Chemistry in Second Life
© Lang et al 2009
Received: 9 July 2009
Accepted: 23 October 2009
Published: 23 October 2009
This review will focus on the current level on chemistry research, education, and visualization possible within the multi-user virtual environment of Second Life. We discuss how Second Life has been used as a platform for the interactive and collaborative visualization of data from molecules and proteins to spectra and experimental data. We then review how these visualizations can be scripted for immersive educational activities and real-life collaborative research. We also discuss the benefits of the social networking affordances of Second Life for both chemists and chemistry students.
With over 80,000 simultaneous users on at any given time, Second Life has emerged as the most popular non game-based 3D virtual world . Users interact with the environment and with each other in the form of avatars, usually lifelike representations of people or animals. Since users are empowered to create objects and environments of their choosing, almost every aspect of real life has been replicated in Second Life. Of course, since virtual worlds do not necessarily suffer the same limitations as reality, creative adaptations abound. Science is no exception and many exhibits in Second Life can be found depicting scientific content .
Chemistry presents some special challenges and opportunities for a platform like Second Life. Full use of 3D space is a real asset, since an understanding of the shape of molecules and orbitals is essential for chemists. We will show how such representations can be made in Second Life and how these have been applied to educational activities. Chemical data can also benefit from use of 3D space and some examples of interactive exhibits will be detailed. Finally, the social networking aspect of Second Life sets this virtual platform aside from others and this will be demonstrated.
This review does not attempt to exhaustively compare Second Life with other currently available technologies and platforms that perform similar operations. It is also not our intent to compare specific educational outcomes from using Second Life compared to alternative approaches or platforms. The targeted readers of this review are educators, students and other chemistry professionals who are curious about ways of using Second Life for chemistry related projects. We do however briefly note that there are several packages  available to display molecules in 3D on the web, such as, Jmol  and RasMol ; and even methods to embed interactive 3D molecular structures into PDF documents. Representations of the dynamics of chemical reactions in 3D are available from browser-based applications; an excellent example is the Mol4D tutorial site . Finally, social networking sites where chemists can interact on the web are multiplying very quickly .
The molecules that Orac makes can be manipulated in many ways. You can easily change the position, size and orientation; you can save the molecules to your inventory for later retrieval, make multiple copies and even distribute them to other users. Also, with a little scripting, you can make the molecules interact with users and even each other.
To achieve a more realistic docking simulation, a docking web-service could be used; and together with human interaction more efficient and sometimes better results (by avoiding local minima), over computer-only docking, can be achieved .
The peptides of Amino World are fully interactive, complete with extensive information available on notecards that users can save to their inventories, and by clicking on the peptide tower controller or the molecule itself you can highlight different structures such as the peptide backbone and the different R-groups. The R-groups can be made to identify themselves and copies can be taken and examined by users.
Another protein rezzer is Monolith scripted by Erich Bremer of Stony Brook University. Like the Protein Rezzing Toolkit, Monolith reads and parses PDB files. Monolith then rezzes the atoms of the structure in 3D. This makes it prim intensive but it rezzes structures relatively quickly - it can rez a 3000+ atom protein in under a minute. The atoms rezzed by Monolith are interactive, allowing the user to set labels, change colors based on residue name/number, set transparency of atoms interactively, and to display subsets of atoms. This makes Monolith a potentially useful tool for dynamic collaborative discussions, though unlike Orac, Hiro's Molecule Rezzer , or the Protein Rezzing Toolkit , it is currently not Open Source or freely available. Also, unlike Orac, which can make any structure, Monolith resembles the Protein Rezzing Toolkit in that it is limited to structures stored in PDB format.
Paul Bourke of the University of Western Australia has also done innovative work in evaluating Second Life for remote collaboration and visualization, including chemistry visualization. His work includes examples of immersive crystal structure visualization, including Hershfield surfaces, using preprocessed spherical projections, a useful low prim visualization technique .
The solubility explorer and 5-dimensional chemical space rezzer allows us to explore the data in real-time to find target solvents for particular combinations of Ugi reactants and analyze the chemical space for solubility trends. It also allows us to easily visualize regions of the data, seeing where the data is sparse, and guiding further research.
In the most recent implementation of these quizzes, content was ported over to a web interface. The resulting ChemTiles game  is now more accessible to everyone, since neither Unreal Tournament nor Second Life need to be installed. However, as will be detailed below, the social aspect of Second Life is absent in the web version. The web version maintains a high score list, so contests do not need to be run in real time in the form of races. During an implementation of the game in the spring of 2009 at Drexel University, students were given about a week to achieve the high score. Students in the class only competed against each other for prizes by signing up under the Drexel group. However, the game is open to anyone in the world to try.
The insertion of new content in the form of bitmap images was streamlined in this version by uploading all the tiles to a Flickr group  and tagging each image according to its category, such as Lewis structures, chirality, etc. The tiles uploaded to Flickr automatically become part of the game via an API provided by Flickr. Hosting the tiles on a Flickr group allows for the crowdsourcing of questions.
The presentation of molecules in 3D was especially helpful for bridged cyclic structures, which are difficult to imagine correctly using 2D representations. The chat interface with the spectral display board was easy to master to zoom into desired regions. With the implementation of the web version of the Spectral Game , most students migrated to that version since it did not require downloading software or learning a new interface. For students who are physically present in a workshop the web version is probably more convenient, whereas teachers who have most students participate remotely may find significant advantage in using the Second Life version.
In addition to teacher generated content, Second Life provides a rich environment for student projects. Students at Drexel University were given the option of creating exhibits for up to 2% extra credit on their final grade. This relatively small reward usually affords on the order of 5% participation, which is useful for large undergraduate courses, where it would be impractical to have 200 students trained and guided within Second Life. Although some training is required, optimally in a face-to-face workshop environment, students are asked to use simple tools.
In addition to providing a rich environment for 3D exhibits, Second Life enjoys a vibrant community of scientists. Students can benefit from spending time in areas with scientific content simply for the people that they meet who happen to be interested in the same topics. In the spring 2009 term, students at Drexel University taking introductory organic chemistry were asked to seek out and interview people on Second Life who are connected somehow to chemistry related fields. Another part of this extra credit assignment involved taking snapshots of areas in Second Life with chemistry content. A convenient way of identifying suitable people on Second Life involved identifying the creator of chemistry objects and contacting them by IM. FriendFeed, another social networking site was made the target of interviews for people involved with chemistry. The results of this assignment were aggregated on the class wiki  and highlight the richness of projects and networks of people working in the field. Such networking, impossible not so long ago, could prove crucial for students to identify opportunities in the course of their education and career.
Chemistry content can also be found at more general conferences and special events covering the sciences most notably on the Elucian Islands Archipelago owned by Nature Publishing Group who host the Nature Podcast  in Second Life and the Sci-Foo Lives On conference , as well as other conferences in science communication related events .
As mentioned above, one of the most useful attributes of Second Life is its ability to promote networking. For educators and researchers, this can turn out to be at least as valuable as leveraging the platform for the creation of 3D exhibits. By simply spending some time on Second Life to create content or assist students, one often accidentally meets people who may ultimately end up as collaborators at some point. People that one meets can be added to a friends list very easily by clicking on their avatar. Whenever one logs in the list of friends currently online is highlighted and any of these people can be contacted by IM or teleported over to interact with a group. The ease with which this can happen in Second Life enables rapid growth of contacts via friend-of-a-friend networks. The authors of this paper represent an excellent example of a collaboration originating from Second Life and evolving to include work in drug discovery, solubility and data visualization, both in Second Life  and on the bench .
Islands with Chemistry Content
The American Chemical Society also provides many free virtual items in its HQ building including amongst other things a molecule rezzer , a 3D periodic table , and clothing such as an ACS branded outfit consisting of a t-shirt, lab coat, and safety goggles.
This article represents a snapshot of some current chemistry related activities in Second Life. The open, immersive, and highly visual 3-dimensional platform combined with the ease of content creation and scripting makes Second Life a valuable tool for conducting chemistry research, education, and collaboration. As with many technological innovations, change can happen quickly. It is expected that chemistry's presence in Second Life will continue to expand in unexpected ways as more people join and bring their creativity to innovate in this virtual world.
Avatar - A user's avatar or agent is a virtual representation of themselves inside Second Life. Chat - In Second Life users communicate with each other via text (chat), voice, and gestures. Text entered into the chat window can be read not only by other users but also by 'listening' scripts within chat range. Orac - A freely available, Open Source, scripted tool that allows users to create conformally realistic molecules from SMILES strings in Second Life. The name Orac comes from a computer character in the British classic science fiction series Blakes 7. Prim - All items/objects in Second Life are created with primitive objects (prims) such as cubes, sphere, cylinders, cones, etc. Rez, Rezzer, Rezzing - To Rez is a verb that means to create or to make an object appear in Second Life. Rezzing an object/prim can be done by dragging items from your inventory or by creating them in directly via the edit window. A scripted object that rezzes other objects, such as molecules, is called a rezzer. The term comes from the science-fiction movie Tron. Smi23d - smi23d is a cheminformatics web-service, originally written by Kevin Gilbert, improved upon by Rajarshi Guha, and is currently hosted by the cheminformatics group at Indiana University . Sim - In Second Life a sim (simulation, more accurately region) is a named 256 m by 256 m area of land hosted by a single simulator process.
The authors would like to thank Joanna Scott and Nature who provided the initial land in Second Life which led to the authors meeting and eventual collaboration, Kate Sellar and the American Chemical Society who provided the land where a number of the tools were created; Sandy Adam of Aldrich Chemical, Peter Miller of the University of Liverpool, David Reeves of Yeshiva University, Joan Slonczewski of Kenyon College, David Wild of Indiana University, Rajarshi Guha at the National Institutes of Health, Antony Williams of ChemSpider, Eloise Pasteur, and Beth Ritter-Guth who all contributed their time and expertise at various points during the author's collaboration.
- Official Second Life statistics. [https://blogs.secondlife.com/community/features/blog/2009/04/16/the-second-life-economy--first-quarter-2009-in-detail]
- McConaghy T: Science Center Group. Second Life science center wiki. [http://science-center-group.wikispaces.com]
- Molecular Graphics Systems. [http://en.wikipedia.org/wiki/List_of_molecular_graphics_systems]
- Herráez A: Biomolecules in the computer: Jmol to the rescue. Biochemistry and Molecular Biology Education. 2006, 34 (4): 255-261. 10.1002/bmb.2006.494034042644.View ArticleGoogle Scholar
- Goodsell DS: Representing structural information with RasMol. Curr Protoc Bioinformatics. 2005, Chapter 5 (Unit 5.4):Google Scholar
- Kumar P, Zieglar A, Zieglar J, Uchanska-Ziegler B, Ziegler A: Grasping molecular structures through publication-integrated 3D models. Trends Biochem Sci. 2008, 33 (9): 408-12. 10.1016/j.tibs.2008.06.004.View ArticleGoogle Scholar
- Mol4D. [http://wetche.cmbi.ru.nl//organic/]
- Social Networking. [http://en.wikipedia.org/wiki/Social_networking]
- Bradley JC: InChI Rezzer in Second Life. [http://usefulchem.blogspot.com/2007/09/inchi-rezzer-in-second-life.html]
- Simplified molecular input line entry specification. [http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification]
- International Chemical Identifier. [http://en.wikipedia.org/wiki/Inchi]
- InChIKey. [http://en.wikipedia.org/wiki/Inchi#InChIKey]
- Bradley JC: Teaching Chemistry Mechanisms in Second Life. [http://drexel-coas-elearning.blogspot.com/2007/08/teaching-chemistry-mechansims-in-second.html]
- Bradley JC, Rosenthal P, Guha R, Mirza K, Gut J: Open Notebook Science - Falcipain-2 Preliminary Results. Nature Precedings. 2008, [http://dx.doi.org/10.1038/npre.2008.2216.1]Google Scholar
- Bradley JC: Molecule Docking in Second Life. [http://usefulchem.blogspot.com/2007/06/molecule-docking-in-second-life.html]
- Subasi E, Basdogan C: A New Haptic Interaction and Visualization Approach for Rigid Molecular Docking. Virtual Environments Presence: Teleoperators & Virtual Environments. 2008, 17 (1): 73-90. 10.1162/pres.17.1.73.View ArticleGoogle Scholar
- Ariantho D: Amino World. [http://daneelariantho.wordpress.com/2008/06/15/amino-world/]
- Miller PGG, et al: Protein Rezzing Toolkit. secondlifemolecules wiki. [http://secondlifemolecules.wikispaces.com/proteins]
- Protein Data Bank. [http://www.pdb.org]
- Greer J, Bush BL: Macromolecular Shape and Surface Maps by Solvent Extrusion. Proc Natl Acad Sci. 1978, 75 (1): 303-307. 10.1073/pnas.75.1.303.View ArticleGoogle Scholar
- Monolith. [http://secondlife.som.stonybrook.edu/monolith]
- Bourke P: Evaluating Second Life As A Tool For Collaborative Scientific Visualization. Computer Games and Allied Technology 2008 conf. 2008, [http://local.wasp.uwa.edu.au/~pbourke/papers/cgat08/]Google Scholar
- Bradley JC: NMR viewer in Second Life. [http://usefulchem.blogspot.com/2008/04/nmr-viewer-in-second-life.html]
- Bradley JC, Mirza KB, Owens K, Osborne T, Williams AJ: Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling. J Vis Exp. 2008, 942-21Google Scholar
- Open Notebook Science Challenge. [http://onschallenge.wikispaces.com]
- Bradley JC: Interactive Visualization of ONS Solubility Data. [http://usefulchem.blogspot.com/2009/01/interactive-visualization-of-ons.html]
- Edufrag project. [http://edufrag.wikispaces.com]
- Steinbeck C, Hoppe C, Kuhn S, Floris M, Guha R, Willighagen EL: Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics. Current pharmaceutical design. 2006, 12: 2111-2220. 10.2174/138161206777585274.View ArticleGoogle Scholar
- Bradley JC, Guha R, Lang ASID, Lindenbaum P, Neylon C, Williams AJ, Willighagen E: Chapter 16: Beautifying Data in the Real World from Beautiful Data. Edited by: Segaran T, Hammerbacher J. 2009, O'Reilly MediaGoogle Scholar
- Bradley JC: Update on games and vodcast for orgo class. [http://drexel-coas-elearning.blogspot.com/2006/04/update-on-games-and-vodcast-for-orgo.html]
- Bradley JC: Spring 07 Post-Mortem. [http://drexel-coas-elearning.blogspot.com/2007/06/spring-07-post-mortem.html]
- Bradley JC: The ChemTiles game. [http://usefulchem.blogspot.com/2009/04/chemtiles-game.html]
- Flickr group for ChemTiles. [http://www.flickr.com/groups/orgogame]
- Bradley JC: Winter 09 term post-mortem: SpectralGame implementation. [http://drexel-coas-elearning.blogspot.com/2009/03/winter-09-term-post-mortem-spectralgame.html]
- Bradley JC, Lancashire RJ, Lang ASID, Williams AJ: The Spectral Game: Leveraging Open Data and Crowdsourcing for Education. Journal of Cheminformatics. 2009, 1: 9-10.1186/1758-2946-1-9. [http://www.jcheminf.com/content/1/1/9]View ArticleGoogle Scholar
- Bradley JC: Spring 2008 post-mortem on organic chemistry courses. [http://drexel-coas-elearning.blogspot.com/2008/07/spring-2008-post-mortem-on-organic.html]
- Networking on Second Life and FriendFeed extra credit page. [http://chem241.wikispaces.com/extracredit]
- Bradley JC: Virtual Poster Session on ACS Island. [http://drexel-coas-elearning.blogspot.com/2008/02/virtual-poster-session-on-acs-island.html]
- Linden Lab: How Meeting In Second Life Transformed IBM's Technology Elite Into Virtual World Believers. [http://secondlifegrid.net.s3.amazonaws.com/docs/Second_Life_Case_IBM_EN.pdf]
- Nature Podcast. [http://www.nature.com/nature/podcast]
- SciFooLivesOn wiki. [http://scifooliveson.wikispaces.com]
- Second Nature Island. [http://www.nature.com/secondnature]
- Bradley JC, Lang ASID: Chemistry Concepts in Second Life. Presentation at the American Chemical Society meeting August 18. 2008, [http://drexel-coas-talks-mp3-podcast.blogspot.com/2008/08/chemistry-concept-in-second-life.html]Google Scholar
- American Chemical Society Island SLurl. [http://slurl.com/secondlife/ACS/87/157/25]
- Sellar K: Welcome to ACS Island on Second Life. [http://www.youtube.com/watch?v=uK5aFfQWcXY]
- Bradley JC: 3D periodic table in Second Life. [http://usefulchem.blogspot.com/2007/10/3d-periodic-table-in-second-life.html]
- Drexel Island wiki. [http://drexelisland.wikispaces.com]
- Elucian Islands Archipelago SLurl. [http://slurl.com/secondlife/Elucian%20Islands/46/62/26]
- Lang ASID, Kobilnyk DC: Visualizing Atomic Orbitals Using Second Life. Journal of Virtual Worlds Research. 2009, 2 (1): [https://journals.tdl.org/jvwr/article/view/448/465]Google Scholar
- Wild D: IU Cheminformatics Web Services find use in Second Life!. 2009, [http://cheminfonews.blogspot.com/2009/07/iu-cheminformatics-web-services-find.html]Google Scholar