scholarly journals Online tools to easily build augmented reality models of biomolecules that run right on the web

2021 ◽  
Author(s):  
Fabio Cortés Rodríguez ◽  
Matteo Dal Peraro ◽  
Luciano Abriata
Keyword(s):  
Structural Biology ◽  
Biology Education ◽  
Biological Macromolecules ◽  
Web Interface ◽  
Substantial Fraction ◽  
Web Based ◽  
Virtual Objects ◽  
Online Tools ◽  
Specialized Hardware ◽  
Consumer Devices

Several groups developed in the last years augmented and virtual reality (AR/VR) programs and apps to visualize 3D molecules, most rather static, limited in content, and requiring software installs, some even requiring specialized hardware. During the Covid-19 pandemic, our team launched moleculARweb (https://molecularweb.epfl.ch), a website that offers interactive content for chemistry and structural biology education through web-based AR that works on consumer devices like smartphones, tablets and laptops. The website quickly got thousands of student and teacher users, a substantial fraction of them accessing from their homes given the pandemic. Teachers have been increasingly requesting more biological macromolecules to be available in AR, a demand that we cannot satisfy individually. Therefore, to allow them to build their own material, and also to help us expedite development of activities, we built a web interface where any user can build any online AR experience in few steps starting from a PDB structure or from virtual objects/scenes exported from VMD. We here briefly describe the tool, that is accessible at https://molecularweb.epfl.ch/pages/pdb2ar.html.

scholarly journals Online tools to easily build augmented reality models of biomolecules that run right on the web

2021 ◽  
Author(s):  
Fabio Cortés Rodríguez ◽  
Matteo Dal Peraro ◽  
Luciano Abriata
Keyword(s):  
Structural Biology ◽  
Biology Education ◽  
Biological Macromolecules ◽  
Web Browsers ◽  
Web Interface ◽  
Web Based ◽  
Virtual Objects ◽  
Online Tools ◽  
Consumer Devices ◽  
The Web

Abstract. Several groups developed in the last years augmented and virtual reality (AR/VR) programs and apps to visualize 3D molecules, most rather static, limited in content, and requiring software installs, some even requiring expensive hardware. During the Covid-19 pandemic, our team launched moleculARweb (https://molecularweb.epfl.ch), a website that offers interactive content for chemistry and structural biology education through commodity web-based AR that works on consumer devices like smartphones, tablets and laptops. Among thousands of users, teachers increasingly request more biological macromolecules to be available, a demand that we cannot satisfy individually. Therefore, to allow users to build their own material, we built a web interface where any user can build any online AR experience in few steps starting from a PDB structure or from virtual objects/scenes exported from VMD. The website also returns a WebXR session for viewing and manipulating the model in high-end immersive VR headsets with web browsers, here tested on the ~400 USD Oculus Quest 2. The tool is accessible at https://molecularweb.epfl.ch/pages/pdb2ar.html.

scholarly journals Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem

2021 ◽  
Vol 8 ◽  
Author(s):  
Rodrigo V. Honorato ◽  
Panagiotis I. Koukos ◽  
Brian Jiménez-García ◽  
Andrei Tsaregorodtsev ◽  
Marco Verlato ◽  
...  
Keyword(s):  
Structural Biology ◽  
Dynamic Properties ◽  
Three Dimensional ◽  
Open Science ◽  
Biological Macromolecules ◽  
Web Based ◽  
Cellular Processes ◽  
User Friendly ◽  
Insight Into ◽  
Gaining Insight

Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of biomolecules and their interactions is critical for understanding the vast majority of cellular processes, with direct applications in health and food sciences. Since 2010, the WeNMR project (www.wenmr.eu) has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers in the field, using the high throughput computing infrastructure provided by EGI. These services have been further developed in subsequent initiatives under H2020 projects and are now operating as Thematic Services in the European Open Science Cloud portal (www.eosc-portal.eu), sending >12 millions of jobs and using around 4,000 CPU-years per year. Here we review 10 years of successful e-infrastructure solutions serving a large worldwide community of over 23,000 users to date, providing them with user-friendly, web-based solutions that run complex workflows in structural biology. The current set of active WeNMR portals are described, together with the complex backend machinery that allows distributed computing resources to be harvested efficiently.

scholarly journals MoleculARweb: A Website for Chemistry and Structural Biology Education Through Interactive Augmented Reality out of the Box in Commodity Devices

2020 ◽  
Author(s):  
Fabio Cortés Rodríguez ◽  
Gianfranco Frattini ◽  
Lucien Krapp ◽  
Hassan Martinez-Huang ◽  
Diego Moreno ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Hydrogen Bonding ◽  
Structural Biology ◽  
Biology Education ◽  
Web Browsers ◽  
X Ray Diffraction ◽  
Acid Base ◽  
Web Based ◽  
X Ray ◽  
Nucleic Acid Structures

<p>Here we introduce <i>MoleculARweb</i>, a purely web-based AR platform for chemistry, molecular and structural biology education that runs out of the box in regular web browsers in ordinary computers, laptops, tablets and smartphones. Through regular-printed markers recognized via the device’s webcam, students and teachers can handle molecules in an AR environment to interactively explore their structure, dynamics and interactions. The release version of <i>MoleculARweb</i> features over 20 activities covering topics about molecular shapes, atomic and molecular orbitals, acid-base equilibria and hydrogen bonding, protein and nucleic acid structures, X-ray diffraction and electron microscopy, and molecular mechanics; applicable from high school to early university levels. <i>MoleculARweb</i> is freely available without registration at <a href="https://molecularweb.epfl.ch">https://MoleculARweb.epfl.ch</a> in 6 languages. </p>

scholarly journals MoleculARweb: A Website for Chemistry and Structural Biology Education Through Interactive Augmented Reality out of the Box in Commodity Devices

2020 ◽  
Author(s):  
Fabio Cortés Rodríguez ◽  
Gianfranco Frattini ◽  
Lucien Krapp ◽  
Hassan Martinez-Huang ◽  
Diego Moreno ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Hydrogen Bonding ◽  
Structural Biology ◽  
Biology Education ◽  
Web Browsers ◽  
X Ray Diffraction ◽  
Acid Base ◽  
Web Based ◽  
X Ray ◽  
Nucleic Acid Structures

<p>Here we introduce <i>MoleculARweb</i>, a purely web-based AR platform for chemistry, molecular and structural biology education that runs out of the box in regular web browsers in ordinary computers, laptops, tablets and smartphones. Through regular-printed markers recognized via the device’s webcam, students and teachers can handle molecules in an AR environment to interactively explore their structure, dynamics and interactions. The release version of <i>MoleculARweb</i> features over 20 activities covering topics about molecular shapes, atomic and molecular orbitals, acid-base equilibria and hydrogen bonding, protein and nucleic acid structures, X-ray diffraction and electron microscopy, and molecular mechanics; applicable from high school to early university levels. <i>MoleculARweb</i> is freely available without registration at <a href="https://molecularweb.epfl.ch">https://MoleculARweb.epfl.ch</a> in 6 languages. </p>

scholarly journals Protein dynamics revealed by NMR relaxation methods

2018 ◽  
Vol 2 (1) ◽  
pp. 93-105 ◽  
Author(s):  
Fa-An Chao ◽  
R. Andrew Byrd
Keyword(s):  
Protein Dynamics ◽  
Structural Biology ◽  
Dynamic Models ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Data Bank ◽  
Biological Macromolecules ◽  
Relaxation Methods ◽  
Genomic Databases ◽  
Wide Range

Structural biology often focuses primarily on three-dimensional structures of biological macromolecules, deposited in the Protein Data Bank (PDB). This resource is a remarkable entity for the worldwide scientific and medical communities, as well as the general public, as it is a growing translation into three-dimensional space of the vast information in genomic databases, e.g. GENBANK. There is, however, significantly more to understanding biological function than the three-dimensional co-ordinate space for ground-state structures of biomolecules. The vast array of biomolecules experiences natural dynamics, interconversion between multiple conformational states, and molecular recognition and allosteric events that play out on timescales ranging from picoseconds to seconds. This wide range of timescales demands ingenious and sophisticated experimental tools to sample and interpret these motions, thus enabling clearer insights into functional annotation of the PDB. NMR spectroscopy is unique in its ability to sample this range of timescales at atomic resolution and in physiologically relevant conditions using spin relaxation methods. The field is constantly expanding to provide new creative experiments, to yield more detailed coverage of timescales, and to broaden the power of interpretation and analysis methods. This review highlights the current state of the methodology and examines the extension of analysis tools for more complex experiments and dynamic models. The future for understanding protein dynamics is bright, and these extended tools bring greater compatibility with developments in computational molecular dynamics, all of which will further our understanding of biological molecular functions. These facets place NMR as a key component in integrated structural biology.

scholarly journals Creation and Use of Online Gateway for School Libraries from Free Web 2.0 Tools

2021 ◽  
Author(s):  
Marion Jude M. Gorospe
Keyword(s):  
Web 2.0 ◽  
Information Needs ◽  
School Library ◽  
Relevant Information ◽  
Information Services ◽  
Web Based ◽  
Web 2.0 Tools ◽  
Online Tools ◽  
Other Information ◽  
Free Search

The school library is challenged to remain relevant in the 21st century learning environment. With young learners always consulting Google and other free search engines for subject assignment and other information needs and with the underwhelming quality of much web-based information, the school library must find an interesting and effective way to deliver authoritative and relevant information services through online tools. However, effective information services online are most often hosted from subscribed or paid Web 2.0 sites. These online services are capable of interactivity among learners and flexibility for individual schools’ administrative concerns. However, the ability to afford these services is frequently beyond the financial capability of schools from developing countries. The researcher explored the possibility of creating a school library website that serves as a pathfinder to online resources and electronically delivers other library-based school services using free Web 2.0 tools.

scholarly journals KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Hugo Mochão ◽  
Pedro Barahona ◽  
Rafael S Costa
Keyword(s):  
Experimental Data ◽  
Metabolic Networks ◽  
Model Simulation ◽  
Web Interface ◽  
Concentration Data ◽  
Web Based ◽  
Share Data ◽  
Visualization Tools ◽  
Filter Mechanism ◽  
Machine Readable

Abstract The KiMoSys (https://kimosys.org), launched in 2014, is a public repository of published experimental data, which contains concentration data of metabolites, protein abundances and flux data. It offers a web-based interface and upload facility to share data, making it accessible in structured formats, while also integrating associated kinetic models related to the data. In addition, it also supplies tools to simplify the construction process of ODE (Ordinary Differential Equations)-based models of metabolic networks. In this release, we present an update of KiMoSys with new data and several new features, including (i) an improved web interface, (ii) a new multi-filter mechanism, (iii) introduction of data visualization tools, (iv) the addition of downloadable data in machine-readable formats, (v) an improved data submission tool, (vi) the integration of a kinetic model simulation environment and (vii) the introduction of a unique persistent identifier system. We believe that this new version will improve its role as a valuable resource for the systems biology community. Database URL:  www.kimosys.org

scholarly journals EVALUASI EKSTRAKSI FITUR KLASIFIKASI TEKS UNTUK PENINGKATAN AKURASI KLASIFIKASI MENGGUNAKAN NAIVE BAYES

2020 ◽  
Vol 13 (1) ◽  
pp. 161-171
Author(s):  
Aji Priyambodo ◽  
Prihati Prihati
Keyword(s):  
Radio Frequency Identification ◽  
Motor Vehicle ◽  
Academic Community ◽  
Security System ◽  
Web Based ◽  
Final Project ◽  
Frequency Identification ◽  
Identity Cards ◽  
Specialized Hardware ◽  
Parking Facilities

Security Parking UIN Walisongo Semarang at this time can be said to be in poor condition. The high case of loss of a motor vehicle cause anxiety for the academic community. Parking system that is traditional that is doing the checking of identity cards at the exit of the campus is less effective. Hence the need for a system of security parking modern and computerized, so that activities out of the vehicle can be recorded and stored automatically. Based on these problems, the authors designed a parking Security System as a WEB-based form of increased security parking campus UIN Walisongo Semarang. By using RFID technology (Radio Frequency Identification) are planted on the card indentitasi, which can later be used as an authentication tool typing will enter and exit the campus area. To provide double security, there are Features of the Live Camera with the base website that serves as a tool for monitoring vehicles that are parked in real time. The output of this final project is to produce a prototype security system parking. Not only specialized hardware, but also software design of the System monitoring of vehicles in live Web-based. So the users of the parking facilities can monitor the vehicle anywhere  

scholarly journals THE CENSUS OF SMS GATEWAY BASED WEB BASED KOTO LUAR PAUH DISTRICTS PADANG CITY

2016 ◽  
Vol 1 (2) ◽  
pp. 169
Author(s):  
Danyl Mallisza
Keyword(s):  
Short Message Service ◽  
Government Performance ◽  
Population Census ◽  
Short Message ◽  
Web Interface ◽  
Web Based ◽  
The World ◽  
Message Service ◽  
Multi Level ◽  
Computerized System

short message service (SMS) plays an important role in the field of IT in the future, SMS GATEWAY can be used as a mobile device for collecting data in the population census in achieving the availability and effectiveness. This research is about the development of software based on short message service (SMS) system to send messages via SMS gateway. The main objective of the proposed system is to provide a multi-level local authentication services to the SMS gateway. This service can be implemented in multi-departmental organizations where SMS service is used for system notifications. The proposed system has a web interface and encryption methods to provide services. Census information system that uses a computerized system is an effort to help smooth in the world of government so that the data obtained more precise and accurate. It can be expected to facilitate the penyensusan population in Koto village of Padang Pauh Subdistrict Affairs effectively, efficiently and accurately to improve government performance.

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