ByoDyn / News: Recent posts

ByoDyn 5.12 release

We are pleased to announce a new release of ByoDyn. The main improvements are the migration to libSBML 4.0.0, an introduction of a small software comparison, fix on a sensitivity calculation bug, implementation of parallel calculations for hybridOnePhase algorithm (our most efficient) and lots of minor bugs fixed.

For the complete list of improvements, please consult the release notes.

In a few days our server ByoDynWeb, http://byodyn.imim.es will be updated to the new version of ByoDyn.... read more

Posted by Adrián López García de Lomana 2009-09-09

ByoDyn 5.11 release

We are pleased to announce a new release of ByoDyn. The main improvements are the implementation of Monte Carlo sampling, clustering and Principal Component Analysis. All routines have been checked, and documented at the user reference manual, tutorial and quick start guide.

More over many bugs have been fixed.

Finally, we would like to say that the current version is in our server, http://byodyn.imim.es. ... read more

Posted by Adrián López García de Lomana 2009-05-29

ByoDyn 5.6

A new release of ByoDyn is ready to download. The main improvements are the error handling of different simulators and many other bugs related to SBML compatibility. Please refer to the RELEASE_HISTORY file for more details. ByoDyn release 5.6 is currently the version of the server, http://byodyn.imim.es. Enjoy it !

Posted by Adrián López García de Lomana 2009-03-23

ByoDynWeb 1.1

In two weeks from our launch of the code of ByoDynWeb we have mainly polished some minor details and we have fixed some bugs:

(1) Fixed bug: The model associated to isomerisation runner in quick start was incorrect.
(2) Fixed bug: The online option for calculations was not executing correctly.
(3) Displayed names for the running environments improved.

The new version is the current one of the server and we provide here the code. Enjoy it!

Posted by Adrián López García de Lomana 2009-03-20

ByoDynWeb code available

We have released now a new package called ByoDynWeb which represents the source code for the server. For the next releases we are working on the documentation of the package, specially a guide for the installation.

Posted by Adrián López García de Lomana 2009-03-14

Release 5.3

A new release of ByoDyn is ready to download. The main improvements are more intuitive and useful figures of optimal experimental design and many bugs were cleaned. Please refer to the RELEASE_HISTORY file for more details. ByoDyn release 5.3 is currently the version of the server, http://byodyn.imim.es.

Enjoy it !

Posted by Adrián López García de Lomana 2009-03-08

Release 5.0

We are proud to announce a new stable release of ByoDyn. Many bugs have been cleaned, please check the RELEASE_HISTORY for further information. More over the structure of the output directory has changed for more easy retrieval of the results. Many other aesthetic issues have been improved.

Finally we invite all users to try our server with full capabilities:
http://byodyn.imim.es/

Posted by Adrián López García de Lomana 2008-12-23

Release 4.8

A new stable release has been delivered. The main new feature is the support for stochastic simulations. Additionally, many bugs have been fixed. Please have a look to the release notes for further information.

Posted by Adrián López García de Lomana 2008-12-17

Minor error corrected at ByoDyn 4.6 release

Thanks to Àlex, a bug has been detected at ByoDyn release 4.6. The error handling was commented. From today on, the line has been fixed and the error handling is done properly. Sorry for the inconveniences.

Posted by Adrián López García de Lomana 2008-12-03

Release 4.6

A new stable release has been delivered. A lot of bugs have been fixed. Please have a look to the release notes for further information.

Posted by Adrián López García de Lomana 2008-11-25

New Release 4.1

A new stable release has been delivered. Main improvements have been the fix of several bugs and the incorporation of png as possible output format of figures.

Posted by Adrián López García de Lomana 2008-06-19

New Release 4.0

We are pleased to announce the release of ByoDyn version 4.0.

ByoDyn version 4.0 represents a stable code version with thorough and precise documentation about the different functionalities of ByoDyn, which are exporting, simulation, optimisation, fitness function calculation, trajectory reconstruction, fitness score surface calculation, sensitivity analysis, identifiability analysis and optimal experimental design. ... read more

Posted by Adrián López García de Lomana 2008-06-09

Documentation identifiability completed

The documentation for identifiability analysis has been completed. It can be found at the CVS.

Posted by Adrián López García de Lomana 2008-06-02

New Release 3.20

ByoDyn version 3.20 has been released. More documentation has been added. Mainly, the documentation for simulation, sensitivityAnalysis and optimization has been updated. Also a major bug on sensitivity analysis has been cleaned out.

Posted by Adrián López García de Lomana 2008-05-13

Parameter Estimation Documentation Completed

The user reference manual compiles the complete documentation for the parameter estimation functionality.

Posted by Adrián López García de Lomana 2008-05-01

Simulation Documentation Completed

The userReferenceManual document contains already detailed descriptions about how to run a simulation using ByoDyn. Different simulation engines are available, SciPy (http://www.scipy.org/), Octave (http://www.gnu.org/software/octave/), Open Modelica (http://www.ida.liu.se/labs/pelab/modelica/OpenModelica.html) and XPPAUT (http://www.math.pitt.edu/~bard/xpp/xpp.html) among others. Moreover we present a table with the SBML (http://www.sbml.org/Main_Page) features supported and the simulation engine that handles them.

Posted by Adrián López García de Lomana 2008-04-01

New Release 3.18

ByoDyn version 3.18 has been released. More documentation has been added. Mainly, the affectors used for the model of LNCS paper has been added. Also the dynamicsReconstruction functionality has been documented.

Posted by Adrián López García de Lomana 2008-03-25

PORT from Netlib from now on

We were using PORT3 library for the local search optimizations, but the link for the source code is broken. We will use from now on PORT library from Netlib.

Posted by Adrián López García de Lomana 2007-12-14

Quick Start Guide and Tutorial Completed

A document consisting on a quick start guide about the functionalities of ByoDyn and a tutorial about some key models has been completed and is available from the CVS server.

Posted by Adrián López García de Lomana 2007-10-30

API Completed

The API for the complete set of functions has been established.

Posted by Adrián López García de Lomana 2007-10-25

New release 3.12

ByoDyn version 3.12 has been released. We highlight some of the new features:

(1) Parallel implementation is finished for the optimization.
(2) Model integration using OpenModelica.
(3) Support for SBML Events and Rules.
(4) Support for identifiability analysis.

Posted by Adrián López García de Lomana 2007-09-18

Installation Guide Available

The installation guide for ByoDyn version 4.0 is ready for users.

Posted by Adrián López García de Lomana 2007-07-25

CVS move completed successfully

From now ever the sources of ByoDyn will be hosted at the CVS repository of the SourceForge.net, not anymore at the developer's machines.

Posted by Adrián López García de Lomana 2007-06-29

CVS up

Today has started the cvs of the project. The code will be uploaded soon and it will be the working repository.

Posted by Adrián López García de Lomana 2007-06-28

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