scholarly journals iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures

2019 ◽  
Vol 36 (1) ◽  
pp. 131-135 ◽  
Author(s):  
Jiyao Wang ◽  
Philippe Youkharibache ◽  
Dachuan Zhang ◽  
Christopher J Lanczycki ◽  
Renata C Geer ◽  
...  
Keyword(s):  
Large Fraction ◽  
3D Structure ◽  
Supplementary Information ◽  
Sequence Annotation ◽  
Web Based ◽  
The Public ◽  
Molecular Features ◽  
Density Maps ◽  
3D Molecular Structure ◽  
3D Representations

Abstract Motivation Build a web-based 3D molecular structure viewer focusing on interactive structural analysis. Results iCn3D (I-see-in-3D) can simultaneously show 3D structure, 2D molecular contacts and 1D protein and nucleotide sequences through an integrated sequence/annotation browser. Pre-defined and arbitrary molecular features can be selected in any of the 1D/2D/3D windows as sets of residues and these selections are synchronized dynamically in all displays. Biological annotations such as protein domains, single nucleotide variations, etc. can be shown as tracks in the 1D sequence/annotation browser. These customized displays can be shared with colleagues or publishers via a simple URL. iCn3D can display structure–structure alignments obtained from NCBI’s VAST+ service. It can also display the alignment of a sequence with a structure as identified by BLAST, and thus relate 3D structure to a large fraction of all known proteins. iCn3D can also display electron density maps or electron microscopy (EM) density maps, and export files for 3D printing. The following example URL exemplifies some of the 1D/2D/3D representations: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1TUP&showanno=1&show2d=1&showsets=1. Availability and implementation iCn3D is freely available to the public. Its source code is available at https://github.com/ncbi/icn3d. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals iCn3D, a Web-based 3D Viewer for Sharing 1D/2D/3D Representations of Biomolecular Structures

2018 ◽  
Author(s):  
Jiyao Wang ◽  
Philippe Youkharibache ◽  
Dachuan Zhang ◽  
Christopher J. Lanczycki ◽  
Renata C. Geer ◽  
...  
Keyword(s):  
Large Fraction ◽  
3D Structure ◽  
Structure Alignment ◽  
Supplementary Information ◽  
Sequence Annotation ◽  
Web Based ◽  
Link Type ◽  
Molecular Features ◽  
Density Maps ◽  
3D Representations

AbstractSummaryiCn3D (I-see-in-3D) is a web-based 3D molecular structure viewer focusing on the interactive structural analysis. It can simultaneously show 3D structure, 2D molecular contacts, and 1D protein and nucleotide sequences through an integrated sequence/annotation browser. Pre-defined and arbitrary molecular features can be selected in any of the 1D/2D/3D windows as sets of residues and these selections are synchronized dynamically in all displays. Biological annotations such as protein domains, single nucleotide variations, etc. can be shown as tracks in the 1D sequence/annotation browser. These customized displays can be shared with colleagues or publishers via a simple URL. iCn3D can display structure-structure alignment obtained from NCBI’s VAST+ service. It can also display the alignment of a sequence with a structure as identified by BLAST, and thus relate 3D structure to a large fraction of all known proteins. iCn3D can also display electron density maps or electron microscopy (EM) density maps, and export files for 3D printing. The following example URL exemplifies some of the 1D/2D/3D representations: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1TUP&showanno=1&show2d=1&showsets=1.Availability and implementationiCn3D is freely available to the public. Its source code is available at https://github.com/ncbi/icn3d.Supplementary informationUser instructions are available at Bioinformatics online

scholarly journals CSynth: an interactive modelling and visualization tool for 3D chromatin structure

2020 ◽  
Author(s):  
Stephen Todd ◽  
Peter Todd ◽  
Simon J McGowan ◽  
James R Hughes ◽  
Yasutaka Kakui ◽  
...  
Keyword(s):  
3D Structure ◽  
Chromosome Conformation Capture ◽  
Third Party ◽  
Supplementary Information ◽  
Chromosome Conformation ◽  
Web Based ◽  
3D Genome ◽  
Interactive 3D ◽  
Interactive Modelling ◽  
Capture Techniques

Abstract Motivation The 3D structure of chromatin in the nucleus is important for gene expression and regulation. Chromosome conformation capture techniques, such as Hi-C, generate large amounts of data showing interaction points on the genome but these are hard to interpret using standard tools. Results We have developed CSynth, an interactive 3D genome browser and real-time chromatin restraint-based modeller to visualize models of any chromosome conformation capture (3C) data. Unlike other modelling systems, CSynth allows dynamic interaction with the modelling parameters to allow experimentation and effects on the model. It also allows comparison of models generated from data in different tissues/cell states and the results of third-party 3D modelling outputs. In addition, we include an option to view and manipulate these complicated structures using Virtual Reality (VR) so scientists can immerse themselves in the models for further understanding. This VR component has also proven to be a valuable teaching and a public engagement tool. Availabilityand implementation CSynth is web based and available to use at https://csynth.org. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals The Glycine Receptor Allosteric Ligands Library (GRALL)

2020 ◽  
Vol 36 (11) ◽  
pp. 3379-3384 ◽  
Author(s):  
Adrien H Cerdan ◽  
Marion Sisquellas ◽  
Gilberto Pereira ◽  
Diego E Barreto Gomes ◽  
Jean-Pierre Changeux ◽  
...  
Keyword(s):  
Binding Site ◽  
Large Fraction ◽  
Glycine Receptor ◽  
Supplementary Information ◽  
Allosteric Modulators ◽  
Structural Annotation ◽  
Pharmacological Targets ◽  
Displacement Experiments ◽  
3D Molecular Structure ◽  
Putative Binding Site

Abstract Motivation Glycine receptors (GlyRs) mediate fast inhibitory neurotransmission in the brain and have been recognized as key pharmacological targets for pain. A large number of chemically diverse compounds that are able to modulate GlyR function both positively and negatively have been reported, which provides useful information for the development of pharmacological strategies and models for the allosteric modulation of these ion channels. Results Based on existing literature, we have collected 218 unique chemical entities with documented modulatory activities at homomeric GlyR-α1 and -α3 and built a database named GRALL. This collection includes agonists, antagonists, positive and negative allosteric modulators and a number of experimentally inactive compounds. Most importantly, for a large fraction of them a structural annotation based on their putative binding site on the receptor is provided. This type of annotation, which is currently missing in other drug banks, along with the availability of cooperativity factors from radioligand displacement experiments are expected to improve the predictivity of in silico methodologies for allosteric drug discovery and boost the development of conformation-based pharmacological approaches. Availability and implementation The GRALL library is distributed as a web-accessible database at the following link: https://ifm.chimie.unistra.fr/grall. For each molecular entry, it provides information on the chemical structure, the ligand-binding site, the direction of modulation, the potency, the 3D molecular structure and quantum-mechanical charges as determined by our in-house pipeline. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

DESIGN AND DEVELOPMENT OF POPULATION SERVICE ADMINISTRATION SYSTEM WITH PIECES METHOD IN KEMIRI VILLAGE HEAD OFFICE BANTEN

2019 ◽  
Vol 1 (1) ◽  
pp. 33-45
Author(s):  
Rosdiana Rosdiana ◽  
Padeli Padeli ◽  
Revi Sajidah Sri Handayani ◽  
Rifky Alfian
Keyword(s):  
Human Error ◽  
Unified Modeling Language ◽  
Integrated System ◽  
Web Based ◽  
Administration System ◽  
Unified Modeling ◽  
The Public ◽  
File Storage ◽  
The Government ◽  
The Village

The public service administration system at the government offices of the Kemiri village office in the Kemiri District currently does not have a computerized and integrated system. Because the system runs, residents who submit letters for administrative completeness, still use the Ms.Word / Ms.Excel application. of course has many weaknesses including human error, not neat in file storage, resulting in the lengthy process of searching and making a cover letter and required reports. The analytical method used in this study is to use PIECES (Performance, Informance, Economy, Control, Efficiency, Service) analysis, the design of the model uses UML (Unified Modeling Language). The results of this study are web-based letter information systems at the Office of the Village Chief of Kemiri that can accessed using a local computer browser. Thus the information letter needed by the Kemiri Village community and more effective and efficient in making the letter.

scholarly journals ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Quantifying Media Effects, Its Content, and Role in Promoting Community Awareness of Chikungunya Epidemic in Bangladesh

Epidemiologia ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 84-94
Author(s):  
Mst. Marium Begum ◽  
Osman Ulvi ◽  
Ajlina Karamehic-Muratovic ◽  
Mallory R. Walsh ◽  
Hasan Tarek ◽  
...  
Keyword(s):  
Social Media ◽  
Web Based ◽  
Study Objective ◽  
The Public ◽  
Mainstream Media ◽  
Related Information ◽  
Vector Borne ◽  
Media Outlet ◽  
And Control

Background: Chikungunya is a vector-borne disease, mostly present in tropical and subtropical regions. The virus is spread by Ae. aegypti and Ae. albopictus mosquitos and symptoms include high fever to severe joint pain. Dhaka, Bangladesh, suffered an outbreak of chikungunya in 2017 lasting from April to September. With the goal of reducing cases, social media was at the forefront during this outbreak and educated the public about symptoms, prevention, and control of the virus. Popular web-based sources such as the top dailies in Bangladesh, local news outlets, and Facebook spread awareness of the outbreak. Objective: This study sought to investigate the role of social and mainstream media during the chikungunya epidemic. The study objective was to determine if social media can improve awareness of and practice associated with reducing cases of chikungunya. Methods: We collected chikungunya-related information circulated from the top nine television channels in Dhaka, Bangladesh, airing from 1st April–20th August 2017. All the news published in the top six dailies in Bangladesh were also compiled. The 50 most viewed chikungunya-related Bengali videos were manually coded and analyzed. Other social media outlets, such as Facebook, were also analyzed to determine the number of chikungunya-related posts and responses to these posts. Results: Our study showed that media outlets were associated with reducing cases of chikungunya, indicating that media has the potential to impact future outbreaks of these alpha viruses. Each media outlet (e.g., web, television) had an impact on the human response to an individual’s healthcare during this outbreak. Conclusions: To prevent future outbreaks of chikungunya, media outlets and social media can be used to educate the public regarding prevention strategies such as encouraging safe travel, removing stagnant water sources, and assisting with tracking cases globally to determine where future outbreaks may occur.

scholarly journals Epidemiological modeling in StochSS Live!

2021 ◽  
Author(s):  
Richard Jiang ◽  
Bruno Jacob ◽  
Matthew Geiger ◽  
Sean Matthew ◽  
Bryan Rumsey ◽  
...  
Keyword(s):  
Stochastic Model ◽  
Epidemiological Model ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Web Based ◽  
Epidemiological Modeling ◽  
Modeling Simulation ◽  
Wide Range ◽  
Biochemical Systems

Abstract Summary We present StochSS Live!, a web-based service for modeling, simulation and analysis of a wide range of mathematical, biological and biochemical systems. Using an epidemiological model of COVID-19, we demonstrate the power of StochSS Live! to enable researchers to quickly develop a deterministic or a discrete stochastic model, infer its parameters and analyze the results. Availability and implementation StochSS Live! is freely available at https://live.stochss.org/ Supplementary information Supplementary data are available at Bioinformatics online.

Perceptions Regarding the Academic and Cognitive Performance of Individuals With Cleft Lip and/or Palate

2021 ◽  
pp. 105566562199530
Author(s):  
İlkem Kara ◽  
Aydan Baştuğ Dumbak ◽  
Maviş Emel Kulak Kayıkcı
Keyword(s):  
Academic Performance ◽  
Cognitive Performance ◽  
General Public ◽  
Cleft Lip ◽  
Group Differences ◽  
Web Based ◽  
The Public ◽  
Adverse Impacts ◽  
Facial Difference ◽  
Self Administered Questionnaire

Introduction: Factors such as teachers’ appropriate support and social interactions have an impact on the academic performance of children with cleft lip and/or palate (CL/P). This study was designed to investigate the perceptions of the teachers and the general public about the academic and cognitive performance of individuals with CL/P. Methods: This study was included 360 (male/female = 102/258) teachers and 640 (male/female = 259/381) participants that represent the general public. Anonymized web-based and paper-and-pencil self-administered questionnaire that included multiple-choice and yes/no questions were administered. Within-group differences and intergroup differences were analyzed in terms of academic and cognitive performance. Results: Most of the teachers and the general public indicated that the academic and cognitive performance of individuals with CL/P is the same as their unaffected peers. A significantly higher proportion of the teachers indicated that the academic performance of children with CL/P is the same as their unaffected peers than the general public. Conclusion: Considering that the general public’s attitudes and appropriate teacher support are crucial to prevent adverse impacts on the lives of individuals with CL/P, it is important to support teachers with the appropriate information and to encourage the public to recognize that everybody with a facial difference should be treated as an individual rather than a disability.

CPVA: a web-based metabolomic tool for chromatographic peak visualization and annotation

2020 ◽  
Vol 36 (12) ◽  
pp. 3913-3915
Author(s):  
Hemi Luan ◽  
Xingen Jiang ◽  
Fenfen Ji ◽  
Zhangzhang Lan ◽  
Zongwei Cai ◽  
...  
Keyword(s):  
False Positive ◽  
Supplementary Information ◽  
Liquid Chromatography Mass Spectrometry ◽  
Targeted Metabolomics ◽  
Metabolomics Data ◽  
Web Based ◽  
Tremendous Amount ◽  
Chromatographic Peaks ◽  
User Friendly

Abstract Motivation Liquid chromatography–mass spectrometry-based non-targeted metabolomics is routinely performed to qualitatively and quantitatively analyze a tremendous amount of metabolite signals in complex biological samples. However, false-positive peaks in the datasets are commonly detected as metabolite signals by using many popular software, resulting in non-reliable measurement. Results To reduce false-positive calling, we developed an interactive web tool, termed CPVA, for visualization and accurate annotation of the detected peaks in non-targeted metabolomics data. We used a chromatogram-centric strategy to unfold the characteristics of chromatographic peaks through visualization of peak morphology metrics, with additional functions to annotate adducts, isotopes and contaminants. CPVA is a free, user-friendly tool to help users to identify peak background noises and contaminants, resulting in decrease of false-positive or redundant peak calling, thereby improving the data quality of non-targeted metabolomics studies. Availability and implementation The CPVA is freely available at http://cpva.eastus.cloudapp.azure.com. Source code and installation instructions are available on GitHub: https://github.com/13479776/cpva. Supplementary information Supplementary data are available at Bioinformatics online.

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