Simbiot: Research Collaboration

As any field matures, it becomes more complex, giving birth to sub-field specialists. The same holds true for molecular biology and related sciences. Perhaps 10 years ago it was possible for a single laboratory to collect the data, analyze them on a personal computer, write a manuscript and publish the results. Today, this process is more complicated. Collecting the data is an expensive and complicated process. It requires a very complex and sophisticated instrument that is very expensive to purchase and maintain and requires specially trained technicians dedicated to using and maintaining the device. None but very well-funded laboratories can afford to purchase and maintain one. So the task of generating data is typically outsourced to either a collaborator or a service provider.

Once the data are generated, they need to be analyzed. This too has become a highly specialized task. With a few tests per experiment, researchers could use standard statistical tools built into a typical spreadsheet. However, more sophisticated experiments such as microarrays require highly specialized tools and algorithms developed specifically to handle these data. These specialized tools are very complex, requiring extensive data formatting, multiple complex parameters and producing ever more complex output. The analysis also requires a specialist. If such a specialist is not available within a lab or institution, which is not unusual since bioinformaticians and biostatisticians are not yet common, the researcher is again required to collaborate with individuals at a remote location or possibly to outsource the analysis project to a service provider.

This collaboration between individuals at separate geographic locations requires much data distribution. If the data quantities are small, this can be achieved using a fairly simple system, such as e-mail and e-mail attachments. A more sophisticated approach could use, for example, public/private FTP sites. However, as data sets continue to grow and increase in complexity, FTP also becomes less viable.

To make the situation even more problematic, the results of analysis frequently are at least as voluminous as the raw files. The analytical results are large and complex, typically consisting of a very large number of complex files. It also should also kept in mind that the results of each run are dependent on the supplied parameters and data, so it would not be unusual for researchers to examine results of multiple runs, with the data from each run being contained in a large number of specially formatted files. These types of results are difficult enough to interpret when they are available locally; it becomes prohibitively complex when the collaboration involves researchers around the country or around the world.

Simbiot: Social Network Services (SNS)

Simbiot makes scientific collaboration easy!

The variety of Communication services, also known as Social Networking Services or SNS built into Simbiot allow users to effectively share information and communicate with collaborators who may be located in a different building, different city or different continent.  This communication is accomplished using a number of tools:

• Document Management System (Projects), which is discussed in a separate document;
• Self-Organizing Groups, which allow users to dynamically form units that will have a simple way to exchange data;
• Share and Copy functionality that allows users to grant access (share) raw data or analysis results with their collaborators within a group as well as to copy (by creating an additional copy) analysis result to another user;
• A multi-lingual Mail tool is another way users can communicate and copy information;
• Integrated, and also multi-lingual, Forums allow access to all users within the server or a more restricted communication within a Group or Project.

Working With Projects

The Projects represent a separate data management system designed to work in parallel with the rest of the Simbiot’s data analysis and management system.  Projects can be used as stand-alone entities to manage and distribute data between different users or they could be used in conjunction with the analysis system to transfer raw data as well as various analysis results into the specified Projects.  Each Project has its own set of members who can communicate within the bounds of that project using project-specific mail and forum options.  The project owner can Invite users to join a project.  The project owner can create an anonymous login for the project.  This login can be sent to, for example, publications to invite reviewers to enter the project and anonymously examine the data.  The owner can “publish” the project which, if approved by the administrator, causes the project to become visible to all users.  Once the project is published, the contents of that project can not be altered.  However, the owner can “duplicate” a project to set up a new unpublished project with the same membership to continue the work post “publication”.

Free demo accounts are available at http://www.simbiot.net.

Please also see more information about Simbiot Single User Accounts and Private Server Installations.