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]

scholarly journals CrosstalkNet: mining large-scale bipartite co-expression networks to characterize epi-stroma crosstalk

2017 ◽  
Author(s):  
Venkata Manem ◽  
George Adam ◽  
Tina Gruosso ◽  
Mathieu Gigoux ◽  
Nicholas Bertos ◽  
...  
Keyword(s):  
Stromal Cells ◽  
Large Scale ◽  
Network Visualization ◽  
Visualization Tool ◽  
Biological Processes ◽  
Web Based ◽  
Link Type ◽  
A Cell ◽  
Large Scale Networks ◽  
User Friendly

ABSTRACTBackground:Over the last several years, we have witnessed the metamorphosis of network biology from being a mere representation of molecular interactions to models enabling inference of complex biological processes. Networks provide promising tools to elucidate intercellular interactions that contribute to the functioning of key biological pathways in a cell. However, the exploration of these large-scale networks remains a challenge due to their high-dimensionality.Results:CrosstalkNet is a user friendly, web-based network visualization tool to retrieve and mine interactions in large-scale bipartite co-expression networks. In this study, we discuss the use of gene co-expression networks to explore the rewiring of interactions between tumor epithelial and stromal cells. We show how CrosstalkNet can be used to efficiently visualize, mine, and interpret large co-expression networks representing the crosstalk occurring between the tumour and its microenvironment.Conclusion:CrosstalkNet serves as a tool to assist biologists and clinicians in exploring complex, large interaction graphs to obtain insights into the biological processes that govern the tumor epithelial-stromal crosstalk. A comprehensive tutorial along with case studies are provided with the application.Availability:The web-based application is available at the following location: http://epistroma.pmgenomics.ca/app/. The code is open-source and freely available from http://github.com/bhklab/EpiStroma-webapp.Contact:[email protected]

scholarly journals SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts

2020 ◽  
Author(s):  
R. Zhang ◽  
M. Mirdita ◽  
E. Levy Karin ◽  
C. Norroy ◽  
C. Galiez ◽  
...  
Keyword(s):  
Open Source ◽  
Protein Level ◽  
De Novo ◽  
False Positives ◽  
Metagenomic Data ◽  
Command Line ◽  
Link Type ◽  
Host Relationships ◽  
User Friendly

SummarySpacePHARER (CRISPR Spacer Phage-Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage-host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER gains sensitivity by comparing spacers and phages at the protein-level, optimizing its scores for matching very short sequences, and combining evidences from multiple matches, while controlling for false positives. We demonstrate SpacePHARER by searching a comprehensive spacer list against all complete phage genomes.Availability and implementationSpacePHARER is available as an open-source (GPLv3), user-friendly command-line software for Linux and macOS at spacepharer.soedinglab.org.

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.

Software Quality in Open Source Software Ecosystems

2011 ◽  
pp. 1496-1501
Author(s):  
Pankaj Kamthan
Keyword(s):  
Software Engineering ◽  
Open Source ◽  
Open Source Software ◽  
Research Literature ◽  
Future Research ◽  
Software Project ◽  
Window System ◽  
Mailing Lists ◽  
Engineering Practices

The steady rise of open source software (OSS) (Raymond, 1999) over the last few decades has made a noticeable impact on many sectors of society where software has a role to play. As reflected from the frequency of media articles, traffic on mailing lists, and growing research literature, OSS has garnered much support in the software community. Indeed, from the early days of GNU software, to X Window System, to Linux and its utilities, and more recently the Apache Software Project, OSS has changed the way software is developed and used. As the deployment of OSS increases, the issue of its quality with respect to its stakeholders arises. We contend that the open source community collectively bears responsibility of producing “high-quality” OSS. Lack of quality raises various risks for organizations adopting OSS (Golden, 2004). This article discusses the manifestation of quality in open source software development (OSSD) from a traditional software engineering standpoint. The organization is as follows. We first outline the background and related work necessary for the discussion that follows, and state our position. This is followed by a detailed treatment of key software engineering practices that directly or indirectly impact the quality of OSS. Next, challenges and directions for future research are outlined and, finally, concluding remarks are given.

Component-Based Deployment for Web Applications

2011 ◽  
pp. 123-137
Author(s):  
Kevin Gary ◽  
Harry Koehnemann
Keyword(s):  
Software Engineering ◽  
Open Source ◽  
Real World ◽  
Cycle Time ◽  
Development Process ◽  
Web Applications ◽  
Web Based ◽  
Component Based Software Engineering ◽  
Reducing Costs ◽  
Downstream Processes

The software engineering community touts component-based software engineering as a solution for many of its woes including reducing cycle time, reducing costs, increasing productivity, allowing easier integration to name just a few. Indeed, many Web-based systems are now built with open-source and vendor provided component technologies. While these advances have led to improvements in the development process, they have also led to a great deal of pressure on downstream processes as these systems must be deployed, tuned, and supported. The complexities in deploying and supporting component- based software for distributed and Web-based applications are not understood in the academic or professional communities. This chapter stresses the need for addressing this problem by presenting component-based software for Web applications from a deployment perspective, characterizing the issues through real-world experiences with highly component-based applications, and presents strategies and directions for the community to pursue.

scholarly journals A repository of web-based bioinformatics resources developed in India

2020 ◽  
Author(s):  
Abhishek Agarwal ◽  
Piyush Agrawal ◽  
Aditi Sharma ◽  
Vinod Kumar ◽  
Chirag Mugdal ◽  
...  
Keyword(s):  
Scientific Community ◽  
Biological Databases ◽  
Web Interface ◽  
Web Based ◽  
Link Type ◽  
Complete Detail ◽  
User Friendly

AbstractIndiaBioDb (https://webs.iiitd.edu.in/raghava/indiabiodb/) is a manually curated comprehensive repository of bioinformatics resources developed and maintained by Indian researchers. This repository maintains information about 543 freely accessible functional resources that include around 258 biological databases. Each entry provides a complete detail about a resource that includes the name of resources, web link, detail of publication, information about the corresponding author, name of institute, type of resource. A user-friendly searching module has been integrated, which allows users to search our repository on any field. In order to retrieve categorized information, we integrate the browsing facility in this repository. This database can be utilized for extracting the useful information regarding the present scenario of bioinformatics inclusive of all research labs funded by government and private bodies of India. In addition to web interface, we also developed mobile to facilitate the scientific community.

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.

A Quantitative Study of the Adoption of Design Patterns by Open Source Software Developers

2008 ◽  
pp. 560-577
Author(s):  
Michael Hahsler
Keyword(s):  
Software Engineering ◽  
Open Source ◽  
Open Source Software ◽  
Design Patterns ◽  
Development Process ◽  
Research Question ◽  
Engineering Practice ◽  
Software Projects ◽  
High Quality ◽  
Engineering Practices

Several successful projects (Linux, Free-BSD, BIND, Apache, etc.) showed that the collaborative and self-organizing process of developing open source software produces reliable, high quality software. Without doubt, the open source software development process differs in many ways from the traditional development process in a commercial environment. An interesting research question is how these differences influence the adoption of traditional software engineering practices. In this chapter we investigate how design patterns, a widely accepted software engineering practice, are adopted by open source developers for documenting changes. We analyze the development process of almost 1,000 open source software projects using version control information and explore differences in pattern adoption using characteristics of projects and developers. By analyzing these differences, we provide evidence that design patterns are an important practice in open source projects and that there exist significant differences between developers who use design patterns and who do not.

scholarly journals Whole-Genome Sequencing Data for Serotyping Escherichia coli—It's Time for a Change!

2015 ◽  
Vol 53 (8) ◽  
pp. 2402-2403 ◽  
Author(s):  
Claire Jenkins
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Content Type ◽  
Link Type ◽  
Article Type ◽  
User Friendly

The accessibility of whole-genome sequencing (WGS) presents the opportunity for national reference laboratories to provide a state-of-the-art public health surveillance service. The replacement of traditional serology-based typing ofEscherichia coliby WGS is supported by user-friendly, freely available data analysis Web tools. Anarticle in this issueof theJournal of Clinical Microbiology(K. G. Joensen, A. M. M. Tetzschner, A. Iguchi, F. M. Aarestrup, and F. Scheutz, J Clin Microbiol, 53:2410–2426, 2015,http://dx.doi.org/10.1128/JCM.00008-15) describes SerotypeFinder, an essential guide to serotypingE. coliin the 21st century.

scholarly journals Tribe: The collaborative platform for reproducible web-based analysis of gene sets

2016 ◽  
Author(s):  
René A. Zelaya ◽  
Aaron K. Wong ◽  
Alex T. Frase ◽  
Marylyn D. Ritchie ◽  
Casey S. Greene
Keyword(s):  
Open Source ◽  
Web Interface ◽  
Web Based ◽  
Gene Set ◽  
Collaborative Editing ◽  
Gene Sets ◽  
Collaborative Platform ◽  
Set Up ◽  
User Friendly ◽  
Multi Server

AbstractBackgroundThe adoption of new bioinformatics webservers provides biological researchers with new analytical opportunities but also raises workflow challenges. These challenges include sharing collections of genes with collaborators, translating gene identifiers to the most appropriate nomenclature for each server, tracking these collections across multiple analysis tools and webservers, and maintaining effective records of the genes used in each analysis.DescriptionIn this paper, we present the Tribe webserver (available at https://tribe.greenelab.com), which addresses these challenges in order to make multi-server workflows seamless and reproducible. This allows users to create analysis pipelines that use their own sets of genes in combinations of specialized data mining webservers and tools while seamlessly maintaining gene set version control. Tribe’s web interface facilitates collaborative editing: users can share with collaborators, who can then view, download, and edit these collections. Tribe’s fully-featured API allows users to interact with Tribe programmatically if desired. Tribe implements the OAuth 2.0 standard as well as gene identifier mapping, which facilitates its integration into existing servers. Access to Tribe’s resources is facilitated by an easy-to-install Python application called tribe-client. We provide Tribe and tribe-client under a permissive open-source license to encourage others to download the source code and set up a local instance or to extend its capabilities.ConclusionsThe Tribe webserver addresses challenges that have made reproducible multi-webserver workflows difficult to implement until now. It is open source, has a user-friendly web interface, and provides a means for researchers to perform reproducible gene set based analyses seamlessly across webservers and command line tools.

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