 Future
Plans for BioEditor
As
we developing BioEditor, we are attempting to make the tool
as intuitive and user-friendly as possible, all the while
retaining powerful features that will appeal to researchers
in areas like bioinformatics, crystallography and structural
genomics, educators at the high school, undergraduate and
graduate levels, and students at those levels as well. We
are planning to address the following issues as we develop
BioEditor:
One
of the challenges in designing this software tool is to incorporate a wide variety
of features, yet make the interface comfortable and familiar to first-time users,
so that the learning curve for BioEditor is not too steep. After some discussion,
we are converting some of the drop-down menus to reflect the traditional menus
that are found in common software products in the Wintel and Mcintosh environments.
The latest versions of the menus are shown here.
|  File
In
addition to traditional menu options (New, Open, etc.) BioEditor will eventually
be able to import files in three different formats and publish the output for
viewing on a web browser or "read-only" version of BioEditor. return
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|
|  Edit
Standard
Edit commands are avaiable in BioEditor and apply differently to the different
BioEditor windows (text, graphics, structure, molecular view). In addition, the
Edit menu has the ability to introduce or remove hyperlinks in the document. |
| |
 View
From
the View menu, the user can choose to view the current document in a web browser,
or to add all the different types of information that BioEditor uses as a new
item in the Folder window. return
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|  Format
The format menu reflects
the fact that BioEditor works with HTML - the options in this menu are the most
commonly used HTML format commands. |
| |  Insert
This
menu enables the user to insert features in a BioEditor text document, including
any unusual symbols or fonts that are avaiable on your system. return
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|  Window
This standard menu item
will be enhanced in the future to enable the user to look at any window that is
currently open in the BioEditor interface. |
| |  Help
One
major future goal is to build effective help files for the use of BioEditor. return
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also include two drop down menus that provide access to the unique features of
BioEditor.
|  Structure
This
menu provides access to a number of web sites that are commonly used for accessing
structural details from the Internet. In addition, this menu is directly connected
to Chime graphics window, either freestanding in BioEditor, or within a text document. return
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|
|  Sequence
This
menu provides direct links to some of the most commonly used bioinformatics tools
for sequence analysis. Clicking on a menu item connects to a WWW site through
a browser window within BioEditor. return
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|
Mouse
FunctionalityCurrently
only the left mouse button is functional in most areas of BioEditor. We plan to
introduce right mouse button functionality soon, with intuitive menus (e.g., copy,
cut, paste when in a text window). In molecular visualization windows (based on
MDLI's Chime), the right mouse button functions as expected in a Chime window.
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|
GraphicsBioEditor
can import and display graphics in three formats: *.gif, *.jpg and *.bmp. Future
editions will also be able to work with *.tiff files, as well as postscript and
*.pdf output that is commonly encountered in many bioinformatics web sites. return
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|
Sequence
Manipulation and DisplayThe
current version of BioEditor is able to manipulate and display sequence data in
a FASTA format. Any more detailed displays must be prepared as graphics (*.gif,
*.jpg, *.bmp). In the future we plan to introduce some simple alignment tools
so that multiple alignments from sources such as ClustalW can be manually manipulated
to improve the alignment. return
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Visualization
InterfaceMolecular
visualization is a very critical part of structural communication. This is often
done through web pages that are built around a very powerful tool call Chime
(MDL Information Systems, San Leandro, CA), which in turn was developed from Rasmol.
There are marvelous resources on the WWW for chime structures, including Eric
Martz's sites at the University of Massachusetts. We
have two concerns about working with Chime. The first is that it is a browser-dependent
plug-in. As such it is subject to the whims of the browser providers. Currently
it is supported by Netscape 4.7x, but not Netscape >6; Chime has never been
completely supported by Internet Explorer and the generous folks at MDL Information
Systems are scrambling to keep up with these developments. The current version
of BioEditor fully supports Chime visualization. As a stand-alone Windows application,
it is not dependent on Netscape or Microsoft for browser support. Our
second concern is with Chime itself. While this is a very powerful program, it
has a very limited Application Program Interface (API) for developers and the
source code is not available. It is in the best interests of structural biologists
that we are independent of commercial software developers and browser distributors.
Therefore, we believe that a new visualization interface should be developed with
a robust API and open source code, and we are looking into this possibility. return
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