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Concurrent interactive visualization and handling of molecular structures over

the Internet in web browsers

Luciano A. Abriata

Laboratory for Biomolecular Modeling, Swiss Federal Institute of Technology (EPFL)

and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland

luciano.abriata@epfl.ch

Abstract. This preprint presents a web app (essentially a web page-based program) with which two or more users

(“peers”) can view and handle 3D molecular structures in a concurrent, interactive way through their web browsers.

This means they can share orientation and zoom level, commands and other operations in almost real time over the

Internet through standard web pages. This web app, open source and built with the open source components JSmol

for molecular visualization and Peer.js for WebRTC connection, provides a practical tool for online collaboration

and teaching at a distance. More broadly, it illustrates the strong integrability of technologies for client-side web

programming, and paves the way for similar apps for concurrent work in other disciplines. Web app is available at:

http://lucianoabriata.altervista.org/jsinscience/concurrent-jsmol/concurrent-jsmol-visualization.html

Keywords: JSmol, Peer.js, web socket, molecular modeling, structural bioinformatics, web technologies

oncurrent visualization of molecular

structures over the Internet is essential for

efficient collaboration and teaching over distant

locations in disciplines like chemistry and

structural biology. A possible way to achieve

concurrent visualization is through screen-sharing

programs; however, this has a number of

disadvantages. First, large amounts of video have

to be streamed over the Internet, potentially

resulting in slow experience and/or decreased

graphics quality for the receiving peer. Second,

confidential information could be captured as the

video streams through Internet. Third, and

probably most important, the receiver has no

control over the visualization. All these

shortcomings are alleviated by the prototypical

web app (program embedded in a web page1,2)

introduced here, which uses simple methods and

existing commodity web software to provide a

unique experience for concurrent, interactive

molecular visualization and handling over the

Internet. As provided, the web app is based on

JSmol3 for molecular visualization and Peer.js4 for

simplified web socket-based connectivity, but

other libraries could be used too. (For the user this

is anyway irrelevant because no software needs to

be installed and the web app works in any standard

web browser.)

Figure 1. Scheme depicting how this web app allows a user to

work on a molecular representation and send states and

commands seamlessly to the other users, yielding a smooth,

computationally inexpensive collaborative experience where

the receiver user can also effectively intervene.

Brief Description for Users

Essentially, this web app provides direct

browser-to-browser connectivity to transmit JSmol

states (like rotations, zoom levels, etc.) and

commands between users. This way, when a user

rotates or zooms the structure on his/her screen,

this induces the same rotations and zooms on the

screens of other users, with subsecond latency.

Likewise, a user can run a JSmol command on

C

his/her visualization and apply the same command

on all the other users’ visualizations. Since the

software system transfers only small pieces of

text-like information about states and commands,

but no graphics, the experience is very fluid even

over average Internet connections. Also, the

molecular files loaded by each user are never sent

over Internet, protecting privacy.

To use the web app, each user (or “peer”)

must direct his or her browser to

http://lucianoabriata.altervista.org/jsinscience/conc

urrent-jsmol/concurrent-jsmol-visualization.html.

When each user’s page loads, he or she gets

assigned a random “PeerJS ID”. At least one user

ID must be communicated to the other users (by e-

mail or any other medium). When the other users

receive the ID of this “master user”, they use it to

connect to him/her. Users can then select whether

they transmit rotations, states and JSmol

commands to the master user as they apply them

to their visualizations, and whether they apply to

their visualizations the rotations, states and

commands received from the master user.

Independently, any other pair of users can

additionally connect to each other to send and

receive states and commands directly between

them.

Within the web app, users can also chat and

send files to each other. And although not

implemented in this web app, the communication

technology employed also allows the

incorporation of video and audio conferencing.

Brief technicalities about the implementation

This web app is self-contained in a single

HTML file. It uses web sockets (here through the

Peer.js library, but others could be used) and a

plugin-less molecular viewer for browsers (here

JSmol, but also other scriptable viewers could be

used). Through HTML and JavaScript code, the

web app controls when it sends rotations and

commands applied by one peer to the other peers,

and whether the rotations and commands received

from another user are applied.

The current implementation runs only over

http, but web socket libraries that handle https

could be used to allow https access (which would

enable JSmol to directly load structures directly

from the Protein Data Bank, instead of the user

having to download it first as in the current

version of the web app).

A last important point is that the web app, as

provided in its single HTML file, can be directly

copied to any other webserver retaining

functionality (a copy of JSmol and proper

reference to it must be given).

Perspectives

Being this web app only a prototype to show

feasibility, there are multiple modifications and

additions worth exploring. For example, it could

be useful to transmit not only commands typed for

the JSmol applet but also any other command

applied directly from the JSmol interface or

console. Also, additional commands prebuilt into

buttons could be implemented, depending on the

intended uses (small molecules or biological

molecules or materials, for research or didactic,

etc.)

This example web app shall promote the

development of interfaces for concurrent work in

other disciplines. Not only for molecular sciences

but for virtually any discipline where transmitting

small pieces of data to transform views on other

users’ devices can help to better communicate

ideas and concepts at a distance.

References

(1) Abriata, L. A. Informatics 2017, 4 (3).

(2) Abriata, L. A.; Rodrigues, J. P. G. L. M.;

Salathé, M.; Patiny, L. Trends Biotechnol.

2017.

(3) Hanson, R. M.; Prilusky, J.; Renjian, Z.;

Nakane, T.; Sussman, J. L. Isr. J. Chem.

2013, 53 (3–4), 207–216.

(4) Bu, M.; Zhang, E. Peer.js.