scholarly journals The Neuroscience Experiments System (NES)–A Software Tool to Manage Experimental Data and Its Provenance

2022 ◽  
Vol 15 ◽  
Author(s):  
Margarita Ruiz-Olazar ◽  
Evandro Santos Rocha ◽  
Claudia D. Vargas ◽  
Kelly Rosa Braghetto
Keyword(s):  
Experimental Data ◽  
Software Tool ◽  
Free Software ◽  
Behavioral Experiments ◽  
Computational Tools ◽  
Modular Software ◽  
Data Formats ◽  
User Friendly ◽  
Neuroscience Community ◽  
Made In

Computational tools can transform the manner by which neuroscientists perform their experiments. More than helping researchers to manage the complexity of experimental data, these tools can increase the value of experiments by enabling reproducibility and supporting the sharing and reuse of data. Despite the remarkable advances made in the Neuroinformatics field in recent years, there is still a lack of open-source computational tools to cope with the heterogeneity and volume of neuroscientific data and the related metadata that needs to be collected during an experiment and stored for posterior analysis. In this work, we present the Neuroscience Experiments System (NES), a free software to assist researchers in data collecting routines of clinical, electrophysiological, and behavioral experiments. NES enables researchers to efficiently perform the management of their experimental data in a secure and user-friendly environment, providing a unified repository for the experimental data of an entire research group. Furthermore, its modular software architecture is aligned with several initiatives of the neuroscience community and promotes standardized data formats for experiments and analysis reporting.

Visualizing 3D Molecular Structures Using an Augmented Reality App

2019 ◽  
Author(s):  
Kristina Eriksen ◽  
Bjarne Nielsen ◽  
Michael Pittelkow
Keyword(s):  
Augmented Reality ◽  
Small Molecules ◽  
Computer Modelling ◽  
Simple Procedure ◽  
3D Structure ◽  
Molecular Structures ◽  
Free Software ◽  
Programming Skills ◽  
2D Space ◽  
Made In

<p>We present a simple procedure to make an augmented reality app to visualize any 3D chemical model. The molecular structure may be based on data from crystallographic data or from computer modelling. This guide is made in such a way, that no programming skills are needed and the procedure uses free software and is a way to visualize 3D structures that are normally difficult to comprehend in the 2D space of paper. The process can be applied to make 3D representation of any 2D object, and we envisage the app to be useful when visualizing simple stereochemical problems, when presenting a complex 3D structure on a poster presentation or even in audio-visual presentations. The method works for all molecules including small molecules, supramolecular structures, MOFs and biomacromolecules.</p>

pLoc_bal-mPlant: Predict Subcellular Localization of Plant Proteins by General PseAAC and Balancing Training Dataset

2019 ◽  
Vol 24 (34) ◽  
pp. 4013-4022 ◽  
Author(s):  
Xiang Cheng ◽  
Xuan Xiao ◽  
Kuo-Chen Chou
Keyword(s):  
Subcellular Localization ◽  
Basic Research ◽  
Training Dataset ◽  
Sequence Information ◽  
Plant Proteins ◽  
Protein Subcellular Localization ◽  
Computational Tools ◽  
Validation Tests ◽  
User Friendly ◽  
Better Than

Knowledge of protein subcellular localization is vitally important for both basic research and drug development. With the avalanche of protein sequences emerging in the post-genomic age, it is highly desired to develop computational tools for timely and effectively identifying their subcellular localization based on the sequence information alone. Recently, a predictor called “pLoc-mPlant” was developed for identifying the subcellular localization of plant proteins. Its performance is overwhelmingly better than that of the other predictors for the same purpose, particularly in dealing with multi-label systems in which some proteins, called “multiplex proteins”, may simultaneously occur in two or more subcellular locations. Although it is indeed a very powerful predictor, more efforts are definitely needed to further improve it. This is because pLoc-mPlant was trained by an extremely skewed dataset in which some subsets (i.e., the protein numbers for some subcellular locations) were more than 10 times larger than the others. Accordingly, it cannot avoid the biased consequence caused by such an uneven training dataset. To overcome such biased consequence, we have developed a new and bias-free predictor called pLoc_bal-mPlant by balancing the training dataset. Cross-validation tests on exactly the same experimentconfirmed dataset have indicated that the proposed new predictor is remarkably superior to pLoc-mPlant, the existing state-of-the-art predictor in identifying the subcellular localization of plant proteins. To maximize the convenience for the majority of experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc_bal-mPlant/, by which users can easily get their desired results without the need to go through the detailed mathematics.

scholarly journals Through what mechanisms do protected areas affect environmental and social outcomes?

2015 ◽  
Vol 370 (1681) ◽  
pp. 20140267 ◽  
Author(s):  
Paul J. Ferraro ◽  
Merlin M. Hanauer
Keyword(s):  
Experimental Data ◽  
Protected Areas ◽  
Empirical Evidence ◽  
Strong Evidence ◽  
Protected Area ◽  
Evidence Base ◽  
Social Outcomes ◽  
Causal Effects ◽  
The Past ◽  
Made In

To develop effective protected area policies, scholars and practitioners must better understand the mechanisms through which protected areas affect social and environmental outcomes. With strong evidence about mechanisms, the key elements of success can be strengthened, and the key elements of failure can be eliminated or repaired. Unfortunately, empirical evidence about these mechanisms is limited, and little guidance for quantifying them exists. This essay assesses what mechanisms have been hypothesized, what empirical evidence exists for their relative contributions and what advances have been made in the past decade for estimating mechanism causal effects from non-experimental data. The essay concludes with a proposed agenda for building an evidence base about protected area mechanisms.

The polarized structure function from the nonextensive statistics

2016 ◽  
Vol 25 (12) ◽  
pp. 1650101 ◽  
Author(s):  
Luis Augusto Trevisan
Keyword(s):  
Experimental Data ◽  
Structure Function ◽  
Nonextensive Statistics ◽  
Made In

In the present work, the effects of the nonextensivity are considered in a model to obtain the polarized structure function for the proton and neutron, including the strange contribution for each one. Any type of symmetry is made in consequence of the experimental data involved.

SAMPA: A free software tool for skin and membrane permeation data analysis

2017 ◽  
Vol 44 ◽  
pp. 361-371 ◽  
Author(s):  
Aleš Bezrouk ◽  
Zdeněk Fiala ◽  
Lenka Kotingová ◽  
Iva Selke Krulichová ◽  
Monika Kopečná ◽  
...  
Keyword(s):  
Data Analysis ◽  
Software Tool ◽  
Free Software ◽  
Membrane Permeation

scholarly journals Demonstration of protocol for computer-aided forensic facial reconstruction with free software and photogrammetry

2014 ◽  
Vol 2 (1) ◽  
pp. 77 ◽  
Author(s):  
Cícero André da Costa Moraes ◽  
Paulo Eduardo Miamoto Dias ◽  
Rodolfo Francisco Haltenhoff Melani
Keyword(s):  
Point Cloud ◽  
Technological Development ◽  
Skin Layer ◽  
Free Software ◽  
Facial Reconstruction ◽  
Digital Cameras ◽  
Basic Training ◽  
3D Mesh ◽  
Computer Aided ◽  
Made In

Purpose: Forensic facial reconstruction (FFR) is an auxiliary technique that approximates a face in order to generate identifications. Technological development allows access to open software that can be applied to FFR. The demonstrated protocol has features from creating 3D replicas of the skull to finishing and displaying the reconstruction. PPT GUI is used for 3D scanning, and the resulting point cloud is converted into a 3D mesh in MeshLab. The sculpture is made in Blender, according to the user’s preferred technique. The adaptation of the skin layer and finishing of the reconstruction is optimized with the use of templates. In this phase, details can also be hand-carved. Allied to basic training in the software featured in this protocol, the open access to these tools and its independence of imaging hardware other than digital cameras is an advantage to its application in forensic and research contexts.

scholarly journals Comparative analysis of methods to determine deflection in steel beams: theoretical analysis, finite element and experimental

2020 ◽  
pp. 32-37
Author(s):  
Gabriela Alor-Saavedra ◽  
Francisco Alejandro Alaffita-Hernández ◽  
Beatris Adriana Escobedo-Trujillo ◽  
Oscar Fernando Silva-Aguilar
Keyword(s):  
Differential Equation ◽  
Experimental Data ◽  
Finite Element ◽  
Comparative Analysis ◽  
Theoretical Analysis ◽  
Comparative Study ◽  
Steel Beams ◽  
Physical Systems ◽  
Theoretical Part ◽  
Made In

This work makes a comparative study of two methods to determine deflection in steel beams: (a) Theoretical and (b) Finite element. For method (a) the solution of the differential equation associated with the modeling of the deflection of a beam is found, while for method (b) a simulation is made in Solidworks. Both methods are compared with experimental data in order to analyze which of the methods presents less uncertainty and show the usefulness of the theoretical part in the modeling of physical systems.

scholarly journals CHR: An Integrated Software Tool for chilling requirements

2020 ◽  
Author(s):  
Chen Chen ◽  
Wanyu Xu ◽  
Ningning Gou ◽  
Lasu Bai ◽  
Lin Wang ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Software Tool ◽  
Fruit Trees ◽  
Cold Weather ◽  
Chilling Requirements ◽  
Deciduous Fruit ◽  
Heat Requirement ◽  
Integrated Software ◽  
User Friendly ◽  
Analyze Data

Abstract Background Bud dormancy in deciduous fruit trees enables plants to survive cold weather. The buds adopt dormant state and resume growth after satisfying the chilling requirements. Chilling requirements play a key role in flowering time. So far, several chilling models, including ≤ 7.2 °C model, the 0–7.2 °C model, Utah model, and Dynamic Model, have been developed; however, it is still time-consuming to determine the chilling requirements employing any model. This calls for efficient tools that can analyze data. Results In this study, we developed novel software Chilling and Heat Requirement (CHR), by flexibly integrating data conversions, model selection, calculations, statistical analysis, and plotting. Conclusion CHR is a tool for chilling requirements estimation, which will be very useful to researchers. It is very simple, easy, and user-friendly.

scholarly journals FIREcaller: Detecting Frequently Interacting Regions from Hi-C Data

2019 ◽  
Author(s):  
Cheynna Crowley ◽  
Yuchen Yang ◽  
Yunjiang Qiu ◽  
Benxia Hu ◽  
Armen Abnousi ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Spatial Organization ◽  
R Package ◽  
Specific Gene ◽  
List Type ◽  
Cell Type ◽  
R Software ◽  
Computational Tools ◽  
Cell Type Specific ◽  
User Friendly

AbstractHi-C experiments have been widely adopted to study chromatin spatial organization, which plays an essential role in genome function. We have recently identified frequently interacting regions (FIREs) and found that they are closely associated with cell-type-specific gene regulation. However, computational tools for detecting FIREs from Hi-C data are still lacking. In this work, we present FIREcaller, a stand-alone, user-friendly R package for detecting FIREs from Hi-C data. FIREcaller takes raw Hi-C contact matrices as input, performs within-sample and cross-sample normalization, and outputs continuous FIRE scores, dichotomous FIREs, and super-FIREs. Applying FIREcaller to Hi-C data from various human tissues, we demonstrate that FIREs and super-FIREs identified, in a tissue-specific manner, are closely related to gene regulation, are enriched for enhancer-promoter (E-P) interactions, tend to overlap with regions exhibiting epigenomic signatures of cis-regulatory roles, and aid the interpretation or GWAS variants. The FIREcaller package is implemented in R and freely available at https://yunliweb.its.unc.edu/FIREcaller.Highlights– Frequently Interacting Regions (FIREs) can be used to identify tissue and cell-type-specific cis-regulatory regions.– An R software, FIREcaller, has been developed to identify FIREs and clustered FIREs into super-FIREs.

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