scholarly journals Biobtree: A tool to search and map bioinformatics identifiers and special keywords

F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 145
Author(s):  
Tamer Gur
Keyword(s):  
Web Services ◽  
Open Source ◽  
Resource Usage ◽  
Web Interface ◽  
Bioinformatics Tool ◽  
Link Type ◽  
As Species ◽  
Storage Resource ◽  
Executable File ◽  
And Storage

Biobtree is a bioinformatics tool to search and map bioinformatics datasets via identifiers or special keywords such as species name. It processes large bioinformatics datasets using a specialized MapReduce-based solution with optimum computational and storage resource usage. It provides uniform and B+ tree-based database output, a web interface, web services and allows performing chain mapping queries between datasets. It can be used via a single executable file or alternatively it can be used via the R or Python-based wrapper packages which are additionally provided for easier integration into existing pipelines. Biobtree is open source and available at GitHub.

scholarly journals Biobtree: A tool to search and map bioinformatics identifiers and special keywords

F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 145
Author(s):  
Tamer Gur
Keyword(s):  
Web Services ◽  
Open Source ◽  
Resource Usage ◽  
Web Interface ◽  
Bioinformatics Tool ◽  
Link Type ◽  
As Species ◽  
Storage Resource ◽  
Executable File ◽  
And Storage

Biobtree is a bioinformatics tool to search and map bioinformatics datasets via identifiers or special keywords such as species name. It processes large bioinformatics datasets using a specialized MapReduce-based solution with optimum computational and storage resource usage. It provides uniform and B+ tree-based database output, a web interface, web services and allows performing chain mapping queries between datasets. It can be used via a single executable file or alternatively it can be used via the R or Python-based wrapper packages which are additionally provided for easier integration into existing pipelines. Biobtree is open source and available at GitHub.

scholarly journals Biobtree: A tool to search and map bioinformatics identifiers and special keywords

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 145
Author(s):  
Tamer Gur
Keyword(s):  
Web Services ◽  
Open Source ◽  
Technical Knowledge ◽  
Resource Usage ◽  
Web Interface ◽  
Bioinformatics Tool ◽  
Binary File ◽  
As Species ◽  
Storage Resource ◽  
And Storage

Biobtree is a bioinformatics tool to search and map bioinformatics datasets via identifiers or special keywords such as species name. It processes large bioinformatics datasets using a specialized MapReduce-based solution with optimum computational and storage resource usage. It provides uniform and B+ tree-based database output, web interface, web services and allows performing chain mapping queries between datasets. It is managed by a single binary file without requiring installation, specific technical knowledge or extra maintenance. Biobtree is open source and available at GitHub.

scholarly journals Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 145
Author(s):  
Tamer Gur
Keyword(s):  
Data Structure ◽  
Web Services ◽  
Software Tools ◽  
Web Interface ◽  
Bioinformatics Tool ◽  
Link Type ◽  
Executable File ◽  
Tree Data ◽  
Tree Data Structure ◽  
Gene Symbols

Due to their nature, bioinformatics datasets are often closely related to each other. For this reason, search, mapping and visualization of these relations are often performed manually or programmatically via identifiers or special keywords such as gene symbols. Although various tools exist for these situations, the growing volume of bioinformatics datasets, emerging new software tools and approaches motivates new solutions. To provide a new tool for these current cases, I present the Biobtree bioinformatics tool. Biobtree effectively fetches and indexes identifiers and special keywords with their related identifiers from supported datasets, optionally with user pre-defined datasets and provides a web interface, web services and direct B+ tree data structure based single uniform database output. Biobtree can handle billions of identifiers and runs via a single executable file with no installation and dependency required. It also aims to provide a relatively small codebase for easy maintenance, addition of new features and extension to larger datasets. Biobtree is available to download from GitHub.

scholarly journals Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords

2019 ◽  
Author(s):  
Tamer Gur
Keyword(s):  
Data Structure ◽  
Web Services ◽  
Software Tools ◽  
Web Interface ◽  
Bioinformatics Tool ◽  
Link Type ◽  
Executable File ◽  
Tree Data ◽  
Tree Data Structure ◽  
Gene Symbols

AbstractDue to their nature, bioinformatics datasets are often closely related to each other. For this reason, search, mapping and visualization of these relations are often performed manual or programmatically via identifiers or special keywords such as gene symbols. Although various tools exist for these situations, the growing volume of bioinformatics datasets, emerging new software tools and approaches motivates new solutions. To provide a new tool for these current cases, I present the Biobtree bioinformatics tool. Biobtree effectively fetches and indexes identifiers and special keywords with their related identifiers from supported datasets, optionally with user pre-defined datasets and provides a web interface, web services and direct B+ tree data structure–based single uniform database output. Biobtree can handle billions of identifiers and runs via a single executable file with no installation and dependency required. It also aims to provide a relatively small codebase for easy maintenance, addition of new features and extension to larger datasets. Biobtree is available to download at https://www.github.com/tamerh/biobtree.

scholarly journals SARS-CoV-2 RECoVERY: a multi-platform open-source bioinformatic pipeline for the automatic construction and analysis of SARS-CoV-2 genomes from NGS sequencing data

2021 ◽  
Author(s):  
Luca De Sabato ◽  
Gabriele Vaccari ◽  
Arnold Knijn ◽  
Giovanni Ianiro ◽  
Ilaria Di Bartolo ◽  
...  
Keyword(s):  
Open Source ◽  
Viral Genome ◽  
Rapid Analysis ◽  
Easy Access ◽  
Sequencing Data ◽  
Bioinformatics Pipeline ◽  
Bioinformatics Analyses ◽  
Sequencing Platform ◽  
Link Type ◽  
And Storage

AbstractBackgroundSince its first appearance in December 2019, the novel Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), spread worldwide causing an increasing number of cases and deaths (35,537,491 and 1,042,798, respectively at the time of writing, https://covid19.who.int). Similarly, the number of complete viral genome sequences produced by Next Generation Sequencing (NGS), increased exponentially. NGS enables a rapid accumulation of a large number of sequences. However, bioinformatics analyses are critical and require combined approaches for data analysis, which can be challenging for non-bioinformaticians.ResultsA user-friendly and sequencing platform-independent bioinformatics pipeline, named SARS-CoV-2 RECoVERY (REconstruction of CoronaVirus gEnomes & Rapid analYsis) has been developed to build SARS-CoV-2 complete genomes from raw sequencing reads and to investigate variants. The genomes built by SARS-CoV-2 RECoVERY were compared with those obtained using other software available and revealed comparable or better performances of SARS–CoV2 RECoVERY. Depending on the number of reads, the complete genome reconstruction and variants analysis can be achieved in less than one hour. The pipeline was implemented in the multi-usage open-source Galaxy platform allowing an easy access to the software and providing computational and storage resources to the community.ConclusionsSARS-CoV-2 RECoVERY is a piece of software destined to the scientific community working on SARS-CoV-2 phylogeny and molecular characterisation, providing a performant tool for the complete reconstruction and variants’ analysis of the viral genome. Additionally, the simple software interface and the ability to use it through a Galaxy instance without the need to implement computing and storage infrastructures, make SARS-CoV-2 RECoVERY a resource also for virologists with little or no bioinformatics skills.Availability and implementationThe pipeline SARS-CoV-2 RECoVERY (REconstruction of COronaVirus gEnomes & Rapid analYsis) is implemented in the Galaxy instance ARIES (https://aries.iss.it).

scholarly journals A RESTful API to serve BAM file with OAuth2 compatible authorization

2017 ◽  
Author(s):  
Julien Delafontaine ◽  
Sylvain Pradervand
Keyword(s):  
Open Source ◽  
Source Code ◽  
Variant Calling ◽  
Use Case ◽  
Web Interface ◽  
Sensitive Data ◽  
Link Type ◽  
Restful Service

AbstractSummaryBam-server is an open-source RESTful service to query slices of BAM files securely and manage their user accesses. A typical use case is the visualization of local read alignments in a web interface for variant calling diagnostic, without exposing sensitive data to unauthorized users through the network, and without moving the original - heavy - file. Bam-server follows the standard implementation of a protected resource server in the context of a typical token-based authorization protocol, supporting HMAC- and RSA-hashed signatures from an authorization server of choice.AvailabilityThe source code is available at https://github.com/chuv-ssrc/bam-server-scala, and a complete documentation can be found at http://bam-server-scala.readthedocs.io/en/latest/[email protected]

scholarly journals GRACC: GRid ACcounting Collector

2019 ◽  
Vol 214 ◽  
pp. 03032
Author(s):  
Derek Weitzel ◽  
Brian Bockelman ◽  
Marian Zvada ◽  
Kevin Retzke ◽  
Shreyas Bhat
Keyword(s):  
Open Source ◽  
Data Storage ◽  
Data Visualization ◽  
Large Data ◽  
Accounting System ◽  
Multiple Agents ◽  
Web Technologies ◽  
Storage Resource ◽  
Database Technology ◽  
And Storage

The OSG has long maintained a central accounting system called Gratia. It uses small probes on each computing and storage resource in order to collect resource usage. The probes report to a central collector which stores the usage in a database. The database is then queried to generate reports. As the OSG aged, the size of the database grew very large. It became too large for the database technology to efficiently query to generate detailed reports. The design of a replacement requires data storage that could be queried efficiently to generate multi-year reports. Additionally, it requires flexibilityto add new attributes to the collected data. In this paper we will describe updates to the GRACC architecture in the last 18 months. GRACC uses modern web technologies that were designed for large data storage, query, and visualization. That includes the open source database Elasticsearch, message broker software RabbitMQ, and Grafana and Kibana as data visualization platforms. It uses multiple agents that perform operations on the data to transform it for easier querying and summarization.

scholarly journals EXPLANe: An Extensible Framework for Poster Annotation with Mobile Devices

2017 ◽  
Author(s):  
Nikhil Gopal ◽  
Andrew Su ◽  
Chunlei Wu ◽  
Sean D. Mooney
Keyword(s):  
Web Services ◽  
Open Source ◽  
Mobile Devices ◽  
Genetic Variants ◽  
Poster Session ◽  
Biological Information ◽  
Text Recognition ◽  
Variant Annotation ◽  
Link Type

AbstractSummaryScientific posters tend to be brief, unstructured, and generally unsuitable for communication beyond a poster session. This paper describes EXPLANe, a framework for annotating posters using optical text recognition and web services on mobile devices. EXPLANe is demonstrated through an interface to the MyVariant.info variant annotation web services, and provides users a list of biological information linked with genetic variants (as found via extracted RSIDs from annotated posters). This paper delineates the architecture of the application, and includes results of a five-part evaluation we conducted. Researchers and developers can use the existing codebase as a foundation from which to generate their own annotation tabs when analyzing and annotating posters.AvailabilityAlpha EXPLANe software is available as an open source application at https://github.com/ngopal/EXPLANeContactSean D. Mooney ([email protected])

scholarly journals Open-source multi-year power generation, consumption, and storage data in a microgrid

2021 ◽  
Vol 13 (2) ◽  
pp. 025301
Author(s):  
Sushil Silwal ◽  
Colton Mullican ◽  
Yi-An Chen ◽  
Avik Ghosh ◽  
John Dilliott ◽  
...  
Keyword(s):  
Power Generation ◽  
Open Source ◽  
And Storage

scholarly journals Monitoring System for Tracking a PV Generator in an Experimental Smart Microgrid: An Open-Source Solution

2021 ◽  
Vol 13 (15) ◽  
pp. 8182
Author(s):  
José María Portalo ◽  
Isaías González ◽  
Antonio José Calderón
Keyword(s):  
Open Source ◽  
Monitoring System ◽  
Smart Grids ◽  
Raspberry Pi ◽  
Operator Interface ◽  
Open Source Hardware ◽  
Real Time Information ◽  
And Storage ◽  
Time Information ◽  
Pv Generator

Smart grids and smart microgrids (SMGs) require proper monitoring for their operation. To this end, measuring, data acquisition, and storage, as well as remote online visualization of real-time information, must be performed using suitable equipment. An experimental SMG is being deployed that combines photovoltaics and the energy carrier hydrogen through the interconnection of photovoltaic panels, electrolyser, fuel cell, and load around a voltage bus powered by a lithium battery. This paper presents a monitoring system based on open-source hardware and software for tracking the temperature of the photovoltaic generator in such an SMG. In fact, the increases in temperature in PV modules lead to a decrease in their efficiency, so this parameter needs to be measured in order to monitor and evaluate the operation. Specifically, the developed monitoring system consists of a network of digital temperature sensors connected to an Arduino microcontroller, which feeds the acquired data to a Raspberry Pi microcomputer. The latter is accessed by a cloud-enabled user/operator interface implemented in Grafana. The monitoring system is expounded and experimental results are reported to validate the proposal.

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