Dataset Information

Web-Based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioral Experiment Definition and Experiment Results Visualization.

ABSTRACT: The Si elegans platform targets the complete virtualization of the nematode Caenorhabditis elegans, and its environment. This paper presents a suite of unified web-based Graphical User Interfaces (GUIs) as the main user interaction point, and discusses their underlying technologies and methods. The user-friendly features of this tool suite enable users to graphically create neuron and network models, and behavioral experiments, without requiring knowledge of domain-specific computer-science tools. The framework furthermore allows the graphical visualization of all simulation results using a worm locomotion and neural activity viewer. Models, experiment definitions and results can be exported in a machine-readable format, thereby facilitating reproducible and cross-platform execution of in silico C. elegans experiments in other simulation environments. This is made possible by a novel XML-based behavioral experiment definition encoding format, a NeuroML XML-based model generation and network configuration description language, and their associated GUIs. User survey data confirms the platform usability and functionality, and provides insights into future directions for web-based simulation GUIs of C. elegans and other living organisms. The tool suite is available online to the scientific community and its source code has been made available.

SUBMITTER: Epelde G

PROVIDER: S-EPMC6243129 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Web-Based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioral Experiment Definition and Experiment Results Visualization.

Epelde Gorka G Morgan Fearghal F Mujika Andoni A Callaly Frank F Leškovský Peter P McGinley Brian B Álvarez Roberto R Blau Axel A Krewer Finn F

Frontiers in neuroinformatics 20181113

The Si elegans platform targets the complete virtualization of the nematode Caenorhabditis elegans, and its environment. This paper presents a suite of unified web-based Graphical User Interfaces (GUIs) as the main user interaction point, and discusses their underlying technologies and methods. The user-friendly features of this tool suite enable users to graphically create neuron and network models, and behavioral experiments, without requiring knowledge of domain-specific compute ...[more]

PMID: 30483089

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Project description:BackgroundCurrently there is a strong need for methods that help to obtain an accurate description of protein interfaces in order to be able to understand the principles that govern molecular recognition and protein function. Many of the recent efforts to computationally identify and characterize protein networks extract protein interaction information at atomic resolution from the PDB. However, they pay none or little attention to small protein ligands and solvent. They are key components and mediators of protein interactions and fundamental for a complete description of protein interfaces. Interactome profiling requires the development of computational tools to extract and analyze protein-protein, protein-ligand and detailed solvent interaction information from the PDB in an automatic and comparative fashion. Adding this information to the existing one on protein-protein interactions will allow us to better understand protein interaction networks and protein function.DescriptionSCOWLP (Structural Characterization Of Water, Ligands and Proteins) is a user-friendly and publicly accessible web-based relational database for detailed characterization and visualization of the PDB protein interfaces. The SCOWLP database includes proteins, peptidic-ligands and interface water molecules as descriptors of protein interfaces. It contains currently 74,907 protein interfaces and 2,093,976 residue-residue interactions formed by 60,664 structural units (protein domains and peptidic-ligands) and their interacting solvent. The SCOWLP web-server allows detailed structural analysis and comparisons of protein interfaces at atomic level by text query of PDB codes and/or by navigating a SCOP-based tree. It includes a visualization tool to interactively display the interfaces and label interacting residues and interface solvent by atomic physicochemical properties. SCOWLP is automatically updated with every SCOP release.ConclusionSCOWLP enriches substantially the description of protein interfaces by adding detailed interface information of peptidic-ligands and solvent to the existing protein-protein interaction databases. SCOWLP may be of interest to many structural bioinformaticians. It provides a platform for automatic global mapping of protein interfaces at atomic level, representing a useful tool for classification of protein interfaces, protein binding comparative studies, reconstruction of protein complexes and understanding protein networks. The web-server with the database and its additional summary tables used for our analysis are available at http://www.scowlp.org.

Project description:BACKGROUND:Virtual stores can be used to identify influences on consumer shopping behavior. Deception is one technique that may be used to attempt to increase the realism of virtual stores. OBJECTIVE:The objective of the experiment was to test whether the purchasing behavior of participants in a virtual shopping task varied based on whether they were told that they would receive the products they selected in a virtual convenience store (a form of deception) or not. METHODS:We recruited a US national sample of 402 adult current smokers by email from an online panel of survey participants. They completed a fully automated randomized virtual shopping experiment with a US $15 or US $20 budget in a Web-based virtual convenience store. We told a random half of participants that they would receive the products they chose in the virtual store or the cash equivalent (intervention condition), and the other random half simply to conduct a shopping task (control condition). We tested for differences in demographics, tobacco use behaviors, and in-store purchases (outcome variable, assessed by questionnaire) by experimental condition. RESULTS:The characteristics of the participants (398/402, 99.0% with complete data) were comparable across conditions except that the intervention group contained slightly more female participants (103/197, 52.3%) than the control group (84/201, 41.8%; P=.04). We did not find any other significant differences in any other demographic variables or tobacco use, or in virtual store shopping behaviors, including purchasing any tobacco (P=.44); purchasing cigarettes (P=.16), e-cigarettes (P=.54), cigars (P=.98), or smokeless tobacco (P=.72); amount spent overall (P=.63) or on tobacco (P=.66); percentage of budget spent overall (P=.84) or on tobacco (P=.74); number of total items (P=.64) and tobacco items purchased (P=.54); or total time spent in the store (P=.07). CONCLUSIONS:We found that telling participants that they will receive the products they select in a virtual store did not influence their purchases. This finding suggests that deception may not affect consumer behavior and, as a result, may not be necessary in virtual shopping experiments.

Dataset Information

Web-Based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioral Experiment Definition and Experiment Results Visualization.

Publications

Web-Based Interfaces for Virtual <i>C. elegans</i> Neuron Model Definition, Network Configuration, Behavioral Experiment Definition and Experiment Results Visualization.

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