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Proceedings Article, Paper
@InProceedings
Beitrag in Tagungsband, Workshop

Author, Editor
Author(s):
Boghossian, Nicolas Pascal
Kohlbacher, Oliver
Lenhof, Hans-Peter
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dblp
dblp
Editor(s):
Vitter, Jeffrey S.
Zaroliagis, Christos D.
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BibTeX cite key*:
BoghossianKohlbacherLenhof1999
Title, Booktitle
Title*:
BALL: Biochemical Algorithms Library
Booktitle*:
Algorithm engineering (WAE-99) : 3rd International Workshop, WAE'99
Event, URLs
Conference URL::
Downloading URL:
Event Address*:
London, UK
Language:
English
Event Date*
(no longer used):
July 19-21
Organization:
Event Start Date:
Incorrect data type for operator or @Function: Time/Date expected Incorrect data type for operator or @Function: Time/Date expected Incorrect data type for operator or @Function: Time/Date expected
Event End Date:
Incorrect data type for operator or @Function: Time/Date expected Incorrect data type for operator or @Function: Time/Date expected Incorrect data type for operator or @Function: Time/Date expected
Publisher
Name*:
Springer
URL:
Address*:
Berlin
Type:
Vol, No, Year, pp.
Series:
Lecture Notes in Computer Science
Volume:
1668
Number:
Month:
Pages:
330-344
Year*:
1999
VG Wort Pages:
ISBN/ISSN:
Sequence Number:
DOI:
Note, Abstract, ©
(LaTeX) Abstract:
In the next century, virtual laboratories will play a key role in
biotechnology. Computer experiments will not only replace
time-consuming and expensive real-world experiments, but they will also
provide insights that cannot be obtained using ``wet'' experiments.
The field that deals with the modeling of atoms, molecules, and their
reactions is called Molecular Modeling. The advent of
Life Sciences gave rise to numerous new developments in this
area. However, the implementation of new simulation tools is extremely
time-consuming. This is mainly due to the large amount of
supporting code (e.g. for data import/export, visualization, and so on)
that is required in addition to the code necessary to implement the new idea. The
only way to reduce the development time is to reuse reliable code,
preferably using object-oriented approaches. We have designed and
implemented BALL, the first object-oriented application framework for rapid
prototyping in Molecular Modeling. By the use
of the composite design pattern and polymorphism we were able to model
the multitude of complex biochemical concepts in a well-structured and
comprehensible class hierarchy, the BALL kernel classes. The
isomorphism between the biochemical structures and the kernel classes
leads to an intuitive interface. Since BALL was designed for rapid software
prototyping, ease of use and flexibility were our principal design
goals. Besides the kernel classes, BALL provides fundamental
components for import/export of data in various file formats,
Molecular Mechanics simulations, three-dimensional visualization, and
more complex ones like a numerical solver for the Poisson-Boltzmann
equation. The usefulness of BALL was shown by the
implementation of an algorithm that checks proteins for
similarity. Instead of the five months that an earlier implementation
took, we were able to implement it within a day using BALL.
Keywords:
Software Libraries, Molecular Modeling, Computational Molecular Biology
Download
Access Level:
Public

Correlation
MPG Unit:
Max-Planck-Institut für Informatik
MPG Subunit:
Algorithms and Complexity Group
Audience:
Expert
Appearance:
MPII WWW Server, MPII FTP Server, MPG publications list, university publications list, working group publication list, Fachbeirat



BibTeX Entry:

@INPROCEEDINGS{BoghossianKohlbacherLenhof1999,
AUTHOR = {Boghossian, Nicolas Pascal and Kohlbacher, Oliver and Lenhof, Hans-Peter},
EDITOR = {Vitter, Jeffrey S. and Zaroliagis, Christos D.},
TITLE = {BALL: Biochemical Algorithms Library},
BOOKTITLE = {Algorithm engineering (WAE-99) : 3rd International Workshop, WAE'99},
PUBLISHER = {Springer},
YEAR = {1999},
VOLUME = {1668},
PAGES = {330--344},
SERIES = {Lecture Notes in Computer Science},
ADDRESS = {London, UK},
}


Entry last modified by Christine Kiesel, 03/02/2010
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Editor(s)
Oliver Kohlbacher
Created
02/17/2000 11:46:36 AM
Revisions
5.
4.
3.
2.
1.
Editor(s)
Christine Kiesel
Anja Becker
Anja Becker
Anja Becker
Anja Becker
Edit Dates
28.08.2006 16:15:52
07.04.2000 09:43:58
29.03.2000 13:05:20
29.03.2000 12:56:59
29.03.2000 12:54:34