38036
2014
2014
eng
277
297
21
3
44
article
Wiley-Blackwell
Hoboken
1
--
--
--
Simplicity-first model-based plug-in development
In this article, we present our experience with over a decade of strict simplicity orientation in the development and evolution of plug-ins. The point of our approach is to enable our graphical modeling framework jABC to capture plug-in development in a domain-specific setting. The typically quite tedious and technical plug-in development is shifted this way from a programming task to the modeling level, where it can be mastered also by application experts without programming expertise. We show how the classical plug-in development profits from a systematic domain-specific API design and how the level of abstraction achieved this way can be further enhanced by defining adequate building blocks for high-level plug-in modeling. As the resulting plug-in models can be compiled and deployed automatically, our approach decomposes plug-in development into three phases where only the realization phase requires plug-in-specific effort. By using our modeling framework jABC, this effort boils down to graphical, tool-supported process modeling. Furthermore, we support the automatic completion of process sketches for executability. All this will be illustrated along the most recent plug-in-based evolution of the jABC framework, which witnessed quite some bootstrapping effects.
Software : practice & experience
10.1002/spe.2243
0038-0644
1097-024X
wos:2014
WOS:000331275900003
Naujokat, S (reprint author), TU Dortmund Univ, D-44227 Dortmund, Germany., stefan.naujokat@tu-dortmund.de
Stefan Naujokat
Johannes Neubauer
Anna-Lena Lamprecht
Bernhard Steffen
Sven Joerges
Tiziana Margaria
eng
uncontrolled
plug-ins
eng
uncontrolled
simplicity
eng
uncontrolled
domain-specific APIs
eng
uncontrolled
process modeling
eng
uncontrolled
bootstrapping
eng
uncontrolled
evolution
eng
uncontrolled
code generation
eng
uncontrolled
loose programming
eng
uncontrolled
dynamic service binding
Institut für Informatik und Computational Science
Referiert
Institut für Informatik
34624
2013
2013
eng
48
54
7
11
46
article
IEEE COMPUTER SOC
LOS ALAMITOS
1
--
--
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Variability Management beyond Feature Models
When new customer and regulatory requirements arise, the ability to quickly adapt business information system processes is crucial to stay ahead of competitors. A proposed synthesis-based framework enables the development of business processes that automatically yield fully executable variants.
COMPUTER
0018-9162
1558-0814
wos:2011-2013
WOS:000327605900017
Lamprecht, AL (reprint author), Univ Potsdam, Inst Comp Sci, Potsdam, Germany.
, lamprecht@cs.uni-potsdam.de; stefan.naujokat@tu-dortmund.de;
i.schaefer@tu-braunschweig.de
Anna-Lena Lamprecht
Stefan Naujokat
Ina Schaefer
43183
2011
2020
eng
23
956
postprint
1
2020-06-12
2020-06-12
--
Semantics-based composition of EMBOSS services
Background
More than in other domains the heterogeneous services world in bioinformatics demands for a methodology to classify and relate resources in a both human and machine accessible manner. The Semantic Web, which is meant to address exactly this challenge, is currently one of the most ambitious projects in computer science. Collective efforts within the community have already led to a basis of standards for semantic service descriptions and meta-information. In combination with process synthesis and planning methods, such knowledge about types and services can facilitate the automatic composition of workflows for particular research questions.
Results
In this study we apply the synthesis methodology that is available in the Bio-jETI workflow management framework for the semantics-based composition of EMBOSS services. EMBOSS (European Molecular Biology Open Software Suite) is a collection of 350 tools (March 2010) for various sequence analysis tasks, and thus a rich source of services and types that imply comprehensive domain models for planning and synthesis approaches. We use and compare two different setups of our EMBOSS synthesis domain: 1) a manually defined domain setup where an intuitive, high-level, semantically meaningful nomenclature is applied to describe the input/output behavior of the single EMBOSS tools and their classifications, and 2) a domain setup where this information has been automatically derived from the EMBOSS Ajax Command Definition (ACD) files and the EMBRACE Data and Methods ontology (EDAM). Our experiments demonstrate that these domain models in combination with our synthesis methodology greatly simplify working with the large, heterogeneous, and hence manually intractable EMBOSS collection. However, they also show that with the information that can be derived from the (current) ACD files and EDAM ontology alone, some essential connections between services can not be recognized.
Conclusions
Our results show that adequate domain modeling requires to incorporate as much domain knowledge as possible, far beyond the mere technical aspects of the different types and services. Finding or defining semantically appropriate service and type descriptions is a difficult task, but the bioinformatics community appears to be on the right track towards a Life Science Semantic Web, which will eventually allow automatic service composition methods to unfold their full potential.
Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-43183
urn:nbn:de:kobv:517-opus4-431830
1866-8372
online registration
Journal of Biomedical Semantics 2 (2011) S5 DOI: 10.1186/2041-1480-2-S1-S5
Anna-Lena Lamprecht
Stefan Naujokat
Tiziana Margaria
Bernhard Steffen
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
956
eng
uncontrolled
service description
eng
uncontrolled
synthesis algorithm
eng
uncontrolled
input type
eng
uncontrolled
synthesis methodology
eng
uncontrolled
electronic tool integration
Biowissenschaften; Biologie
Medizin und Gesundheit
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/43183/pmnr956.pdf