libRoadRunner - A high performance SBML JIT compiler and simulation library.
For details, see http://www.libroadrunner.org
LibRoadRunner is brought to you by
E. T. Somogyi 1, M. Swat 1, and H. M Sauro 2 and J. A. Glazier 1
1 Biocomplexity Institute, Indiana University, Simon Hall MSB1, Bloomington, IN 47405
2 Department of Bioengineering, University of Washington, Seattle, WA, 98195
Files
-----
This directory contains a number of files, the files starting with pylibroadrunner
contain the python distutils based package installer, and the ones starting with
cpp contain the c++ libraries, header files, and command line programs.
Acknowledgements
----------------
This work is funded by NIGMS grant: GM081070
Licence
Licensed under the Apache License, Version 2.0 (the License); you may not use this
file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
News
----
-- Version 1.2.1
* Added models and data files from the Discrete Stochastic Models Test Suite,
https://code.google.com/p/dsmts/
to the roadrunner.testing package.
* New function in the roadrunner.testing package to enumerate testing data files.
* Clean up of SBML warning messages (thanks Lucian)
* Fixed major bug with how absolute and relative tolerances are handled (major thanks to Matthias
Koenig)
* Added support for reading values of reaction rates inside the model (identified by Matthias)
* Event status is not available as a selection, i.e. r.model["my_event_id"] will return 1 or -1
depending on whether or not the event is triggered.
* The plot method no longer tries to parse labels from SBML ids as LaTeX.
* made structuredResult behavior backward compatible (some users like the structured result).
* major revamp of the Python simulate method, it now accepts a variety of positional and named
arguments.
* fix bug when compiling with clang3.4 in c++ 11 mode (identified by Andrew Millspaugh)
* Gillespie integrator now supports fixed and variable time step mode.
* Variable time step mode fixes with deterministic solver.
-- Version 1.2.0
* Enabled mutable initial conditions when conserved moities are used, implemented Jacobian
calculation when conserved moieties are used.
* Fixed memory leaks related to how CVODE is used. With the mem leaks fixed, we leak a total of 16
bytes ONCE, in a 3rd party library in the beginning for running the entire test suite.
* Fixed bugs with stiff solver not being selected
* New getValue / setValue methods on SimulationOptions to set arbitrary settings, will be used by
future integrators.
* Prototype Gillespie stochastic integrator
* Added missing init amount method to python API
* Clean up IL code generation
* Structured result disabled by default
* New parameters in simulate and plot methods (Herbert has these, waiting on feedback),
simulate now accepts all SimulateOptions field names as keywords and has plot option,
i.e. simulate(plot=True)
* Raise exception on invalid selection strings
* Removed pointless bool return value on exception raising methods.
* All instance variables in public classes moved to private internal struct -- result is that we
can now add and remove instance variables and never break binary compatibility. Relevant to C++
users.
* Future versions may accept more complex types for configuration settings, API is set up so we
never break binary compatibility as we add new features like this.
* Continuous documentation updates and enhancements.
-- Version 1.1.0
* Config system. RoadRunner can now read and write most default configuration parameters
from / to a config file
* fixed memory leak in moiety conservation converter
* new colored logging
* Can read SBML files through HTTP on all platforms. The RoadRunner constructor
or load methods are smart in that accept a string which can be either:
a: the contents of a SBML document
b: a local file path, i.e. /home/andy/feedback.xml
c: a full URI identifier that can be either a local file or a remote file,
this can even be a BioModels identifier, i.e.
r=roadrunner.RoadRunner("http://www.ebi.ac.uk/biomodels-main/download?mid=BIOMD0000000275")
* upgraded to standard Poco 1.5 distribution. RoadRunner's Poco is now linked
directly to the official Poco git repository.
* lots of integrator tuning parameters are now accessible via the SimulateOptions object.
* Can run the integrator in new MULTI_STEP mode where the integrator determines
time step size.
* New SBML events -- users can register listeners for any SBML event. Whenever a
SBML event is triggered or assigned, the user can be notified.
* New integrator events -- users can register listeners for integrator events
such as when a time step completes or an event was detected.
* Significantly improved integrator error handling. Whenever CVODE encounters any
error such as numeric instability, the error is written directly to the Roadrunner
logging system with exact details about the error. Descriptive exceptions are
now raised detailing the exact source of the error.
* cleanup of integrator code.
* new distutils based python installation system. We now provide binaries for
32/64 bit Linux (Intel), 64 bit Mac OSX and 32 bit Windows.
-- Version 1.0.1
* Fixed bug where nested SBML functions were not handled properly. Now
it correctly reports when SBML functions are called with invalid
number of args.
* Fixed bug where where a log trace message incorrectly created.
* Display version info correctly in the command line rr program.
* Cache selection types and indices in model.getValue / setValue,
significant improvement in SBML symbol access times.
* Fixed memory leaks in Python API, performance improvements in
selections.
* New RoadRunner constructor which takes a URI and load options.
* Plugins moved to Tellurium project.
* Added getStateVectorRate and getStateVectorIds to ExecutableModel interface,
readily allows roadrunner to be used with external integrators.
* SBML variable access performance improvements.
-- Version 1.0.0
* Initial release
Download Latest Version
libroadrunner-1.0.0-src.tar.gz (26.0 MB)
