Filters








17,887 Hits in 4.5 sec

PathwayAnalyser: A Systems Biology Tool for Flux Analysis of Metabolic Pathways

Karthik Raman, Nagasuma Chandra
2008 Nature Precedings  
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]

John Kodumal, Alex Aiken
2005 Lecture Notes in Computer Science  
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]

Miroslav Kratochvil, Laurent Heirendt, St. Elmo Wilken, Taneli Pusa, Sylvain Arreckx, Alberto Noronha, Marvin van Aalst, Venkata P. Satagopam, Oliver Ebenhoeh, Reinhard Schneider, Christophe Trefois, Wei Gu
2021 bioRxiv   pre-print
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

Torbjörn Ekman, Max Schäfer, Mathieu Verbaere
2008 Proceedings of the 2nd Workshop on Refactoring Tools - WRT '08  
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

Julien Lange, Emilio Tuosto
2011 Electronic Proceedings in Theoretical Computer Science  
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]

Jesse Doherty, Laurie Hendren
2012 Lecture Notes in Computer Science  
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

Emden R. Gansner, Stephen C. North
2000 Software, Practice & Experience  
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

Emden R. Gansner, Stephen C. North
2000 Software, Practice & Experience  
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

Zachary H. Seeskin, A. Rupa Datta, Gabriel Ugarte
2019 International Journal of Population Data Science  
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

P. Mishra, N. Dutt
2005 IEE Proceedings - Computers and digital Techniques  
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

Michael Eichberg, Andreas Sewe
2011 Electronical Notes in Theoretical Computer Science  
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

Adam L. Bazinet, Daniel S. Myers, John Fuetsch, Michael P. Cummings
2007 Future generations computer systems  
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]

Michael Eichberg, Martin Monperrus, Sven Kloppenburg, Mira Mezini
2010 Lecture Notes in Computer Science  
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

John Kodumal, Alex Aiken
2007 Proceedings of the 2007 ACM SIGPLAN conference on Programming language design and implementation - PLDI '07  
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]

Danilo Ansaloni, Walter Binder, Christoph Bockisch, Eric Bodden, Kardelen Hatun, Lukáš Marek, Zhengwei Qi, Aibek Sarimbekov, Andreas Sewe, Petr Tůma, Yudi Zheng
2012 Lecture Notes in Computer Science  
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
« Previous Showing results 1 — 15 out of 17,887 results