scholarly journals META-pipe Authorization service

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 32
Author(s):  
Inge Alexander Raknes ◽  
Lars Ailo Bongo
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Service Providers ◽  
Storage System ◽  
Web Based ◽  
Single Sign On ◽  
Link Type ◽  
Metagenomics Data ◽  
Access To Data

We describe the design, implementation, and use of the META-pipe Authorization service. META-pipe is a complete workflow for the analysis of marine metagenomics data. We will provide META-pipe as a web based data analysis service for ELIXIR users. We have integrated our Authorization service with the ELIXIR Authorization and Authentication Infrastructure (AAI) that allows single sign-on to services across the ELIXIR infrastructure. We use the Authorization service to authorize access to data on the META-pipe storage system and jobs in the META-pipe job queue. Our Authorization server was among the first SAML2 service providers  that integrated with ELIXIR AAI. The code is open source at: https://gitlab.com/uit-sfb/AuthService2.

scholarly journals META-pipe Authorization service

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 32 ◽  
Author(s):  
Inge Alexander Raknes ◽  
Lars Ailo Bongo
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Storage System ◽  
Web Based ◽  
Single Sign On ◽  
Link Type ◽  
Metagenomics Data ◽  
Access To Data

We describe the design, implementation, and use of the META-pipe Authorization service. META-pipe is a complete workflow for the analysis of marine metagenomics data. We will provide META-pipe as a web based data analysis service for ELIXIR users. We have integrated our Authorization service with the ELIXIR Authorization and Authentication Infrastructure (AAI) that allows single sign-on to services across the ELIXIR infrastructure. We use the Authorization service to authorize access to data on the META-pipe storage system and jobs in the META-pipe job queue. Our Authorization server was among the first services that integrated with ELIXIR AAI. The code is open source at: https://gitlab.com/uit-sfb/AuthService2.

scholarly journals NASQAR: A web-based platform for high-throughput sequencing data analysis and visualization

2019 ◽  
Author(s):  
Ayman Yousif ◽  
Nizar Drou ◽  
Jillian Rowe ◽  
Mohammed Khalfan ◽  
Kristin C Gunsalus
Keyword(s):  
New York ◽  
Data Analysis ◽  
Open Source ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Web Applications ◽  
Rna Seq ◽  
Sequencing Data ◽  
Web Based ◽  
Link Type

AbstractBackgroundAs high-throughput sequencing applications continue to evolve, the rapid growth in quantity and variety of sequence-based data calls for the development of new software libraries and tools for data analysis and visualization. Often, effective use of these tools requires computational skills beyond those of many researchers. To ease this computational barrier, we have created a dynamic web-based platform, NASQAR (Nucleic Acid SeQuence Analysis Resource).ResultsNASQAR offers a collection of custom and publicly available open-source web applications that make extensive use of a variety of R packages to provide interactive data analysis and visualization. The platform is publicly accessible at http://nasqar.abudhabi.nyu.edu/. Open-source code is on GitHub at https://github.com/nasqar/NASQAR, and the system is also available as a Docker image at https://hub.docker.com/r/aymanm/nasqarall. NASQAR is a collaboration between the core bioinformatics teams of the NYU Abu Dhabi and NYU New York Centers for Genomics and Systems Biology.ConclusionsNASQAR empowers non-programming experts with a versatile and intuitive toolbox to easily and efficiently explore, analyze, and visualize their Transcriptomics data interactively. Popular tools for a variety of applications are currently available, including Transcriptome Data Preprocessing, RNA-seq Analysis (including Single-cell RNA-seq), Metagenomics, and Gene Enrichment.

Open Source in Web-Based Applications

2009 ◽  
pp. 83-97
Author(s):  
Claudio Agostino Ardagna ◽  
Fulvio Frati ◽  
Gabriele Gianini
Keyword(s):  
Open Source ◽  
Global Communication ◽  
Communication Infrastructure ◽  
Community Patterns ◽  
Web Based ◽  
Recreational Activities ◽  
Single Sign On ◽  
Open Source Systems

Business and recreational activities on the global communication infrastructure are increasingly based on the use of remote resources and services, and on the interaction between different, remotely located parties. In such a context, Single Sign-On technologies simplify the log-on process allowing automatic access to secondary domains through a unique log-on operation to the primary domain. In this paper, we evaluate different Single Sign-On implementations focusing on the central role of Open Source in the development of Web-based systems. We outline requirements for Single Sign-On systems and evaluate four existing Open Source implementations in terms of degree of fulfilment of those requirements. Finally we compare those Open Source systems with respect to some specific Open Source community patterns.

scholarly journals PlateEditor: A web-based application for the management of multi-well plate layouts and associated data

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0252488
Author(s):  
Vincent Delorme ◽  
Minjeong Woo ◽  
Virginia Carla de Almeida Falcão ◽  
Connor Wood
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Dose Response ◽  
Response Curves ◽  
Web Based ◽  
Speed Up ◽  
Definition Of ◽  
Client Side ◽  
Associated Data ◽  
Multiple Conditions

Multi-well plates are convenient tools to work with in biology experiments, as they allow the probing of multiple conditions in a compact and economic way. Although both free and commercial software exist for the definition of plate layout and management of plate data, we were looking for a more flexible solution, available anywhere, free from download, installation and licensing constraints. In this context, we created PlateEditor, a free web-based, client-side application allowing rapid creation of even complex layouts, including dose-response curves and multiple combination experiments for any plate format up to 1536 wells. PlateEditor also provides heatmap visualization and aggregation features to speed-up the process of data analysis and formatting for export in other application. Written in pure JavaScript, it is fully open-source, can be integrated in various workflows and has the potential to be extended with more functionalities in the future.

scholarly journals MightyScreen: An Open-Source Visualization Application for Screening Data Analysis

2017 ◽  
Vol 23 (2) ◽  
pp. 218-223
Author(s):  
Longfei Wang ◽  
Qin Yang ◽  
Adriana Jaimes ◽  
Tianyu Wang ◽  
Hendrik Strobelt ◽  
...  
Keyword(s):  
Data Analysis ◽  
Data Quality ◽  
Open Source ◽  
Biomedical Research ◽  
Data Evaluation ◽  
Selection Methods ◽  
Visual Data ◽  
Web Based ◽  
Visualization Application

Screening is a methodology widely used in biological and biomedical research. There are numerous visualization methods to validate screening data quality but very few visualization applications capable of hit selection. Here, we present MightyScreen ( mightyscreen.net ), a novel web-based application designed for visual data evaluation as well as visual hit selection. We believe MightyScreen is an intuitive and interactive addition to conventional hit selection methods. We also provide study cases showing how MightyScreen is used to visually explore screening data and make hit selections.

scholarly journals HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps

2017 ◽  
Author(s):  
Peter Kerpedjiev ◽  
Nezar Abdennur ◽  
Fritz Lekschas ◽  
Chuck McCallum ◽  
Kasper Dinkla ◽  
...  
Keyword(s):  
Open Source ◽  
Visual Exploration ◽  
Visualization Tool ◽  
Data Types ◽  
Experimental Conditions ◽  
Web Based ◽  
Web Technologies ◽  
Link Type

AbstractWe present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, allowing users to combine various data types, synchronize multiple visualization modalities, and share fully customizable views with others. We demonstrate its utility in exploring different experimental conditions, comparing the results of analyses, and creating interactive snapshots to share with collaborators and the broader public. HiGlass is accessible online athttp://higlass.ioand is also available as a containerized application that can be run on any platform.

scholarly journals BPG: Seamless, Automated and Interactive Visualization of Scientific Data

2017 ◽  
Author(s):  
Christine P’ng ◽  
Jeffrey Green ◽  
Lauren C. Chong ◽  
Daryl Waggott ◽  
Stephenie D. Prokopec ◽  
...  
Keyword(s):  
Open Source ◽  
Interactive Visualization ◽  
Scientific Data ◽  
High Dimensional ◽  
Seamless Integration ◽  
Web Based ◽  
Link Type ◽  
Interactive Tool ◽  
High Dimensional Datasets ◽  
Publication Quality

AbstractWe introduce BPG, an easy-to-use framework for generating publication-quality, highly-customizable plots in the R statistical environment. This open-source package includes novel methods of displaying high-dimensional datasets and facilitates generation of complex multi-panel figures, making it ideal for complex datasets. A web-based interactive tool allows online figure customization, from which R code can be downloaded for seamless integration with computational pipelines. BPG is available at http://labs.oicr.on.ca/boutros-lab/software/bpg

scholarly journals SoS Notebook: An Interactive Multi-Language Data Analysis Environment

2018 ◽  
Author(s):  
Bo Peng ◽  
Gao Wang ◽  
Jun Ma ◽  
Man Chong Leong ◽  
Chris Wakefield ◽  
...  
Keyword(s):  
Data Analysis ◽  
Data Collection ◽  
Bioinformatic Analysis ◽  
Web Based ◽  
Link Type ◽  
Language Data ◽  
Scripting Language ◽  
Cross Language ◽  
Analysis Environment ◽  
Different Parts

AbstractMotivationComplex bioinformatic data analysis workflows involving multiple scripts in different languages can be difficult to consolidate, share, and reproduce. An environment that streamlines the entire processes of data collection, analysis, visualization and reporting of such multi-language analyses is currently lacking.ResultsWe developed Script of Scripts (SoS) Notebook, a web-based notebook environment that allows the use of multiple scripting language in a single notebook, with data flowing freely within and across languages. SoS Notebook enables researchers to perform sophisticated bioinformatic analysis using the most suitable tools for different parts of the workflow, without the limitations of a particular language or complications of cross-language communications.AvailabilitySoS Notebook is hosted at http://vatlab.github.io/SoS/ and is distributed under a BSD [email protected]

scholarly journals GiraFFe Browse: A lightweight web based tool for inspecting GFF and FASTA data

2018 ◽  
Author(s):  
Owen Garland ◽  
Amanda Clare ◽  
Wayne Aubrey
Keyword(s):  
Escherichia Coli ◽  
Software Engineering ◽  
Open Source ◽  
Fasta File ◽  
Web Based ◽  
Link Type ◽  
European Nucleotide Archive ◽  
Specialist Knowledge ◽  
Engineering Practices ◽  
User Friendly

AbstractSummaryGiraFFe Browse is a tool aimed at making GFF and FASTA data more useful and accessible to researchers. Existing solutions are large in scope and difficult to maintain without specialist knowledge of computer systems. GiraFFe Browse is a lightweight alternative, built using modern software engineering practices with a focus on being developer and user friendly.Availability and implementationGiraFFe Browse is open source (GPL) software that is available from the Github repository: https://github.com/bag-man/giraffe-browseDemo versionAn example installation of the application is available at http://giraffe.owen.cymru, using a GFF and FASTA file of Escherichia coli from the European Nucleotide [email protected]

Perceptions of a Collaborative Professional Learning Program: Seeing the “Bigger Picture”

2020 ◽  
Vol 5 (1) ◽  
pp. 290-303
Author(s):  
P. Charlie Buckley ◽  
Kimberly A. Murza ◽  
Tami Cassel
Keyword(s):  
Data Analysis ◽  
Professional Learning ◽  
Social Communication ◽  
Special Educators ◽  
Service Providers ◽  
Integrative Approach ◽  
Theory Approach ◽  
Learning Program ◽  
Speech Language Pathologists ◽  
Related Service

Purpose The purpose of this study was to explore the perceptions of special education practitioners (i.e., speech-language pathologists, special educators, para-educators, and other related service providers) on their role as communication partners after participation in the Social Communication and Engagement Triad (Buckley et al., 2015 ) yearlong professional learning program. Method A qualitative approach using interviews and purposeful sampling was used. A total of 22 participants who completed participation in either Year 1 or Year 2 of the program were interviewed. Participants were speech-language pathologists, special educators, para-educators, and other related service providers. Using a grounded theory approach (Glaser & Strauss, 1967 ) to data analysis, open, axial, and selective coding procedures were followed. Results Three themes emerged from the data analysis and included engagement as the goal, role as a communication partner, and importance of collaboration. Conclusions Findings supported the notion that educators see the value of an integrative approach to service delivery, supporting students' social communication and engagement across the school day but also recognizing the challenges they face in making this a reality.

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