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PathwayAnalyser: A Systems Biology Tool for Flux Analysis of Metabolic Pathways
2008
Nature Precedings
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PathwayAnalyser interfaces with the open-source GNU Linear Programming Toolkit (GLPK) for linear programming/ FBA and Object Oriented Quadratic Programming (OOQP) for quadratic programming/MoMA. ...
Stoichiometric and constraint-based analyses of metabolic pathways has been gaining ground in the recent past with the increase in the quality and number of pathway databases available and the curation ...
programming problem) solved using Object-Oriented Quadratic Programming (OOQP) library [9] * PathwayAnalyser outputs: * fluxes for the wild type and the various in silico deletion mutants * a gene deletion ...
doi:10.1038/npre.2008.1868.1
fatcat:5mjvgvbjwjhrxggbkozxbrhq2q
Banshee: A Scalable Constraint-Based Analysis Toolkit
[chapter]
2005
Lecture Notes in Computer Science
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We introduce Banshee, a toolkit for constructing constraintbased analyses. ...
Banshee's novel features include a code generator for creating customized constraint resolution engines, incremental analysis based on backtracking, and fast persistence. ...
We have built Banshee, a constraint-based analysis toolkit that addresses these problems [14] . Banshee succeeds Bane, our first generation toolkit for constraint-based program analysis [2] . ...
doi:10.1007/11547662_16
fatcat:ma27gswyvrdaniurstkitre6ba
COBREXA.jl: constraint-based reconstruction and exascale analysis
[article]
2021
bioRxiv
pre-print
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COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. ...
We report the architecture of the package, and demonstrate its scalability by benchmarking the task distribution overhead incurred when performing analyses of many variants of multi-organism community ...
of constraint-based biological models. ...
doi:10.1101/2021.06.04.447038
fatcat:eizxeoqsqbejdenooygvo5zyfi
Refactoring is not (yet) about transformation
2008
Proceedings of the 2nd Workshop on Refactoring Tools - WRT '08
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These preconditions usually involve subtle analyses of the program to be refactored, and as long as there is no good support for implementing them, refactoring is not about transformation, but about analysis ...
The second building block encapsulates data flow and control flow analyses, enabling the developer to specify precise conditions for validity of a transformation in terms of concepts like dominance and ...
The naming toolkit proved useful in this setting as well, for instance to detect accidental overriding and to construct type accesses for the throws clauses in the extracted method. ...
doi:10.1145/1636642.1636647
dblp:conf/oopsla/EkmanSV08
fatcat:5m7o6g4worhu7bynxjwv3qvesm
A Modular Toolkit for Distributed Interactions
2011
Electronic Proceedings in Theoretical Computer Science
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We discuss the design, architecture, and implementation of a toolkit which supports some theories for distributed interactions. ...
With the help of some examples, we illustrate the main features of our toolkit. ...
The main contribution of this paper is the description of the design choice and the implementation of a modular toolkit that features the main algorithms necessary to analyse systems using theories based ...
doi:10.4204/eptcs.69.7
fatcat:aif465sfxbbsbejfs7rxv3rnye
McSAF: A Static Analysis Framework for MATLAB
[chapter]
2012
Lecture Notes in Computer Science
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a variety of flow data types; and support for depth-first and structure-based analyses. ...
family of structure-based traversals for forward and backward flow-sensitive analyses. ...
doi:10.1007/978-3-642-31057-7_7
fatcat:i5ksldtj75hmba4yqvavookt4u
An open graph visualization system and its applications to software engineering
2000
Software, Practice & Experience
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We describe a package of practical tools and libraries for manipulating graphs and their drawings. ...
Our design, which aimed at facilitating the combination of the package components with other tools, includes stream and event interfaces for graph operations, high-quality static and dynamic layout algorithms ...
In particular, the authors would like to thank Yih-Farn Chen, Eleftherios Koutsofios, John Mocenigo and Kiem-Phong Vo of AT&T Labs -Research, and John Ellson of Lucent Corporation, for their crucial input ...
doi:10.1002/1097-024x(200009)30:11<1203::aid-spe338>3.3.co;2-e
fatcat:e6aowek2fzfj7aqfpzjyhex6qu
An open graph visualization system and its applications to software engineering
2000
Software, Practice & Experience
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We describe a package of practical tools and libraries for manipulating graphs and their drawings. ...
Our design, which aimed at facilitating the combination of the package components with other tools, includes stream and event interfaces for graph operations, high-quality static and dynamic layout algorithms ...
In particular, the authors would like to thank Yih-Farn Chen, Eleftherios Koutsofios, John Mocenigo and Kiem-Phong Vo of AT&T Labs -Research, and John Ellson of Lucent Corporation, for their crucial input ...
doi:10.1002/1097-024x(200009)30:11<1203::aid-spe338>3.0.co;2-n
fatcat:nyubu7ojofeajfzoeytcwulhqa
Constructing a toolkit to evaluate quality of state and local administrative data
2019
International Journal of Population Data Science
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In the United States, state and local agencies administering government assistance programs have in their administrative data a powerful resource for policy analysis to inform evaluation and guide improvement ...
While we seek to develop general tools for common data quality analyses, most administrative datasets have particularities that can benefit from a customized analysis building on our toolkit. ...
for Children and Families, U.S Department of Health and Human Services to the University of Chicago, with NORC at the University of Chicago as a sub-grantee. ...
doi:10.23889/ijpds.v4i1.937
pmid:32935025
pmcid:PMC7479930
fatcat:iltjduulhbfy5jaydqgwvr4bbu
Architecture description languages for programmable embedded systems
2005
IEE Proceedings - Computers and digital Techniques
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Architecture description languages (ADL) enable exploration of programmable architectures for a given set of application programs under various design constraints such as area, power and performance. ...
Shrinking time-to-market, coupled with short product lifetimes, create a critical need for rapid exploration and evaluation of candidate architectures. ...
Software ADLs are used for representing and analysing software architectures [3, 4] . ...
doi:10.1049/ip-cdt:20045071
fatcat:sznyga75n5hk3pongpmyrmffgq
Encoding the Java Virtual Machine's Instruction Set
2011
Electronical Notes in Theoretical Computer Science
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New toolkits that parse, analyze, and transform Java Bytecode are frequently developed from scratch to obtain a representation suitable for a particular purpose. ...
But, while the functionality implemented by these toolkits to read in class files and do basic control-and data-flow analyses is comparable, it is implemented over and over again. ...
Acknowledgement The authors would like to thank Lucas Satabin for implementing the type checker. This work was supported by www.cased.de. ...
doi:10.1016/j.entcs.2011.02.004
fatcat:4pu6yaondbhqdbl3harqjctaya
Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services
2007
Future generations computer systems
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The library has been extensively tested and used for computational biology research in a Globus Toolkit-based Grid system, in which no fewer than twenty Grid services written with this API are deployed ...
The Grid Services Base Library (GSBL) is a procedural application programming interface (API) that abstracts many of the high-level functions performed by Globus Grid services, thus dramatically lowering ...
Acknowledgments We thank Deji Akinyemi, Jonathan Howard, Stephen McLellan and Christopher Milliron for developing some of the Grid services; Borja Sotomayor for his tutorials on creating Globus Grid services ...
doi:10.1016/j.future.2006.07.009
fatcat:oegks5qixjdtpppmc77dlex6sy
Model-Driven Engineering of Machine Executable Code
[chapter]
2010
Lecture Notes in Computer Science
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We show how to leverage model-driven engineering to facilitate the design and implementation of programs doing static analyses. ...
to express a metamodel, and using XSLT to implement (a) transformations and (b) a lint like tool. ...
, built-in support for XML and tuple types. ...
doi:10.1007/978-3-642-13595-8_10
fatcat:h7cgznudzvdsxllj2i54cmj4tq
Regularly annotated set constraints
2007
Proceedings of the 2007 ACM SIGPLAN conference on Programming language design and implementation - PLDI '07
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type-based flow analysis, and pushdown model checking. ...
A general class of program analyses can be characterized as a combination of context-free and regular language reachability. ...
We have implemented an algorithm for solving regularly annotated constraints within BAN-SHEE, our constraint-based program analysis toolkit. ...
doi:10.1145/1250734.1250772
dblp:conf/pldi/KodumalA07
fatcat:y7qi4vjt4jgpbn4jwj537rxgoi
Challenges for Refinement and Composition of Instrumentations: Position Paper
[chapter]
2012
Lecture Notes in Computer Science
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Instrumentation techniques are widely used for implementing dynamic program analysis tools like profilers or debuggers. ...
While there are many toolkits and frameworks to support the development of such low-level instrumentations, there is little support for the refinement or composition of instrumentations. ...
[6] propose a framework for composing different small and simple analyses for concurrent programs. ...
doi:10.1007/978-3-642-30564-1_6
fatcat:xsyuzlvmv5hf3cj7u2whsfsg4e
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