Jmol - Jmol is a Java molecular viewer for
three-dimensional chemical structures. Features include reading a variety of
file types and output from quantum chemistry programs, and animation of
multi-frame files and computed normal modes from quantum
programs.
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- Development Status: 4 - Beta
- Environment: Web Environment ,
Win32 (MS Windows) ,
X11 Applications
- Intended Audience: Developers , End
Users/Desktop ,
Science/Research
- License: GNU Library or Lesser General Public License (LGPL)
- Natural Language: Dutch ,
English ,
Spanish
- Operating System: OS Independent
- Programming Language: Java
- Topic: Computer Aided Instruction (CAI) , 3D
Rendering ,
Bio-Informatics ,
Chemistry ,
Visualization
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Gene Ontology - This is the home of
the Gene OntologyTM Consortium.
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- Development Status: 4 - Beta , 5
- Production/Stable
- Intended Audience: Developers , End
Users/Desktop
- License: Artistic License
- Natural Language: English
- Operating System: OS Independent ,
POSIX
- Programming Language: C ,
Java ,
Perl
- Topic: Bio-Informatics
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Semantic Web Ontology Editor for
Protege - The Protege-OWL plugin extends the Protégé platform
(http://protege.stanford.edu) into an ontology editor for the Web Ontology
Language (OWL). The plugin is written in Java and uses the Jena library
(http://www.hpl.hp.com/semweb/index.html) for OWL and R
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- Development Status: 2 - Pre-Alpha
- Environment: Cocoa (MacOS X) ,
Win32 (MS Windows) ,
Gnome ,
KDE
- Intended Audience: Developers ,
Education ,
End Users/Desktop ,
Healthcare Industry ,
Information Technology ,
Science/Research
- License: Mozilla Public License 1.1 (MPL 1.1)
- Natural Language: English
- Operating System: OS Independent
- Programming Language: Java
- Topic: Artificial Intelligence ,
Bio-Informatics ,
Information Analysis ,
Visualization
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JAligner - JAligner is a Java
implementation of biological sequence alignment
algorithms.
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- Development Status: 1 - Planning
- Intended Audience: Developers ,
Science/Research
- License: GNU General Public License (GPL)
- Natural Language: English
- Operating System: OS Independent
- Programming Language: Java
- Topic: Bio-Informatics
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XML tree viewer component - Universal
java component to display content and structure of the XML document.
Bioinformatics.
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- Development Status: 5 - Production/Stable
- Environment: Win32 (MS Windows) ,
Gnome
- Intended Audience: Developers
- License: Apache Software License ,
GNU General Public License (GPL)
- Natural Language: English
- Operating System: Windows ,
OS Independent
- Programming Language: Java
- Topic: Viewers ,
Bio-Informatics
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74. Protein Family Alignment Annotation Tool -
The Pfaat protein family alignment annotation tool is a Java-based multiple
sequence alignment editor and viewer designed for protein family analysis. The
application merges display features such as dendrograms, secondary and tertiary
protein structures.
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- Development Status: 5 - Production/Stable
- Intended Audience: Healthcare Industry ,
Science/Research
- License: GNU General Public License (GPL)
- Operating System: OS Independent
- Programming Language: Java
- Topic: Bio-Informatics
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Protein 3D Printing - This
project provides software resources for creating solid models of proteins that
can be printed on color 3D printers. The main focus is a java program that reads
in a PDB file and produces a PLY format stick representation of the
protein.
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- Development Status: 3 - Alpha
- Environment: Console (Text Based) ,
Web Environment
- Intended Audience: Developers , End
Users/Desktop
- License: Public Domain
- Natural Language: English
- Programming Language: Java
- Topic: Bio-Informatics ,
Visualization
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Geneview - Genbank Visualisation Tool -
Geneview is a visualisation tool to display genetic sequence data stored in
nucleic sequence databases like <A
HREF="http://www.ncbi.nlm.nih.gov/Genbank/">GenBank</A>.
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- Development Status: 4 - Beta
- Intended Audience: Developers , End
Users/Desktop
- License: GNU Library or Lesser General Public License (LGPL)
- Natural Language: English
- Operating System: OS Independent
- Programming Language: Java
- Topic: Bio-Informatics ,
Visualization
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130. SPedit - Swiss-Prot curation environment -
SPedit is a new curation environment for the Swiss-Prot and TrEMBL databases.
For more information about these databases see http://www.expasy.ch/sprot/ and
http://www.ebi.ac.uk/swissprot/
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- Development Status: 1 - Planning
- Intended Audience: Developers , End
Users/Desktop
- License: GNU Library or Lesser General Public License (LGPL)
- Natural Language: English ,
French ,
German
- Operating System: OS Independent
- Programming Language: Java
- Topic: Front-Ends ,
Bio-Informatics ,
Visualization
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