June 8, 2004
Added three more mailing list archives to the links page. I find that
casual reading through these kinds of archives can be an enjoyable way of becoming familiar
with the history and issues surrounding molecular dynamics, computational biology and software development.
Warning: opinions about what is 'enjoyable' may vary.
June 4, 2004
The guide for writing Rbq-Lua unit tests has been
updated with information about 'tick' unit tests, a new kind of unit test needed for rbq-lua functions that
exhibit delayed behaviour. Because of infrastructure work, the completion of
unit tests is still only at 30%.
May 27, 2004
The Screenshots page has been updated with a table of thumbnail images
and additional screenshots.
May 23, 2004
A Links page has been added to the project web pages.
The progress of the Rbq-Lua unit
test development is now at 29.5%.
May 10, 2004
A calculation of percent completion of Rbq-Lua unit tests has been added to
the progress report.
Currently, 20% of the tests have been completed!
May 7, 2004
A guide for writing Rbq-Lua unit tests has been
added to the development page.
May 5, 2004
Another rbq-lua unit test has been added and the TestUtil.lua library has
been updated. Currently, there are a grand total of 4 unit tests. Hopefully,
as the test framework matures, the addition rate will increase.
May 2, 2004
A test driver file has been added for running the rbq-lua unit tests. The test
driver file can be run from a menu item in the 'Script', 'Other', 'Testing' menu.
At present, it successfully runs the single unit test that has been created, as
reported in the Rbq-Lua Unit Test Creation table.
May 1, 2004
The development page has been updated, with a better description of the near-term
goals, including creation of unit tests for the rbq-lua API.
April 29, 2004
A new file release
has been uploaded, ver 0.3.1. This is a quick fix of a bad
bug in the previous release, ver 0.1.13. Since the new release has
been built from the source code on the SourceForge CVS server, the
version has been bumped up to 0.3. In addition to the GNU/Linux port,
there is another near-term development goal: addition of
automated tests into the make and distribution process.
The exp and pdb supplementary project directories have been added to CVS
with module names 'exp' and 'pdb'. The pdb module is rather large in size
(~40 MB). It should not change very much in the future, typically, only
new files will be added to it.
April 28, 2004
The first commit of project source code to the SouceForge CVS server has been done. The 'bas' module is available for checkout.
This module contains the source code for the base functionality of the program. The pdb and
exp modules will be added in the near future.
To checkout the code, you can do the following:
cvs -z3 -d:pserver:firstname.lastname@example.org:/cvsroot/rbuilder co bas
For additional information on using CVS, refer to the excellent SourceForge documentation pages:
The immediate work will now focus on porting the current code to GNU/Linux, while keeping it functional
on the existing Win32 platform.
To track the porting progress, a table has
been created which lists all the modules in the program and the
completion dates for the modules that have been successfully ported.
April 27, 2004
Created a Development section on the project home page. This page documents
ongoing development work on the Ribosome Builder project.
April 24, 2004
Version 0.1.13, the first SourceForge release, has been uploaded.
It is available at the Files page.
The release consists of a full distribution (binary, source, documentation and experimental data files) in a self-extracting zip file for Win32 platforms.
There are also two zipped movie demo files (rather large). Online documentation and CVS files will be added soon.
April 21, 2004
The project is in the process of being moved to SourceForge! Until the move is
complete, you can access the current hosting site
at the University of Montana.
March 19, 2004
Version 0.1.12 has been released. Significant changes include addition of a force to restrict dynamic
models to a cubical volume, a script to add waters around a model, and a script to apply springs to
torsion angles. See the the download page for the complete list of changes for this version.
February 10, 2004
Version 0.1.11 has been released. Significant changes include a modification of the hydrogen
bonding function to improve bonding and a bug fix in the torsion potential to eliminate the
rotation drift that occurred for long sims. There have also been some additions to the rbd file format
to better support loading of dynamic models. See the the download page for the complete list of
changes for this version.
January 28, 2004
Version 0.1.10 has been released. A working version of the geometrical interpolation component of a
hypothetical initiation sequence has been added to the exp/dev/simpanel directory. See the
the download page for the complete list of changes for this version.
January 16, 2004
Created 'setup-rbofull-0.1.9.exe', a self-extracting executeable for the 0.1.9 distribution that includes
the core program, source code, pdb and exp components in a single package.
January 09, 2004
Version 0.1.9 has been released. The most significant changes include the creation of a script,
called 'thermal.lua', to add thermal input during folding, the option to create single-atom nodes
in dynamic models, and initial development of the exp/dev/simpanel project, which is intended to
provide building blocks for the construction of hypothetical sequences of movements of components
in the translation process. Refer to the download page for the complete list of changes.
December 15, 2003
A new version of the Experiments component has been released, version 0.1.9. In addition
a movie files download page as been added that has a movie of the wrapping of a 27
residue mRNA around the path of PDB model 1jgo chain 1.
December 8, 2003
Version 0.1.8 has been released. The main changes center around scripted input of forces
to the forcefield, which wasn't really working in the previous version. Also, in the
exp-0.1.8.zip distribution, an mRNA folding script was added in exp/dev/mrna/rkp.
November 25, 2003
Version 0.1.7 has been released. Support for dynamic modeling of proteins has been added.
However, this is in a very preliminary state and will need further testing
and development. Also, a demo of translation initiation has been added to the 'Script', 'Demos' menu.
October 27, 2003
Version 0.1.6 has been released. The most significant addition is a custom force container that attempts
to enable more rapid simulations by specifying a subset of the dynamic residues as static and skips
intra-group force calculations for those residues.
October 22, 2003
Version 0.1.5 has been released. This release attempts to fix the contraction observed in a-form
RNA helix simulations by increasing the van der waals radii by a factor of 1.2 (for non-torsion
steric interactions). Also, the implementation of electrostatic interactions has been changed from
non-bonded electron pairs of hydrogen bond acceptors to specific charged atoms - currently, the
phosphate oxygens O1P and O2P. In addition, the valence configuration of O2P has been changed
from sp3 to sp2, resulting in a reduction of the number of nodes in a dynamic residue. This
has the unfortunate side-effect of causing movies recorded in prior versions of the program
to be incompatible with this version. Since the program is still at an early stage of development,
this should not be much of a problem. Finally, support for positively-charged counter-ions has
been added. Also, a link to the molecular modeling forum on the lab homepage has been created
so that any current users of this program can post questions and feedback there.
October 17, 2003
Version 0.1.4 has been released. This release includes an important security fix for the web browser
interface and support for scripted input of forces. Also, the web page has been redesigned. Coming
soon: modeling metal ions.