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Developing science gateways for drug discovery in a grid environment

Horacio Pérez-Sánchez, Vahid Rezaei, Vitaliy Mezhuyev, Duhu Man, Jorge Peña-García, Helena den-Haan, Sandra Gesing
2016 SpringerPlus  
Results: To this end, we recently integrated the biophysics-based drug-screening program FlexScreen into a service, applicable for large-scale parallel screening and reusable in the context of scientific  ...  As these techniques become more complex and computationally costly we are faced with an increasing problem to provide the research community of life sciences with a convenient tool for high-throughput  ...  This work was partially supported by the computing facilities of Extremadura Research Centre for Advanced Technologies (CETA-CIEMAT), funded by the European Regional Development Fund (ERDF).  ... 
doi:10.1186/s40064-016-2914-x pmid:27547674 pmcid:PMC4978646 fatcat:oulkcqzd7zemdiagyo6bcencla

Advancing software architecture modeling for large scale heterogeneous systems

Ian Gorton, Yan Liu
2010 Proceedings of the FSE/SDP workshop on Future of software engineering research - FoSER '10  
In this paper we describe how incorporating technology-specific modeling at the architecture level can help reduce risks and produce better designs for large, heterogeneous software applications.  ...  We then describe the advances in modeling, analysis and tooling that are required to bring sophisticated modeling and development methods within reach of software architects.  ...  Figure 1 Iterative modeling workflow for geoscientists Geoscientists initially build 3 dimensional models of the subsurface geology.  ... 
doi:10.1145/1882362.1882393 dblp:conf/sigsoft/GortonL10 fatcat:x3h2ujqvubfonl5tjvewx5v5nq

A characterization of workflow management systems for extreme-scale applications

Rafael Ferreira da Silva, Rosa Filgueira, Ilia Pietri, Ming Jiang, Rizos Sakellariou, Ewa Deelman
2017 Future generations computer systems  
Automation of the execution of computational tasks is at the heart of improving scientific productivity.  ...  As the resource requirements of today's computational and data science applications that process vast amounts of data keep increasing, there is a compelling case for a new generation of advances in high-performance  ...  With the large volume of data generated from the different iterations, support for in situ analysis and visualization within workflow ensembles may become crucial for extreme-scale.  ... 
doi:10.1016/j.future.2017.02.026 fatcat:3ri627jyy5a47hgh5r343f5ife

Machine Learning-Based Prototyping of Graphical User Interfaces for Mobile Apps [article]

Kevin Moran and Carlos Bernal-Cárdenas and Michael Curcio and Richard Bonett and Denys Poshyvanyk
2018 arXiv   pre-print
It is common practice for developers of user-facing software to transform a mock-up of a graphical user interface (GUI) into code.  ...  In this paper, we present an approach that automates this process by enabling accurate prototyping of GUIs via three tasks: detection, classification, and assembly.  ...  This work is supported in part by the NSF CCF-1525902 grant. Any opinions, findings, and conclusions expressed herein are the authors and do not necessarily reflect those of the sponsors.  ... 
arXiv:1802.02312v2 fatcat:j6nchfpks5f5jiwsq2wc7nctbi

A Template-Based Methodology for the Specification and Automated Composition of Performability Models

Leonardo Montecchi, Paolo Lollini, Andrea Bondavalli
2019 IEEE Transactions on Reliability  
For the evaluation of large systems, reusable submodels are typically adopted as an effective way to address the complexity and to improve the maintainability of models.  ...  This paper provides a solution to this problem focusing on: formally defining the concept of model templates, defining a specification language for model templates, defining an automated instantiation  ...  ACKNOWLEDGMENT This work is related to the activities of the H2020 MSCA-RISE-2018 Project ADVANCE "Addressing Verification and Validation Challenges in Future Cyber-Physical Systems."  ... 
doi:10.1109/tr.2019.2898351 fatcat:jyz3ohuoubfipghis5z2goguwy

Report of the Workshop on Program Synthesis for Scientific Computing [article]

Hal Finkel, Ignacio Laguna
2021 arXiv   pre-print
This report reviews the relevant areas of program synthesis work for scientific computing, discusses successes to date, and outlines opportunities for future work.  ...  This report is the result of the Workshop on Program Synthesis for Scientific Computing was held virtually on August 4-5 2020 (https://prog-synth-science.github.io/2020/).  ...  Automated machine learning (AutoML) [44] is a technique for automating the design and development of an ML pipeline.  ... 
arXiv:2102.01687v1 fatcat:vaq33ohgq5aczmiq5rci5hbpdi

Composable Modular Models for Synthetic Biology

Goksel Misirli, Jennifer Hallinan, Anil Wipat
2014 ACM Journal on Emerging Technologies in Computing Systems  
Modelling and computational simulation are crucial for the large-scale engineering of biological circuits since they allow the system under design to be simulated prior to implementation in vivo.  ...  Modelling and computational simulation are crucial for the large-scale engineering of biological circuits since they allow the system under design to be simulated prior to implementation in vivo.  ...  ACKNOWLEDGMENTS The authors would like to thank Dr. Michael Cooling, Owen Gilfellon, Dr. Matthew Pocock, the UK Flowers consortium and the SBOL community for helpful discussions.  ... 
doi:10.1145/2631921 fatcat:zz3khigjhneotnu3f2sxu73dlq

Code Generation in Computational Neuroscience: A Review of Tools and Techniques

Inga Blundell, Romain Brette, Thomas A. Cleland, Thomas G. Close, Daniel Coca, Andrew P. Davison, Sandra Diaz-Pier, Carlos Fernandez Musoles, Padraig Gleeson, Dan F. M. Goodman, Michael Hines, Michael W. Hopkins (+17 others)
2018 Frontiers in Neuroinformatics  
Large-scale, biophysically detailed cell models pose a particular set of computational challenges, and this has led to the development of a number of domain-specific simulators.  ...  At the other level of detail, the ever growing variety of point neuron models increases the implementation barrier even for those based on the relatively simple integrate-and-fire neuron model.  ...  , the Initiative and Networking Fund of the Helmholtz Association, and the Hemholtz Portfolio Theme Simulation and Modeling for the Human Brain.  ... 
doi:10.3389/fninf.2018.00068 pmid:30455637 pmcid:PMC6230720 fatcat:u2hxo6y46jcwpbkq7zbmdtgeuq

Model-driven Engineering Tools and Languages for Cyber-physical Systems -A Systematic Literature Review

Mustafa Abshir Mohamed, Geylani Kardas, Moharram Challenger
2021 IEEE Access  
Moharram Challenger and Geylani Kardas would like to thank the European Cooperation in Science & Technology COST Action networking mechanisms and support of COST Action IC1404: Multi-Paradigm Modelling  ...  for Cyber-Physical Systems (MPM4CPS).  ...  [65] used UML profile to develop a meta-model for modeling cyber-physical assembly systems.  ... 
doi:10.1109/access.2021.3068358 fatcat:7daa32lsgjagdkbryifoqjddra

A Model-Based Approach to Support Safety-Related Decisions in the Petroleum Domain

Leonardo Montecchi, Atle Refsdal, Paolo Lollini, Andrea Bondavalli
2016 2016 46th Annual IEEE/IFIP International Conference on Dependable Systems and Networks (DSN)  
In this paper we propose an approach to provide an automated decision support to the work permit system, which consists in the evaluation of quantitative measures of the risk associated with the execution  ...  The approach relies on state-based stochastic models, which can be automatically composed based on the work permit to be examined.  ...  ACKNOWLEDGMENT This work has been partially supported by the ARTEMIS-JU CONCERTO project (n.333053), and by CECRIS, "CErtification of CRItical Systems", FP7-Marie Curie (IAPP) number 324334.  ... 
doi:10.1109/dsn.2016.33 dblp:conf/dsn/MontecchiRLB16 fatcat:6ff4secgxrf37g363xu3j6psmu

White Paper from Workshop on Large-scale Parallel Numerical Computing Technology (LSPANC 2020): HPC and Computer Arithmetic toward Minimal-Precision Computing [article]

Roman Iakymchuk, Daichi Mukunoki, Artur Podobas, Fabienne Jézéquel, Toshiyuki Imamura, Norihisa Fujita, Jens Huthmann, Shuhei Kudo, Yiyu Tan, Jens Domke, Kai Torben Ohlhus, Takeshi Fukaya (+6 others)
2020 arXiv   pre-print
However, precision generally plays a contrary role for both.  ...  Several studies have been already conducted for it so far (e.g. Precimoniuos and Verrou), but the scope of those studies is limited to the precision-tuning alone.  ...  Among the common wisdom in High-Performance Computing is the applications' need for large amount of double-precision support in hardware.  ... 
arXiv:2004.04628v2 fatcat:7fo3kfaa7zfnhg4mlz62ljnvee

ExaStencils: Advanced Multigrid Solver Generation [chapter]

Christian Lengauer, Sven Apel, Matthias Bolten, Shigeru Chiba, Ulrich Rüde, Jürgen Teich, Armin Größlinger, Frank Hannig, Harald Köstler, Lisa Claus, Alexander Grebhahn, Stefan Groth (+5 others)
2020 Lecture Notes in Computational Science and Engineering  
Project ExaStencils pursued a domain-specific approach with a language, called ExaSlang, that is stratified into four layers of abstraction, the most abstract being the formulation in continuous mathematics  ...  At every layer, the corresponding language expresses not only computational directives but also domain knowledge of the problem and platform to be leveraged for optimization.  ...  We are grateful to Rochus Schmid for letting us have the RSDFT code for the molecular dynamics simulation.  ... 
doi:10.1007/978-3-030-47956-5_14 fatcat:xhbxnt45ynhilgh6vv2ui2n76i

Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey

Muhammad Usman Tariq, Muhammad Haseeb, Mohammed Aledhari, Rehma Razzak, Reza M. Parizi, Fahad Saeed
2020 IEEE Access  
experimental MS spectra against a six-frame translation genome database, and automating the process of annotating genome sequences.  ...  These state-of-the-art tools can take more than half a month to process a small-scale dataset of one million spectra against a genome of 3 GB.  ...  In case of low sequence depth and the availability of a closely related reference, genome mapping can also be used for assembly.  ... 
doi:10.1109/access.2020.3047588 pmid:33537181 pmcid:PMC7853650 fatcat:2eqqiahepjearai7aospb32tgy

RLOps: Development Life-cycle of Reinforcement Learning Aided Open RAN [article]

Peizheng Li, Jonathan Thomas, Xiaoyang Wang, Ahmed Khalil, Abdelrahim Ahmad, Rui Inacio, Shipra Kapoor, Arjun Parekh, Angela Doufexi, Arman Shojaeifard, Robert Piechocki
2021 arXiv   pre-print
Based on these principles, we propose the best practices for RLOps to achieve an automated and reproducible model development process.  ...  We provide a taxonomy of the challenges faced by ML/RL models throughout the development life-cycle: from the system specification to production deployment (data acquisition, model design, testing and  ...  As discussed in [36] , DTs offer a wide range of benefits for communications networks, including reducing the deployment costs for new services and supporting network automation and optimization.  ... 
arXiv:2111.06978v1 fatcat:g4tj7q7pevde5funhd2u3nqhoi

Automating Software Development for Mobile Computing Platforms

Kevin Moran
2018 2018 IEEE International Conference on Software Maintenance and Evolution (ICSME)  
Finally, we design a novel approach for automated testing of mobile apps, called CrashScope, that explores a given Android app using systematic input generation with the intrinsic goal of triggering crashes  ...  The GUI-based input generation engine is driven by a combination of static and dynamic analyses that create a model of an app's GUI and targets common, empirically derived root causes of crashes in Android  ...  In contrast, ReDraw is trained on a large scale dataset collected through a novel application of automated dynamic analysis for user interface mining.  ... 
doi:10.1109/icsme.2018.00094 dblp:conf/icsm/Moran18 fatcat:idlcmxdceza67ecd7fk4llnfxm
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