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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