scholarly journals Annotating and prioritising genomic variants using the Ensembl Variant Effect Predictor - a tutorial

2021 ◽  
Author(s):  
Sarah Hunt ◽  
Benjamin Moore ◽  
M. Amode ◽  
Irina Armean ◽  
Diana Lemos ◽  
...  
Keyword(s):  
Application Programming Interface ◽  
Access Methods ◽  
Variant Effect Predictor ◽  
Genomic Variants ◽  
Representational State Transfer ◽  
Gene Sets ◽  
Command Line Tool ◽  
Application Programming ◽  
Variant Effect ◽  
User Friendly

The Ensembl Variant Effect Predictor (VEP) is a freely available, open source tool for the annotation and filtering of genomic variants. It predicts variant molecular consequence using the Ensembl/GENCODE or RefSeq gene sets. It also reports phenotype associations from databases such as ClinVar, allele frequencies from studies including gnomAD, and predictions of deleteriousness from tools such as SIFT and CADD. Ensembl VEP includes filtering options to customise variant prioritisation. It is well supported and updated roughly quarterly to incorporate the latest gene, variant and phenotype association information. Ensembl VEP analysis can be performed using a highly configurable, extensible command-line tool, a Representational State Transfer (REST) application programming interface (API) and a user-friendly web interface. These access methods are designed to suit different levels of bioinformatics experience and meet different needs in terms of data size, visualisation and flexibility. In this tutorial, we will describe performing variant annotation using the Ensembl VEP web tool, which enables sophisticated analysis through a simple interface.

As-RaD System as a Design Model of the Network Automation Configuration System Based on the REST-API and Django Framework

2020 ◽  
pp. 291-298
Author(s):  
Adian Fatchur Rochim ◽  
Abda Rafi ◽  
Adnan Fauzi ◽  
Kurniawan Teguh Martono
Keyword(s):  
Information Technology ◽  
Application Programming Interface ◽  
Design Model ◽  
Automation System ◽  
Network Configuration ◽  
Web Based ◽  
Representational State Transfer ◽  
Application Programming ◽  
Rest Api ◽  
Python Programming

The use of information technology these days are very high. From business through education activities tend to use this technology most of the time. Information technology uses computer networks for integration and management data. To avoid business problems, the number of network devices installed requires a manageable network configuration for easier maintenance. Traditionally, each of network devices has to be manually configured by network administrators. This process takes time and inefficient. Network automation methods exist to overcome the repetitive process. Design model uses a web-based application for maintenance and automates networking tasks. In this research, the network automation system implemented and built a controller application that used REST API (Representational State Transfer Application Programming Interface) architecture and built by Django framework with Python programming language. The design modeled namely As-RaD System. The network devices used in this research are Cisco CSR1000V because it supports REST API communication to manage its network configuration and could be placed on the server either. The As-RaD System provides 75% faster performance than Paramiko and 92% than NAPALM.

scholarly journals An IoT-Based Smart Home Automation System

Sensors ◽  
2021 ◽  
Vol 21 (11) ◽  
pp. 3784
Author(s):  
Cristina Stolojescu-Crisan ◽  
Calin Crisan ◽  
Bogdan-Petru Butunoi
Keyword(s):  
Application Programming Interface ◽  
Smartphone Application ◽  
Raspberry Pi ◽  
Automation System ◽  
Home Automation ◽  
Network Connection ◽  
Communication Scheme ◽  
Application Programming ◽  
Home Automation System ◽  
User Friendly

Home automation has achieved a lot of popularity in recent years, as day-to-day life is getting simpler due to the rapid growth of technology. Almost everything has become digitalized and automatic. In this paper, a system for interconnecting sensors, actuators, and other data sources with the purpose of multiple home automations is proposed. The system is called qToggle and works by leveraging the power of a flexible and powerful Application Programming Interface (API), which represents the foundation of a simple and common communication scheme. The devices used by qToggle are usually sensors or actuators with an upstream network connection implementing the qToggle API. Most devices used by qToggle are based on ESP8266/ESP8285 chips and/or on Raspberry Pi boards. A smartphone application has been developed that allows users to control a series of home appliances and sensors. The qToggle system is user friendly, flexible, and can be further developed by using different devices and add-ons.

Pemantauan dan Pengendalian Parameter Akuaponik Menggunakan Representational State Transfer Application Programming Interface

2020 ◽  
Vol 9 (4) ◽  
pp. 394-402
Author(s):  
Helmy ◽  
Athadhia Febyana ◽  
Agung Al Rasyid ◽  
Arif Nursyahid ◽  
Thomas Agung Setyawan ◽  
...  
Keyword(s):  
Application Programming Interface ◽  
Total Dissolved Solids ◽  
Data Loss ◽  
Representational State Transfer ◽  
State Transfer ◽  
Application Programming ◽  
Representational State ◽  
Rest Api ◽  
E Mail ◽  
Programming Interface

Akuaponik merupakan penggabungan antara akuakultur dengan hidroponik. Salah satu sistem hidroponik yaitu sistem drip (tetes). Parameter yang perlu diperhatikan dalam budidaya akuaponik antara lain keasaman larutan nutrisi yaitu pH, suhu air, dan larutan nutrisi yang ditunjukkan oleh kepekatan zat padat terlarut dalam air (Total Dissolved Solids, TDS). Nutrisi tanaman diperoleh dari kotoran ikan yang mengandung nitrogen. Oleh karena itu, diperlukan pemantauan pH, TDS, dan suhu secara realtime dan pengendalian kelembapan tanah pada tanaman akuaponik agar tanaman tidak kekurangan nutrisi. Proses pengendalian menggunakan Representational State Transfer Application Programming Interface (REST API) dalam menerima nilai batas ambang yang ditentukan petani akuaponik melalui situs web dan mengirimkan nilai kelembapan tanah dan parameter kolam ikan berupa pH, suhu dan TDS ke server. Pengujian data loss dan delay pada sistem pemantauan dan pengendalian ini diperlukan untuk mengetahui keandalan alat dalam pengiriman dan penerimaan data. Selain itu, diperlukan notifikasi berupa e-mail kepada petani apabila nilai kelembapan tanah kurang dari batas ambang. Hasil pengujian menunjukkan sistem dapat mengirimkan notifikasi berupa e-mail kepada petani apabila nilai kelembapan tanah kurang dari batas ambang, rerata delay pemantauan node-gateway sebesar 6,01 detik, sedangkan rerata delay pemantauan gateway–server sebesar 10,02 detik, dan rerata delay pengendalian server–gateway sebesar 92,55 detik.

Leveraging Web 2.0 technologies to add value to the IUPAC Solubility Data Series: development of a REST style website and application programming interface (API)

2015 ◽  
Vol 87 (11-12) ◽  
pp. 1127-1137
Author(s):  
Stuart J. Chalk
Keyword(s):  
Application Programming Interface ◽  
Scientific Data ◽  
Lessons Learned ◽  
Data Series ◽  
Representational State Transfer ◽  
Database Construction ◽  
Series Development ◽  
Application Programming ◽  
Rest Api ◽  
Program Interface

AbstractThis paper details an approach to re-purposing scientific data as presented on a web page for the sole purpose of making the data more available for searching and integration into other websites. Data ‘scraping’ is used to extract metadata from a set of pages on the National Institute of Standards and Technology (NIST) website, clean, organize and store the metadata in a MySQL database. The metadata is then used to create a new website at the authors institution using the CakePHP framework to create a representational state transfer (REST) style application program interface (API). The processes used for website analysis, schema development, database construction, metadata scraping, REST API development, and remote data integration are discussed. Lessons learned and tips and tricks on how to get the most out of the process are also included.

scholarly journals Participation Reports help Crossref members drive research further

2021 ◽  
Vol 8 (2) ◽  
pp. 180-185
Author(s):  
Anna Tolwinska
Keyword(s):  
Text Mining ◽  
Full Text ◽  
Application Programming Interface ◽  
Representational State Transfer ◽  
State Transfer ◽  
Application Programming ◽  
Funding Information ◽  
Rest Api ◽  
Machine Readable ◽  
Programming Interface

This article aims to explain the key metadata elements listed in Participation Reports, why it’s important to check them regularly, and how Crossref members can improve their scores. Crossref members register a lot of metadata in Crossref. That metadata is machine-readable, standardized, and then shared across discovery services and author tools. This is important because richer metadata makes content more discoverable and useful to the scholarly community. It’s not always easy to know what metadata Crossref members register in Crossref. This is why Crossref created an easy-to-use tool called Participation Reports to show editors, and researchers the key metadata elements Crossref members register to make their content more useful. The key metadata elements include references and whether they are set to open, ORCID iDs, funding information, Crossmark metadata, licenses, full-text URLs for text-mining, and Similarity Check indexing, as well as abstracts. ROR IDs (Research Organization Registry Identifiers), that identify institutions will be added in the future. This data was always available through the Crossref ’s REST API (Representational State Transfer Application Programming Interface) but is now visualized in Participation Reports. To improve scores, editors should encourage authors to submit ORCIDs in their manuscripts and publishers should register as much metadata as possible to help drive research further.

scholarly journals The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

2018 ◽  
Author(s):  
Alberto Noronha ◽  
Jennifer Modamio ◽  
Yohan Jarosz ◽  
Nicolas Sompairac ◽  
German Preciat Gonzàlez ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Current Knowledge ◽  
Application Programming Interface ◽  
Data Interpretation ◽  
Human Metabolism ◽  
Human Genes ◽  
Application Programming ◽  
Underlying Mechanisms ◽  
User Friendly ◽  
Programming Interface

AbstractA multitude of factors contribute to complex diseases and can be measured with “omics” methods. Databases facilitate data interpretation for underlying mechanisms. Here, we describe the Virtual Metabolic Human (VMH, http://vmh.life) database encapsulating current knowledge of human metabolism within five interlinked resources “Human metabolism”, “Gut microbiome”, “Disease”, “Nutrition”, and “ReconMaps”. The VMH captures 5,180 unique metabolites, 17,730 unique reactions, 3,288 human genes, 255 Mendelian diseases, 818 microbes, 632,685 microbial genes, and 8,790 food items. The VMH’s unique features are i) the hosting the metabolic reconstructions of human and gut microbes amenable for metabolic modeling; ii) seven human metabolic maps for data visualization; iii) a nutrition designer; iv) a user-friendly webpage and application-programming interface to access its content; and v) user feedback option for community engagement. We demonstrate with four examples the VMH’s utility. The VMH represents a novel, interdisciplinary database for data interpretation and hypothesis generation to the biomedical community.

scholarly journals Molint 1.0: An Application Programming Interface Framework for the Computation of Molecular Integrals and Their First Derivatives for the Density-Fitted Methods

2020 ◽  
Author(s):  
Uğur Bozkaya
Keyword(s):  
Tensor Decomposition ◽  
Application Programming Interface ◽  
Efficient Computation ◽  
Property Evaluation ◽  
Hybrid Code ◽  
Programming Techniques ◽  
Molecular Integrals ◽  
Application Programming ◽  
User Friendly ◽  
Programming Interface

The efficient computation of molecular integrals and their derivatives is a crucial step in molecular property evaluation in modern quantum chemistry. As an integral tensor decomposition technique, the density-fitting (DF) approach becomes a popular tool to reduce the memory and disk requirements for the electron repulsion integrals. In this study, an application programming interface (API) framework, denoted Molint (MFW), for the computation of molecular integrals and their first derivatives, over contracted Gaussian functions, for the density-fitted methods is reported. The MFW is free software and it includes overlap, dipole, kinetic, potential, metric, and 3-index integrals, and their first derivatives. Furthermore, the MFW provides a smooth approach to build the Fock matrix and evaluate analytic gradients for the density-fitted methods. The MFW is a C++/Fortran hybrid code, which can take advantage of shared-memory parallel programming techniques. Our results demonstrate that the MFW is an efficient and user-friendly API for the computation of molecular integrals and their first derivatives.

scholarly journals Annotating and prioritising genomic variants using the Ensembl Variant Effect Predictor ‐ a tutorial

2021 ◽  
Author(s):  
Sarah E. Hunt ◽  
Benjamin Moore ◽  
Ridwan M. Amode ◽  
Irina M. Armean ◽  
Diana Lemos ◽  
...  
Keyword(s):  
Variant Effect Predictor ◽  
Genomic Variants ◽  
Variant Effect

scholarly journals Innovative management of accelerometry, inertial, acoustic, and satellite data using netCDF and Postgres

2018 ◽  
Author(s):  
Alex Nunes ◽  
Damian Lidgard ◽  
Franziska Broell
Keyword(s):  
High Resolution ◽  
Satellite Data ◽  
Large Scale ◽  
Cluster Computing ◽  
Movement Ecology ◽  
Application Programming Interface ◽  
Easy Access ◽  
Application Programming ◽  
Original Size ◽  
User Friendly

In 2015, as part of the Ocean Tracking Network’s bioprobe initiative, 20 grey seals (Halichoerus grypus) were tagged with a high-resolution (> 30 Hz) inertial tags (> 30 Hz), a depth-temperature satellite tag (0.1 Hz), and an acoustic transceiver on Sable Island for 6 months. Comparable to similar large-scale studies in movement ecology, the unprecedented size of the data (gigabytes for a single seal) collected by these instruments raises new challenges in efficient database management. Here we propose the utility of Postgres and netCDF for storing the biotelemetry data and associated metadata. While it was possible to write the lower-resolution (acoustic and satellite) data to a Postgres database, netCDF was chosen as the format for the high-resolution movement (acceleration and inertial) records. Even without access to cluster computing, data could be efficiently (CPU time) recorded, as 920 million records were written in < 3 hours. ERDDAP was used to access and link the different datastreams with a user-friendly Application Programming Interface. This approach compresses the data to a fifth of its original size, and storing the data in a tree-like structure enables easy access and visualization for the end user.

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