Developing a Collaboratory for Environmental Molecular Sciences


A Collaboratory is a "...'center without walls' in which the nation's researchers can perform their research without regard to geogrphical location - interacting with colleagues, accessing instrumentation, sharing data and computational resources, and accessing information in digital libraries." Bill Wulf (1989)

Collaboratory Images - Collaboratory Presentation:

Environmental Molecular Sciences Collaboratory

The Environmental Molecular Sciences Collaboratory, through the support of the Office of Energy Research of the US Department of Energy, will revolutionize the nature of scientific collaboration by using computing technology to create a virtual place in which collaborations take place naturally, without interference from the tools which make them possible.

Collaboratory Examples

Collaboratories have been successfully implemented in several areas of science.

EMSL Collaborations

The Environmental Molecular Sciences Collaboratory will contain many one of a kind instruments of interest to scientists around the world. The process of doing science collaboratively is an iterative one. The collaborative software environment (CSE) is being created to facilitate the scientific process for all participants.

The Collaborative Software Environment Tools

The Collaborative Software Environment (CSE) as presently implemented in a prototype at PNL consists of an extensible set of software tools loosely integrated through an Executive Toolbar. One requirement for the CSE for the Environmental Molecular Sciences is that it be implemented as a cross platform (Unix, Mac, pc) environment. The CSE Executive (written at PNL) provides for connecting individuals to a collaborative session, and displays the tools presently used by each collaborator.

The six tools presently available in the CSE include:
1) A Chat Box (part of the CSE Executive) providing the exchange of text messages between participants.
2) Audio and video tele-conferencing are available in the LBL Mbone nv and vat software (as well as commercial applications).
3) A shared whiteboard provides a common writing surface for all particiapants. We are presently using the LBL Mbone wb software. Tele-conferencing and the whiteboard provide a real-time, non-permanent interaction mechanism.
4) The tele-viewer provides the ability for multiple collaborators to simultaneously observe (and potentially interact) with an analysis program or an instrument console. We are developing a cross-platform tele-viewer since we have not located a public tool which satisfies this need.
5) A collaborative scientific notebook provides a shared, integrated, cross-platform, permanent data storage mechanism for scientific information. Virtual Notebook System (VNS) from The Forefront Group is a commercial tool of his nature, available for Macintosh, MS Windows, and Unix platforms. A scientific notebook allows users to create text, images, and other 'objects', arranged on pages in notebooks that can be viewed and changed by multiple simultaneous users. The notebook allows real-time interaction between collaborators and provides a permanent record of the interaction.
6) The Informatics (integrated, comprehensive information accessed) requirement of of the CSE is satisfied by NSCA Mosaic which provides a World Wide Web hyypertext document browser as well as a platform for integrating information access which is required for the collaborative environment. The web provides text, graphics, audio and video in a relatively non-interactive, but permanent, form.

The CSE is adaptable to each specific collaborative interaction., with the appropriate tools being chosen for the circumstance of the moment. Usage includes:
1) Tele-analysis where collaborators interact in the data analysis or development process;
2) Tele-experimentation where collaborators interact with an instrument (or a computational experiment). This does not necessarily imply remote control, since being a voyeur may be all that is required.
3) The CSE provides multimedia tele-conferencing, with a richer environment for interaction between peers.
4) Tele-mentoring may occur for example in an educational environment such as a scientist consulting with a student or a class, or between an expert and a technician on site with an instrument.
5) Tele-medicine is the usage of such tools and processes described above in the context of health care, and includes access to medical images and shared diagnosis.
6) Tele-presence represents the extension of the CSE multimedia capability into a moree immersive and rich environment of tools, such as multi-dimensional viewing, sonification, and force feedback.

Collaborative Software Environment

The desktop computer display shows the prototype CSE in use. The upper left window on the screen is the Executive toolbar, where each tool (VNS, Mosaic, Mbone WhiteBoard, Mbone Audio/Video teleconferencing) is launched by a (blue) button. The Chat Box is seen below the toolbar with text exchange between the participants. Not shown is the Executive display of the conference particpants and their selected tools. The picture in the upper center is the Mbone video of one participant. The upper right window is a fragment of a Mosaic informatics display relevent to the Rotational Coherence Spectroscopy instrument being discussed. The lower right is a part of the Mbone whiteboard being used to exchange comments about the spectroscopy experiment. The lower left window is a display of the RCS-TRID analysis program being shared via the tele-viewer in this shared analysis session.

The picture at lower left is the other collaborator in this session pointing to the sensor on a part of the instrument being discussed, as seen by the Mbone video.

The picture at lower middle is a computational chemistry result showing channels in zeolite, a theoretical input of relevence to the collaborative interaction.

The lower right picture is a KSR 2 supercomputer with 80 nodes, used at PNL for computational chemistry. Compute jobs can result from a collaborative interaction, and be sent to remote systems for computation, with results returned to the collaborators in the CSE.

The upper right picture shows a Fourier Transform Ion Cycltron Resonance Mass Spectrometer instrument, one of the shared instruments in the EMSL at PNL.

CSE Client-Server Model

The CSE has a client-server structure.

CSE Executive

The Collaborative Software Environment Executive lauches applications, makes connections with collaborators, shows the present collaborations, and provides the chat box.

CSE Tools

The CSE tools provide varying functionality, with the mix of tools being selected by the user in the context of the specific collaboration.

Accessing Unique EMSL Instruments

The Environmental Molecular Sciences Collaboratory will provide collaborators with access to unique instruments within the laboratory.

Accessing EMSL Instruments

The Environmental Molecular Sciences Collaboratory will include sharing of instruments, analysis and data between researchers in all aspects of chemical physics.

CSE Usage

For example, the CSE might be used in an interaction between PNL researchers, local instruments, and remote researchers, such as collaborators at the University of Utah. Multiple instruments in the Environmental Molecular Sciences Laboratory at PNL are being implemented with a common data format, to ease the exchange of information. Experimentalists and theorists are interacting on common problems using CSE tools. Remote collaborators can share the data format and interact through the CSE tools with their PNL peers.

Electronic Scientific Notebook

A collaborative electronic scientific notebook provides a shared, integrated, cross-platform, permanent data storage mechanism for scientific information. Virtual Notebook System (VNS) from The Forefront Group is a commercial tool of his nature, available for Macintosh, MS Windows, and Unix platforms. A scientific notebook allows users to create text, images, and other 'objects', arranged on pages in notebooks that can be viewed and changed by multiple simultaneous users. The notebook allows real-time interaction between collaborators and provides a permanent record of the interaction..

Multicast Backbone

Audio and video tele-conferencing for Unix systems are available in the LBL Mbone nv and vat software. A shared whiteboard provides a common writing surface for all particiapants. We are presently using the LBL Mbone wb software. The CU-SeeMe tool from Cornell provides multi-cast access to Mac's and pc's. Tele-conferencing and the whiteboard provide a real-time, non-permanent interaction mechanism.

Different Views of Information

Information is viewed within a context. Ask different scientists what a molecule is, and you will get different answers based upon their perspective. A theorist might specify a molecule as input parameters to a calculation, where an experimentalist might view it by its image upon a detector after breaking up in a collision, and an engineer might view it in the context of a complex mixture.

Environmental Molecular Sciences Laboratory WWW Pages

The Environmental Molecular Sciences Laboratory is using the World Wide Web to provide for all the informatics needs of our center. The EMSL pages are found at http://www.emsl.pnl.gov:2080.

EMSL Mosaic Extensions

The EMSL is using Mosaic as a mechanism for documentation and is building extensions such as specialized viewers to support the Collaboratory development.

Forms Usage in EMSL

The forms capability provided by Mosaic is being used to provide interactive access to computing resources, scientific information, and computation at the EMSL.

The InCINC Conference

The EMSL is sponsoring a network based conference on chemometrics, InCINC '94.

Environmental Molecular Sciences Collaboratory Goals

The Environmental Molecular Sciences Collaboratory will provide a rich environment for scientific collaboration.

Psycho-Social Issues

A Collaboratory is a new environment for scientific research. The presentation on Psycho-social Issues of Collaboratories gives some of the issues to be considered.


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