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Conveyor: a workflow engine for bioinformatic analyses

Burkhard Linke, Robert Giegerich, Alexander Goesmann
2011 Computer applications in the biosciences : CABIOS  
Results: We have developed the Conveyor software library, a multitiered generic workflow engine for composition, execution and monitoring of complex workflows.  ...  Two example use cases illustrate the application of the versatile Conveyor engine to common bioinformatics problems. Availability: The Conveyor application including client and server are available at  ...  ACKNOWLEDGEMENTS The authors further thank the BRF system administrators for technical support.  ... 
doi:10.1093/bioinformatics/btr040 pmid:21278189 fatcat:e2f74dgfvbbjvhnor47tbxtnba

Flexible metagenome analysis using the MGX framework

Sebastian Jaenicke, Stefan P. Albaum, Patrick Blumenkamp, Burkhard Linke, Jens Stoye, Alexander Goesmann
2018 Microbiome  
Results: We present MGX, a flexible and extensible client/server-framework for the management and analysis of metagenomic datasets; MGX features a comprehensive set of adaptable workflows required for  ...  At the same time, MGX allows to include own data sources and devise custom analysis pipelines, thus enabling researchers to perform basic as well as highly specific analyses within a single application  ...  " (grant 031A533) within the German Network for Bioinformatics Infrastructure (de.NBI).  ... 
doi:10.1186/s40168-018-0460-1 pmid:29690922 pmcid:PMC5937802 fatcat:a5sd3o6lpbbcjdioaoo6jar2zq

SciPipe—Turning Scientific Workflows into Computer Programs

Samuel Lampa, Martin Dahlo, Jonathan Alvarsson, Ola Spjuth
2019 Computing in science & engineering (Print)  
We have reviewed the top dozen workflow tools popular in our field of bioinformatics.  ...  This tendency can also be seen in popular workflow engines building on domain specific languages (DSLs).  ... 
doi:10.1109/mcse.2019.2907814 fatcat:kpx6opbk2bdb5lwfjik76dnxii

Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support

Mohamed Abouelhoda, Shadi Issa, Moustafa Ghanem
2012 BMC Bioinformatics  
Over the past decade the workflow system paradigm has evolved as an efficient and userfriendly approach for developing complex bioinformatics applications.  ...  Results In this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns.  ...  We thank Sondos Seif from Nile University for helping us in software engineering tasks.  ... 
doi:10.1186/1471-2105-13-77 pmid:22559942 pmcid:PMC3583125 fatcat:arnykmuzbnehnnk73kmfroe36a

Understanding Design Concept Identification [chapter]

Ivey Chiu, Filippo A. Salustri
2014 Design Computing and Cognition '12  
In general, automated concept identification may lead to better integration of early conceptual design with more detailed and computable downstream processes, resulting in a unified design workflow.  ...  Concepts and concept identification are also of interest in other fields such as archaeology, bioinformatics and education.  ...  Acknowledgements The authors wish to acknowledge the financial support of the Natural Sciences and Engineering Research Council of Canada (NSERC).  ... 
doi:10.1007/978-94-017-9112-0_34 fatcat:exqpbhrqrjefzoqxx2ggpn4sfa

Scientific workflow design for mere mortals

Timothy McPhillips, Shawn Bowers, Daniel Zinn, Bertram Ludäscher
2009 Future generations computer systems  
With these users in mind, we identify a set of desiderata for scientific workflow systems crucial for enabling scientists to model and design the workflows they wish to automate themselves.  ...  Regardless of how a workflow is ultimately deployed -within a local desktop computer, web server, or distributed computing environment -scientists must have models and tools for designing scientific workflows  ...  Finally, while the assembly-line approach can make it easier for scientists to design and understand their workflows, a naïve implementation of a comad workflow enactment engine can result in a greater  ... 
doi:10.1016/j.future.2008.06.013 fatcat:cjgaj5lvy5edrd5qhsdnuoc6bu

Quantitative monitoring of Arabidopsis thaliana growth and development using high-throughput plant phenotyping

Daniel Arend, Matthias Lange, Jean-Michel Pape, Kathleen Weigelt-Fischer, Fernando Arana-Ceballos, Ingo Mücke, Christian Klukas, Thomas Altmann, Uwe Scholz, Astrid Junker
2016 Scientific Data  
engineering and bioinformatics.  ...  Therefore the here presented dataset has been annotated using the standardized ISA-Tab format and considering the recently published recommendations for the semantical description of plant phenotyping  ...  Acknowledgements We thank Hanna Ćwiek-Kupczyńska and Pawe" Krajewski from the Polish Academy of Sciences and Philippe Rocca-Serra from the Oxford e-Research Centre for fruitful discussions and their support  ... 
doi:10.1038/sdata.2016.55 pmid:27529152 pmcid:PMC4986541 fatcat:6w222or54zbdjjvi4gr6sxguju

Modeling and optimization of scientific workflows

Daniel Zinn
2008 Proceedings of the 2008 EDBT Ph.D. workshop on - Ph.D. '08  
Scientific workflow systems are built for modeling and automation of scientific applications, to increase scientists' productivity.  ...  Simulation and computer-aided data analysis have become an integral part of many traditional sciences and have spawned virtual observatories and even entirely new disciplines, e.g. bioinformatics.  ...  For this purpose, I am implementing a COMAD-execution engine for a cluster environment.  ... 
doi:10.1145/1387150.1387152 fatcat:7d3dgy23vjhovhsmghwfaqgbc4

A Semantic Lab Notebook - Report on a Use Case Modelling an Experiment of a Microwave-based Quarantine Method

Nico Adams, Armin Haller, Alexander Krumpholz, Kerry L. Taylor
2013 International Semantic Web Conference  
A recent trend in a number of academic disciplines is the publication of results of experiments together with the scientific article for a better reproducibility of the published experiments and algorithms  ...  Together, the ontologies, the experimental data and the computational services constitute the elements needed for a semantically enabled lab notebook, facilitating research studies over multiple experiments  ...  SADI is a semantic Web service framework that is predominantly used in the bioinformatics domain.  ... 
dblp:conf/semweb/AdamsHKT13 fatcat:fbiumersinhktcvywy23xuwlj4

Automation in the Clinical Microbiology Laboratory

C.-A. D. Burnham, W. M. Dunne, G. Greub, S. M. Novak, R. Patel
2013 Clinical Chemistry  
For example, if plates are transferred via a conveyor below to a smart incubator with a digital camera and a colony is chosen for identification or susceptibility testing, the plate must be sent to a piece  ...  However, these cost analyses are as yet completely lacking for automated microbiology systems.  ...  This is especially true for automated inoculation systems that help in terms of traceability and in getting high-quality spreading of the inoculum over the agar plate, with a higher number of isolated  ... 
doi:10.1373/clinchem.2012.201038 pmid:23690497 fatcat:f6jouzahyngo7gd6aftwy5wnx4

A survey of biodiversity informatics: Concepts, practices, and challenges

Luiz M. R. Gadelha, Pedro C. Siracusa, Eduardo Couto Dalcin, Luís Alexandre Estevão Silva, Douglas A. Augusto, Eduardo Krempser, Helen Michelle Affe, Raquel Lopes Costa, Maria Luiza Mondelli, Pedro Milet Meirelles, Fabiano Thompson, Marcia Chame (+2 others)
2020 Wiley Interdisciplinary Reviews Data Mining and Knowledge Discovery  
The transformation of these raw data into synthesized information that is fit for use requires going through many refinement steps.  ...  Biodiversity data follow a life cycle consisting of planning, collection, certification, description, preservation, discovery, integration, and analysis.  ...  These analyses typically employ several different applications executed in a loosely coupled manner, being a typical use case for scientific workflow management tools (J.  ... 
doi:10.1002/widm.1394 fatcat:m4zuuvmtjzbvfgsjkzarwrvaze

Single muscle fiber proteomics reveals unexpected mitochondrial specialization

M. Murgia, N. Nagaraj, A. S. Deshmukh, M. Zeiler, P. Cancellara, I. Moretti, C. Reggiani, S. Schiaffino, M. Mann
2015 EMBO Reports  
Here, we developed a high-sensitivity workflow to characterize the proteome of single fibers.  ...  The fiber type-resolved proteomes can be applied to a variety of physiological and pathological conditions and illustrate the utility of single cell type analysis for dissecting proteomic heterogeneity  ...  Bioinformatic analysis Analyses were performed with the Perseus software (version 1.4.2.23), part of the MaxQuant environment (http://www.perseusframework.org).  ... 
doi:10.15252/embr.201439757 pmid:25643707 pmcid:PMC4364878 fatcat:w7dfstiykjcoxcp7ig7n5t4gei

Generic Software Frameworks for GC-MS Based Metabolomics [chapter]

Nils Hoffmann, Jens Stoye
2012 Metabolomics  
and for kindly providing us with the datasets.  ...  We finally thank our students Mathias Wilhelm for his work on ChromA4D and Kai-Bernd Stadermann for his work on the RMI-based remote execution framework.  ...  A typical workflow for a metabolomics experiment.  ... 
doi:10.5772/31224 fatcat:dqt23nueeje53mm23zmbohbu54

EMPHASIS-PREP Deliverable 2.5: Report on current and future user demands

Michela Janni, Silvana Moscatelli, Francesco Loreto
2020 Zenodo  
Rationale: Exploring the user and stakeholder demands is a continues and evolving process that is fundamental for the long-term sustainability of EMPHA [...]  ...  Executive Summary Objectives: The improvement of crop performance to address the challenges imposed by climate change and in view of a continuous increases of the world population (and its needs for wellbeing  ...  User access is for one or more installations at a time, resulting in specific datasets that can be analysed per se.  ... 
doi:10.5281/zenodo.4544532 fatcat:l7q5extponcddb2kprouruhn7a

The MGX framework for microbial community analysis

Sebastian Jaenicke
2020
Acknowledgements Alexander Goesmann and Jens Stoye are acknowledged for the opportunity and supervision of this PhD thesis.  ...  I'm also grateful to Peter Belmann and Patrick Blumenkamp for the contribution of software components which they developed during their B.Sc. and M.Sc. theses under my supervision.  ...  analysis pipelines to a different data processing 5.2 Outlook engine, implementing cloud support for the Conveyor workflow engine or adding support for an additional workflow system to MGX that is able  ... 
doi:10.4119/unibi/2940338 fatcat:ef3zg6nqlrhdzm4ysj533576ee
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