scholarly journals USMI Galaxy Demonstrator (UGD): a collection of tools to integrate microorganisms information

2017 ◽  
Author(s):  
Daniele Pierpaolo Colobraro ◽  
Paolo Romano
Keyword(s):  
Service Providers ◽  
Basic Information ◽  
Unique Identifier ◽  
Web Based ◽  
Representational State Transfer ◽  
Biological Resource Centres ◽  
The Galaxy ◽  
Science Domain ◽  
On Line ◽  
Strain Number

Due to the fragmentation of microbial information and the several branch of human activities encompassed by microorganism applications, a comprehensive approach for merging information on microbes is needed. Although on line service providers collect several data on microorganisms and provide services for microbial Biological Resource Centres (mBRCs), such services are still limited both in contents and aims. The USMI Galaxy Demonstrator (UGD), an implementation of the Galaxy framework exploiting the XML-based Microbiological Common Language (MCL), is meant to support researchers to make an integrated access to enriched information from microbial catalogues, as well as to help mBRC curators in validating and enriching the contents of their catalogues. Researchers and mBRC curators may exploit the UGD to avoid manual, potentially long, searches on the web and to identify and select microorganisms of interest. UGD tools are written in Python, version 2.7. They allow to enrich the basic information provided by catalogues with related taxonomy, literature, sequence and chemical compound data retrieved from some of the main databases on the basis of the strain number, i.e. the unique identifier for a given culture, and the species names. The data is retrieved by querying database Web Services using either the Simple Object Access Protocol (SOAP) or the Representational State Transfer (REST) access protocols. The MCL format provides a versatile way to archive and exchange data among mBRCs. Galaxy is a well-known, open, web-based platform which offers many tools to retrieve, manage and analyze different kind of information arising from any life science domain. By exploiting Galaxy flexibility,UGD implements some tools and workflows that can be used to find and integrate several information on microorganisms. UGD tools integrate basic information which may support mBRC staff in the insertion of all fundamental strain information in a proper format allowing integration and interoperability with external databases. They also extend the output by adding information on source materials, including species and strain numbers, and retrieve associated microorganisms which use a compound or an enzyme in whatever metabolic pathway by returning the accession number, synonyms, links to external databases, taxon name, and strain number of the requested molecule.

scholarly journals USMI Galaxy Demonstrator (UGD): a collection of tools to integrate microorganisms information

2017 ◽  
Author(s):  
Daniele Pierpaolo Colobraro ◽  
Paolo Romano
Keyword(s):  
Service Providers ◽  
Basic Information ◽  
Unique Identifier ◽  
Web Based ◽  
Representational State Transfer ◽  
Biological Resource Centres ◽  
The Galaxy ◽  
Science Domain ◽  
On Line ◽  
Strain Number

Due to the fragmentation of microbial information and the several branch of human activities encompassed by microorganism applications, a comprehensive approach for merging information on microbes is needed. Although on line service providers collect several data on microorganisms and provide services for microbial Biological Resource Centres (mBRCs), such services are still limited both in contents and aims. The USMI Galaxy Demonstrator (UGD), an implementation of the Galaxy framework exploiting the XML-based Microbiological Common Language (MCL), is meant to support researchers to make an integrated access to enriched information from microbial catalogues, as well as to help mBRC curators in validating and enriching the contents of their catalogues. Researchers and mBRC curators may exploit the UGD to avoid manual, potentially long, searches on the web and to identify and select microorganisms of interest. UGD tools are written in Python, version 2.7. They allow to enrich the basic information provided by catalogues with related taxonomy, literature, sequence and chemical compound data retrieved from some of the main databases on the basis of the strain number, i.e. the unique identifier for a given culture, and the species names. The data is retrieved by querying database Web Services using either the Simple Object Access Protocol (SOAP) or the Representational State Transfer (REST) access protocols. The MCL format provides a versatile way to archive and exchange data among mBRCs. Galaxy is a well-known, open, web-based platform which offers many tools to retrieve, manage and analyze different kind of information arising from any life science domain. By exploiting Galaxy flexibility,UGD implements some tools and workflows that can be used to find and integrate several information on microorganisms. UGD tools integrate basic information which may support mBRC staff in the insertion of all fundamental strain information in a proper format allowing integration and interoperability with external databases. They also extend the output by adding information on source materials, including species and strain numbers, and retrieve associated microorganisms which use a compound or an enzyme in whatever metabolic pathway by returning the accession number, synonyms, links to external databases, taxon name, and strain number of the requested molecule.

Patient and Provider Perspectives Regarding Criteria for Patient Prioritization in Rehabilitation Programs (Preprint)

2019 ◽  
Author(s):  
Julien Déry ◽  
Angel Ruiz ◽  
François Routhier ◽  
Marie-Pierre Gagnon ◽  
André Côté ◽  
...  
Keyword(s):  
Service Providers ◽  
Quebec City ◽  
Web Based ◽  
Rehabilitation Programs ◽  
Provider Perspectives ◽  
Patient Prioritization ◽  
Services Sociaux ◽  
Multiple Case ◽  
Patient And Provider Perspectives

BACKGROUND Queueing patients on waiting lists is a common practice to manage access to rehabilitation services. To increase fairness and equity in access, a strategy emerging from the literature is patient prioritization. The goal is for patients with the greatest needs to be treated first and for patient wait times to be determined objectively on the basis of explicit criteria. Selecting criteria, however, is a complex task because it is important to simultaneously consider the objectives of all stakeholders. OBJECTIVE The aim of this study was to compare service users’ and service providers’ perspectives regarding patient prioritization criteria in two rehabilitation programs. METHODS We conducted a multiple case study in two rehabilitation programs at the Centre intégré universitaire de santé et de services sociaux de la Capitale-Nationale in Quebec City (Canada), i.e. a driving evaluation program (DEP) and a compression garment manufacturing program (CGMP). We sent a web-based survey asking two groups (patients and providers) of informed stakeholders to individually produce a set of criteria. We then conducted an inductive thematic analysis where each group’s individual answers were coded and combined in a single set of criteria. RESULTS Stakeholders from the DEP identified a total of 22 criteria to prioritize patients while those from the CGMP listed 27 criteria. Providers shared 76% of the criteria mentioned by patients. Some criteria, such as age, occupation, functional level, pain, absence of caregiver, and time since referral, were considered important by both stakeholders in both programs. CONCLUSIONS Patients and providers tended to have similar opinions about a majority of the criteria to prioritize patients in waitlists. Nonetheless, our study confirms that patients and providers base their choices on different types of knowledge and values, which explains some of the differences observed. Taking into consideration the opinions of all stakeholders concerning prioritization criteria is an important part of the decision-making process, based on a multiple constituency approach.

As-RaD System as a Design Model of the Network Automation Configuration System Based on the REST-API and Django Framework

2020 ◽  
pp. 291-298
Author(s):  
Adian Fatchur Rochim ◽  
Abda Rafi ◽  
Adnan Fauzi ◽  
Kurniawan Teguh Martono
Keyword(s):  
Information Technology ◽  
Application Programming Interface ◽  
Design Model ◽  
Automation System ◽  
Network Configuration ◽  
Web Based ◽  
Representational State Transfer ◽  
Application Programming ◽  
Rest Api ◽  
Python Programming

The use of information technology these days are very high. From business through education activities tend to use this technology most of the time. Information technology uses computer networks for integration and management data. To avoid business problems, the number of network devices installed requires a manageable network configuration for easier maintenance. Traditionally, each of network devices has to be manually configured by network administrators. This process takes time and inefficient. Network automation methods exist to overcome the repetitive process. Design model uses a web-based application for maintenance and automates networking tasks. In this research, the network automation system implemented and built a controller application that used REST API (Representational State Transfer Application Programming Interface) architecture and built by Django framework with Python programming language. The design modeled namely As-RaD System. The network devices used in this research are Cisco CSR1000V because it supports REST API communication to manage its network configuration and could be placed on the server either. The As-RaD System provides 75% faster performance than Paramiko and 92% than NAPALM.

scholarly journals How the Covid-19 Pandemic Is Changing Online Food Shopping Human Behaviour in Italy

2020 ◽  
Vol 12 (22) ◽  
pp. 9594
Author(s):  
Leonardo Salvatore Alaimo ◽  
Mariantonietta Fiore ◽  
Antonino Galati
Keyword(s):  
Online Shopping ◽  
Grocery Shopping ◽  
Competitive Advantages ◽  
Web Based ◽  
Explanatory Variables ◽  
Food Shopping ◽  
Cumulative Logit Model ◽  
Level Of Satisfaction ◽  
Shopping Experience ◽  
On Line

The advent of the Internet has significantly changed consumption patterns and habits. Online grocery shopping is a way of purchasing food products using a web-based shopping service. The current COVID-19 pandemic is determining a rethinking of purchase choice elements and of consumers’ behavior. This work aims to investigate which characteristics can affect the decision of online food shopping during the pandemic emergency in Italy. In particular, the work aims to analyze the effects of a set of explanatory variables on the level of satisfaction for the food online shopping experience. For achieving this aim, the proportional odds version of the cumulative logit model is carried out. Data derive from an anonymous on-line questionnaire administrated during the first months of the pandemic and filled by 248 respondents. The results of this work highlight that people having familiarity with buying food online, that have a higher educational level and consider food online channels easy to use, appear more satisfied for the food online shopping experience. These findings can be crucial for the future green global challenges as online shopping may help to reach competitive advantages for company sustainability.

scholarly journals Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy

GigaScience ◽  
2020 ◽  
Vol 9 (5) ◽  
Author(s):  
Katarzyna Murat ◽  
Björn Grüning ◽  
Paulina Wiktoria Poterlowicz ◽  
Gillian Westgate ◽  
Desmond J Tobin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Association Studies ◽  
Methylation Analysis ◽  
Web Based ◽  
Array Platform ◽  
Complex Evaluation ◽  
The Galaxy ◽  
Population Epigenetics ◽  
Analyse Data ◽  
Dna Methylation Analysis

Abstract Background Infinium Human Methylation BeadChip is an array platform for complex evaluation of DNA methylation at an individual CpG locus in the human genome based on Illumina’s bead technology and is one of the most common techniques used in epigenome-wide association studies. Finding associations between epigenetic variation and phenotype is a significant challenge in biomedical research. The newest version, HumanMethylationEPIC, quantifies the DNA methylation level of 850,000 CpG sites, while the previous versions, HumanMethylation450 and HumanMethylation27, measured >450,000 and 27,000 loci, respectively. Although a number of bioinformatics tools have been developed to analyse this assay, they require some programming skills and experience in order to be usable. Results We have developed a pipeline for the Galaxy platform for those without experience aimed at DNA methylation analysis using the Infinium Human Methylation BeadChip. Our tool is integrated into Galaxy (http://galaxyproject.org), a web-based platform. This allows users to analyse data from the Infinium Human Methylation BeadChip in the easiest possible way. Conclusions The pipeline provides a group of integrated analytical methods wrapped into an easy-to-use interface. Our tool is available from the Galaxy ToolShed, GitHub repository, and also as a Docker image. The aim of this project is to make Infinium Human Methylation BeadChip analysis more flexible and accessible to everyone.

scholarly journals On Line Validation Exercise (OLIVE): A Web Based Service for the Validation of Medium Resolution Land Products. Application to FAPAR Products

2014 ◽  
Vol 6 (5) ◽  
pp. 4190-4216 ◽  
Author(s):  
Marie Weiss ◽  
Frédéric Baret ◽  
Tom Block ◽  
Benjamin Koetz ◽  
Alessandro Burini ◽  
...  
Keyword(s):  
Web Based ◽  
Medium Resolution ◽  
On Line

scholarly journals Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Shawna Spoor ◽  
Connor Wytko ◽  
Brian Soto ◽  
Ming Chen ◽  
Abdullah Almsaeed ◽  
...  
Keyword(s):  
Workflow Management ◽  
Application Programming Interface ◽  
Scientific Workflow ◽  
Biological Databases ◽  
Web Based ◽  
Job Management ◽  
The Galaxy ◽  
Application Programming ◽  
Computational Resources ◽  
Programming Interface

Abstract Online biological databases housing genomics, genetic and breeding data can be constructed using the Tripal toolkit. Tripal is an open-source, internationally developed framework that implements FAIR data principles and is meant to ease the burden of constructing such websites for research communities. Use of a common, open framework improves the sustainability and manageability of such as site. Site developers can create extensions for their site and in turn share those extensions with others. One challenge that community databases often face is the need to provide tools for their users that analyze increasingly larger datasets using multiple software tools strung together in a scientific workflow on complicated computational resources. The Tripal Galaxy module, a ‘plug-in’ for Tripal, meets this need through integration of Tripal with the Galaxy Project workflow management system. Site developers can create workflows appropriate to the needs of their community using Galaxy and then share those for execution on their Tripal sites via automatically constructed, but configurable, web forms or using an application programming interface to power web-based analytical applications. The Tripal Galaxy module helps reduce duplication of effort by allowing site developers to spend time constructing workflows and building their applications rather than rebuilding infrastructure for job management of multi-step applications.

Automated medical citation records creation for Web-based on-line journals

2002 ◽  
Author(s):  
D.X. Le ◽  
L.Q. Tran ◽  
J. Chow ◽  
Joogwoo Kim ◽  
S.E. Hauser ◽  
...  
Keyword(s):  
Web Based ◽  
On Line
Sign in / Sign up

Export Citation Format

Share Document