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Scaling Up Bioinformatics Workflows with Dynamic Job Expansion: A Case Study Using Galaxy and Makeflow

Nicholas Hazekamp, Joseph Sarro, Olivia Choudhury, Sandra Gesing, Scott Emrich, Douglas Thain
2015 2015 IEEE 11th International Conference on e-Science  
Logical workflow management systems provide a user-friendly portal through which data can be processed using a sequence of standard tools.  ...  To demonstrate this technique, we have applied job expansion to a selection of bioinformatics applications running in the Galaxy workflow management system.  ...  We have implemented dynamic job expansion using Galaxy as a logical workflow manager, Makeflow [6] as the performance workflow manager, and Work Queue [7] as a remote execution system.  ... 
doi:10.1109/escience.2015.39 dblp:conf/eScience/HazekampSCGET15 fatcat:e4dbpumrfbaxthlwmxfo5gpdma

Conceptual-level workflow modeling of scientific experiments using NMR as a case study

Kacy K Verdi, Heidi Jc Ellis, Michael R Gryk
2007 BMC Bioinformatics  
Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data.  ...  Using the approach, we were able to accurately document, in a short amount of time, numerous steps in the process of conducting an experiment using NMR spectroscopy.  ...  Maciejewski in the validation of the workflows. This work was supported by NIH grant EB001496 to H.J.C.E. and M.R.G.  ... 
doi:10.1186/1471-2105-8-31 pmid:17263870 pmcid:PMC1796901 fatcat:cqm7qqutbfg75gclixxzawdm7i

Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case

Thomas A Russ, Cartic Ramakrishnan, Eduard H Hovy, Mihail Bota, Gully APC Burns
2011 BMC Bioinformatics  
This is presented as a possible biocuration interface and supplementary reasoning toolkit for a larger, more specialized bioinformatics system: the Brain Architecture Management System (BAMS).  ...  It uses Persevere (a noSQL database) as a flexible data store and PowerLoom ® (a mature First Order Logic reasoning system) to execute queries using spatial reasoning over the BAMS neuroanatomical ontology  ...  for the 'BioScholar' project http://bmkeg.isi.edu/ with some additional contributions from NIH grant (1R01MH079068-01A2) and from the non-specific funding program from the Michael J Fox Foundation ('A  ... 
doi:10.1186/1471-2105-12-351 pmid:21859449 pmcid:PMC3176268 fatcat:6mhn4gtoknetndkbfzkg6vyuqy

Application of whole genome data for in silico evaluation of primers and probes routinely employed for the detection of viral species by RT-qPCR using dengue virus as a case study

Kevin Vanneste, Linda Garlant, Sylvia Broeders, Steven Van Gucht, Nancy H. Roosens
2018 BMC Bioinformatics  
Using dengue virus as a case study, we evaluated 18 published RT-qPCR methods using more than 3000 publically available genomes in the NCBI Virus Variation Resource, and provide a systematic overview of  ...  Results: We present a bioinformatics approach that enables in silico evaluation of primers and probes intended for routinely employed RT-qPCR methods.  ...  KV and LG conducted the bioinformatics analysis. All authors aided in interpretation of the results and writing of the final manuscript. All authors read and approved the final manuscript.  ... 
doi:10.1186/s12859-018-2313-0 pmid:30180800 pmcid:PMC6123964 fatcat:qgizfencvbealba53ih723tv2m

RetroMine, or how to provide in-depth retrospective studies from Medline in a glance: the hepcidin use-case

Bertrand Ameline de Cadeville, Olivier Loréal, Fouzia Moussouni-Marzolf
2015 Journal of Integrative Bioinformatics  
However, bioinvestigators are still reluctant to use these tools for two reasons: i) a large volume of events is often extracted upon a query, and this volume is hard to manage, and ii) background events  ...  This work is illustrated by a case study regarding Hepcidin gene publications over a decade, a duration that is sufficiently long enough to generate alternative views on the overall data extracted.  ...  We have used a workflow centered on web-service to generate massive amounts of data on events for each month of D.  ... 
doi:10.2390/biecoll-jib-2015-275 pmid:26673791 fatcat:nfyuq5ygrres3cvvtiyeefbh3u

RetroMine, or how to provide in-depth retrospective studies from Medline in a glance: the hepcidin use-case

Bertrand Ameline de Cadeville, Olivier Loréal, Fouzia Moussouni-Marzolf
2015 Journal of Integrative Bioinformatics  
However, bioinvestigators are still reluctant to use these tools for two reasons: i) a large volume of events is often extracted upon a query, and this volume is hard to manage, and ii) background events  ...  This work is illustrated by a case study regarding Hepcidin gene publications over a decade, a duration that is sufficiently long enough to generate alternative views on the overall data extracted.  ...  We have used a workflow centered on web-service to generate massive amounts of data on events for each month of D.  ... 
doi:10.1515/jib-2015-275 fatcat:gf7hq5pwhzaidaw3dgotcwhnoe

Using prototyping to choose a bioinformatics workflow management system

Michael Jackson, Kostas Kavoussanakis, Edward W. J. Wallace, Francis Ouellette
2021 PLoS Computational Biology  
a workflow management system.  ...  Many workflow management systems enhance portability by supporting the use of containers, high-performance computing (HPC) systems, and clouds.  ...  The intent of this article is not to make a recommendation as to the use of a specific workflow management system for all bioinformatics projects.  ... 
doi:10.1371/journal.pcbi.1008622 pmid:33630841 fatcat:3lltosvobrey7o37akej3orwxq

Technical Perspectives on Knowledge Management in Bioinformatics Workflow Systems

Walaa N., M.Sabih Aksoy
2015 International Journal of Advanced Computer Science and Applications  
This article focuses on the knowledge management of in silico experimentation in bioinformatics workflow systems.  ...  Workflow systems by it's nature can help bioinformaticians to plan for their experiments, store, capture and analysis of the runtime generated data.  ...  for a particular use case.  ... 
doi:10.14569/ijacsa.2015.060126 fatcat:wskynuwvzvfijb4cymmpu4to4e

Designing for Recommending Intermediate States in A Scientific Workflow Management System [article]

Debasish Chakroborti, Banani Roy, Sristy Sumana Nath
2020 arXiv   pre-print
In this paper, we present and evaluate a GUI version of such a novel approach of intermediate data management with two use cases (Plant Phenotyping and Bioinformatics).  ...  We integrated GUI-RISPTS with an existing workflow management system called SciWorCS.  ...  Case Studies, Technology Integrations and Evaluations A number of studies [23] [34] have been done on Use-case analysis of system integration and architecture implementation in the domain of Scientific  ... 
arXiv:2010.04880v1 fatcat:h4mtd24rdzfjnbvuiwyxdy6xam

Using rapid prototyping to choose a bioinformatics workflow management system [article]

Michael Jackson, Edward Wallace, Kostas Kavoussanakis
2020 bioRxiv   pre-print
a workflow management system.  ...  Many workflow management systems enhance portability by supporting the use of containers, high-performance computing systems and clouds.  ...  To avoid being rendered indecisive through 186 188 Baichoo et al. [19] describe a case study of a project, H3ABioNet, who sought a workflow 189 management system both in common use within the bioinformatics  ... 
doi:10.1101/2020.08.04.236208 fatcat:xzgov53yizb63efaor4ziutn6y

Bioinformatics algorithm development for Grid environments

Fotis E. Psomopoulos, Pericles A. Mitkas
2010 Journal of Systems and Software  
Bioinformatics applications stand to gain in such a distributed environment in terms of increased availability, reliability and efficiency of computational resources.  ...  In this paper we introduce a unifying methodology coupling the strengths of the Grid with the specific needs and constraints of the major bioinformatics approaches.  ...  the locations of intermediate data are managed by a distributed data management system.  ... 
doi:10.1016/j.jss.2010.01.051 fatcat:ss5fenza55c5nk4o6ksmemstxe

Guided Composition of Tasks with Logical Information Systems - Application to Data Analysis Workflows in Bioinformatics [chapter]

Mouhamadou Ba
2013 Lecture Notes in Computer Science  
This doctorial work will address the composition of tasks using Logical Information Systems (LIS).  ...  In a number of domains, particularly in bioinformatics, there is a need for complex data analysis. For that issue, elementary data analysis operations called tasks are composed as workflows.  ...  The platform offers a suitable environment to evaluate and validate our approach. We will use datasets and real cases of the GenOuest platform for evaluation.  ... 
doi:10.1007/978-3-642-38288-8_47 fatcat:qvzfu62ytnbfdfdkehyqfr4n7y

Web Service management system for bioinformatics research: a case study

Kai Xu, Qi Yu, Qing Liu, Ji Zhang, Athman Bouguettaya
2011 Service Oriented Computing and Applications  
In this paper, we present a case study of the design and development of a Web Service management system for bioinformatics research.  ...  The described system is a prototype that provides a complete solution to manage the entire life cycle of Web Services in bioinformatics domain, which include semantic service description, service discovery  ...  We would like to thank Mark Hepburn for his contribution to the implementation of the system.  ... 
doi:10.1007/s11761-011-0076-9 fatcat:aggzwybqgrhnjfk7hi55i4q7lu

Renewing bioinformatics workflow systems by using a Web 2.0 approach

Roberto Colella, Bachir Balech, Antonella Vaccina, Pietro Leo, Gaetano Scioscia
2015 EMBnet journal  
In this study, a Web 2.0 technology was adopted to promote a key field of bioinformatics research through the management and automation of bioinformatics workflows.  ...  plausible alternative environment for supporting bioinformatics workflow design, management and execution.  ...  To that end, we provide a complete description of this workflow management and storage system, presented as a prototype and tested on two locally assembled bioinformatics workflows in a mashup framework  ... 
doi:10.14806/ej.21.0.840 fatcat:bcxednt5fzadlezro5fqnf2s4a

information management system [chapter]

Martin H. Weik
2000 Computer Science and Communications Dictionary  
Therefore it is portable and flexible and can also be used as a stand alone tool to manage a microarray laboratory workflow.  ...  In this project a Microarray Laboratory Information Management System (Microarray LIMS) was designed and developed to become part of the integrated bioinformatics infrastructure for the Organon GeneChip  ...  Therefore it is portable and flexible and can also be used as a stand alone tool to manage a microarray laboratory workflow.  ... 
doi:10.1007/1-4020-0613-6_8939 fatcat:7nlcguakhze4zbhlvofxazmjby
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