Filters








695 Hits in 9.3 sec

A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects

Gerhard Mayer, Christian Quast, Janine Felden, Matthias Lange, Manuel Prinz, Alfred Pühler, Chris Lawerenz, Uwe Scholz, Frank Oliver Glöckner, Wolfgang Müller, Katrin Marcus, Martin Eisenacher
2017 Briefings in Bioinformatics  
In this article, a generally applicable lightweight method is described by which bioinformatics infrastructure projects can estimate the value of tools and services offered without determining exactly  ...  Four examples are presented for the calculation of the value of tools and services provided by the German Network for Bioinformatics Infrastructure (de.NBI): one for tool usage, one for (Web-based) database  ...  Consequently, there is a need for a generally applicable lightweight cost model.  ... 
doi:10.1093/bib/bbx140 pmid:29092005 fatcat:lzqav62rvbfe7i4ujdzrqimdsi

CNSMO: A Network Services Manager/Orchestrator Tool for Cloud Federated Environments [article]

J. Aznar, E. Escalona, I. Canyameres, O. Moya, A. Viñes
2016 arXiv   pre-print
Application service providers (ASPs) now develop, deploy, and maintain complex computing platforms within multiple cloud infrastructures to improve resilience, responsiveness and elasticity of their applications  ...  In this paper, we propose the CNSMO (CYCLONE Network Services Manager/Orchestrator) tool to bring the innovation at federated cloud environments by bridging these network service capabilities to cloud  ...  ACKNOWLEDGMENT The work presented in this paper is supported by the EU funded Horizon2020 project CYCLONE under Grant agreement no. 644925  ... 
arXiv:1609.01043v1 fatcat:2j7umsi2frfujg3rwpvmfb47g4

The eBioKit, a stand-alone educational platform for bioinformatics

Rafael Hernández-de-Diego, Etienne P. de Villiers, Tomas Klingström, Hadrien Gourlé, Ana Conesa, Erik Bongcam-Rudloff, Francis Ouellette
2017 PLoS Computational Biology  
The eBioKit is a stand-alone educational platform that hosts numerous tools and databases for bioinformatics research and allows training to take place in a controlled environment.  ...  providing small research groups with a platform to incorporate bioinformatics analysis in their research.  ...  Acknowledgments We thank the EMBnet, H3Abionet, SANBio, and BECA/ILRI communities and members for valuable discussions and for providing logistics and resources.  ... 
doi:10.1371/journal.pcbi.1005616 pmid:28910280 pmcid:PMC5598936 fatcat:7mke2s2wjvdnvdwjp22plk577e

Container-based bioinformatics with Pachyderm

Jon Ander Novella, Payam Emami Khoonsari, Stephanie Herman, Daniel Whitenack, Marco Capuccini, Joachim Burman, Kim Kultima, Ola Spjuth, Jonathan Wren
2018 Bioinformatics  
We adapted Pachyderm and demonstrated its attractive properties in bioinformatics. A Helm Chart was created so that researchers can use Pachyderm in multiple scenarios.  ...  A wrapper for initiating Pachyderm on cloud-agnostic virtual infrastructures was created.  ...  System and methods Kubernetes Kubernetes is a tool that efficiently orchestrates containerised applications in a cluster of computers, without tying containers specifically to individual machines.  ... 
doi:10.1093/bioinformatics/bty699 pmid:30101309 fatcat:etdpz4xxrrbfde4zbsyuagp32a

Container-based bioinformatics with Pachyderm [article]

Jon Ander Novella, Payam Emami Khoonsari, Stephanie Herman, Daniel Whitenack, Marco Capuccini, Joachim Burman, Kim Kultima, Ola Spjuth
2018 bioRxiv   pre-print
We adapted Pachyderm and demonstrated its attractive properties in bioinformatics. A Helm Chart was created so that researchers can use Pachyderm in multiple scenarios.  ...  A wrapper for initiating Pachyderm on cloud-agnostic virtual infrastructures was created.  ...  System and methods Kubernetes Kubernetes is a tool that efficiently orchestrates containerised applications in a cluster of computers, without tying containers specifically to individual machines.  ... 
doi:10.1101/299032 fatcat:khv7fvuhobfitjwkp7ydzxwyly

A Framework of Intelligent Middleware for DNA Sequence Analysis in Cloud Computing Environment
DNA 서열 분석을 위한 클라우드 컴퓨팅 기반 지능형 미들웨어 설계

Junseok Oh, Yoonjae Lee, Bong Gyou Lee
2014 Journal of Internet Computing and services  
The workflow-based middleware, which supports Web services, DBMS, and cloud computing, is proposed in this paper for expecting to reduceanalysis time and aiding lightweight virtual instances.  ...  It uses DBMS for managing the pipeline status and supporting the creation of lightweight virtual instances in the cloud environment.  ...  In this paper, we have developed workflow-based middleware as a part of a national project. The project is aimed for developing the next generation bioinformatics platform.  ... 
doi:10.7472/jksii.2014.15.1.29 fatcat:wrrehounhzdq3eewiymx6uh37q

JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes

Michael Richter, Thierry Lombardot, Ivaylo Kostadinov, Renzo Kottmann, Melissa Duhaime, Jörg Peplies, Frank Glöckner
2008 BMC Bioinformatics  
The lightweight software solution allows the user to easily take advantage of advanced back-end database structures by providing a programming and graphical user interface to answer biological questions  ...  Based on a pre-computed GenDB database project, JCoast offers a flexible graphical user interface (GUI), as well as an application programming interface (API) that facilitates back-end data access.  ...  Acknowledgements We thank Marga Schüler, Stefka Tyanova, Christian Quast, Elmar Prüsse, Anke Meyerdierks, and Beatriz Fernández Gómez for testing the application at early stages of the development and  ... 
doi:10.1186/1471-2105-9-177 pmid:18380896 pmcid:PMC2311307 fatcat:vbdqmtjs6nceril6d4snhltvre

e!DAL - a framework to store, share and publish research data

Daniel Arend, Matthias Lange, Jinbo Chen, Christian Colmsee, Steffen Flemming, Denny Hecht, Uwe Scholz
2014 BMC Bioinformatics  
DAL is a lightweight software framework for publishing and sharing research data.  ...  The infrastructures currently available for managing and publishing data are often designed to meet domain-specific or project-specific requirements, resulting in the repeated development of proprietary  ...  Acknowledgements We thank Joscha Joel Benz for the initial WebDAV code and Thomas Münch, Heiko Miehe as administrator of the project website, code, and artifact repositories.  ... 
doi:10.1186/1471-2105-15-214 pmid:24958009 pmcid:PMC4080583 fatcat:37kjtgzyybdmde5nw6z2mfen6e

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines

Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti, Raffaele A Calogero
2018 BMC Bioinformatics  
Reproducible Bioinformatics Project provides a general schema and an infrastructure to distribute robust and reproducible workflows.  ...  Reproducibility of a research is a key element in the modern science and it is mandatory for any industrial application.  ...  However, Bioconductor does not cover all the steps of any possible bioinformatics workflow, e.g. in RNAseq wolkflow fastq trimming and alignment steps are generally done using tools not implemented in  ... 
doi:10.1186/s12859-018-2296-x pmid:30367595 pmcid:PMC6191970 fatcat:svttxrofbndzla5lduo2ntozfy

BioInstaller: a comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform

Jianfeng Li, Bowen Cui, Yuting Dai, Ling Bai, Jinyan Huang
2018 PeerJ  
The increase in bioinformatics resources such as tools/scripts and databases poses a great challenge for users seeking to construct interactive and reproducible biological data analysis applications.  ...  interfaces, and a docker image.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.7717/peerj.5853 pmid:30402350 pmcid:PMC6215441 fatcat:6u5v3tdljncq3iirzns37v5mlq

Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes

Tiziana Margaria, Christian Kubczak, Bernhard Steffen
2008 BMC Bioinformatics  
Methods: Bio-jETI uses the jABC environment for service-oriented modeling and design as a graphical process modeling tool and the jETI service integration technology for remote tool execution.  ...  With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R  ...  This article has been published as part of BMC Bioinformatics Volume 9 Supplement 4, 2008: A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications.  ... 
doi:10.1186/1471-2105-9-s4-s12 pmid:18460173 pmcid:PMC2367639 fatcat:y7fq43ei7zdwla3f7cb6xhz3ae

West-Life: a virtual research environment for structural biology

Chris Morris, Paolo Andreetto, Lucia Banci, Alexandre M.J.J. Bonvin, Grzegorz Chojnowski, Laura del Cano, José Marıa Carazo, Pablo Conesa, Susan Daenke, George Damaskos, Andrea Giachetti, Natalie E.C. Haley (+19 others)
2019 Journal of Structural Biology: X  
The West-Life project (https://about.west-life.eu/) is a Horizon 2020 project funded by the European Commission to provide data processing and data management services for the international community of  ...  Through this work it has striven to make the benefits of European e-Infrastructures more accessible to life-science researchers in general and structural biologists in particular.  ...  Most users in general only access a limited number of options, but for challenging projects or particular experiment types more control can be useful.  ... 
doi:10.1016/j.yjsbx.2019.100006 pmid:32647812 pmcid:PMC7337051 fatcat:i5kgwmdfpzg5nibcwt2wkaz4qi

Scalability and Validation of Big Data Bioinformatics Software

Andrian Yang, Michael Troup, Joshua W.K. Ho
2017 Computational and Structural Biotechnology Journal  
Scalability is defined as the ability for a program to scale based on workload. It has always been an important consideration when developing bioinformatics algorithms and programs.  ...  We discuss how modern cloud computing and big data programming frameworks such as MapReduce and Spark are being used to effectively implement divide-and-conquer in a distributed computing environment.  ...  (1105271), Amazon Web Services (AWS) Credits for Research, and an Australian Postgraduate Award.  ... 
doi:10.1016/j.csbj.2017.07.002 pmid:28794828 pmcid:PMC5537105 fatcat:nnkrlwg35fd3hkpbg2jtosdicq

SNPflow: A Lightweight Application for the Processing, Storing and Automatic Quality Checking of Genotyping Assays

Hansi Weissensteiner, Margot Haun, Sebastian Schönherr, Mathias Neuner, Lukas Forer, Günther Specht, Anita Kloss-Brandstätter, Florian Kronenberg, Stefan Coassin, Paul Taylor
2013 PLoS ONE  
SNPflow is a lightweight, intuitive and easily deployable application, which processes genotype data from Sequenom MassARRAY (iPLEX) and ABI 7900HT (TaqMan, KASPar) systems and is extendible to other genotyping  ...  , provides a module for the processing of SNPs, which allow sex determination for DNA quality control purposes and, finally, stores all data in a relational database.  ...  Hibernate is a powerful object-relational mapping tool for persistence and query services. The passwords of the different users are stored in the database securely encoded by MD5 hash.  ... 
doi:10.1371/journal.pone.0059508 pmid:23527209 pmcid:PMC3602247 fatcat:2bjcz3cgvbhexcfjeeouegruce

Phenomenal Services Virtual Machine Image To Facilitate The Phenomenal Toolsets And Pipelines, Both Locally And In The Grid - D9.2.3

PhenoMeNal Consortium
2016 Zenodo  
The chosen cloud and software architectures are well-aligned with emerging bioinformatics efforts for use in national and European scientific cloud infrastructures.  ...  Description of the architecture of the service VMIs with user-facing web interfaces and how service VMIs performing the container orchestration are installed in the Virtual Research Environment (VRE).  ...  Candidate molecules of different databases are fragmented in silico and matched against mass to charge values, and a score is calculated using the fragment peak matches.  ... 
doi:10.5281/zenodo.832594 fatcat:sapubhpg6jbxrfiguda2fjdctm
« Previous Showing results 1 — 15 out of 695 results