TRIANGLE Portal: An User-Friendly Web Interface for Remote Experimentation

2018 ◽  
pp. 110-117 ◽  
Author(s):  
Almudena Díaz-Zayas ◽  
Alberto Salmerón Moreno ◽  
Gustavo García Pascual ◽  
Pedro Merino Gómez
Keyword(s):  
Web Interface ◽  
User Friendly ◽  
Remote Experimentation

MetaADEDB 2.0: a comprehensive database on adverse drug events

2020 ◽  
Author(s):  
Zhuohang Yu ◽  
Zengrui Wu ◽  
Weihua Li ◽  
Guixia Liu ◽  
Yun Tang
Keyword(s):  
Safety Assessment ◽  
Adverse Drug Events ◽  
Adverse Event Reporting System ◽  
Adverse Event Reporting ◽  
Supplementary Information ◽  
Online Database ◽  
Web Interface ◽  
Drug Discovery And Development ◽  
Comprehensive Information ◽  
User Friendly

Abstract Summary MetaADEDB is an online database we developed to integrate comprehensive information on adverse drug events (ADEs). The first version of MetaADEDB was released in 2013 and has been widely used by researchers. However, it has not been updated for more than seven years. Here, we reported its second version by collecting more and newer data from the U.S. FDA Adverse Event Reporting System (FAERS) and Canada Vigilance Adverse Reaction Online Database, in addition to the original three sources. The new version consists of 744 709 drug–ADE associations between 8498 drugs and 13 193 ADEs, which has an over 40% increase in drug–ADE associations compared to the previous version. Meanwhile, we developed a new and user-friendly web interface for data search and analysis. We hope that MetaADEDB 2.0 could provide a useful tool for drug safety assessment and related studies in drug discovery and development. Availability and implementation The database is freely available at: http://lmmd.ecust.edu.cn/metaadedb/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals VIP-HL: Semi-automated ACMG/AMP variant interpretation platform for genetic hearing loss

2020 ◽  
Author(s):  
Jiguang Peng ◽  
Jiale Xiang ◽  
Xiangqian Jin ◽  
Junhua Meng ◽  
Nana Song ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Expert Panel ◽  
Sequence Variant ◽  
Variant Interpretation ◽  
Web Interface ◽  
Online Tool ◽  
Genetic Hearing Loss ◽  
Genetics And Genomics ◽  
Evidence Based Guidelines ◽  
User Friendly

The American College of Medical Genetics and Genomics, and the Association for Molecular Pathology (ACMG/AMP) have proposed a set of evidence-based guidelines to support sequence variant interpretation. The ClinGen hearing loss expert panel (HL-EP) introduced further specifications into the ACMG/AMP framework for genetic hearing loss. This study developed a tool named VIP-HL, aiming to semi-automate the HL ACMG/AMP rules. VIP-HL aggregates information from external databases to automate 13 out of 24 ACMG/AMP rules specified by HL-EP, namely PVS1, PS1, PM1, PM2, PM4, PM5, PP3, BA1, BS1, BS2, BP3, BP4, and BP7. We benchmarked VIP-HL using 50 variants where 83 rules were activated by the ClinGen HL-EP. VIP-HL concordantly activated 96% (80/83) rules, significantly higher than that of by InterVar (47%; 39/83). Of 4948 ClinVar star 2+ variants from 142 deafness-related genes, VIP-HL achieved an overall variant interpretation concordance in 88.0% (4353/4948). VIP-HL is an integrated online tool for reliable automated variant classification in hearing loss genes. It assists curators in variant interpretation and provides a platform for users to share classifications with each other. VIP-HL is available with a user-friendly web interface at http://hearing.genetics.bgi.com/.

scholarly journals The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics

2018 ◽  
Vol 2 ◽  
pp. 3 ◽  
Author(s):  
Heba Shaaban ◽  
David A. Westfall ◽  
Rawhi Mohammad ◽  
David Danko ◽  
Daniela Bezdan ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Large Scale ◽  
Research Effort ◽  
Gram Stain ◽  
Web Interface ◽  
Ongoing Effort ◽  
Student Researchers ◽  
User Friendly ◽  
Optimal Ph ◽  
Online Web

The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes’ characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses, allowing one to interpret and explore their taxonomic classifications to have a deeper understanding of the microbial ecosystem they are studying. Such characteristics include, but are not limited to: optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, antimicrobial resistance, and COGEM class risk rating. The database has been manually curated by trained student-researchers from Weill Cornell Medicine and CUNY—Hunter College, and its analysis remains an ongoing effort with open-source capabilities so others can contribute. Available in SQL, JSON, and CSV (i.e. Excel) formats, the Microbe Directory can be queried for the aforementioned parameters by a microorganism’s taxonomy. In addition to the raw database, The Microbe Directory has an online counterpart (https://microbe.directory/) that provides a user-friendly interface for storage, retrieval, and analysis into which other microbial database projects could be incorporated. The Microbe Directory was primarily designed to serve as a resource for researchers conducting metagenomic analyses, but its online web interface should also prove useful to any individual who wishes to learn more about any particular microbe.

scholarly journals COVID-19 preVIEW: Semantic Search to Explore COVID-19 Research Preprints

2021 ◽  
Author(s):  
Lisa Langnickel ◽  
Roman Baum ◽  
Johannes Darms ◽  
Sumit Madan ◽  
Juliane Fluck
Keyword(s):  
Search Engine ◽  
Access Point ◽  
Semantic Search ◽  
Web Interface ◽  
Disease Trajectory ◽  
Human Genes ◽  
Central Access ◽  
Semantic Information Retrieval ◽  
User Friendly ◽  
Semantic Search Engine

During the current COVID-19 pandemic, the rapid availability of profound information is crucial in order to derive information about diagnosis, disease trajectory, treatment or to adapt the rules of conduct in public. The increased importance of preprints for COVID-19 research initiated the design of the preprint search engine preVIEW. Conceptually, it is a lightweight semantic search engine focusing on easy inclusion of specialized COVID-19 textual collections and provides a user friendly web interface for semantic information retrieval. In order to support semantic search functionality, we integrated a text mining workflow for indexing with relevant terminologies. Currently, diseases, human genes and SARS-CoV-2 proteins are annotated, and more will be added in future. The system integrates collections from several different preprint servers that are used in the biomedical domain to publish non-peer-reviewed work, thereby enabling one central access point for the users. In addition, our service offers facet searching, export functionality and an API access. COVID-19 preVIEW is publicly available at https://preview.zbmed.de.

scholarly journals Arabic-English Parallel Corpus: A New Resource for Translation Training and Language Teaching

2017 ◽  
Author(s):  
Arab World English Journal ◽  
Hind M. Alotaibi
Keyword(s):  
Language Teaching ◽  
Data Driven ◽  
Text Segmentation ◽  
Web Interface ◽  
King Saud University ◽  
Parallel Corpora ◽  
Parallel Corpus ◽  
Source Language ◽  
User Friendly ◽  
Ongoing Project

Parallel corpora can be defined as collections of aligned, translated texts of two or more languages. They play a major role in translation and contrastive studies, and are also becoming popular in translation training and language teaching, with the advent of the data-driven learning (DDL) approach. Despite their significance, however, Arabic seems to lack a satisfactory general-use parallel corpus resource. The literature describes few Arabic–English parallel corpora, and these few are usually inaccurate and/or expensive. Some are small in size, while others are restricted in terms of genre, failing to meet the requirements of many academics and researchers. This paper describes an ongoing project at the College of Languages and Translation, King Saud University, to compile a 10-million-word Arabic–English parallel corpus to be used as a resource for translation training and language teaching. The bidirectional corpus can be used to compare translated and source language and identify differences. The corpus has been manually verified at different stages, including translation, text segmentation, alignment, and file preparation; it is available as full-text in XML format and through a user-friendly web interface that provides a concordancer to support bilingual search queries and several filtering options.

scholarly journals miR2Diabetes: A Literature-Curated Database of microRNA Expression Patterns, in Diabetic Microvascular Complications

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 784 ◽  
Author(s):  
Sungjin Park ◽  
SeongRyeol Moon ◽  
Kiyoung Lee ◽  
Ie Byung Park ◽  
Dae Ho Lee ◽  
...  
Keyword(s):  
Association Studies ◽  
Microvascular Complications ◽  
Expression Patterns ◽  
Disease Model ◽  
Model Organisms ◽  
Web Interface ◽  
Diabetic Microvascular Complications ◽  
User Friendly ◽  
Rats And Mice ◽  
Kidney Liver

microRNAs (miRNAs) have been established as critical regulators of the pathogenesis of diabetes mellitus (DM), and diabetes microvascular complications (DMCs). However, manually curated databases for miRNAs, and DM (including DMCs) association studies, have yet to be established. Here, we constructed a user-friendly database, “miR2Diabetes,” equipped with a graphical web interface for simple browsing or searching manually curated annotations. The annotations in our database cover 14 DM and DMC phenotypes, involving 156 miRNAs, by browsing diverse sample origins (e.g., blood, kidney, liver, and other tissues). Additionally, we provide miRNA annotations for disease-model organisms (including rats and mice), of DM and DMCs, for the purpose of improving knowledge of the biological complexity of these pathologies. We assert that our database will be a comprehensive resource for miRNA biomarker studies, as well as for prioritizing miRNAs for functional validation, in DM and DMCs, with likely extension to other diseases.

scholarly journals SpatialDB: a database for spatially resolved transcriptomes

2019 ◽  
Author(s):  
Zhen Fan ◽  
Runsheng Chen ◽  
Xiaowei Chen
Keyword(s):  
Spatial Organization ◽  
Expression Patterns ◽  
Functional Enrichment ◽  
Web Interface ◽  
Current Version ◽  
Transcriptomic Data ◽  
Spatially Resolved ◽  
User Friendly ◽  
New Strategies

Abstract Spatially resolved transcriptomic techniques allow the characterization of spatial organization of cells in tissues, which revolutionize the studies of tissue function and disease pathology. New strategies for detecting spatial gene expression patterns are emerging, and spatially resolved transcriptomic data are accumulating rapidly. However, it is not convenient for biologists to exploit these data due to the diversity of strategies and complexity in data analysis. Here, we present SpatialDB, the first manually curated database for spatially resolved transcriptomic techniques and datasets. The current version of SpatialDB contains 24 datasets (305 sub-datasets) from 5 species generated by 8 spatially resolved transcriptomic techniques. SpatialDB provides a user-friendly web interface for visualization and comparison of spatially resolved transcriptomic data. To further explore these data, SpatialDB also provides spatially variable genes and their functional enrichment annotation. SpatialDB offers a repository for research community to investigate the spatial cellular structure of tissues, and may bring new insights into understanding the cellular microenvironment in disease. SpatialDB is freely available at https://www.spatialomics.org/SpatialDB.

E Learning in Engineering Education

2010 ◽  
Vol 8 (2) ◽  
pp. 14-27
Author(s):  
Jagadeesh Chandra A.P. ◽  
R.D. Sudhaker Samuel
Keyword(s):  
Distance Learning ◽  
Engineering Education ◽  
Learning By Doing ◽  
Ongoing Research ◽  
Life Goal ◽  
Communication Circuits ◽  
E Learning ◽  
User Friendly ◽  
Remote Experimentation ◽  
Goal Distance

Attaining excellence in technical education is a worthy challenge to any life goal. Distance learning opportunities make these goals easier to reach with added quality. Distance learning in engineering education is possible only through successful implementations of remote laboratories in a learning-by-doing environment. This paper presents one such technology to carry out laboratory experiments from remote locations. The technology is demonstrated by handling the web interface, which supports the remote experimentation on communication circuits, power system and an embedded board. The implemented system environment facilitates users to perform the experiment remotely and efficiently using only a commonly available, user-friendly web browser. It describes the ongoing research in this area exploiting current telematics techniques, which supports remote experimentation with real hardware via the Internet.

scholarly journals MESPEUS: a database of the geometry of metal sites in proteins

2008 ◽  
Vol 41 (5) ◽  
pp. 963-968 ◽  
Author(s):  
K. Hsin ◽  
Y. Sheng ◽  
M. M. Harding ◽  
P. Taylor ◽  
M. D. Walkinshaw
Keyword(s):  
Protein Molecule ◽  
Data Bank ◽  
Web Interface ◽  
Coordination Numbers ◽  
Data Resolution ◽  
Metal Metal ◽  
Set Up ◽  
Stored Information ◽  
Interacting Atoms ◽  
User Friendly

A database with details of the geometry of metal sites in proteins has been set up. The data are derived from metalloprotein structures that are in the Protein Data Bank [PDB; Berman, Henrick, Nakamura & Markley (2006).Nucleic Acids Res.35, D301–D303] and have been determined at 2.5 Å resolution or better. The database contains all contacts within the crystal asymmetric unit considered to be chemical bonds to any of the metals Na, Mg, K, Ca, Mn, Fe, Co, Ni, Cu or Zn. The stored information includes PDB code, crystal data, resolution of structure determination, refinement program andRfactor, protein class (from PDB header), contact distances, atom names of metal and interacting atoms as they appear in the PDB, site occupancies,Bvalues, coordination numbers, information on coordination shapes, and metal–metal distances. This may be accessed by SQL queries, or by a user-friendly web interface which searches for contacts between specified types of atoms [for example Ca and carboxylate O of aspartate, Co and imidazole Nδ of histidine] or which delivers details of all the metal sites in a specified protein. The web interface allows graphical display of the metal site, on its own or within the whole protein molecule, and may be accessed at http://eduliss.bch.ed.ac.uk/MESPEUS/. Some applications are briefly described, including a study of the characteristics of Mg sites that bind adenosine triphosphate, the derivation of an average Mg—Ophosphatedistance and some problems that arise when average bond distances with high precision are required.

scholarly journals Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

2017 ◽  
Vol 4 (1) ◽  
Author(s):  
Kamal Choudhary ◽  
Faical Yannick P. Congo ◽  
Tao Liang ◽  
Chandler Becker ◽  
Richard G. Hennig ◽  
...  
Keyword(s):  
Interatomic Potentials ◽  
Web Interface ◽  
User Friendly
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