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A comparison of three programming languages for a full-fledged next-generation sequencing tool [article]

Pascal Costanza, Charlotte Herzeel, Wilfried Verachtert
2019 bioRxiv   pre-print
We therefore investigated three alternative programming languages: Go and Java using a concurrent, parallel garbage collector on the one hand, and C++17 using reference counting on the other hand for handling  ...  Conclusions: Based on our benchmark results, we selected Go as our new implementation language for elPrep, and recommend considering Go as a good candidate for developing other bioinformatics tools for  ...  Ashby and Tom Haber for indepth discussions about memory management techniques in various programming languages.  ... 
doi:10.1101/558056 fatcat:zjywgjicmjf4rfuokn57gliy5a

A comparison of three programming languages for a full-fledged next-generation sequencing tool

Pascal Costanza, Charlotte Herzeel, Wilfried Verachtert
2019 BMC Bioinformatics  
We therefore investigated three alternative programming languages: Go and Java using a concurrent, parallel garbage collector on the one hand, and C++17 using reference counting on the other hand for handling  ...  Conclusions: Based on our benchmark results, we selected Go as our new implementation language for elPrep, and recommend considering Go as a good candidate for developing other bioinformatics tools for  ...  Ashby and Tom Haber for in-depth discussions about memory management techniques in various programming languages.  ... 
doi:10.1186/s12859-019-2903-5 fatcat:wojcekiaz5debcuo36mcczsb64

Programming languages for synthetic biology

P. Umesh, F. Naveen, Chanchala Uma Maheswara Rao, Achuthsankar S. Nair
2010 Journal of Systems and Synthetic Biology  
This paper introduces Kera, a state of the art programming language for synthetic biology which is arguably ahead of similar languages or tools such as GEC, Antimony and GenoCAD.  ...  Kera is a full-fledged object oriented programming language which is tempered by biopart rule library named Samhita which captures the knowledge regarding the interaction of genome components and catalytic  ...  These are in the form of full-fledged or non-full-fledged programming languages, aimed at giving finer control over representation and modeling.  ... 
doi:10.1007/s11693-011-9070-y pmid:22132053 pmcid:PMC3065592 fatcat:qiv3thwglzcrpjiuwflzqfx62i

EasyAccept

Jacques Philippe Sauvé, Osório Lopes Abath Neto, Walfredo Cirne
2006 Proceedings of the 2006 international workshop on Automation of software test - AST '06  
This paper introduces EasyAccept, a tool to create and run clientreadable acceptance tests easily, and describes how it can be used to allow a simple but powerful acceptance-test driven software development  ...  Results of experiments with undergraduate students demonstrate the benefits of the ATDD approach using EasyAccept and show that this tool can also help to teach and train good testing and development practices  ...  Due to space limitations, we have summarized the exposition of the approach. For a full-fledged discussion, see reference [13].  ... 
doi:10.1145/1138929.1138951 dblp:conf/icse/SauveNC06 fatcat:iwcyzcg4gngsxi5hzyzfts2gsi

Comparison and evaluation of code clone detection techniques and tools: A qualitative approach

Chanchal K. Roy, James R. Cordy, Rainer Koschke
2009 Science of Computer Programming  
We begin with background concepts, a generic clone detection process and an overall taxonomy of current techniques and tools.  ...  In this paper, we provide a qualitative comparison and evaluation of the current state-of-the-art in clone detection techniques and tools, and organize the large amount of information into a coherent conceptual  ...  Acknowledgements We thank the anonymous reviewers for their valuable comments and suggestions in improving this paper.  ... 
doi:10.1016/j.scico.2009.02.007 fatcat:wsjwomcyn5ahri3sbcxegg3d5e

From Grammars to Parameters: Automatic Iterated Greedy Design for the Permutation Flow-Shop Problem with Weighted Tardiness [chapter]

Franco Mascia, Manuel López-Ibáñez, Jérémie Dubois-Lacoste, Thomas Stützle
2013 Lecture Notes in Computer Science  
In particular, we first propose a grammar that generates iterated greedy (IG) algorithms for the permutation flow-shop problem with weighted tardiness minimization.  ...  Next, we show how this grammar can be represented in terms of parameters.  ...  The size and complexity of the building blocks is set at a level that is below a full-fledged heuristic, but still allows us to easily combine them in a modular way to generate a very large number of different  ... 
doi:10.1007/978-3-642-44973-4_36 fatcat:st342qbfnvgxfi564y4v7hbvt4

The UCSC Kestrel Application-Unspecific Processor

Richard Hughey, Andrea Blas
2006 IEEE 17th International Conference on Application-specific Systems, Architectures and Processors (ASAP'06)  
The result has been a readily programmable and efficient co-processor for many applications.  ...  Address Generator  ...  One of the best ways to discover the information relationship between two sequences and is by using one of a family of related dynamic programming algorithms for pairwise sequence comparison.  ... 
doi:10.1109/asap.2006.66 dblp:conf/asap/HugheyB06 fatcat:zl7dyipt6zaktbxr4tkrs3wuxq

On the automated translational execution of the action language for foundational UML

Federico Ciccozzi
2016 Journal of Software and Systems Modeling  
In this paper, we provide a solution for the fully automated translational execution of ALF towards C++.  ...  Additionally, we give an insight on how to simplify the transition from the use of programming languages for modelling fine-grained behaviours to model-aware action languages in industrial MDE.  ...  Moreover, the author would like to thank Thomas Åkerlund and Knightec AB, for the essential contribution to the implementation of the translational execution.  ... 
doi:10.1007/s10270-016-0556-7 pmid:30220904 pmcid:PMC6132576 fatcat:jgzdpfnzdjfhzdpkawls4g6mtm

Combining Model Checking and Testing [chapter]

Patrice Godefroid, Koushik Sen
2018 Handbook of Model Checking  
One way to do this consists of adapting model checking into a form of systematic testing that is applicable to industrial-size software.  ...  Model checking and testing have a lot in common.  ...  directly on a program implementation written in a full-fledged programming language.  ... 
doi:10.1007/978-3-319-10575-8_19 fatcat:o7z7rus4ebesdlatlvgockypjy

Does My Model Work? Evaluation Abstractions of Cognitive Modelers

Christopher Bogart, Margaret Burnett, Scott Douglass, David Piorkowski, Amber Shinsel
2010 2010 IEEE Symposium on Visual Languages and Human-Centric Computing  
From these results, we derive design implications for several categories of persistent, first-class evaluation abstractions in future debugging tools for modelers.  ...  Are the abstractions that scientific modelers use to build their models in a modeling language the same abstractions they use to evaluate the correctness of their models?  ...  Acknowledgments We thank the Air Force Office of Scientific Research for partial support of this work under FA9550-10-1-0326.  ... 
doi:10.1109/vlhcc.2010.16 dblp:conf/vl/BogartBDPS10 fatcat:tqd5uhfgxrexvlrg2k3rir3rne

A language independent approach for detecting duplicated code

S. Ducasse, M. Rieger, S. Demeyer
1999 Proceedings IEEE International Conference on Software Maintenance - 1999 (ICSM'99). 'Software Maintenance for Business Change' (Cat. No.99CB36360)  
In this paper we show that is possible to circumvent this hindrance by applying a language independent and visual approach, i.e. a tool that requires no parsing, yet is able to detect a significant amount  ...  Techniques for detecting duplicated code exist but rely mostly on parsers, technology that has proven to be brittle in the face of different languages and dialects.  ...  It reports similar code sequences and proposes unifying macros to replace the found clones. Their approach requires, however, a full-fledged parser.  ... 
doi:10.1109/icsm.1999.792593 dblp:conf/icsm/DucasseRD99 fatcat:75hh7qubirffpo726jk7cxa7py

An End-to-End Configuration-Based Framework for Automatic SWS Composition

Patrick Albert, Laurent Henocque, Mathias Kleiner
2008 2008 20th IEEE International Conference on Tools with Artificial Intelligence  
We describe a theoretical and experimental framework based upon finite model search for constrained object models to address this problem.  ...  Composing is first performed at the abstract level of goals (each roughly representing a discovery request), which yields a composition request at the workflow level.  ...  Among the benefits, the knowledge representation is close to existing SWS formalisms (description logics for data and workflows for services behaviour), solving is done using well-known constraint programming  ... 
doi:10.1109/ictai.2008.145 dblp:conf/ictai/AlbertHK08a fatcat:d3bvxwhdvvcejotdrlwgoh4zku

Past Time LTL Runtime Verification for Microcontroller Binary Code [chapter]

Thomas Reinbacher, Jörg Brauer, Martin Horauer, Andreas Steininger, Stefan Kowalewski
2011 Lecture Notes in Computer Science  
This paper presents a method for runtime verification of microcontroller binary code based on past time linear temporal logic (ptLTL).  ...  We show how to implement a framework that, owing to a dedicated hardware unit, does not require code instrumentation, thus, allowing the program under scrutiny to remain unchanged.  ...  Ideally, we would favor a full-fledged hardware-only solution allowing for arbitrary atomic propositions to be checked on-the-fly.  ... 
doi:10.1007/978-3-642-24431-5_5 fatcat:pdmmbanhx5dg7cybtp72ubwlqa

Textual modeling tools

Bernhard Merkle
2010 Proceedings of the ACM international conference companion on Object oriented programming systems languages and applications companion - SPLASH '10  
Currently the number of new emerging Programming Languages is significant [1] but GPL (General Purpose Languages) do often not fit the specific need of the end-user.  ...  Domain Specific Languages (DSL) attract more and more users as they are specialized and optimized for a certain problem area.  ...  They were very helpful with my questions and bug reports for their tools. Thank you again!  ... 
doi:10.1145/1869542.1869564 dblp:conf/oopsla/Merkle10a fatcat:sm2rsivm7rh6zkr5cj3oisdtjq

HFST Tools for Morphology – An Efficient Open-Source Package for Construction of Morphological Analyzers [chapter]

Krister Lindén, Miikka Silfverberg, Tommi Pirinen
2009 Communications in Computer and Information Science  
We evaluate their efficiency in comparison to some similar tools and libraries. In particular, we evaluate them using several full-fledged morphological descriptions.  ...  Morphological analysis of a wide range of languages can be implemented efficiently using finite-state transducer technologies.  ...  Acknowledgments We are grateful to the Finnish Academy and to the Finnish Ministry of Education for funding the project.  ... 
doi:10.1007/978-3-642-04131-0_3 fatcat:h2aqipzlf5ftdpqocnrq4f7ugi
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