Blind and Visually Impaired Students Can Perform Computer-Aided Molecular Design with an Assistive Molecular Fabricator

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• 作者：Val猫re Lounnas (20)
  Henry B. Wedler (21)
  Timothy Newman (21)
  Jon Black (20)
  Gert Vriend (20)
  
  20. CMBI Radboudumc ; Geert Grooteplein 26-28 ; 6525 GA ; Nijmegen ; The Netherlands
  21. Department of Chemistry ; University of Davis ; Davis ; CA ; 95616 ; USA
  
• 关键词：Blind ; visually impaired ; chemistry ; molecular editor ; assistive software ; computer ; aided molecular design ; Braille ; science ; higher education
• 刊名：Lecture Notes in Computer Science
• 出版年：2015
• 出版时间：2015
• 年：2015
• 卷：9043
• 期：1
• 页码：18-29
• 全文大小：504 KB
• 参考文献：1. Lounnas V., Wedler H.B., Newman T., Schaftenaar G., Harrison J.G., Nepomuceno G., Pem-berton R., Tantillo D.J., Vriend G.: Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol. J. Comput. Aided Mol. Des. (August 5, 2014) (Epub. ahead of print)
  2. Wedler, H.B., Boyes, L., Davis, R.L., Flynn, D., Franz, A.K., Hamann, C.S., Harrison, J.G., Lodewyk, M.W., Milinkevich, K.R., Shaw, J.T., Tantillo, D.J., Wang, S.C. (2014) Nobody Can See Atoms: Science Camps Highlighting Approaches for Making Chemistry Accessible to Blind and Visually-Impaired Students. J. Chem. Educ. 91: pp. 188-194 21/ed300600p" target="_blank" title="It opens in new window">CrossRef
  3. Albright professor helps blind students discover chemistry at summer camps, ofessor-helps-blind-students-discover-chemistry-at-summer-camps#.VEFIsb5OKpp" class="a-plus-plus"> http://readingeagle.com/news/article/albright-professor-helps-blind-students-discover-chemistry-at-summer-camps#.VEFIsb5OKpp
  4. History of Analytical Chemistry by Ferenc Szabadvary, Gordon and Breach Sciences Pub-lishers, Yverdon, Switzerland Horstmann, August (1843 鈥?1929) studied at the University of Heidelberg, and later became a professor there. He became blind quite young as the re-sult of a disease
  5. Blind students confront chemistry lab, 2009/aug/18/blind-students-confront-chemistry-lab/" class="a-plus-plus"> http://www.kpbs.org/news/2009/aug/18/blind-students-confront-chemistry-lab/
  6. Which problems would a blind person have when applying for a professorship, 23421/which-problems-would-a-blind-person-have-when-applying-for-a-professorship" class="a-plus-plus"> http://academia.stackexchange.com/questions/23421/which-problems-would-a-blind-person-have-when-applying-for-a-professorship
  7. Skawinski, W.J., Busanic, T.J., Ofsievich, A.D., Luzhkov, V.B., Venanzi, T.J., Venanzi, C.A.: The Use of Laser Stereolithography to Produce Three-Dimensional Tactile Molecular Models for Blind and Visually-Impaired Scientists and Students. Inf. Technol. Disabil. 1(4), Article 6 (1994)
  8. Chemistry by touch: blind scientist fashions new models of molecules, of+molecules.-a016723790" class="a-plus-plus"> http://www.thefreelibrary.com/Chemistry+by+touch%3A+blind+scientist+fashions+new+models+of+molecules.-a016723790 (accessed April 30, 2014)
  9. Fartaria, R.P.S., Pereira, F., Bonif谩cio, V.B.D., Mata, P., Aires-de-Sousa, J., Lobo, A.M.: NavMol 2.0: a molecular structure navigator/editor for blind and visually impaired users. Eur. J. Org. Chem. 1415鈥?419 (2013)
  10. Lounnas, V., Vriend, G. (2012) AsteriX: A Web Server To Automatically Extract Ligand Coordinates from Figures in PDF Articles. J. Chem. Inf. Model. 52: pp. 568-576 21/ci2004303" target="_blank" title="It opens in new window">CrossRef
  11. SMILES 鈥?A Simplified Chemical Language, http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
  12. ChemAxon Home Page, http://www.chemaxon.com/ (accessed April 30, 2014)
  13. O鈥橞oyle, N.M., Banck, M., James, C.A., Morley, C., Vandermeersch, T., Hutchison, G.R. (2011) Open Babel: An open chemical toolbox. Journal of Cheminformatics 3: pp. 33 2946-3-33" target="_blank" title="It opens in new window">CrossRef
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• 作者单位：Bioinformatics and Biomedical Engineering
• 丛书名：978-3-319-16482-3
• 刊物类别：Computer Science
• 刊物主题：Artificial Intelligence and Robotics
  Computer Communication Networks
  Software Engineering
  Data Encryption
  Database Management
  Computation by Abstract Devices
  Algorithm Analysis and Problem Complexity
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1611-3349

文摘

Life science in general and chemistry in particular are inaccessible to blind and visually impaired (BVI) students at the exception of very few individ-uals who have overcome, in a seemingly miraculous way, the hurdles that pave the way to higher education and professional competency. AsteriX-BVI a publicly accessible web server, developed at the Radboud University in the Netherlands already allows BVI scientists to perform a complete series of tasks to automatically manage results of quantum chemical calculations and produce a 3D representation of the optimized structures into a 3D printable, haptic-enhanced format that includes Braille annotations.1 We report here the implementation of Molecular Fabricator 1.0, a molecular editor which is a new assistive feature of AsteriX-BVI. This molecular editor allows BVI scientists to conceptualize complex organic molecules in their mind and subsequently create them via the server. It was developed around the concept that molecules are composed of chemical fragments connected together. Fragments from either a predefined dictionary or defined as short SMILES strings can be used, ensuring that almost any structure can be generated. A fragment-based relative atom-numbering scheme that can be mentally tracked is used together with the support of an automatically generated report in Braille providing topological information and a clean 2D sketch of the constructed molecule, that can be unambiguously recognized tactilely. The R or S stereo-chemical configuration of asymmetric centers is controlled via feedback provided in the Braille report. The molecular fabricator creates output files in a variety of formats currently used in drug design and theoretical chemistry. It was tested and refined with the help of HBW, the blind co-author of this article, who pursues a PhD in chemistry at UC Davis, California. With Molecular Fab-ricator 1.0 HBW can now create molecules very fast and verify their structures without external help as was the case before. Molecular Fabricator 1.0 and its tutorial are accessible at: http://swift.cmbi.ru.nl/bitmapb/access/runit_bvi.html .