Virtual Notebook Environment FAQ

What does ViNE do?

ViNE provides an interactive, web-based notebook interface for scientists to store, analyze, and visualize their data. ViNE connects the notebook interface to tools within the scientist's computational environment. These tools (simulation, storage, analysis, and presentational tools) maybe located on different computer systems. ViNE associates the tool and data objects in the notebook interface with their location in the scientist's environment in a user-transparent way.

ViNE allows scientists to describe and name their data and computational tools within their notebooks, and then construct experiments graphically without worrying about where the tools and data are located. ViNE handles connecting tools and data within the environment, relieving the scientist to focus on more important tasks than how data is transported between different platforms. In addition to running experiments, scientists can arrange for the results to be displayed on a notebook page for review. This page may become a permanent page in their notebook if the scientists decides to save the results. ViNE provides computational scientists with a secure, flexible organizational system for their data and analysis.

Who should use ViNE?

Scientists who want an easy and simple way to organize their observations, data, tools, and experiments should use ViNE. ViNE also has some nice features for those who wish to share information across the web.

How does ViNE work?

ViNE uses web technology to provide a consistent interface that can be accessed anywhere. Once a scientist has a notebook in ViNE, they can login and be presented with a list of notebooks that they have permission to access, including their own. From here they can look at other notebooks for ideas and information, or begin working in their own notebook.

What platforms does ViNE run on?

The ViNE interface is made up of web pages and can be viewed on all platforms - Unix, Mac, and PC - without any modifications. The interface can run (inside a browser) on a machine outside the ViNE system, and the scientist can still access and interact with the environment across the web in the same way they would if they were on a machine that was part of the system. This gives the scientist a great deal of freedom in where and how they access ViNE.

The underlying implementation will run on any system that is running a web server, Perl 5, and Expect with little or no modifications. In addition, some parts of ViNE are Java enhanced and will run on Java compatible platforms. ViNE's interface is platform independent and the back-end is extremely easy to port.

What databases does ViNE work with?

At this time, ViNE works mostly with data stored in files; no default database is used. However, a database could be added to the backend of ViNE with some minor additions for ViNE to communicate with the database interface. ViNE does not have any inherent traits that would make it impossible to work with most common database tools. Once the communication interface between ViNE and the database has been created, the database should work smoothly in the environment

What kind of tools can be used?

Any type of tool that has a command line interface works with ViNE without any modification. Other tools with input file interfaces will need to be "wrapped" in order for ViNE to interact directly with them. Finally, tools that only have graphical interfaces can not be used in ViNE at this time, except in a standalone manner. We are looking at ways to incorporate graphical interfaces in browsers.

What is an experiment?

An experiment consists of one or more tools acting on one or more data sets. The scientist describes the flow of the experiment in ViNE's graphical experiment sequencer by connecting tools and data together. Once the experiment has been described, it can be stored and executed. The scientist can monitor the experiment as it is running to find out its current status. After the experiment has finished, the output data is displayed, and the scientist is given the option to save the data in their notebook.

Is ViNE Secure?

Yes, ViNE insures the security of notebooks and the data they contain. All users that login to the system are given a cookie that identifies them. Without this identification, the user is not allowed to browse any notebooks or areas of ViNE. Cookies are checked frequently to guarantee that users only access the pages they are permitted to.

Scientists have control over who can look at their data and results. They can choose to have a completely secure notebook where no one is allowed to browse through their information, or give notebook access to specified individuals that may also be involved in similar work. Also, they can change or view this information at any time from within their notebook.

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