Difference between revisions of "Literature"
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Please add additional literature (sorted on descending publication year): | Please add additional literature (sorted on descending publication year): | ||
| + | |||
| + | === 2011 === | ||
| + | * Tim Wallace: '''Using Java applets to enhance online teaching and assessment in Blackboard'''. In ''Symposium on the Benefits of eLearning Technologies''. University of Manchester, 2011. | ||
| + | *: [http://www.elearning.eps.manchester.ac.uk/wp-content/uploads/2011/05/Symposium_Publication.pdf#page=12 Article] | ||
=== 2010 === | === 2010 === | ||
| − | |||
* Robert M. Hanson: '''''Jmol'' â a paradigm shift in crystallographic visualization'''. ''Journal of Applied Crystallography'', 43(5): 1250-1260 '''(2010)''' | * Robert M. Hanson: '''''Jmol'' â a paradigm shift in crystallographic visualization'''. ''Journal of Applied Crystallography'', 43(5): 1250-1260 '''(2010)''' | ||
*:doi:10.1107/S0021889810030256 - [http://dx.doi.org/10.1107/S0021889810030256 Abstract and article] | *:doi:10.1107/S0021889810030256 - [http://dx.doi.org/10.1107/S0021889810030256 Abstract and article] | ||
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=== 2009 === | === 2009 === | ||
| − | |||
* Jeroen Logtenberg: '''Multi-user interaction with molecular visualizations on a multi-touch table.''' MSc Thesis, University of Twente, Enschede, The Netherlands '''(2009)'''. | * Jeroen Logtenberg: '''Multi-user interaction with molecular visualizations on a multi-touch table.''' MSc Thesis, University of Twente, Enschede, The Netherlands '''(2009)'''. | ||
*: [http://purl.org/utwente/e59199 Full document] | *: [http://purl.org/utwente/e59199 Full document] | ||
=== 2008 === | === 2008 === | ||
| − | |||
* Clifton Forlines, Ryan Lilien: '''Adapting a single-user, single-display molecular visualization application for use in a multi-user, multi-display environment.''' In: ''Proceedings of the Working Conference on Advanced Visual Interfaces'', pp. 367-371 '''(2008)'''. | * Clifton Forlines, Ryan Lilien: '''Adapting a single-user, single-display molecular visualization application for use in a multi-user, multi-display environment.''' In: ''Proceedings of the Working Conference on Advanced Visual Interfaces'', pp. 367-371 '''(2008)'''. | ||
*: doi:10.1145/1385569.1385635 - [http://www.cliftonforlines.com/papers/2008_forlines_molvis.pdf] | *: doi:10.1145/1385569.1385635 - [http://www.cliftonforlines.com/papers/2008_forlines_molvis.pdf] | ||
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=== 2007 === | === 2007 === | ||
| − | |||
* Angel Herráez: '''How to use Jmol to study and present molecular structures, Vol.1'''. Lulu Enterprises: Morrisville, NC, USA '''(2007)'''. | * Angel Herráez: '''How to use Jmol to study and present molecular structures, Vol.1'''. Lulu Enterprises: Morrisville, NC, USA '''(2007)'''. | ||
*: ''A manual to learn the use of Jmol and scripting, and how to include JmolApplet into web pages. Volume 1 covers beginner and intermediate levels.'' - [http://biomodel.uah.es/Jmol-handbook.htm Info, preview and on-line shop] - ISBN 978-1-84799-259-8 <br />An update and an extra chapter: [http://www.lulu.com/product/15672160 Supplement 2011] | *: ''A manual to learn the use of Jmol and scripting, and how to include JmolApplet into web pages. Volume 1 covers beginner and intermediate levels.'' - [http://biomodel.uah.es/Jmol-handbook.htm Info, preview and on-line shop] - ISBN 978-1-84799-259-8 <br />An update and an extra chapter: [http://www.lulu.com/product/15672160 Supplement 2011] | ||
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=== 2006 === | === 2006 === | ||
| − | |||
* Angel Herráez: '''Biomolecules in the computer: Jmol to the rescue'''. ''Biochemistry and Molecular Biology Education'' 34(4): 255-261 '''(2006)'''. | * Angel Herráez: '''Biomolecules in the computer: Jmol to the rescue'''. ''Biochemistry and Molecular Biology Education'' 34(4): 255-261 '''(2006)'''. | ||
*: ''A review of Jmol project and features, in comparison to Rasmol and Chime.'' [http://dx.doi.org/10.1002/bmb.2006.494034042644 doi:10.1002/bmb.2006.494034042644] - ''Now freely available in full-text.'' | *: ''A review of Jmol project and features, in comparison to Rasmol and Chime.'' [http://dx.doi.org/10.1002/bmb.2006.494034042644 doi:10.1002/bmb.2006.494034042644] - ''Now freely available in full-text.'' | ||
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=== 2005 === | === 2005 === | ||
| − | |||
* Marion E. Cass, Henry S. Rzepa, David R. Rzepa, Charlotte K. Williams: '''The use of the free, open-source program Jmol to generate an interactive web site to teach molecular symmetry'''. ''Journal of Chemical Education'' 82(11):1736-1740 '''(2005)'''. | * Marion E. Cass, Henry S. Rzepa, David R. Rzepa, Charlotte K. Williams: '''The use of the free, open-source program Jmol to generate an interactive web site to teach molecular symmetry'''. ''Journal of Chemical Education'' 82(11):1736-1740 '''(2005)'''. | ||
*: [http://jchemed.chem.wisc.edu/Journal/Issues/2005/Nov/abs1736.html Abstract] | *: [http://jchemed.chem.wisc.edu/Journal/Issues/2005/Nov/abs1736.html Abstract] | ||
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=== 2004 === | === 2004 === | ||
| − | |||
* Martin Reitz, Oliver Sacher, Aleksey Tarkhov, Dietrich Trumbach, Johann Gasteiger: '''Enabling the exploration of biochemical pathways'''. ''Organic and Biomolecular Chemistry'' 2(2): 3226-3237 '''(2004)'''. | * Martin Reitz, Oliver Sacher, Aleksey Tarkhov, Dietrich Trumbach, Johann Gasteiger: '''Enabling the exploration of biochemical pathways'''. ''Organic and Biomolecular Chemistry'' 2(2): 3226-3237 '''(2004)'''. | ||
*: ''Introduces a [http://www2.chemie.uni-erlangen.de/services/biopath/ pathway] database that uses Jmol to visualize molecules.'' - doi:10.1039/B410949J - [http://www.rsc.org/Publishing/Journals/OB/article.asp?doi=B410949J Abstract and article] | *: ''Introduces a [http://www2.chemie.uni-erlangen.de/services/biopath/ pathway] database that uses Jmol to visualize molecules.'' - doi:10.1039/B410949J - [http://www.rsc.org/Publishing/Journals/OB/article.asp?doi=B410949J Abstract and article] | ||
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=== 2003 === | === 2003 === | ||
| − | |||
* Christoph Steinbeck, Yongquan Han, Stefan Kuhn, Oliver Horlacher, Edgar Luttmann, Egon Willighagen: '''The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics'''. ''Journal of Chemical Information and Computer Sciences'' 43(2): 493-500 '''(2003)'''. | * Christoph Steinbeck, Yongquan Han, Stefan Kuhn, Oliver Horlacher, Edgar Luttmann, Egon Willighagen: '''The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics'''. ''Journal of Chemical Information and Computer Sciences'' 43(2): 493-500 '''(2003)'''. | ||
*: ''Describes CDK, the library on which Jmol v6 to v9 is built.'' - doi:10.1021/ci025584y - [http://pubs.acs.org/cgi-bin/abstract.cgi/jcisd8/2003/43/i02/abs/ci025584y.html Abstract] | *: ''Describes CDK, the library on which Jmol v6 to v9 is built.'' - doi:10.1021/ci025584y - [http://pubs.acs.org/cgi-bin/abstract.cgi/jcisd8/2003/43/i02/abs/ci025584y.html Abstract] | ||
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=== 2001 === | === 2001 === | ||
| − | |||
* Egon L. Willighagen: '''Processing CML Conventions in Java'''. ''Internet Journal of Chemistry'' 4 '''(2001)'''. | * Egon L. Willighagen: '''Processing CML Conventions in Java'''. ''Internet Journal of Chemistry'' 4 '''(2001)'''. | ||
*: ''Describes how Jmol upto and including v9 read CML.'' - [http://www.ijc.com/abstracts/abstract4n4.html Abstract] | *: ''Describes how Jmol upto and including v9 read CML.'' - [http://www.ijc.com/abstracts/abstract4n4.html Abstract] | ||
Revision as of 13:08, 30 June 2011
- Websites Using J(S)mol
- J(S)mol in the Classroom
- Journals Using J(S)mol
- J(S)mol Literature
- Articles Using J(S)mol
- Books Using J(S)mol
- Wikis Using J(S)mol
- Blogs Using J(S)mol
- CMS Using J(S)mol (Moodle and others)
Course Management Systems, Learning Management Systems, Virtual Learning Environments, e-Learning Platforms - Applications Embedding Jmol
- Distributions Including Jmol
- Blue Obelisk
This section is devoted to published articles and books that describe Jmol features or uses.
Please add additional literature (sorted on descending publication year):
2011
- Tim Wallace: Using Java applets to enhance online teaching and assessment in Blackboard. In Symposium on the Benefits of eLearning Technologies. University of Manchester, 2011.
2010
- Robert M. Hanson: Jmol â a paradigm shift in crystallographic visualization. Journal of Applied Crystallography, 43(5): 1250-1260 (2010)
- doi:10.1107/S0021889810030256 - Abstract and article
- J. H. Gutow, Easy Jmol Web Pages using the Jmol Export to Web Function. Journal of Chemical Education WebWare. Publication Date (Web): April 8, 2010.
2009
- Jeroen Logtenberg: Multi-user interaction with molecular visualizations on a multi-touch table. MSc Thesis, University of Twente, Enschede, The Netherlands (2009).
2008
- Clifton Forlines, Ryan Lilien: Adapting a single-user, single-display molecular visualization application for use in a multi-user, multi-display environment. In: Proceedings of the Working Conference on Advanced Visual Interfaces, pp. 367-371 (2008).
- doi:10.1145/1385569.1385635 - [1]
- Brian McMahon, Robert M. Hanson: A toolkit for publishing enhanced figures. Journal of Applied Crystallography, 41(4): 811-814 (2008)
- doi:10.1107/S0021889808015616 - Abstract and article
2007
- Angel Herráez: How to use Jmol to study and present molecular structures, Vol.1. Lulu Enterprises: Morrisville, NC, USA (2007).
- A manual to learn the use of Jmol and scripting, and how to include JmolApplet into web pages. Volume 1 covers beginner and intermediate levels. - Info, preview and on-line shop - ISBN 978-1-84799-259-8
An update and an extra chapter: Supplement 2011
- A manual to learn the use of Jmol and scripting, and how to include JmolApplet into web pages. Volume 1 covers beginner and intermediate levels. - Info, preview and on-line shop - ISBN 978-1-84799-259-8
- Angel Herráez: Cómo utilizar Jmol para estudiar y presentar estructuras moleculares, Vol.1. Lulu Enterprises: Morrisville, NC, USA (2007).
- (In Spanish) - Info, preview and on-line shop - ISBN 978-1-84753-710-2
- Egon Willighagen, Miguel Howard: Fast and scriptable molecular graphics in web browsers without Java3D. Nature Precedings 14 June (2007).
- David A. Evans, Michael J. Bodkin, S. Richard Baker, Gary J. Sharman: Janocchio - a Java applet for viewing 3D structures and calculating NMR couplings and NOEs. Magnetic Resonance in Chemistry 45(7): 595-600 (2007).
- Janocchio is a Java applet based on Jmol; it calculates both H-H and H-C 3-bond coupling constants and NOEs from a three-dimensional structure. - doi:10.1002/mrc.2016
2006
- Angel Herráez: Biomolecules in the computer: Jmol to the rescue. Biochemistry and Molecular Biology Education 34(4): 255-261 (2006).
- A review of Jmol project and features, in comparison to Rasmol and Chime. doi:10.1002/bmb.2006.494034042644 - Now freely available in full-text.
- Interview with Martin Walker. Reactive Reports 54 (2006).
- Joost Van Durme, Florence Horn, Sabine Costagliola, Gert Vriend, Gilbert Vassart: GRIS: Glycoprotein-hormone Receptor Information System. Molecular Endocrinology 20(9): 2247-2255 (2006).
- doi:10.1210/me.2006-0020 - Abstract and article
2005
- Marion E. Cass, Henry S. Rzepa, David R. Rzepa, Charlotte K. Williams: The use of the free, open-source program Jmol to generate an interactive web site to teach molecular symmetry. Journal of Chemical Education 82(11):1736-1740 (2005).
- Jason E. Donald, Isaac A. Hubner, Veronica M. Rotemberg, Eugene I. Shakhnovich, Leonid A. Mirny: CoC: a database of universally conserved residues in protein folds. Bioinformatics 21: 2539-2540 (2005).
- Describes the CoC database which uses Jmol for visualisation. - doi:10.1093/bioinformatics/bti360 - Abstract
- Egon Willighagen, Miguel Howard: Jmol as 3D Viewer for CDK. CDK News 2(1): 17-20 (2005).
- Shows how Jmol can be embedded in other Java programs, in this case the Chemistry Development Kit specifically. - Article
2004
- Martin Reitz, Oliver Sacher, Aleksey Tarkhov, Dietrich Trumbach, Johann Gasteiger: Enabling the exploration of biochemical pathways. Organic and Biomolecular Chemistry 2(2): 3226-3237 (2004).
- Introduces a pathway database that uses Jmol to visualize molecules. - doi:10.1039/B410949J - Abstract and article
- Peter Murray-Rust, Henry S. Rzepa, Mark J. Williamson, Egon L. Willighagen: Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators. Journal of Chemical Information and Computer Sciences 44(2): 462-469 (2004).
- Describes a CDK plugin that acts as a RSS agregator and show its application as pluged in Jmol. - doi:0.1021/ci034244p - Abstract
- Andreas Bohne-Lang, Elke Lang: 3D-Molekülvisualisiering im Internet - Schwerpunkt Java-Applets. BIOspektrum 2004(2): 167-169 (2004).
- Compares Jmol with other chemistry visualisation applets. - Article
2003
- Christoph Steinbeck, Yongquan Han, Stefan Kuhn, Oliver Horlacher, Edgar Luttmann, Egon Willighagen: The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics. Journal of Chemical Information and Computer Sciences 43(2): 493-500 (2003).
- Describes CDK, the library on which Jmol v6 to v9 is built. - doi:10.1021/ci025584y - Abstract
- Francis T. Marchese, Jude Mercado, Yi Pan: Adapting single-user visualization software for collaborative use. In: Proceedings of the Seventh International Conference on Information Visualization - An International Conference on Computer Visualization and Graphics Applications, pp. 252-257 (2003).
- ISBN 0-7695-1988-1 - Article
2001
- Egon L. Willighagen: Processing CML Conventions in Java. Internet Journal of Chemistry 4 (2001).
- Describes how Jmol upto and including v9 read CML. - Abstract
Contributors
AngelHerraez, Rzepa, Gutow, NicolasVervelle, BrianMcMahon, Pimpim
