummaryThe MMseqs2 desktop and web server app facilitates interactive sequence searches through custom protein sequence and profile databases on personal workstations. By eliminating MMseqs2’s runtime overhead, we reduced response times to a few seconds at sensitivities close to BLAST.Availability and implementationThe app is easy to install for non-experts. Source code, prebuilt desktop app packages for Windows, macOS and Linux, Docker images for the web server application, and a demo web server are available at https://[email protected] or [email protected]

scholarly journals MMseqs2 desktop and local web server app for fast, interactive sequence searches

2019 ◽  
Vol 35 (16) ◽  
pp. 2856-2858 ◽  
Author(s):  
Milot Mirdita ◽  
Martin Steinegger ◽  
Johannes Söding
Keyword(s):  
Protein Sequence ◽  
Response Times ◽  
Web Server ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Server Application ◽  
The Web

Abstract Summary The MMseqs2 desktop and web server app facilitates interactive sequence searches through custom protein sequence and profile databases on personal workstations. By eliminating MMseqs2’s runtime overhead, we reduced response times to a few seconds at sensitivities close to BLAST. Availability and implementation The app is easy to install for non-experts. GPLv3-licensed code, pre-built desktop app packages for Windows, MacOS and Linux, Docker images for the web server application and a demo web server are available at https://search.mmseqs.com. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Matchathon: A guide to student-faculty connections in PhD programs

2020 ◽  
Author(s):  
Haley Amemiya ◽  
Zena Lapp ◽  
Cathy Smith ◽  
Margaret Durdan ◽  
Michelle DiMondo ◽  
...  
Keyword(s):  
Open Source ◽  
Source Code ◽  
Faculty Members ◽  
Retention Rates ◽  
Link Type ◽  
Shiny App ◽  
R Shiny ◽  
Web App ◽  
Phd Programs ◽  
The Web

AbstractRelevant and impactful mentors are essential to a graduate student’s career. Finding mentors can be challenging in umbrella programs with hundreds of faculty members. To foster connections between potential mentors and students with similar research interests, we created a Matchathon event, which has successfully enabled students to find mentors. We developed an easy-to-use R Shiny app (https://github.com/UM-OGPS/matchathon/) to facilitate matching and organizing the event that can be used at any institution. It is our hope that this resource will improve the environment and retention rates for students in the academy.The open source app is publicly available on the web (app: https://UM-OGPS.shinyapps.io/matchathon/; source code: https://github.com/UM-OGPS/matchathon/).

scholarly journals A Python-WSGI and PHP-Apache Web Server Performance Analysis by Search Page Generator (SPG)

2021 ◽  
Vol 5 (1) ◽  
pp. 132-138
Author(s):  
Hataw Jalal Mohammed ◽  
Kamaran Hama Ali Faraj
Keyword(s):  
Computer Architecture ◽  
Source Code ◽  
Web Server ◽  
The Other ◽  
Web Database ◽  
Web Servers ◽  
Web Technologies ◽  
Server Side ◽  
The One ◽  
The Web

The web servers (WSGI-Python) and (PHP-Apache) are in middleware tier architecture. Middleware architecture is between frontend tier and backend tier, otherwise it’s a connection between frontend tier and backend tier for three tier architecture. The ELearning systems are designed by two different dynamic web technologies. First is by Python-WSGI and the second is by Personal Home Page (PHP-Apache). The two websites were designed with different open source and cross platform web technologies programming language namely; Python and PHP in the same structure and weight will evaluate perform over two different operating systems (OSs): 1) Windows-16 and 2) Linux-Ubuntu 20.4. Both systems run over the same computer architecture (64bit) as a server side with a common backend MySQL web database for both of them. Nevertheless, the middleware for PHP is a cross Apache MySQL PHP Perl (XAMPP), but the middleware for Python is Pycharm and the web server gateway interface (WSGI). WSGI and Apache are both web servers and this paper will show which of them has a better response time (RT). On the one hand, the experimental results demonstrate that the Python-WSGI is even weightier in Mbyte than PHP-Apache, on the other hand Python is still faster and more accurate than PHP. The designed SPG is by handwriting codes: one time designed the SPG by PHP source code and the other time designed by Python source code. Both Python-WSGI and PHP-Apache results are targeted to compare by the least time in milliseconds and take in to account enhanced performance.

scholarly journals Active Control Parameters Monitoring for Freight Trains, Using Wireless Sensor Network Platform and Internet of Things

Processes ◽  
2020 ◽  
Vol 8 (6) ◽  
pp. 639 ◽  
Author(s):  
Adrian Brezulianu ◽  
Cristian Aghion ◽  
Marius Hagan ◽  
Oana Geman ◽  
Iuliana Chiuchisan ◽  
...  
Keyword(s):  
Web Server ◽  
Global Market ◽  
Wireless Sensor ◽  
Control Parameters ◽  
The Status ◽  
Train Driver ◽  
On Line ◽  
Network Platform ◽  
Server Application ◽  
The Web

Operating in a dynamic and competitive global market, railway companies have realized many years ago that better management of their logistical operations will enhance their strategic positions on the market. The financial component of daily operations is of utmost importance these days and many companies concluded that maximizing the profit relies on the integration of logistical activities with better income management. This paper presents a system consisting of three components: Ferodata BOX, Ferodata MOBILE, and Ferodata SYS, used to transmit to a web-server the status and operating information of an electric or diesel train. Train information includes data from locomotives, wagons, train driver, route, direction, fuel or electric consumption, speed, etc. All this information is processed in real-time and can be viewed in the web-server application. Additionally, the web-server application could manage and report details that are coming from the wagons, such as valuable information regarding the bogie wear, the identification of the wagons attached to a gasket, and identification the situations in which a wagon or group of wagons comes off the gasket configuration. All information about the status of trains is available on-line and at any moment the person responsible for management can use these data in their work.

scholarly journals Automated Gene Data Integration with Databio

2019 ◽  
Author(s):  
Robert W Reid ◽  
Jacob W Ferrier ◽  
Jeremy J Jay
Keyword(s):  
Data Structures ◽  
Computational Analysis ◽  
Source Code ◽  
Data Provenance ◽  
Data Sets ◽  
Time Data ◽  
Specialized Knowledge ◽  
Link Type ◽  
Gene Data ◽  
The Web

AbstractSummaryDatabio is capable of providing fast and accurate annotation of gene-oriented data sets, coupled with an integrated identifier conversion service to empower downstream data mining and computational analysis. Databio is enabled by fast real-time data structures applied to over 137 million unique identifiers, and uses automated heuristics to permit accurate data provenance without highly specialized knowledge and bioinformatics training.Availability and ImplementationFreely available on the web at https://datab.io/. Source code and binaries are freely available for download at https://github.com/joiningdata/databio/, implemented in Go and supported on Linux, Windows, and macOS.

scholarly journals A decoupled, modular and scriptable architecture for tools to curate data platforms

2020 ◽  
Author(s):  
Moritz Langenstein ◽  
Henning Hermjakob ◽  
Manuel Bernal Llinares
Keyword(s):  
Web Application ◽  
Production Systems ◽  
Source Code ◽  
Black Box ◽  
Command Line ◽  
Web Interface ◽  
Link Type ◽  
Data Platform ◽  
The Web

AbstractMotivationCuration is essential for any data platform to maintain the quality of the data it provides. Existing databases, which require maintenance, and the amount of newly published information that needs to be surveyed, are growing rapidly. More efficient curation is often vital to keep up with this growth, requiring modern curation tools. However, curation interfaces are often complex and difficult to further develop. Furthermore, opportunities for experimentation with curation workflows may be lost due to a lack of development resources, or a reluctance to change sensitive production systems.ResultsWe propose a decoupled, modular and scriptable architecture to build curation tools on top of existing platforms. Instead of modifying the existing infrastructure, our architecture treats the existing platform as a black box and relies only on its public APIs and web application. As a decoupled program, the tool’s architecture gives more freedom to developers and curators. This added flexibility allows for quickly prototyping new curation workflows as well as adding all kinds of analysis around the data platform. The tool can also streamline and enhance the curator’s interaction with the web interface of the platform. We have implemented this design in cmd-iaso, a command-line curation tool for the identifiers.org registry.AvailabilityThe cmd-iaso curation tool is implemented in Python 3.7+ and supports Linux, macOS and Windows. Its source code and documentation are freely available from https://github.com/identifiers-org/cmd-iaso. It is also published as a Docker container at https://hub.docker.com/r/identifiersorg/[email protected]

scholarly journals Pengujian Distribusi Beban Kerja Web Secara Statis pada Sistem Server Web Berbasis Cluster dengan Algoritma Never Queue

2019 ◽  
Vol 2 (3) ◽  
pp. 266
Author(s):  
Nongki Angsar
Keyword(s):  
Response Times ◽  
Web Server ◽  
Web Traffic ◽  
Average Output ◽  
Network Bandwidth ◽  
Server Systems ◽  
The One ◽  
Microprocessor Technology ◽  
Server System ◽  
The Web

The increase in web traffic and the development of network bandwidth that is relatively faster than the development of microprocessor technology today causes the one point server platform to be no longer sufficient to meet the scalability requirements of web server systems. Multiple server platforms are the answer. One known solution is cluster-based web server systems. In this study, a cluster-based web server system would be designed with the Never Queue algorithm and continued with testing the distribution of web workload on this system. The tests were carried out by generating HTTP workloads statically (with fast HTTP requests per fixed second) and dynamically (rapid HTTP requests per second that change or rise regularly) from the client to the web server system pool. Followed by analyzing data package traffic. In this study, the results of static testing with rapid HTTP requests per second which still showed that the Never Queue algorithm distributed HTTP requests to the web server system pool properly and got HTTP replies that tend to be stable at the HTTP average of 1031.8 replies/s. As for the rapid parameters of TCP connections, response times and errors increased with the rapid increasing HTTP requests generated. The average output was at 2,983 Mbps.

Development and Implementation of Ship Maintenance Management Spot Inspection Information System

2014 ◽  
Vol 644-650 ◽  
pp. 6233-6237
Author(s):  
Lei Feng
Keyword(s):  
Information System ◽  
System Design ◽  
Current System ◽  
Web Server ◽  
Mobile Terminal ◽  
Maintenance Management ◽  
System Structure ◽  
Ship Maintenance ◽  
Server Application ◽  
The Web

A engineering ship as the object, This paper analyzed the application of equipment Inspection, and discussed the PDCA management system, developed a set of spot inspection Information system based on the web server application & intelligent mobile terminal application which has the current system better regulated. Introduced the development background, expounded the system structure, functions and technology solutions, and discussed the main functions of the system design scheme.

scholarly journals ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases

2018 ◽  
Author(s):  
Daniel Domingo-Fernández ◽  
Charles Tapley Hoyt ◽  
Carlos Bobis-Álvarez ◽  
Josep Marín-Llaó ◽  
Martin Hofmann-Apitius
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Web Application ◽  
Biological Systems ◽  
Source Code ◽  
Major Pathway ◽  
Link Type ◽  
Pathway Databases ◽  
The Web

AbstractAlthough pathways are widely used for the analysis and representation of biological systems, their lack of clear boundaries, their dispersion across numerous databases, and the lack of interoperability impedes the evaluation of the coverage, agreements, and discrepancies between them. Here, we present ComPath, an ecosystem that supports curation of pathway mappings between databases and fosters the exploration of pathway knowledge through several novel visualizations. We have curated mappings between three of the major pathway databases and present a case study focusing on Parkinson’s disease that illustrates how ComPath can generate new biological insights by identifying pathway modules, clusters, and cross-talks with these mappings. The ComPath source code and resources are available at https://github.com/ComPath and the web application can be accessed at http://compath.scai.fraunhofer.de/.

scholarly journals libsbmljs — Enabling Web–Based SBML Tools

2019 ◽  
Author(s):  
J Kyle Medley ◽  
Joseph Hellerstein ◽  
Herbert M Sauro
Keyword(s):  
Systems Biology ◽  
Model Building ◽  
Source Code ◽  
Stochastic Simulations ◽  
Web Based ◽  
Server Side ◽  
Link Type ◽  
Software Distribution ◽  
Api Documentation ◽  
The Web

The SBML standard is used in a number of online repositories for storing systems biology models, yet there is currently no Web–capable JavaScript library that can read and write the SBML format. This is a severe limitation since the Web has become a universal means of software distribution, and the graphical capabilities of modern web browsers offer a powerful means for building rich, interactive applications. Also, there is a growing developer population specialized in web technologies that is poised to take advantage of the universality of the web to build the next generation of tools in systems biology and other fields. However, current solutions require server– side processing in order to support existing standards in modeling. We present libsbmljs, a JavaScript / WebAssembly library for Node.js and the Web with full support for all SBML extensions. Our library is an enabling technology for online SBML editors, model–building tools, and web–based simulators, and runs entirely in the browser without the need for any dedicated server resources. We provide NPM packages, an extensive set of examples, JavaScript API documentation, and an online demo that allows users to read and validate the SBML content of any model in the BioModels and BiGG databases. We also provide instructions and scripts to allow users to build a copy of libsbmljs against any libSBML version. Although our library supports all existing SBML extensions, we cover how to add additional extensions to the wrapper, should any arise in the future. To demonstrate the utility of this implementation, we also provide a demo at https://libsbmljsdemo.github.io/ with a proof–of–concept SBML simulator that supports ODE and stochastic simulations for SBML core models. Our project is hosted at https://libsbmljs.github.io/, which contains links to examples, API documentation, and all source code files and build scripts used to create libsbmljs. Our source code is licensed under the Apache 2.0 open source license.

Sign in / Sign up

Export Citation Format

Share Document