Why use BioCoRE?

BioCoRE offers a broad online extension to the conventional way of doing research and training. A problem-solving environment, BioCoRE bridges people and resources across distances and time zones, via high bandwidth, as well as normal-speed computer networks.

Research and Research Management

BioCoRE facilitates individual and collaborative research and research management

Productive research relies on extensive and intensive interactions between scientists across disciplines and at different levels. Equally essential is the ability to easily and rapidly exchange both textual and visual information. This is particularly critical in the biomedical sciences, where discussions of molecular graphics images and the transfer of extremely large data files are a daily routine. To facilitate effective communication among collaborators, BioCoRE offers tools such as a message board, allowing for an easy exchange of textual information. For visual communication, scientists can use JMV and VMD to view, manipulate and store molecular graphics images. BioCoRE's storage capability enables researchers to depict specific views of a given biological system and store them; later other project members, whenever and wherever they are, can virtually share the stored views, modify them, and review the system alone or with their colleagues. Researchers can use a Lab Book to track current progress within the project team, and can share relevant web-based resources with other researchers via a Website Link Library. Aiding dissemination efforts, BioCoRE publically accessible areas can be used for sharing data and findings whose significance cuts across projects, making them viewable to the entire BioCoRE user community.

As research projects often generate trajectory files of biomolecular simulations easily reaching sizes of several gigabytes, the resulting datasets often preclude simple email discussions of findings. BioCoRE meets the challenge by allocating each project its own file space (BioFS) , thereby creating a central hub where all project-data, e.g. structure files, simulation data, and analysis results of files can be stored and accessed. WebDAV support makes the BioFS especially transparent and friendly.

Joint research is mostly performed by scientists from different institutions, each in need of an environment with expert assistance tools to harness the quality of their work. Accordingly, BioCoRE features tools to set up computer simulations, submit jobs to local or remote computing resources, using Globus or SSH, and to perform run time job monitoring. BioCoRE also supplies a unified environment in which researchers can manage multiple accounts at multiple computer sites. BioCoRE's archiving features make it particularly beneficial for scientists who join the project after inception, as well as for those who are at times unavailable and inaccessible.

BioCoRE facilitates training

Many of the same communication and publication tools important for collaborative research are as valuable for training purposes. The shared filesystem is ideal as a repository of PDF, PowerPoint and other class-level documents. Class materials placed there can be continuously updated as they evolve. Windows, Macintosh, and Linux users can use WebDAV to "mount" the file system and have it appear as a normal folder on their desktop. Standard Unix-style filesystem permissions enable read-only files, allowing students to review relevant material before the class actually begins, while preventing inadvertent and unauthorized modifications. BioCoRE public and private areas allow students and trainees to present information in the public area for others to view and comment on, while protecting their unpublished work in their private areas. BioCoRE has tools for exporting data from the private area to HTML, and a student or instructor may present his/her class-related work directly to other students and instructors. The BioCoRE Message Board and Control Panel enhance communication, and can be used for sharing information among students and instructors.

BioCoRE's simplified graphical interface to structural biology tools is conducive for hosting tutorials, and for training non-expert research-oriented students to use these tools. Tutorials using BioCoRE could be administered in a variety of ways, including instructor-led and self-guided sessions. BioCoRE's features such as the online chat and message board allow instructors to interact with students and monitor their progress within BioCoRE. BioCoRE will soon incorporate tools to allow researchers to design and deliver tutorials about their own accomplishments and on subjects of their choice. The NAMD Configuration File Generator is an invaluable asset for MD beginners. Users are able to create an NAMD configuration file that can be saved to the shared file system or to one's local machine. Once students have their NAMD configuration file in the shared file system (along with other files required for the simulation), the instructor can show them how to submit a job to the supercomputer in which they have active accounts, using the Job Management feature of BioCoRE. The students would tell what files they need to have uploaded and what files they expect back, and BioCoRE will perform the operation for them. Instructors who offer their sessions in computer labs could go even further and project the BioCoRE session for the entire class to view. Throughout the transmission process the instructor can explain relevant values to students, giving them the opportunity to explore the configuration file options and see results in the text file in real time.

Other BioCoRE features with special training significance include the Link Library that is used to store and share relevant website links with the rest of the class. Another training advantage BioCoRE offers is the sharing of visual displays with the class, via the VMD Load/Save state features. By preparing a view (state) of a molecular structure with VMD and saving it to BioCoRE, students can easily re-load the view and work with it, assuming they have VMD installed on their local machine. If they don't have VMD installed, BioCoRE provides a static image file of the state, viewable in their web browser. Once the class ends, final class materials could be placed on the web by 'exporting' the entire project to a webpage.

BioCoRE facilitates Mentoring

BioCoRE, as a research and training platform, presents an ideal venue to supervise and mentor students and staff within one's department/unit/institution and between facilities and organizations across any distance, exploiting readily available fast (and ever-faster) communication networks. BioCoRE built-in evaluation capabilities enable 'on-site' coaching and systematic assessment of trainees progress and performance.


The BioCoRE team welcomes any comments, questions, or suggestions that you might have concerning our software! Please email us or fill out our feedback form.