scholarly journals ORCAE-AOCC: A Centralized Portal for the Annotation of African Orphan Crop Genomes

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 950
Author(s):  
Anna E. J. Yssel ◽  
Shu-Min Kao ◽  
Yves Van de Peer ◽  
Lieven Sterck
Keyword(s):  
Gene Model ◽  
Underutilized Crops ◽  
Knowledge Based ◽  
Online Resource ◽  
Or Gene ◽  
Genome Annotations ◽  
Expression Evidence ◽  
User Friendly ◽  
Community Annotation ◽  
Orphan Crop

ORCAE (Online Resource for Community Annotation of Eukaryotes) is a public genome annotation curation resource. ORCAE-AOCC is a branch that is dedicated to the genomes published as part of the African Orphan Crops Consortium (AOCC). The motivation behind the development of the ORCAE platform was to create a knowledge-based website where the research-community can make contributions to improve genome annotations. All changes to any given gene-model or gene description are stored, and the entire annotation history can be retrieved. Genomes can either be set to “public” or “restricted” mode; anonymous users can browse public genomes but cannot make any changes. Aside from providing a user- friendly interface to view genome annotations, the platform also includes tools and information (such as gene expression evidence) that enables authorized users to edit and validate genome annotations. The ORCAE-AOCC platform will enable various stakeholders from around the world to coordinate their efforts to annotate and study underutilized crops.

scholarly journals ONTOLOGY-BASED WEB TOOLS FOR RETRIEVING PHOTOGRAMMETRIC CULTURAL HERITAGE MODELS

2019 ◽  
Vol XLII-2/W10 ◽  
pp. 31-38 ◽  
Author(s):  
M. Ben Ellefi ◽  
P. Drap ◽  
O. Papini ◽  
D. Merad ◽  
J. P. Royer ◽  
...  
Keyword(s):  
Cultural Heritage ◽  
Specific Knowledge ◽  
Domain Specific ◽  
Knowledge Based ◽  
Web Tools ◽  
Domain Specific Knowledge ◽  
Visualization Systems ◽  
User Friendly ◽  
Machine Readable ◽  
Associated Knowledge

<p><strong>Abstract.</strong> A key challenge in cultural heritage (CH) sites visualization is to provide models and tools that effectively integrate the content of a CH data with domain-specific knowledge so that the users can query, interpret and consume the visualized information. Moreover, it is important that the intelligent visualization systems are interoperable in the semantic web environment and thus, capable of establishing a methodology to acquire, integrate, analyze, generate and share numeric contents and associated knowledge in human and machine-readable Web. In this paper, we present a model, a methodology and a software Web-tools that support the coupling of the 2D/3D Web representation with the knowledge graph database of <i>Xlendi</i> shipwreck. The Web visualization tools and the knowledge-based techniques are married into a photogrammetry driven ontological model while at the same time, user-friendly web tools for querying and semantic consumption of the shipwreck information are introduced.</p>

scholarly journals Application of Parameter Optimization to Search for Oscillatory Mass-Action Networks Using Python

Processes ◽  
2019 ◽  
Vol 7 (3) ◽  
pp. 163 ◽  
Author(s):  
Veronica Porubsky ◽  
Herbert Sauro
Keyword(s):  
Regulatory Networks ◽  
Differential Evolution Algorithm ◽  
Mass Action ◽  
Oscillatory Dynamics ◽  
Metabolic Protein ◽  
Evolution Algorithm ◽  
Or Gene ◽  
Action Networks ◽  
User Friendly

Biological systems can be described mathematically to model the dynamics of metabolic, protein, or gene-regulatory networks, but locating parameter regimes that induce a particular dynamic behavior can be challenging due to the vast parameter landscape, particularly in large models. In the current work, a Pythonic implementation of existing bifurcation objective functions, which reward systems that achieve a desired bifurcation behavior, is implemented to search for parameter regimes that permit oscillations or bistability. A differential evolution algorithm progressively approximates the specified bifurcation type while performing a global search of parameter space for a candidate with the best fitness. The user-friendly format facilitates integration with systems biology tools, as Python is a ubiquitous programming language. The bifurcation–evolution software is validated on published models from the BioModels Database and used to search populations of randomly-generated mass-action networks for oscillatory dynamics. Results of this search demonstrate the importance of reaction enrichment to provide flexibility and enable complex dynamic behaviors, and illustrate the role of negative feedback and time delays in generating oscillatory dynamics.

scholarly journals Application of Differential Network Enrichment Analysis for Deciphering Metabolic Alterations

Metabolites ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 479
Author(s):  
Gayatri R. Iyer ◽  
Janis Wigginton ◽  
William Duren ◽  
Jennifer L. LaBarre ◽  
Marci Brandenburg ◽  
...  
Keyword(s):  
Simultaneous Detection ◽  
Enrichment Analysis ◽  
Data Sets ◽  
Complex Data ◽  
Metabolomics Data ◽  
Knowledge Based ◽  
Differential Network ◽  
Complex Data Sets ◽  
User Friendly

Modern analytical methods allow for the simultaneous detection of hundreds of metabolites, generating increasingly large and complex data sets. The analysis of metabolomics data is a multi-step process that involves data processing and normalization, followed by statistical analysis. One of the biggest challenges in metabolomics is linking alterations in metabolite levels to specific biological processes that are disrupted, contributing to the development of disease or reflecting the disease state. A common approach to accomplishing this goal involves pathway mapping and enrichment analysis, which assesses the relative importance of predefined metabolic pathways or other biological categories. However, traditional knowledge-based enrichment analysis has limitations when it comes to the analysis of metabolomics and lipidomics data. We present a Java-based, user-friendly bioinformatics tool named Filigree that provides a primarily data-driven alternative to the existing knowledge-based enrichment analysis methods. Filigree is based on our previously published differential network enrichment analysis (DNEA) methodology. To demonstrate the utility of the tool, we applied it to previously published studies analyzing the metabolome in the context of metabolic disorders (type 1 and 2 diabetes) and the maternal and infant lipidome during pregnancy.

ORCAE: online resource for community annotation of eukaryotes

2012 ◽  
Vol 9 (11) ◽  
pp. 1041-1041 ◽  
Author(s):  
Lieven Sterck ◽  
Kenny Billiau ◽  
Thomas Abeel ◽  
Pierre Rouzé ◽  
Yves Van de Peer
Keyword(s):  
Online Resource ◽  
Community Annotation

scholarly journals Conceptual Design of a Comprehensive Farm Nitrogen Management System

Agronomy ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 2501
Author(s):  
Fabian Weckesser ◽  
Frank Leßke ◽  
Marco Luthardt ◽  
Kurt-Jürgen Hülsbergen
Keyword(s):  
Management System ◽  
Nutrient Management ◽  
Management Tools ◽  
Knowledge Based ◽  
Innovation Potential ◽  
Digital Format ◽  
N Management ◽  
User Friendly ◽  
Data Requirements

Data that are required for nutrient management are becoming increasingly available in digital format, leading to a high innovation potential for digital nitrogen (N) management applications. However, it is currently difficult for farmers to analyze, assess, and optimize N flows in their farms using the existing software. To improve digital N management, this study identified, evaluated, and systematized the requirements of stakeholders. Furthermore, digital farm N management tools with varying objectives in terms of system boundaries, data requirements, used methods and algorithms, performance, and practicality were appraised and categorized. According to the identified needs, the concept of a farm N management system (FNMS) software is presented which includes the following modules: (1) management of site and farm data, (2) determination of fertilizer requirements, (3) N balancing and cycles, (4) N turnover and losses, and (5) decision support. The aim of FNMS is to support farmers in their farming practices for increasing N efficiency and reducing environmentally harmful N surpluses. In this study, the conceptual requirements from the agricultural and computer science perspectives were determined as a basis for developing a consistent, scientifically sound, and user-friendly FNMS, especially applicable in European countries. This FNMS enables farmers and their advisors to make knowledge-based decisions based on comprehensive and integrated data.

scholarly journals BORDERLESS GEOSPATIAL WEB (BOLEGWEB)

2016 ◽  
Vol XLI-B4 ◽  
pp. 677-682
Author(s):  
V. Cetl ◽  
T. Kliment ◽  
M. Kliment
Keyword(s):  
Spatial Data ◽  
The European Union ◽  
Geospatial Information ◽  
User Perspective ◽  
Knowledge Based ◽  
Discovery Service ◽  
Seventh Framework Programme ◽  
Data Infrastructures ◽  
User Friendly ◽  
The Web

The effective access and use of geospatial information (GI) resources acquires a critical value of importance in modern knowledge based society. Standard web services defined by Open Geospatial Consortium (OGC) are frequently used within the implementations of spatial data infrastructures (SDIs) to facilitate discovery and use of geospatial data. This data is stored in databases located in a layer, called the invisible web, thus are ignored by search engines. SDI uses a catalogue (discovery) service for the web as a gateway to the GI world through the metadata defined by ISO standards, which are structurally diverse to OGC metadata. Therefore, a crosswalk needs to be implemented to bridge the OGC resources discovered on mainstream web with those documented by metadata in an SDI to enrich its information extent. A public global wide and user friendly portal of OGC resources available on the web ensures and enhances the use of GI within a multidisciplinary context and bridges the geospatial web from the end-user perspective, thus opens its borders to everybody. &lt;br&gt;&lt;br&gt; Project “Crosswalking the layers of geospatial information resources to enable a borderless geospatial web” with the acronym BOLEGWEB is ongoing as a postdoctoral research project at the Faculty of Geodesy, University of Zagreb in Croatia (http://bolegweb.geof.unizg.hr/). The research leading to the results of the project has received funding from the European Union Seventh Framework Programme (FP7 2007-2013) under Marie Curie FP7-PEOPLE-2011-COFUND. The project started in the November 2014 and is planned to be finished by the end of 2016. This paper provides an overview of the project, research questions and methodology, so far achieved results and future steps.

scholarly journals CEDAR, an online resource for the reporting and exploration of complexome profiling data

2020 ◽  
Author(s):  
Joeri van Strien ◽  
Alexander Haupt ◽  
Uwe Schulte ◽  
Hans-Peter Braun ◽  
Alfredo Cabrero-Orefice ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Complexes ◽  
Mass Spectrometry Data ◽  
Analysis Tool ◽  
Data Resource ◽  
Online Resource ◽  
Comprehensive Information ◽  
Central Resource ◽  
Rest Api ◽  
User Friendly

Complexome profiling is an emerging 'omics approach that systematically interrogates the composition of protein complexes (the complexome) of a sample, by combining biochemical separation of native protein complexes with mass-spectrometry based quantitation proteomics. The resulting fractionation profiles hold comprehensive information on the abundance and composition of the complexome, and have a high potential for reuse by experimental and computational researchers. However, the lack of a central resource that provides access to these data, reported with adequate descriptions and an analysis tool, has limited their reuse. Therefore, we established the ComplexomE profiling DAta Resource (CEDAR, www3.cmbi.umcn.nl/cedar/), an openly accessible database for depositing and exploring mass spectrometry data from complexome profiling studies. Compatibility and reusability of the data is ensured by a standardized data and reporting format containing the "minimum information required for a complexome profiling experiment" (MIACE). The data can be accessed through a user-friendly web interface, as well as programmatically using the REST API portal. Additionally, all complexome profiles available on CEDAR can be inspected directly on the website with the profile viewer tool that allows the detection of correlated profile sand inference of potential complexes. In conclusion, CEDAR is a unique,growing and invaluable resource for the study of protein complex composition and dynamics across biological systems.

scholarly journals A comprehensive resource for retrieving, visualizing, and integrating functional genomics data

2019 ◽  
Vol 3 (1) ◽  
pp. e201900546
Author(s):  
Matthias Blum ◽  
Pierre-Etienne Cholley ◽  
Valeriya Malysheva ◽  
Samuel Nicaise ◽  
Julien Moehlin ◽  
...  
Keyword(s):  
Functional Genomics ◽  
High Performance ◽  
Large Scale ◽  
Quality Data ◽  
Multidimensional Data ◽  
Online Resource ◽  
Public Data ◽  
User Friendly ◽  
Quality Assessments ◽  
Multidimensional Data Integration

The enormous amount of freely accessible functional genomics data is an invaluable resource for interrogating the biological function of multiple DNA-interacting players and chromatin modifications by large-scale comparative analyses. However, in practice, interrogating large collections of public data requires major efforts for (i) reprocessing available raw reads, (ii) incorporating quality assessments to exclude artefactual and low-quality data, and (iii) processing data by using high-performance computation. Here, we present qcGenomics, a user-friendly online resource for ultrafast retrieval, visualization, and comparative analysis of tens of thousands of genomics datasets to gain new functional insight from global or focused multidimensional data integration.

An Intelligent Wearable Platform for Real Time Pilot's Health Telemonitoring

2008 ◽  
pp. 777-784
Author(s):  
Christos Papadelis ◽  
Chrysoula Kourtidou-Papadeli ◽  
Fotini Lazaridou ◽  
Eleni Perantoni
Keyword(s):  
Health Status ◽  
Real Time ◽  
Vital Signs ◽  
Health And Safety ◽  
National Research Council ◽  
Pilot Performance ◽  
Clustering Techniques ◽  
Knowledge Based ◽  
Pressure Changes ◽  
User Friendly

Aviators engage in a variety of outdoor activities where their health status, the environment, and the degree of workload and fatigue affect their performance. An innovative tool has been developed, which supports the real-time health monitoring of pilots using new algorithms based on intelligent clustering techniques for the recognition of possible health problems in flight. The Smart Profiler and the Intelligent Advisor modules of this system exploit the use of knowledge based expert systems and intelligent classification techniques. Coupled with the Portal, which also exploits the use of intelligent clustering techniques, it estimates the pilot’s performance in unknown environments. The new system targets recognizing possible problems at the time of flying, but it can also be used for the monitoring of the pilot performance and progress throughout a period of time, as it stores information from different flying sessions. The system was applied in 20 private pilots during the flight of a Cessna 152 aerobatic. The device was reliable and user-friendly, enabling us to monitor real-time health status of aviators in order to detect possible problems caused by the actual environmental conditions to which individuals are exposed, thus contributing to their health and safety in their working environments. Despite the automation and increasing technological complexity of modern aircrafts, the human operator still plays an important role in controlling those demanding systems. Piloting an aircraft is a highly complex task that requires the pilot to be proficient in numerous skills (Wilson & Eggemeier, 1991) in a hostile environment of cabin pressure changes and circadian rhythm disturbances particularly in long duration flights. The resulting overload of the pilots mandates the need for real time health telemonitoring (Charles, Winget, Charles, De- Roshia, Markley, & Holley, 1984; Denison, Ledwith, & Poulton, 1966; U.S. National Research Council, 2002; Ustinaviciene, Obelenis, & Ereminas, 2004). Real time health telemonitoring would be crucial to early detect and prevent conditions affecting aviator’s vital signs and cognitive performance.

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