Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges
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{"title"=>"Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges", "type"=>"journal", "authors"=>[{"first_name"=>"Zhihan", "last_name"=>"Lv", "scopus_author_id"=>"55925162500"}, {"first_name"=>"Alex", "last_name"=>"Tek", "scopus_author_id"=>"35073072500"}, {"first_name"=>"Franck", "last_name"=>"Da Silva", "scopus_author_id"=>"56875173700"}, {"first_name"=>"Charly", "last_name"=>"Empereur-mot", "scopus_author_id"=>"55614271300"}, {"first_name"=>"Matthieu", "last_name"=>"Chavent", "scopus_author_id"=>"24376265100"}, {"first_name"=>"Marc", "last_name"=>"Baaden", "scopus_author_id"=>"6601957611"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84874639659", "pmid"=>"23483961", "isbn"=>"1932-6203; 1932-6203", "pui"=>"368465784", "issn"=>"19326203", "scopus"=>"2-s2.0-84874639659", "doi"=>"10.1371/journal.pone.0057990"}, "id"=>"b29741c0-4405-3a73-bbc2-8c2943cc2f5a", "abstract"=>"The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists? This approach points to an extension of open computer programs, not only providing access to the source code, but also delivering an easily modifiable and extensible scientific research tool. In this work, we will explore these questions using the Unity3D game engine to develop and prototype a biological network and molecular visualization application for subsequent use in research or education. We have compared several routines to represent spheres and links between them, using either built-in Unity3D features or our own implementation. These developments resulted in a stand-alone viewer capable of displaying molecular structures, surfaces, animated electrostatic field lines and biological networks with powerful, artistic and illustrative rendering methods. We consider this work as a proof of principle demonstrating that the functionalities of classical viewers and more advanced novel features could be implemented in substantially less time and with less development effort. Our prototype is easily modifiable and extensible and may serve others as starting point and platform for their developments. A webserver example, standalone versions for MacOS X, Linux and Windows, source code, screen shots, videos and documentation are available at the address: http://unitymol.sourceforge.net/.", "link"=>"http://www.mendeley.com/research/game-science-video-game-technology-help-biologists-tackle-visualization-challenges", "reader_count"=>108, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Librarian"=>2, "Researcher"=>18, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>3, "Other"=>8, "Student > Master"=>26, "Student > Bachelor"=>11, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Librarian"=>2, "Researcher"=>18, "Student > Doctoral Student"=>7, "Student > Ph. D. 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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/978749"], "description"=>"<p>A – Human hemoglobin (PDB id: 1HHO) rendered with a stylized blood effect. B – Binding of a DNA molecule on the DNA-binding domain of Myb (PDB id: 1MSE). The secondary structure object was imported from PyMol. C - Contour outlining combined with glow. D – Green fluorescent protein shown as glowing carbon alpha spline (PDB id: 1KYS). E - Artistic molecule rendering : leucotoxin S component from <i>Staphylococcus Aureus</i> (PDB id: 1T5R) with a gold material. A,E – Background creation using a skybox.</p>", "links"=>[], "tags"=>["Computational biology", "computer science", "physics", "mathematics"], "article_id"=>645639, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Physics"], "users"=>["Zhihan Lv", "Alex Tek", "Franck Da Silva", "Charly Empereur-mot", "Matthieu Chavent", "Marc Baaden"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057990.g005", "stats"=>{"downloads"=>3, "page_views"=>128, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Several_visual_effects_available_in_Unity_/645639", "title"=>"Several visual effects available in Unity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-07 09:11:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/978746"], "description"=>"<p>A - All possible lighting and shading components of an arbitrary object (right) can be represented on a 2D image of a sphere (left). Colored arrows depict locations of equivalent surface orientation. B - Different lit-spheres applied to a molecular surface creating different effects : hand drawing (left), green glass (center), cartoon shading (right). C – Illustrative rendering using lit spheres and Hyperballs. Van der Waals (left) and backbone (right) representation of the BLT2 GPCR receptor with hand drawn lit spheres.</p>", "links"=>[], "tags"=>["spheres"], "article_id"=>645638, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Physics"], "users"=>["Zhihan Lv", "Alex Tek", "Franck Da Silva", "Charly Empereur-mot", "Matthieu Chavent", "Marc Baaden"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057990.g004", "stats"=>{"downloads"=>1, "page_views"=>41, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Lit_spheres_concept_/645638", "title"=>"Lit spheres concept.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-07 09:10:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/1006333"], "description"=>"<p>Performance comparison between UnityMol using HyperBalls (with Unity 3D Engine Version 3.5 and 4), VMD and PyMol to display molecules with Ball & Stick representation on two different configurations.</p>", "links"=>[], "tags"=>["unitymol", "hyperballs", "3d", "vmd", "pymol", "molecules"], "article_id"=>666946, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Physics"], "users"=>["Zhihan Lv", "Alex Tek", "Franck Da Silva", "Charly Empereur-mot", "Matthieu Chavent", "Marc Baaden"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057990.t002", "stats"=>{"downloads"=>6, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Performance_comparison_between_UnityMol_using_HyperBalls_with_Unity_3D_Engine_Version_3_5_and_4_VMD_and_PyMol_to_display_molecules_with_Ball_amp_Stick_representation_on_two_different_configurations_/666946", "title"=>"Performance comparison between UnityMol using HyperBalls (with Unity 3D Engine Version 3.5 and 4), VMD and PyMol to display molecules with Ball & Stick representation on two different configurations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-06 01:55:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/978761"], "description"=>"<div><p>The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists? This approach points to an extension of open computer programs, not only providing access to the source code, but also delivering an easily modifiable and extensible scientific research tool. In this work, we will explore these questions using the Unity3D game engine to develop and prototype a biological network and molecular visualization application for subsequent use in research or education. We have compared several routines to represent spheres and links between them, using either built-in Unity3D features or our own implementation. These developments resulted in a stand-alone viewer capable of displaying molecular structures, surfaces, animated electrostatic field lines and biological networks with powerful, artistic and illustrative rendering methods. We consider this work as a proof of principle demonstrating that the functionalities of classical viewers and more advanced novel features could be implemented in substantially less time and with less development effort. Our prototype is easily modifiable and extensible and may serve others as starting point and platform for their developments. A webserver example, standalone versions for MacOS X, Linux and Windows, source code, screen shots, videos and documentation are available at the address: <a href=\"http://unitymol.sourceforge.net/\" target=\"_blank\">http://unitymol.sourceforge.net/</a>.</p> </div>", "links"=>[], "tags"=>["biologists", "visualization", "challenges"], "article_id"=>645647, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Physics"], "users"=>["Zhihan Lv", "Alex Tek", "Franck Da Silva", "Charly Empereur-mot", "Matthieu Chavent", "Marc Baaden"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057990", "stats"=>{"downloads"=>13, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Game_On_Science_How_Video_Game_Technology_May_Help_Biologists_Tackle_Visualization_Challenges__/645647", "title"=>"Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-07 09:13:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/978732"], "description"=>"<p>A – Rendering efficiency for ferrocytochrome C (PDB-id 1KX2) shown as atoms and bonds measured in Frames Per Second (FPS) for a 1344×1008 viewport. B - FPS values for molecules of increasing size rendered by a particle system, HyperBalls or Unity spheres. The red dashed line divides the graph in two parts: above this line the FPS step is 50, below this line the FPS step is 5.</p>", "links"=>[], "tags"=>["graphical"], "article_id"=>645628, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Physics"], "users"=>["Zhihan Lv", "Alex Tek", "Franck Da Silva", "Charly Empereur-mot", "Matthieu Chavent", "Marc Baaden"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057990.g002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Benchmark_of_graphical_methods_/645628", "title"=>"Benchmark of graphical methods.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-07 09:07:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/1006348"], "description"=>"<p>Set of molecules used to evaluate the rendering performance of UnityMol.</p>", "links"=>[], "tags"=>["molecules", "rendering"], "article_id"=>666975, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Physics"], "users"=>["Zhihan Lv", "Alex Tek", "Franck Da Silva", "Charly Empereur-mot", "Matthieu Chavent", "Marc Baaden"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057990.t001", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Set_of_molecules_used_to_evaluate_the_rendering_performance_of_UnityMol_/666975", "title"=>"Set of molecules used to evaluate the rendering performance of UnityMol.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-06 01:56:15"}

PMC Usage Stats | Further Information

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Relative Metric

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