Last updated August 12, 2009.

About the document

This document is a user manual for the Boltzmann Likelihood software written by Mirela Andronescu.


1. Introduction to BL

Boltzmann Likelihood (BL) is a computational approach to RNA free energy parameter estimation. It maximizes the conditional likelihood of the known structures in a set of RNA sequences with known secondary structures used for training. This algorithm is similar to the CONTRAfold algorithm (Do et al, 2006).

2. Copyright and disclaimer


The BL algorithm and code is copyrighted under GNU General Public Licence by Mirela Andronescu, Anne Condon and Holger Hoos, Department of Computer Science, University of British Columbia.


Although the authors have made every effort to ensure that BL correctly implements the underlying models and fullfills the functions described in the documentation, neither the authors nor the University of British Columbia guarantee its correctness, fitness for a particular purpose, or future availability.

3. Using BL 

BL uses the IPOPT non-linear optimizer. In order to run BL with IPOPT, you have to have the following packages:
To run BL, type:
        bin/ config/config_example.txt

This will create a directory with a complicated name in results.

4. Troubleshooting

Please let know andrones at cs dot ubc dot ca if you have problems running BL.

5. History

6. References

Please cite one of the above if you use BL in your work.
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