scholarly journals VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences

2019 ◽  
Vol 47 (W1) ◽  
pp. W632-W635 ◽  
Author(s):  
Lukas Bartonek ◽  
Bojan Zagrovic
Keyword(s):  
Nucleic Acids ◽  
Physicochemical Properties ◽  
Sequence Data ◽  
Structural Disorder ◽  
Biological Sequence ◽  
Web Based ◽  
Starting Point ◽  
User Friendly ◽  
Insight Into ◽  
Sequence Position

Abstract The structure, dynamics and, ultimately, biological function of proteins and nucleic acids are determined by the physicochemical properties of their primary sequences. Such properties are frequently captured via one-dimensional profile plots depicting a given physicochemical variable as a function of sequence position. Hydrophobicity, charge or structural disorder in proteins or nucleobase-density in nucleic acids are routinely visualized in this manner to analyze sequences at a glance. Such visualizations, however, are typically created case-by-case in a purely static manner, employ fixed visualization parameters only and do not enable a quantitative comparison between different sequences. Here, we present VOLPES (volpes.univie.ac.at), a user-friendly web server and the corresponding JavaScript library that enable a fully interactive, multifunctional visualization, analysis and comparison of the physicochemical properties of protein and nucleic-acid sequences, allowing unprecedented insight into biological sequence data and creating a starting point for further in-depth exploration.

scholarly journals Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem

2021 ◽  
Vol 8 ◽  
Author(s):  
Rodrigo V. Honorato ◽  
Panagiotis I. Koukos ◽  
Brian Jiménez-García ◽  
Andrei Tsaregorodtsev ◽  
Marco Verlato ◽  
...  
Keyword(s):  
Structural Biology ◽  
Dynamic Properties ◽  
Three Dimensional ◽  
Open Science ◽  
Biological Macromolecules ◽  
Web Based ◽  
Cellular Processes ◽  
User Friendly ◽  
Insight Into ◽  
Gaining Insight

Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of biomolecules and their interactions is critical for understanding the vast majority of cellular processes, with direct applications in health and food sciences. Since 2010, the WeNMR project (www.wenmr.eu) has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers in the field, using the high throughput computing infrastructure provided by EGI. These services have been further developed in subsequent initiatives under H2020 projects and are now operating as Thematic Services in the European Open Science Cloud portal (www.eosc-portal.eu), sending >12 millions of jobs and using around 4,000 CPU-years per year. Here we review 10 years of successful e-infrastructure solutions serving a large worldwide community of over 23,000 users to date, providing them with user-friendly, web-based solutions that run complex workflows in structural biology. The current set of active WeNMR portals are described, together with the complex backend machinery that allows distributed computing resources to be harvested efficiently.

KNIndex: a comprehensive database of physicochemical properties for k-tuple nucleotides

2020 ◽  
Author(s):  
Wen-Ya Zhang ◽  
Junhai Xu ◽  
Jun Wang ◽  
Yuan-Ke Zhou ◽  
Wei Chen ◽  
...  
Keyword(s):  
Physicochemical Properties ◽  
High Throughput Sequencing ◽  
Genomic Sequences ◽  
Biological Sequences ◽  
Sequencing Technology ◽  
Learning Methods ◽  
Rna Sequences ◽  
Web Based ◽  
Comprehensive Database ◽  
User Friendly

Abstract With the development of high-throughput sequencing technology, the genomic sequences increased exponentially over the last decade. In order to decode these new genomic data, machine learning methods were introduced for genome annotation and analysis. Due to the requirement of most machines learning methods, the biological sequences must be represented as fixed-length digital vectors. In this representation procedure, the physicochemical properties of k-tuple nucleotides are important information. However, the values of the physicochemical properties of k-tuple nucleotides are scattered in different resources. To facilitate the studies on genomic sequences, we developed the first comprehensive database, namely KNIndex (https://knindex.pufengdu.org), for depositing and visualizing physicochemical properties of k-tuple nucleotides. Currently, the KNIndex database contains 182 properties including one for mononucleotide (DNA), 169 for dinucleotide (147 for DNA and 22 for RNA) and 12 for trinucleotide (DNA). KNIndex database also provides a user-friendly web-based interface for the users to browse, query, visualize and download the physicochemical properties of k-tuple nucleotides. With the built-in conversion and visualization functions, users are allowed to display DNA/RNA sequences as curves of multiple physicochemical properties. We wish that the KNIndex will facilitate the related studies in computational biology.

Developing Client-Side Mashups

2013 ◽  
Vol 5 (1) ◽  
pp. 34-52
Author(s):  
Arto Salminen ◽  
Tommi Mikkonen ◽  
Feetu Nyrhinen ◽  
Antero Taivalsaari
Keyword(s):  
Software Development ◽  
Web Sites ◽  
Reference Architecture ◽  
Web Based ◽  
Starting Point ◽  
Practical Experiences ◽  
Client Side ◽  
Insight Into

Software mashups that combine content from multiple web sites to an integrated experience are a popular trend. However, methods, tools and architectures for creating mashups are still rather undeveloped, and there is little engineering support behind them. In this paper the authors present guidelines that can serve as a helpful starting point for the design of new mashups. Guidelines focus mainly on mashup creation methods. Furthermore, they describe a reference architecture for client-side mashup development. In addition, the authors provide insight into mashup development based on their practical experiences in implementing various sample client-side mashup applications and tools for creating them. The long term goal of the authors’ work is to facilitate the development of compelling, robust and maintainable mashup applications, and more generally ease the transition towards web-based software development.

scholarly journals ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

2019 ◽  
Author(s):  
Silas Kieser ◽  
Joseph Brown ◽  
Evgeny M. Zdobnov ◽  
Mirko Trajkovski ◽  
Lee Ann McCue
Keyword(s):  
Data Processing ◽  
Sequence Data ◽  
Microbial Populations ◽  
Valuable Insight ◽  
Genome Databases ◽  
Abundance Estimates ◽  
And Function ◽  
User Friendly ◽  
Insight Into ◽  
Metagenome Sequence

AbstractBackgroundMetagenomics and metatranscriptomics studies provide valuable insight into the composition and function of microbial populations from diverse environments, however the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers.ResultsHere we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome and metatranscriptome data. Genome-centric resolution and abundance estimates are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license.ConclusionATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome and metatranscriptome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.

The Role of Web Based Accounting Online System 2.0 as the Company's Income and Expense Management

2017 ◽  
Vol 1 (1) ◽  
pp. 44-49
Author(s):  
Nur Azizah ◽  
Dedeh Supriyanti ◽  
Siti Fairuz Aminah Mustapha ◽  
Holly Yang
Keyword(s):  
Financial Management ◽  
Accounting System ◽  
Bank Account ◽  
Web Based ◽  
Online System ◽  
Version 2.0 ◽  
User Friendly ◽  
The Impact ◽  
A Company

In a company, the process of income and expense of money must have a profit-generating goal base. The success of financial management within the company, can be monitored from the ability of the financial management in managing the finances and utilize all the opportunities that exist with as much as possible with the aim to control the company's cash (cash flow) and the impact of generating profits in accordance with expectations. With a web-based online accounting system version 2.0, companies can be given the ease to manage money in and out of the company's cash. It has a user friendly system with navigation that makes it easy for the financial management to use it. Starting from the creation of a company's cash account used as a cash account and corporate bank account on the system, deletion or filing of cash accounts, up to the transfer invoice creation feature, receive and send money. Thus, this system is very effective and efficient in the management of income and corporate cash disbursements.   Keywords:​Accounting Online System, Financial Management, Cash and Bank

The Word Class Adjective in English Business Magazines Online

2018 ◽  
Vol 6 (2) ◽  
pp. 99-115
Author(s):  
Borislav Marušić ◽  
Sanda Katavić-Čaušić
Keyword(s):  
Empirical Study ◽  
Empirical Analysis ◽  
Word Formation ◽  
Word Class ◽  
Business English ◽  
Starting Point ◽  
Comprehensive Picture ◽  
English Syntax ◽  
The Empirical Analysis ◽  
Insight Into

Abstract The aim of this paper is to research the word class adjective in one sequence of the ESP: Business English, more precisely English business magazines online. It is an empirical study on the corpus taken from a variety of business magazines online. The empirical analysis allows a comprehensive insight into the word class adjective in this variety of Business English and makes its contribution to English syntax, semantics and word formation. The syntactic part analyses the adjective position in the sentence. The semantic part of the study identifies the most common adjectives that appear in English business magazines online. Most of the analysis is devoted to the word formation of the adjectives found in the corpus. The corpus is analysed in such a way that it enables its division into compounds, derivatives and conversions. The results obtained in this way will give a comprehensive picture of the word class adjective in this type of Business English and can act as a starting point for further research of the word class adjective.

PubChem and ChEMBL Beyond Lipinski

2019 ◽  
Author(s):  
Jean-Louis Reymond ◽  
Mahendra Awale ◽  
Daniel Probst ◽  
Alice Capecchi
Keyword(s):  
Nearest Neighbor ◽  
Molecular Shape ◽  
Biological Properties ◽  
Web Based ◽  
Large Molecules ◽  
Interactive Tools ◽  
Small Molecule Drugs ◽  
Pubchem Database ◽  
Nearest Neighbor Searches ◽  
Insight Into

<p>Seven million of the currently 94 million entries in the PubChem database break at least one of the four Lipinski constraints for oral bioavailability, 183,185 of which are also found in the ChEMBL database. These non-Lipinski PubChem (NLP) and ChEMBL (NLC) subsets are interesting because they contain new modalities that can display biological properties not accessible to small molecule drugs. Unfortunately, the current search tools in PubChem and ChEMBL are designed for small molecules and are not well suited to explore these subsets, which therefore remain poorly appreciated. Herein we report MXFP (macromolecule extended atom-pair fingerprint), a 217-D fingerprint tailored to analyze large molecules in terms of molecular shape and pharmacophores. We implement MXFP in two web-based applications, the first one to visualize NLP and NLC interactively using Faerun (http://faerun.gdb.tools/), the second one to perform MXFP nearest neighbor searches in NLP (http://similaritysearch.gdb.tools/). We show that these tools provide a meaningful insight into the diversity of large molecules in NLP and NLC. The interactive tools presented here are publicly available at http://gdb.unibe.ch and can be used freely to explore and better understand the diversity of non-Lipinski molecules in PubChem and ChEMBL.</p>

Web-Based Peer and Self-Assessment System Design and Development for Elementary School Students

2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Mehmet EMIN KORTAK
Keyword(s):  
Elementary School ◽  
Elementary School Students ◽  
Primary Schools ◽  
Peer Assessment ◽  
Assessment System ◽  
Assessment Process ◽  
School Students ◽  
Self Assessment ◽  
Web Based ◽  
User Friendly

This research aimed at designing and improving the web-based integrated peer and self- assessment. WesPASS (web-based peer-assessment system), developed in this research, allows students to assess their own or their peers’ performance and project assignments and to report about the result of these assessments so that they correct their assignments. This study employed design-based research. The participants included 102 fourth grade primary school students and their 4 teachers from 2 state and 2 private primary schools in Ankara, Kecioren (Turkey) who employed the system and were engaged in a questionnaire survey to assess its quality. The findings were analyzed through quantitative data analysis. The findings revealed that the system can be used by elementary school students for peer and self-assessment system. The participants stated that WesPASS is simple and user-friendly, and it accelerates the assessment process by employing information technology and allows to share opinions 

scholarly journals The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases

Metabolites ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 113
Author(s):  
Julia Koblitz ◽  
Sabine Will ◽  
S. Riemer ◽  
Thomas Ulas ◽  
Meina Neumann-Schaal ◽  
...  
Keyword(s):  
Metabolic Networks ◽  
Point Of View ◽  
Use Cases ◽  
Mathematical Methods ◽  
State Behavior ◽  
Web Based ◽  
Research Fields ◽  
Balance Analysis ◽  
Metabolic Models ◽  
User Friendly

Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental conditions. However, many existing applications for flux optimizations do not provide a metabolite-centric view on fluxes. Metano is a standalone, open-source toolbox for the analysis and refinement of metabolic models. While flux distributions in metabolic networks are predominantly analyzed from a reaction-centric point of view, the Metano methods of split-ratio analysis and metabolite flux minimization also allow a metabolite-centric view on flux distributions. In addition, we present MMTB (Metano Modeling Toolbox), a web-based toolbox for metabolic modeling including a user-friendly interface to Metano methods. MMTB assists during bottom-up construction of metabolic models by integrating reaction and enzymatic annotation data from different databases. Furthermore, MMTB is especially designed for non-experienced users by providing an intuitive interface to the most commonly used modeling methods and offering novel visualizations. Additionally, MMTB allows users to upload their models, which can in turn be explored and analyzed by the community. We introduce MMTB by two use cases, involving a published model of Corynebacterium glutamicum and a newly created model of Phaeobacter inhibens.

scholarly journals An Interactive Web Application for the Statistical Analysis of Continuous Glucose Monitoring Data in Epidemiological Studies

2021 ◽  
pp. 193229682098557
Author(s):  
Alysha M. De Livera ◽  
Jonathan E. Shaw ◽  
Neale Cohen ◽  
Anne Reutens ◽  
Agus Salim
Keyword(s):  
Continuous Glucose Monitoring ◽  
Web Application ◽  
Diabetes Management ◽  
Glucose Monitoring ◽  
Epidemiological Studies ◽  
Interactive Software ◽  
Web Based ◽  
Software Applications ◽  
Visualization Of Data ◽  
User Friendly

Motivation: Continuous glucose monitoring (CGM) systems are an essential part of novel technology in diabetes management and care. CGM studies have become increasingly popular among researchers, healthcare professionals, and people with diabetes due to the large amount of useful information that can be collected using CGM systems. The analysis of the data from these studies for research purposes, however, remains a challenge due to the characteristics and large volume of the data. Results: Currently, there are no publicly available interactive software applications that can perform statistical analyses and visualization of data from CGM studies. With the rapidly increasing popularity of CGM studies, such an application is becoming necessary for anyone who works with these large CGM datasets, in particular for those with little background in programming or statistics. CGMStatsAnalyser is a publicly available, user-friendly, web-based application, which can be used to interactively visualize, summarize, and statistically analyze voluminous and complex CGM datasets together with the subject characteristics with ease.

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