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Grids and Clouds: Making Workflow Applications Work in Heterogeneous Distributed Environments

Ewa Deelman
2009 The international journal of high performance computing applications  
Scientific workflows are frequently being used to model complex phenomena, to analyze instrumental data, to tie together information from distributed sources, and to pursue other scientific endeavors.  ...  Although clouds were first introduced in the business arena, they have a potential to be provide ondemand resources for scientific computations.  ...  Acknowledgements This work was funded by the NSF under Cooperative Agreement OCI-0438712 and grant # CCF-0725332.  ... 
doi:10.1177/1094342009356432 fatcat:dielha3lpnftzcrp6y7ykwjqaq

EOSC-Life Report on the work of the initial demonstrators

Frauke Leitner, Jose Maria Carazo, Johanna Bischof, Natalie Haley, Pauline Audergon, Carlos Oscar Sorzano, Laura del Cano, Pablo Conesa, Cymon J. Cox, Gianluca De Moro, Corre Erwan, Katrina Exter (+32 others)
2021 Zenodo  
work done in EOSC-Life to build an open digital and collaborative space for biological and medical research.  ...  from the demonstrator experience and improve the integration of the new pilot project within EOSC-Life.  ...  This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 824087.  ... 
doi:10.5281/zenodo.4817722 fatcat:r4rso6bxcrdfdon7iaznxaql6i

Analysis of Information Technologies Used to Insure Working Efficiency of Personnel [article]

V.Ya. Vilisov, D.A. Dyatlova
2017 arXiv   pre-print
The work is devoted to a modern state, methods and tools of monitoring, assessment and prediction of the indicators showing physical condition of a person and his/her capabilities to perform work duties  ...  The analysis showing significant interconnections and factors that determine a necessary level of working capacity and productivity of personnel allows organizing Work & Rest Schedule of employees in an  ...  The parameters of Work & Rest Schedule (WRS) are very important for these work categories.  ... 
arXiv:1705.03507v1 fatcat:nphd6wierbdrvkc3vglnevge6u

Telescope: an interactive tool for managing large scale analysis from mobile devices [article]

Jaqueline J. Brito, Thiago Mosqueiro, Jeremy Rotman, Victor Xue, Douglas J. Chapski, Juan De la Hoz, Paulo Matias, Lana Martin, Alex Zelikovsky, Matteo Pellegrinni, Serghei Mangul
2019 arXiv   pre-print
biology techniques and bioinformatics tools.  ...  High-performance computational facilities are capable of processing considerable volumes of data, yet often lack an easy-to-use interface to guide the user in supervising and adjusting bioinformatics analysis  ...  Telescope was initially developed to work with SGE, but it is designed to be configurable to other scheduling systems.  ... 
arXiv:1909.12469v3 fatcat:2iqbwvh66bhavct55wilpqwxla

Coinami: A Cryptocurrency with DNA Sequence Alignment as Proof-of-work [article]

Atalay M. Ileri, Halil I. Ozercan, Alper Gundogdu, Ahmet K. Senol, M. Yusuf Ozkaya, Can Alkan
2016 arXiv   pre-print
The Coinami protocol includes mechanisms to ensure that jobs performed by volunteers are correct, and provides genomic data privacy.  ...  However, since HTS read mapping requires substantial computational resources and fast analysis turnout is desired, Coinami uses the HTS read mapping as proof-of-work to generate valid blocks to main its  ...  The miners requests jobs from the authority to to work on, which are tracked by a job scheduler that also imposes "deadlines" on the assignments to prevent deadlocks.  ... 
arXiv:1602.03031v2 fatcat:xasefyfq3zfapb3vrvdxudegyu

A task framework for the web interface W2H

P. Ernst, K.-H. Glatting, S. Suhai
2003 Bioinformatics  
The W3H task framework allows the execution of compound jobs utilizing the description of work and data flows in a heterogeneous bioinformatics environment using meta-data information.  ...  Authors of task descriptions can base their work on the underlying classes and objects to be able to describe dependency rules between previously independent applications.  ...  ACKNOWLEDGEMENTS We would like to thank the task designers Mechthilde Falkenhahn, Agnes Hotz-Wagenblatt, Barbara Pardon and Coral del Val for their valuable comments and Artjom Tarasenko for his participation  ... 
doi:10.1093/bioinformatics/19.2.278 pmid:12538250 fatcat:6z3gjbffr5h6phs3dddxvu6cpa

A Review of Scalable Bioinformatics Pipelines

Bjørn Fjukstad, Lars Ailo Bongo
2017 Data Science and Engineering  
The pipelines used to implement analyses must therefore scale with respect to the resources on a single compute node, the number of nodes on a cluster, and also to cost-performance.  ...  Scalability is increasingly important for bioinformatics analysis services, since these must handle larger datasets, more jobs, and more users.  ...  Toil uses file caching and data streaming, and it schedules work on the same portions of a dataset to the same compute node.  ... 
doi:10.1007/s41019-017-0047-z fatcat:7wyzccy7ffhjdd46pfmljrzioy

Working out aerobic fitness

Ole Johan Kemi, Per Magnus Haram, Ulrik Wisløff, Øyvind Ellingsen
2006 Physiology News  
Acknowledgements Work in our laboratory has been supported by the Canadian Institutes of Health Research and the Saskatchewan Health Research Foundation through the CIHR Regional Partnership Program by  ...  an operating grant and by a New Investigator Award to TEF.  ...  the job.  ... 
doi:10.36866/pn.634.18 fatcat:volnq3nxnfcwjgoiq6aaw5azyq

What Worked, What Did Not: University Instruction during a Pandemic

Neil A. Manson, Randy M. Wadkins
2021 The Biophysicist  
We discuss our experiences of what went right and what went wrong with each approach.  ...  The instructional approaches that we attempted would be significantly more difficult to implement at universities with larger class sizes, geographically more restricted with regard to climate, or more  ...  ACKNOWLEDGMENTS The authors thank Dr. Laura Antonow (University of Mississippi) for her helpful editing of this manuscript.  ... 
doi:10.35459/tbp.2021.000181 fatcat:c47uu4w6hvaf7fe5hearkqwczi

Contribution to the collaborative work in virtual organization - a case study

Fernando A. Crespo, Chandra Sekhar Pedamallu, Linet Özdamar, Gerhard Wilhelm Weber
2012 Organizacija  
The six dimensions that are normally used to analyze virtual organizations are the use of technologies, sense of belonging, success factors, level of trust from members, virtual community management, and  ...  It is also helpful to the group in broadening its presence and involving more researchers, practitioners and students in the field of operational research.  ...  Hans Ittman for their great contributions and support to the working group.  ... 
doi:10.2478/v10051-012-0023-3 fatcat:25cooouejbe27e27ri4rkdyk4e

Workflow management systems

2004 8th International Conference on Computer Supported Cooperative Work in Design CSCWD-04  
If the working hours are approved, the supervisor sends the timesheet to the payroll office. The payroll office then schedules the payment on payment day.  ...  Supervisors assigned work to resources, and clerks passed the work from one resource to another. Lists were made to keep track of the work so that nothing could get away, or to measure performance.  ...  Future work It would be very interesting to develop the WMS further on to fully utilize the workflow technology.  ... 
doi:10.1109/cacwd.2004.1349048 fatcat:q65kmdefofbzpehmqzqcylrtc4

Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package

Mohamed El-Kalioby, Mohamed Abouelhoda, Jan Krüger, Robert Giegerich, Alexander Sczyrba, Dennis P Wall, Peter Tonellato
2012 BMC Bioinformatics  
Acknowledgements We thank Shady Issa from Nile University for this help and support during the development of the elasticHPC. We thank the Amazon team for providing us with AWS compute hours.  ...  This article has been published as part of BMC Bioinformatics Volume 13 Supplement  ...  Right: a tool page in the NUBIOS server where the user can select to run this tool on the cloud.  ... 
doi:10.1186/1471-2105-13-s17-s22 pmid:23281941 pmcid:PMC3521398 fatcat:jbyd47v4tff2fjesf5eaj5qlnm

WeBIAS: a web server for publishing bioinformatics applications

Paweł Daniluk, Bartek Wilczyński, Bogdan Lesyng
2015 BMC Research Notes  
One of the requirements for a successful scientific tool is its availability.  ...  When publishing bioinformatic applications, such attitude puts additional burden on the reviewers who have to cope with poorly designed interfaces in order to assess quality of presented methods, as well  ...  Competing interests The authors declare that they have no competing interests.  ... 
doi:10.1186/s13104-015-1622-x pmid:26526344 pmcid:PMC4629404 fatcat:qxf7hrtcubdoxggacufl7qgmia

Capturing and supporting contexts for scientific data sharing via the biological sciences collaboratory

George Chin, Carina S. Lansing
2004 Proceedings of the 2004 ACM conference on Computer supported cooperative work - CSCW '04  
Today, a movement is afoot within the scientific computing community to shift "collaboratory" development from traditional tool-centric approaches to more data-centric ones.  ...  Overall, BSC strives to identify and capture the various social and scientific contexts in which data sharing collaborations in biology take place and to provide collaboration tools and capabilities that  ...  ACKNOWLEDGMENTS The research described in this paper was conducted under the Laboratory-Directed Research and Development (LDRD) Program at the Pacific Northwest National Laboratory, a multiprogram national  ... 
doi:10.1145/1031607.1031677 dblp:conf/cscw/ChinL04 fatcat:pgwhxmj7czghxm5ineaocldqsu

Microbase2.0: A Generic Framework for Computationally Intensive Bioinformatics Workflows in the Cloud

Keith Flanagan, Sirintra Nakjang, Jennifer Hallinan, Colin Harwood, Robert P. Hirt, Matthew R. Pocock, Anil Wipat
2012 Journal of Integrative Bioinformatics  
We used Microbase2.0 to develop an automated Cloud-based bioinformatics workflow executing simultaneously on two different Amazon EC2 data centres and the Newcastle University Condor Grid.  ...  One solution is to apply Grid and Cloud technologies to address the computational requirements of analysing high throughput datasets.  ...  This work was also supported by funding from the EPSRC (EP/G061394/1 and EP/C536444/1). JH was supported by an RCUK Academic Fellowship.  ... 
doi:10.1515/jib-2012-212 fatcat:dr2ntuyggbalfcut75lb6liv2y
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