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Walter Cazzola, Antonio Cisternino, Diego Colombo
2005 Proceedings of the 2005 ACM symposium on Applied computing - SAC '05  
A set of operations on annotated code blocks to retrieve annotations and manipulate bytecode is introduced.  ...  In this paper we describe [a]C#, 1 an extension of the C# programming language, that allows programmers to annotate statements or code blocks and retrieve these annotations at run-time.  ...  This is a pity because several programs whose goal consists of administering and manipulating other programs would benefit from a finer grain model for annotations.  ... 
doi:10.1145/1066677.1066964 dblp:conf/sac/CazzolaCC05 fatcat:zt76irrpfzh33bfc6laqbzh4oi

Inking in the IDE: Experiences with Pen-based Design and Annotatio

B. Plimmer, J. Grundy, J. Hosking, R. Priest
2006 Visual Languages and Human-Centric Computing (VL/HCC'06)  
a programming tool.  ...  We describe our research experiences of adding support for hand-drawn design and annotation to three Integrated Development Environments (IDEs): a software design tool; a user interface design tool; and  ...  Marama provides conventional CASE tool diagramming support via drag-and-drop within a form, a tool palette, and diagram content manipulation.  ... 
doi:10.1109/vlhcc.2006.28 dblp:conf/vl/PlimmerGHP06 fatcat:acpoorkpmngk7jdysd5sz43jgm

Freely Annotating C#

Walter Cazzola, Antonio Cisternino, Diego Colombo
2005 Journal of Object Technology  
A set of operations on annotated code blocks to retrieve annotations and manipulate bytecode is introduced.  ...  Finally, we show how our model for custom attributes has been realized. a The name [a]C# should be pronounced as annotated C sharp.  ...  We believe that code annotations can be useful to develop software that meets the always increasing demand for flexibility and dynamic adaptation.  ... 
doi:10.5381/jot.2005.4.10.a2 fatcat:td6oio2ao5fhhfr7qks6hekn6y

Mutual satellites

Lars Thorup, Sune Gynthersen, Kristian Dupont
2006 Companion to the 21st ACM SIGPLAN conference on Object-oriented programming systems, languages, and applications - OOPSLA '06  
The tool manipulates all three application layers of conventional enterprise applications, currently with support for SQL, C# and XAML.  ...  During the presentation we will demonstrate a new modeling tool, implemented as an Add-In for Microsoft Visual Studio.  ...  Other tools (typically UML and database modeling) succeed in providing round-trip capabilities but then lack support for more than a single application layer.  ... 
doi:10.1145/1176617.1176683 dblp:conf/oopsla/ThorupGD06 fatcat:4eokz6d3jzef5dyxr7l4ct6dsu

BuddySuite: Command-line toolkits for manipulating sequences, alignments, and phylogenetic trees [article]

Stephen R Bond, Karl E Keat, Sofia Barreira, Andreas D Baxevanis
2016 bioRxiv   pre-print
Most common sequence, alignment, and tree file formats are automatically detected and parsed, and over 100 tools have been implemented for manipulating these data.  ...  Documentation for each BuddySuite tool, including usage examples, is available at  ...  Funding This work has been supported by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health.  ... 
doi:10.1101/040675 fatcat:cwhlghaeozcuji7h5bmk5ufmwy

GoBean: a Java GUI application for visual exploration of GO term enrichments

Sang-Hyuk Lee, Ji-Young Cha, Hyeon-Jin Kim, Ung-Sik Yu
2012 BMB Reports  
It was designed to be a comprehensive and flexible GUI tool for GO term enrichment analysis, combining the merits of other programs and incorporating extensive graphic exploration of enrichment results  ...  We have developed a biologist-friendly, Java GUI application (GoBean) for GO term enrichment analysis.  ...  Acknowledgements This work was supported by a GIST systems biology infrastructure establishment grant (2011).  ... 
doi:10.5483/bmbrep.2012.45.2.120 pmid:22360891 fatcat:k2wtdqniozglrcbo75o6k5haji

Towards Tierless Web Development without Tierless Languages

Laure Philips, Coen De Roover, Tom Van Cutsem, Wolfgang De Meuter
2014 Proceedings of the 2014 ACM International Symposium on New Ideas, New Paradigms, and Reflections on Programming & Software - Onward! '14  
This not only reduces the complexity that developers are exposed to, but also precludes the need for new development tools.  ...  Tierless programming languages enable developing the typical server, client and database tiers of a web application as a single mono-linguistic program.  ...  Laure Philips is supported by a doctoral scholarship granted by the Agency for Innovation by Science and Technology in Flanders, Belgium (IWT).  ... 
doi:10.1145/2661136.2661146 dblp:conf/oopsla/PhilipsRCM14 fatcat:fcvddqn7qvg3zf6owuxzadwiqe

BuddySuite: Command-Line Toolkits for Manipulating Sequences, Alignments, and Phylogenetic Trees

Stephen R. Bond, Karl E. Keat, Sofia N. Barreira, Andreas D. Baxevanis
2017 Molecular biology and evolution  
Most common sequence, alignment, and tree file formats are automatically detected and parsed, and over 100 tools have been implemented for manipulating these data.  ...  Documentation for each BuddySuite tool, including usage examples  ...  As an alternative we present BuddySuite, a 1 Bond et al. comprehensive set of general-purpose commandline tools for manipulating sequence, alignment, and phylogenetic tree data that can be joined into  ... 
doi:10.1093/molbev/msx089 pmid:28333216 pmcid:PMC5850830 fatcat:w3sruhtjbnfq3dzz62zdyspknm

Three Tools to Aid Visualisation of FITS Files for Astronomy [article]

P. Mohan, C. Hawkins, R. Klapaukh, M. Johnston-Hollitt
2016 arXiv   pre-print
It also supports annotations which can be placed without affecting the underlying data. The final tool is an R package for applying high dynamic range compression techniques to 2D fits images.  ...  This paper describes three new tools for astronomical visualisation and image manipulation that are the result of a collaboration between software engineers and radio astronomers.  ...  MJ-H is supported in this work by a Marsden Grant. We thank L. Pratley & L. Hindson for discussions on limitations of existing astronomical tools.  ... 
arXiv:1601.00264v1 fatcat:nxj4hcoaavdzxajwrejfdmcueq

Rational Metaprogramming

Diomidis Spinellis
2008 IEEE Software  
tools of the trade 78 I E E E S o f t w a r E P u b l i s h e d b y t h e I E E E C o m p u t e r S o c i e t y 0 7 4 0 -7 4 5 9 / 0 8 / $ 2 5 . 0 0 © 2 0 0 8 I E E E  ...  Tools for a DSL will always be inferior to those for a mainstream language and will always require an expert to maintain them.  ...  Rational Metaprogramming Diomidis Spinellis M etaprogramming, using programs to manipulate other programs, is as old as programming.  ... 
doi:10.1109/ms.2008.15 fatcat:7fs72n36wvcnfgsiunqhhru2ty

GOGrapher: A Python library for GO graph representation and analysis

Brian Muller, Adam J Richards, Bo Jin, Xinghua Lu
2009 BMC Research Notes  
Conclusions: The GOGrapher project provides a reusable programming library designed for the manipulation and analysis of Gene Ontology graphs.  ...  ., a graph-based multi-label text classifier for protein annotation.  ...  Acknowledgments This research is partially supported by the following NIH grants: R01LM009153-01A1, T15LM07438, and  ... 
doi:10.1186/1756-0500-2-122 pmid:19583843 pmcid:PMC2714316 fatcat:op5i44xuqfet3m7cl4iprms7ge

Learning Assertions to Verify Linked-List Programs [chapter]

Jan Tobias Mühlberg, David H. White, Mike Dodds, Gerald Lüttgen, Frank Piessens
2015 Lecture Notes in Computer Science  
C programs that manipulate list-based dynamic data structures remain a challenging target for static verification.  ...  In this paper we employ a dynamic analysis to locate and identify data structure operations in a program, so as to automatically annotate that program with assertions in separation logic.  ...  verification tool VeriFast, which are suitable for the automated verification of operations that manipulate list-based data structures.  ... 
doi:10.1007/978-3-319-22969-0_3 fatcat:dkympayt4vfincospvvr7uv6eu

An Incremental Compilation Approach for OpenMP Applications [chapter]

Maurizio Giordano, Mario Mango Furnari
2005 Lecture Notes in Computer Science  
This work presents a new approach to software development framework design for parallel programming: the Graphical Parallelizing Environment 1 (GPE ).  ...  It adopts an incremental compilation process for OpenMP programming based on automatic detection of parallelism and user interaction for its calibration.  ...  The OpenMP editing module is a GPE extension providing an easy-to-use editor, based on graph manipulation, to assist users in inserting/modifying OpenMP annotations.  ... 
doi:10.1007/11577188_33 fatcat:hmiprd4omjcpzapcukqyrk47wq

Toward on-chip JIT synthesis on Xilinx VirtexII-Pro FPGAs

Etienne Bergeron, Marc Feeley, Jean Pierre David
2007 2007 IEEE Northeast Workshop on Circuits and Systems  
Xilinx also supplies JBits, but this tool does not support the VirtexII Pro FPGA and later devices. We aim to dynamically produce digital circuits.  ...  Xilinx VirtexII Pro FPGAs support dynamic reconfiguration.  ...  The problem we address consists in finding the positions of the configuration bits related to a given programming point, for all programming points.  ... 
doi:10.1109/newcas.2007.4487978 fatcat:bvgidiwla5hwrdbfmir7fee5uy

Critique of 'files as directories: some thoughts on accessing structured data within files' (1)

Philip Tchernavskij
2018 Conference Companion of the 2nd International Conference on Art, Science, and Engineering of Programming - Programming'18 Companion  
In this critique of Files as Directories (FAD) by Raphael Wimmer, I argue that FAD as presented applies primarily to traditional programming tasks, consider FAD as a broader subversion of app-like software  ...  , and speculate about the hypothetical design space of FAD beyond programming.  ...  ACKNOWLEDGEMENTS This work was partially supported by European Research Council (ERC) grant nº 695464 ONE: Unified Principles of Interaction.  ... 
doi:10.1145/3191697.3214324 dblp:conf/programming/Tchernavskij18 fatcat:m74shpfs7ndd7p3isx4rsiwtue
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