scholarly journals NetWheels: A web application to create high quality peptide helical wheel and net projections

2018 ◽  
Author(s):  
A.R. Mól ◽  
M.S. Castro ◽  
W. Fontes
Keyword(s):  
Web Application ◽  
Secondary Structures ◽  
Two Dimensions ◽  
Helical Structures ◽  
High Quality ◽  
Web Based ◽  
Link Type ◽  
Helical Wheel ◽  
Intramolecular Bonding

AbstractHelices are one of the most common secondary structures found in peptides and proteins. The wheel and net projections have been proposed to represent in two dimensions the tridimensional helical structures and facilitate the observation of their properties, especially in terms of residues polarity and intramolecular bonding. Nevertheless, there are few software options to create these projections. We have developed a web-based application that has several futures to create, customize and export these projections and is freely available at http://lbqp.unb.br/NetWheels.

scholarly journals LandScape: a web application for interactive genomic summary visualization

2019 ◽  
Author(s):  
Wenlong Jia ◽  
Hechen Li ◽  
Shiying Li ◽  
Shuaicheng Li
Keyword(s):  
Genetic Information ◽  
Web Application ◽  
Genomic Research ◽  
File Format ◽  
Data Types ◽  
Web Based ◽  
Link Type ◽  
Level Data ◽  
Real Time Visualization ◽  
Information Landscape

ABSTRACTSummaryVisualizing integrated-level data from genomic research remains a challenge, as it requires sufficient coding skills and experience. Here, we present LandScapeoviz, a web-based application for interactive and real-time visualization of summarized genetic information. LandScape utilizes a well-designed file format that is capable of handling various data types, and offers a series of built-in functions to customize the appearance, explore results, and export high-quality diagrams that are available for publication.Availability and implementationLandScape is deployed at bio.oviz.org/demo-project/analyses/landscape for online use. Documentation and demo data are freely available on this website and GitHub (github.com/Nobel-Justin/Oviz-Bio-demo)[email protected]

scholarly journals Radiator: a cloud-based framework for deploying re-usable bioinformatics tools

2019 ◽  
Author(s):  
Emily K.W. Lo ◽  
Remy M. Schwab ◽  
Zak Burke ◽  
Patrick Cahan
Keyword(s):  
User Interfaces ◽  
Web Application ◽  
Web Applications ◽  
Cloud Provider ◽  
Web Based ◽  
Lightweight Framework ◽  
Link Type ◽  
Bioinformatics Tools ◽  
Command Line Tool ◽  
Amazon Web Services

AbstractSummaryAccessibility and usability of compute-intensive bioinformatics tools can be increased with simplified web-based graphic user interfaces. However, deploying such tools as web applications presents additional barriers, including the complexity of developing a usable interface, network latency in transferring large datasets, and cost, which we encountered in developing a web-based version of our command-line tool CellNet. Learning and generalizing from this experience, we have devised a lightweight framework, Radiator, to facilitate deploying bioinformatics tools as web applications. To achieve reproducibility, usability, consistent accessibility, throughput, and cost-efficiency, Radiator is designed to be deployed on the cloud. Here, we describe the internals of Radiator and how to use it.Availability and ImplementationCode for Radiator and the CellNet Web Application are freely available at https://github.com/pcahan1 under the MIT license. The CellNet WebApp, Radiator, and Radiator-derived applications can be launched through public Amazon Machine Images from the cloud provider Amazon Web Services (AWS) (https://aws.amazon.com/).

scholarly journals MiBiOmics: an interactive web application for multi-omics data exploration and integration

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Johanna Zoppi ◽  
Jean-François Guillaume ◽  
Michel Neunlist ◽  
Samuel Chaffron
Keyword(s):  
Web Application ◽  
Biological Systems ◽  
Easy Access ◽  
Omics Data ◽  
Web Based ◽  
Link Type ◽  
Interactive Interface ◽  
Shiny App ◽  
Ordination Techniques ◽  
Scale Characterization

Abstract Background Multi-omics experimental approaches are becoming common practice in biological and medical sciences underlining the need to design new integrative techniques and applications to enable the multi-scale characterization of biological systems. The integrative analysis of heterogeneous datasets generally allows to acquire additional insights and generate novel hypotheses about a given biological system. However, it can become challenging given the often-large size of omics datasets and the diversity of existing techniques. Moreover, visualization tools for interpretation are usually non-accessible to biologists without programming skills. Results Here, we present MiBiOmics, a web-based and standalone application that facilitates multi-omics data visualization, exploration, integration, and analysis by providing easy access to dedicated and interactive protocols. It implements classical ordination techniques and the inference of omics-based (multilayer) networks to mine complex biological systems, and identify robust biomarkers linked to specific contextual parameters or biological states. Conclusions MiBiOmics provides easy-access to exploratory ordination techniques and to a network-based approach for integrative multi-omics analyses through an intuitive and interactive interface. MiBiOmics is currently available as a Shiny app at https://shiny-bird.univ-nantes.fr/app/Mibiomics and as a standalone application at https://gitlab.univ-nantes.fr/combi-ls2n/mibiomics.

scholarly journals GenFam: A web application and database for gene family-based classification and functional enrichment analysis

2018 ◽  
Author(s):  
Renesh Bedre ◽  
Kranthi Mandadi
Keyword(s):  
Gene Family ◽  
Web Application ◽  
High Throughput Sequencing ◽  
Source Code ◽  
Enrichment Analysis ◽  
Gene Families ◽  
Functional Enrichment ◽  
Multiple Testing Correction ◽  
Web Based ◽  
Link Type

ABSTRACTGenome-scale studies using high-throughput sequencing (HTS) technologies generate substantial lists of differentially expressed genes under different experimental conditions. These gene lists need to be further mined to narrow down biologically relevant genes and associated functions in order to guide downstream functional genetic analyses. A popular approach is to determine statistically overrepresented genes in a user-defined list through enrichment analysis tools, which rely on functional annotations of genes based on Gene Ontology (GO) terms. Here, we propose a new approach, GenFam, which allows classification and enrichment of genes based on their gene family, thus simplifying identification of candidate gene families and associated genes that may be relevant to the query. GenFam and its integrated database comprises of three-hundred and eighty-four unique gene families and supports gene family classification and enrichment analyses for sixty plant genomes. Four comparative case studies with plant species belonging to different clades and families were performed using GenFam which demonstrated its robustness and comprehensiveness over preexisting functional enrichment tools. To make it readily accessible for plant biologists, GenFam is available as a web-based application where users can input gene IDs and export enrichment results in both tabular and graphical formats. Users can also customize analysis parameters by choosing from the various statistical enrichment tests and multiple testing correction methods. Additionally, the web-based application, source code and database are freely available to use and download. Website: http://mandadilab.webfactional.com/home/. Source code and database: http://mandadilab.webfactional.com/home/dload/.

scholarly journals MiBiOmics: An interactive web application for multi-omics data exploration and integration

2020 ◽  
Author(s):  
Johanna Zoppi ◽  
Jean-François Guillaume ◽  
Michel Neunlist ◽  
Samuel Chaffron
Keyword(s):  
Web Application ◽  
Biological Systems ◽  
Easy Access ◽  
Omics Data ◽  
Medical Sciences ◽  
Web Based ◽  
Link Type ◽  
Interactive Interface ◽  
Shiny App ◽  
Ordination Techniques

AbstractBackgroundMulti-omics experimental approaches are becoming common practice in biological and medical sciences underlying the need to design new integrative techniques and applications to enable the holistic characterization of biological systems. The integrative analysis of heterogeneous datasets generally allows us to acquire additional insights and generate novel hypotheses about a given biological system. However, it can often become challenging given the large size of omics datasets and the diversity of existing techniques. Moreover, visualization tools for interpretation are usually non-accessible to biologists without programming skills.ResultsHere, we present MiBiOmics, a web-based and standalone application that facilitates multi-omics data visualization, exploration, integration, and analysis by providing easy access to dedicated and interactive protocols. It implements advanced ordination techniques and the inference of omics-based (multi-layer) networks to mine complex biological systems, and identify robust biomarkers linked to specific contextual parameters or biological states.ConclusionsThrough an intuitive and interactive interface, MiBiOmics provides easy-access to ordination techniques and to a network-based approach for integrative multi-omics analyses. MiBiOmics is currently available as a Shiny app at https://shiny-bird.univ-nantes.fr/app/Mibiomics and as a standalone application at https://gitlab.univ-nantes.fr/combi-ls2n/mibiomics.

scholarly journals CircularLogo: A lightweight web application to visualize intra-motif dependencies

2017 ◽  
Author(s):  
Zhenqing Ye ◽  
Tao Ma ◽  
Michael T. Kalmbach ◽  
Surendra Dasari ◽  
Jean-Pierre A. Kocher ◽  
...  
Keyword(s):  
Binding Sites ◽  
Web Application ◽  
Source Code ◽  
Sequence Logo ◽  
Rna Motifs ◽  
Biomolecular Structure ◽  
Web Based ◽  
Link Type ◽  
Web Framework ◽  
Interactive Application

AbstractBackgroundThe sequence logo has been widely used to represent DNA or RNA motifs for more than three decades. Despite its intelligibility and intuitiveness, the traditional sequence logo is unable to display the intra-motif dependencies and therefore is insufficient to fully characterize nucleotide motifs. Many methods have been developed to quantify the intra-motif dependencies, but fewer tools are available for visualization.ResultWe developed CircularLogo, a web-based interactive application, which is able to not only visualize the position-specific nucleotide consensus and diversity but also display the intra-motif dependencies. Applying CircularLogo to HNF6 binding sites and tRNA sequences demonstrated its ability to show intra-motif dependencies and intuitively reveal biomolecular structure. CircularLogo is implemented in JavaScript and Python based on the Django web framework. The program’s source code and user’s manual are freely available at http://circularlogo.sourceforge.net. CircularLogo web server can be accessed from http://bioinformaticstools.mayo.edu/circularlogo/index.html.ConclusionCircularLogo is an innovative web application that is specifically designed to visualize and interactively explore intra-motif dependencies.

scholarly journals Development and operational experience of the web based application to collect, manage, and release the alignment and calibration configurations for data processing at CMS

2019 ◽  
Vol 214 ◽  
pp. 04006
Author(s):  
Hasbuddin Md ◽  
Arun Kumar ◽  
Giacomo Govi ◽  
Giovanni Franzoni ◽  
Luca Pernie ◽  
...  
Keyword(s):  
Data Processing ◽  
Data Management ◽  
Compact Muon Solenoid ◽  
Web Application ◽  
Operational Experience ◽  
High Quality ◽  
Management Tools ◽  
Web Based ◽  
Cms Experiment ◽  
The Web

The alignment and calibration workflows at the Compact Muon Solenoid (CMS) experiment are fundamental to provide a high quality physics data and to maintain the design performance of the experiment. To facilitate the operational efforts required by the experiment, the alignment and calibration team has developed and deployed a set of web-based applications to search, navigate and prepare a consistent set of calibrations to be consumed in reconstruction of data for physics, accessible through the Condition DB Browser. The Condition DB Browser hosts also various data management tools, including a vi-sualization tool that allows to easily inspect alignment an calibration contents, an user-defined notification agent for delivering updates on modification to the database, a logging service for the user and the automatic online-to-offline condition uploads. In this paper we report on the operational experience of this web application from 2017 data taking, with focus on new features and tools incorporated during this period.

scholarly journals Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison

2020 ◽  
Author(s):  
Tobias Schmidt ◽  
Patroklos Samaras ◽  
Viktoria Dorfer ◽  
Christian Panse ◽  
Tobias Kockmann ◽  
...  
Keyword(s):  
Web Application ◽  
Mass Spectra ◽  
Seamless Integration ◽  
Web Based ◽  
Tandem Mass Spectra ◽  
Learning Framework ◽  
Time Prediction ◽  
Link Type ◽  
Comparison Results ◽  
Universal Spectrum

AbstractHere we present the Universal Spectrum Explorer (USE), a web-based tool based on IPSA for cross-resource (peptide) spectrum visualization and comparison (https://www.proteomicsdb.org/use/). Mass spectra under investigation can either be provided manually by the user (table format), or automatically retrieved from online repositories supporting access to spectral data via the universal spectrum identifier (USI), or requested from other resources and services implementing a newly designed REST interface. As a proof of principle we implemented such an interface in ProteomicsDB thereby allowing the retrieval of spectra acquired within the ProteomeTools project. In addition, USE can retrieve real-time prediction of tandem mass spectra from the deep learning framework Prosit. Comparison results like annotated mirror spectrum plots can be exported from USE as editable scalable high quality vector graphics. The USE was designed and implemented with minimal external dependencies allowing local usage and seamless integration into websites (https://github.com/kusterlab/universal_spectrum_explorer).

ANALYZING AND IMPROVING WEB APPLICATION QUALITY USING DESIGN PATTERNS

2012 ◽  
Vol 2 (2) ◽  
pp. 112-116
Author(s):  
Shikha Bhatia ◽  
Mr. Harshpreet Singh
Keyword(s):  
Web Application ◽  
Design Pattern ◽  
Design Patterns ◽  
Web Applications ◽  
Past Research ◽  
Software Systems ◽  
Interactive Software ◽  
Web Based ◽  
Software Application ◽  
Execution Speed

With the mounting demand of web applications, a number of issues allied to its quality have came in existence. In the meadow of web applications, it is very thorny to develop high quality web applications. A design pattern is a general repeatable solution to a generally stirring problem in software design. It should be noted that design pattern is not a finished product that can be directly transformed into source code. Rather design pattern is a depiction or template that describes how to find solution of a problem that can be used in many different situations. Past research has shown that design patterns greatly improved the execution speed of a software application. Design pattern are classified as creational design patterns, structural design pattern, behavioral design pattern, etc. MVC design pattern is very productive for architecting interactive software systems and web applications. This design pattern is partition-independent, because it is expressed in terms of an interactive application running in a single address space. We will design and analyze an algorithm by using MVC approach to improve the performance of web based application. The objective of our study will be to reduce one of the major object oriented features i.e. coupling between model and view segments of web based application. The implementation for the same will be done in by using .NET framework.

eMap: A Web Application for Identifying and Visualizing Electron or Hole Hopping Pathways in Proteins

2019 ◽  
Author(s):  
Ruslan N. Tazhigulov ◽  
James R. Gayvert ◽  
Melissa Wei ◽  
Ksenia B. Bravaya
Keyword(s):  
Web Application ◽  
Shortest Paths ◽  
Coarse Grained ◽  
Decay Parameter ◽  
Electron Hole ◽  
Web Based ◽  
Aromatic Amino Acid Residue ◽  
Pathways Model ◽  
Visualization Tools ◽  
Effective Decay

<p>eMap is a web-based platform for identifying and visualizing electron or hole transfer pathways in proteins based on their crystal structures. The underlying model can be viewed as a coarse-grained version of the Pathways model, where each tunneling step between hopping sites represented by electron transfer active (ETA) moieties is described with one effective decay parameter that describes protein-mediated tunneling. ETA moieties include aromatic amino acid residue side chains and aromatic fragments of cofactors that are automatically detected, and, in addition, electron/hole residing sites that can be specified by the users. The software searches for the shortest paths connecting the user-specified electron/hole source to either all surface-exposed ETA residues or to the user-specified target. The identified pathways are ranked based on their length. The pathways are visualized in 2D as a graph, in which each node represents an ETA site, and in 3D using available protein visualization tools. Here, we present the capability and user interface of eMap 1.0, which is available at https://emap.bu.edu.</p>

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