scholarly journals Comparing protein structures with RINspector automation in Cytoscape

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 563 ◽  
Author(s):  
Guillaume Brysbaert ◽  
Théo Mauri ◽  
Marc F. Lensink
Keyword(s):  
Protein Structures ◽  
Application Programming Interface ◽  
Easy Access ◽  
Network Centrality ◽  
Backbone Flexibility ◽  
Residue Interaction ◽  
Application Programming ◽  
Quaternary Structures ◽  
The Impact ◽  
Programming Interface

Residue interaction networks (RINs) have been shown to be relevant representations of the tertiary or quaternary structures of proteins, in particular thanks to network centrality analyses. We recently developed the RINspector 1.0.0 Cytoscape app, which couples centrality analyses with backbone flexibility predictions. This combined approach permits the identification of crucial residues for the folding or function of the protein that can constitute good targets for mutagenesis experiments. Here we present an application programming interface (API) for RINspector 1.1.0 that enables interplay between Cytoscape, RINspector and external languages, such as R or Python. This API provides easy access to batch centrality calculations and flexibility predictions, and allows for the easy comparison of results between different structures. These comparisons can lead to the identification of specific and conserved central residues, and show the impact of mutations to these and other residues on the flexibility of the proteins. We give two use cases to demonstrate the interest of these functionalities and provide the corresponding scripts: the first concerns NMR conformers, the second focuses on mutations in a structure.

scholarly journals Comparing protein structures with RINspector automation in Cytoscape

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 563 ◽  
Author(s):  
Guillaume Brysbaert ◽  
Théo Mauri ◽  
Marc F. Lensink
Keyword(s):  
Protein Structures ◽  
Application Programming Interface ◽  
Easy Access ◽  
Network Centrality ◽  
Backbone Flexibility ◽  
Residue Interaction ◽  
Application Programming ◽  
Quaternary Structures ◽  
The Impact ◽  
Programming Interface

Residue interaction networks (RINs) have been shown to be relevant representations of the tertiary or quaternary structures of proteins, in particular thanks to network centrality analyses. We recently developed the RINspector Cytoscape app, which couples centrality analyses with backbone flexibility predictions. This combined approach permits the identification of crucial residues for the folding or function of the protein that can constitute good targets for mutagenesis experiments. Here we present an application programming interface (API) for RINspector that enables interplay between Cytoscape, RINspector and external languages, such as R or Python. This API provides easy access to batch centrality calculations and flexibility predictions, and allows for the easy comparison of results between different structures. These comparisons can lead to the identification of specific and conserved central residues, and show the impact of mutations to these and other residues on the flexibility of the proteins. We give two use cases to demonstrate the interest of these functionalities and provide the corresponding scripts: the first concerns NMR conformers, the second focuses on mutations in a structure.

scholarly journals Sentiment Analysis on Overseas Tweets on the Impact of COVID-19 in Indonesia

2021 ◽  
Vol 5 (2) ◽  
pp. 304-313
Author(s):  
Tigor Nirman Simanjuntak ◽  
Setia Pramana
Keyword(s):  
Big Data ◽  
Application Programming Interface ◽  
Text Format ◽  
Python Programming Language ◽  
Application Programming ◽  
Python Programming ◽  
Negative Sentiment ◽  
Analytical Tools ◽  
The Impact ◽  
Programming Interface

This study aims to conduct analysis to determine the trend of sentiment on tweets about Covid-19 in Indonesia from the Twitter accounts overseas on big data perspective. The data was obtained from Twitter in the period of April 2020, with the word query "Indonesian Corona Virus" from foreign user accounts in English. The process of retrieving data comes from Twitter tweets by crawling the text using Twitter's API (Application Programming Interface) by employing Python programming language. Twitter was chosen because it is very fast and easy to spread through status updates from and among the user accounts. The number of tweets obtained was 8,740 in text format, with a total engagement of 217,316. The data was sorted from the tweets with the largest to smallest engagement, then cleaned from unnecessary fonts and symbols as well as typo words and abbreviations. The sentiment classification was carried out by analytical tools, extracting information with text mining, into positive, negative, and neutral polarity. To sharpen the analysis, the cleaned data was selected only with the largest engagement until those with 100 engagements; then was grouped into 30 sub-topics to be analyzed. The interesting facts are found that most tweets and sub-topics were dominated by the negative sentiment; and some unthinkable sub-topics were talked by many users.

VirES for Aeolus - Virtual Research Environment (VRE)

2021 ◽  
Author(s):  
Daniel Santillan Pedrosa ◽  
Alexander Geiss ◽  
Isabell Krisch ◽  
Fabian Weiler ◽  
Peggy Fischer ◽  
...  
Keyword(s):  
Application Programming Interface ◽  
Data Access ◽  
Easy Access ◽  
Research Environment ◽  
Web Browser ◽  
Explorer Mission ◽  
Virtual Research Environment ◽  
Application Programming ◽  
Open Service ◽  
Programming Interface

<p><span>The VirES for Aeolus service (https://aeolus.services) has been successfully running </span><span>by EOX </span><span>since August 2018. The service </span><span>provides</span><span> easy access </span><span>and</span><span> analysis functions for the entire data archive of ESA's Aeolus Earth Explorer mission </span><span>through a web browser</span><span>.</span></p><p><span>This </span>free and open service <span>is being extended with a Virtual Research Environment (VRE). </span><span>The VRE </span><span>builds on the available data access capabilities of the service and provides </span><span>a </span><span>data access Application Programming Interface (API) a</span><span>s part of a </span><span>developing environment </span><span>i</span><span>n the cloud </span><span>using </span><span>JupyterHub and </span><span>JupyterLab</span><span> for processing and exploitation of the Aeolus data. </span>In collaboration with Aeolus DISC user requirements are being collected, implemented and validated.</p><p>Jupyter Notebook templates, an extensive set of tutorials, and documentation are being made available to enable a quick start on how to use VRE in projects. <span>The VRE is intended to support and simplify </span><span>the </span><span>work of (citizen-) scientists </span><span>interested in</span><span> Aeolus data by being able to </span><span>quickly develop processes or algorithms that can be </span><span>shar</span><span>ed or used to create </span><span>visualizations</span><span> for publications. Having a unified constant platform could potentially also be very helpful for calibration and validation activities </span><span>by </span><span>allowing easier result comparisons. </span></p>

Sistem Pengawasan Aktifitas Penggunaan Smartphone Android

2018 ◽  
Vol 9 (1) ◽  
pp. 24-31
Author(s):  
Rudianto Rudianto ◽  
Eko Budi Setiawan
Keyword(s):  
Application Programming Interface ◽  
Third Party ◽  
Image Content ◽  
Image File ◽  
Application Programming ◽  
Index Terms ◽  
Programming Interface

Availability the Application Programming Interface (API) for third-party applications on Android devices provides an opportunity to monitor Android devices with each other. This is used to create an application that can facilitate parents in child supervision through Android devices owned. In this study, some features added to the classification of image content on Android devices related to negative content. In this case, researchers using Clarifai API. The result of this research is to produce a system which has feature, give a report of image file contained in target smartphone and can do deletion on the image file, receive browser history report and can directly visit in the application, receive a report of child location and can be directly contacted via this application. This application works well on the Android Lollipop (API Level 22). Index Terms— Application Programming Interface(API), Monitoring, Negative Content, Children, Parent.

scholarly journals Advanced soft robot modeling in ChainQueen

Robotica ◽  
2021 ◽  
pp. 1-31
Author(s):  
Andrew Spielberg ◽  
Tao Du ◽  
Yuanming Hu ◽  
Daniela Rus ◽  
Wojciech Matusik
Keyword(s):  
Application Programming Interface ◽  
Material Point ◽  
Soft Robotics ◽  
Soft Robot ◽  
Inference Control ◽  
Simulation And Optimization ◽  
Efficient Simulation ◽  
Application Programming ◽  
Robot Modeling ◽  
Programming Interface

Abstract We present extensions to ChainQueen, an open source, fully differentiable material point method simulator for soft robotics. Previous work established ChainQueen as a powerful tool for inference, control, and co-design for soft robotics. We detail enhancements to ChainQueen, allowing for more efficient simulation and optimization and expressive co-optimization over material properties and geometric parameters. We package our simulator extensions in an easy-to-use, modular application programming interface (API) with predefined observation models, controllers, actuators, optimizers, and geometric processing tools, making it simple to prototype complex experiments in 50 lines or fewer. We demonstrate the power of our simulator extensions in over nine simulated experiments.

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