A Collaborative Virtual Reality Environment for Molecular Biology

Jun Lee1, PhamSy Quy1, Jee-In Kim1*, Lin-Woo Kang1

Dept. of Advanced Technology Fusion1 Konkuk University

Seoul, Korea junlee@konkuk.ac.kr

Anna Seo2, HyungSeok Kim3 Dept. of {Computer Science & Engineering2, Internet

and Multimedia Engineering3} Konkuk University

Seoul, Korea jnkm@konkuk.ac.kr

Abstract— A collaborative virtual reality environment (CRVE) can be used in molecular biology because it can provide users with virtual experiences of three dimensional molecular models in cyberspaces. Therefore, we developed a remote collaboration system for molecular docking and crystallography using virtual reality techniques. The collaborative works of molecular docking were successfully exercised. We also conducted visualization and manipulation of three dimensional biomolecular models and supported discussions of remote participants for crystallography using the collaborative system.

Keywords: Collaborative Virtual Reality; Molecular Simulation; Virtual Reality Applications

I. INTRODUCTION The collaboration of several users can improve

performance of completing their tasks. The concept of computer supported cooperative work (CSCW) can be applied to such collaboration. CSCW is used in wide areas of applications such as chatting, e-mail, version control and so on.

In networked virtual reality (VR), multiple users can attend collaborative works which can be classified as collaborative virtual reality [1]. Its application areas include military training, medical surgery, computer aided design (CAD) and so on.

Biological researches such as molecular modeling and crystallography aim to investigate three dimensional (3D) structures of molecules such as viruses and proteins. The researches include simulations of characteristics of the molecules using equations of quantum and classical physics. With the simulations, scientists can develop new materials and new drugs. VMD [2] and VRMMS [3] are software tools for the scientists to manipulate 3D molecular models in virtual reality. The tools could execute simulation software using distributed or parallel computing system for real-time calculations. Several visualization and simulation algorithms have been developed for visualizing large scale molecular models. Also, various applications have been suggested for collaboration and education using the Internet [4].

* Corresponding Author

Most tools for collaborative virtual reality are mainly focusing on real-time collaboration between distributed co-workers [4]. However, it is difficult for co-workers in geographically distant locations and different time zones to perform simulations at the same time. They have to adjust their life cycles for their partners during the collaboration. Some co-workers must join the collaborative simulations too late at night or too early in the morning. It could decrease performances of the co-workers.

We plan to develop a new collaborative tool which enhances such collaborative activities in networked virtual reality. The proposed system aims to solve the time conflicts between researchers from different regions. One of our solutions is to provide with version control concepts for collaborative works. That is, the system records intermediate simulation results as movie files, 3D replay files and data files. These files are stored in the collaboration server and other co-workers can download these files, review the previous works and resume the works, if necessary. The co-workers can analyze the intermediate results, give feedbacks as comments and decide whether they reject or accept the previous works. It is similar to the version control concept in software engineering.

II. RELATED WORKS Bhandarkar et al.[4] developed BioCore which facilitates

cooperative works for molecular modeling. It consists of Workbench, Notebook, Conferences, and Documents. They perform molecular energy simulation, real-time monitoring, communication among participants and document management, respectively. Also, BioCore can be combined with existing tools a visualization tool VMD [2] and a computational system NAMD [5]. However, its users complain that the rendering speed becomes slow if they use ordinary PC class computers or notebooks. This means that real-time collaboration through the Internet with various types of computers does not seem to become highly active. Also, the network module of BioCore is not ‘open standard’. Therefore, its flexibility is not quite high.

Park et al. [3] proposed a collaborative environment with various communication channels such as chatting and commenting. It also supported haptic feedbacks and an adaptive level of detail (LOD) technique in order to provide

2009 International Symposium on Ubiquitous Virtual Reality

978-0-7695-3704-7/09 $25.00 © 2009 IEEE

DOI 10.1109/ISUVR.2009.14

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the remote users with precise 3D images, though they have different types of computing systems such as ordinary PC’s and notebooks.

III. SYSTEM OVERVIEW

Figure 1. System Overview.

Figure 2. Synchronous Collaboration Server.

The proposed environment can be described as show in

Figure 1. User 1 enters Portal Server and registers a collaborative simulation. After the registration, users may attend two types of collaborations, ‘synchronous’ (where co-workers collaborate at the same time) or ‘asynchronous’ (co-workers may not be required to be present at the same time to collaborate) collaboration. Asynchronous Collaboration Server records actions of the users into movie files, replay files and information files. If another user attends the collaboration, he could analyzes the previous works using

the files and attach additional works subsequently to the previous works. If synchronous collaboration is required, Synchronous Collaboration Server is used. In this case, the proposed system provides a concurrency control mechanism [7] to avoid conflicts among multiple participants.

In Synchronous Collaboration Server, sessions for collaboration are created for multiple participants. In order to solve the concurrency control problem, ‘floor control’ [7], which manages the access control of 3D molecular models, is implemented.

For geographically separated co-workers of collaborative biomolecular researches, Asynchronous Collaborations Server must provide with functions to modify and update previous research results. Version control mechanisms are implemented and recording mechanisms such as movie files, VR replay files and information files such as log data files are also implemented.

Figure 3. Asynchronous Collaboration Server.

Figure 4. VR Replays according to time-step information.

The proposed system requires network connection, file

management and various virtual reality interfaces. As presented in Figure 5, Connection Manager gets collaboration information from Collaboration Servers which is to be sorted in buffers of Streaming Manager. Operation Manager reads the collaboration information from Streaming Manager and sends it to Representation Platform for visualization and animation of 3D molecular models. Operation Manager uses IO Parser to build 3D models of molecules. Also, users can operate various interfaces such as a haptic interface for exercising more realistic and convenient experiments.

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Figure 5. Collaborative Client.

IV. COLLABORATIVE SIMULATION

A. Molecular Docking Simulation Molecular docking procedure aims to find a candidate

molecule (a ligand) which can be combined with a receptor at a specific position called as ‘active site’. Molecular docking process needs to manipulate two molecules simultaneously to find out active site with physically calculation. Collaboration greatly helps co-workers, because the docking requires hand skills, experiences and knowledge.

Figure 6. (A) Before an AIDS virus model and a new drug model are combined. (B) After the AIDS virus model and the new drug model are

combined.

B. Crystallography Simulation Crystallography gets information of structures of patterns

in crystals of molecular models using X-ray diffractions and refinements. The pattern data are used to create a new 3D molecular model. It aims to develop new materials or medicines. The crystallography simulation takes much time and costs because researchers should start from real reagent sources and to use computer software to refine 3D molecular models. Since knowledge and experiences of experts are essential to succeed, collaboration is the most important.

We expanded a widely used program called COOT (Crystallographic Object-Oriented Toolkit) [8]. The extension is called CO-COOT. It was installed and beta-tested in the Global lab at Konkuk University and the Roger Kornberg lab at Stanford University with the high speed connection 1.

Figure 7. (Human RNA polymerase II 1SFO[9], Info of electronic density

and refined 3D molecular model.

V. CONCLUDING REMARKS In this paper, we propose a virtual reality biomolecular

simulation system supporting synchronous and asynchronous collaboration. The proposed system consists of synchronous collaboration and asynchronous collaboration. In synchronous collaboration, the proposed system provides a floor control mechanism to avoid conflicts problem between multi users. The proposed system supports features of recording movie, VR replay and chemical data for asynchronous collaboration. So any users who participate into the collaboration attend analysis and gave comments the collaboration. Our experiments demonstrated that the proposed environment worked quite well in both synchronous and asynchronous collaboration.

The computing performance of the proposed system still needs to be improved for bilmolecular simulations. A possible solution for high performance could be GRID computing[10], NAMD parallel processing[5], and so on.

1 We are supported by the KREONET and GLORIAD connection for high speed collaboration between Korea and USA by KISTI’s Cyber Network Infrastructure Program.

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Also, the concurrency control mechanism of the proposed system offers a simple and primitive method to access shared objects during synchronous collaboration. We will enhance performance of current concurrency control mechanism and version control mechanism by testing and applying various control mechanisms.

ACKNOWLEDGMENT This work was supported by the Seoul R&BD

Program(10581).

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