[Savannah-register-public] [task #5371] Submission of TaxonDNA

[Gaurav Vaidya]

URL:
  <http://savannah.nongnu.org/task/?func=detailitem&item_id=5371>

                 Summary: Submission of TaxonDNA
                 Project: Savannah Administration
            Submitted by: ggvaidya
            Submitted on: Sat 04/01/06 at 00:01
         Should Start On: Sat 04/01/06 at 00:00
   Should be Finished on: Tue 04/11/06 at 00:00
                Category: Project Approval
                Priority: 5 - Normal
                  Status: None
                 Privacy: Public
             Assigned to: None
        Percent Complete: 0%
             Open/Closed: Open
                  Effort: 0.00

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Details:

A new project has been registered at Savannah 
The project account will remain inactive until a site admin approve or
discard the registration.


######### REGISTRATION ADMINISTRATION #########

While this item will be useful to track the registration process, approving
or discarding the registration must be done using the specific "Group
Administration" page, accessible only to site administrators, effectively
logged as site administrators (superuser):

  <https://savannah.nongnu.org/admin/groupedit.php?group_id=8442>


######### REGISTRATION DETAILS ######### 

Full Name:
----------
  TaxonDNA

System Group Name:
-----------------
  taxondna

Type:
-----
  non-GNU software & documentation

License:
-------- 
  GNU General Public License V2 or later

Description:
------------
  TaxonDNA evolved as an undergraduate student project of mine (which I am
still maintaining for my lab at NUS: http://evolution.science.nus.edu.sg/).

I aim to create a simple biological sequence editor, allowing
bioinformaticians to open, edit, and export to many of the dozens of file
formats commonly used in bioinformatics. Additionally, I want to make it
extremely easy for programmers to write modules which can process the
sequences in some way. Thus, programmers who need to write a program to
perform some sort of data analysis on biological sequence data can just write
the algorithm, relying to TaxonDNA to provide them with a user interface, file
import/export functionality, functions for dealing with sequence data, and so
on.

TaxonDNA is currently at version 0.9.1 (although some urgent bugfixes will be
coming out shortly, bumping us to 0.9.1.1). It is being used in several
projects in my lab, and is thus going through a "beta" phase preparatory to
full 1.0 release (probably in June/July). While the interface needs
polishing, it is very usable and easy to work with. Some of the code needs
rewriting, but I am 80-90% ready for 1.0. 

TaxonDNA was written in Java, using the AWT. With two modifications not yet
in CVS, it can be compiled on Jikes using the Kaffe classes. However, some
parts of the code still need work to work around bugs Kaffe, and I still
haven't completely finished testing the code on Kaffe. However, complete
Jikes compatibility will be a goal for version 1.0, and complete Kaffe
compatibility for 2.0.

TaxonDNA is released under the GPL. The code can be viewed online on our
SourceForge archive, at http://cvs.sourceforge.net/viewcvs.py/taxondna/.

Other Software Required:
------------------------
  We use BrowserLauncher
[http://cvs.sourceforge.net/viewcvs.py/taxondna/TaxonDNA/Others/BrowserLauncher.java?view=markup],
which "may be redistributed or modified in any form without restrictions as
long as the portion of this comment from this paragraph [the license] through
the end of the comment is not removed" according to its license, which I take
to be a BSD-compatible license.

The current version of the program can (with two modifications) compile on
Jikes; however, while it works fine on GNU/Linux/JDK, it doesn't seem to work
completely in Kaffe. These bugs will be rectified by version 2.0 of the
software.

Other Comments:
---------------
  As you can see, all of our code is currently hosted on SourceForge. I was
pushed into looking for other hosting solutions due to very erratic CVS
access in the last few weeks, although I'm already very impressed by the
simplicity of the Savannah interface. Although I might continue to use sf.net
for the final distribution, I'd much prefer using Savannah for bug/task/cvs
and the website. The community also seems "tighter" here, allowing for more
collaboration (I hope!).








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