Multiscale Systems Biology Collaboration

Talks

• Ding Ma, Ken Judd, Dominique Orban and Michael Saunders (2019), Algorithm NCL for constrained optimization, 23rd International Symposium on Mathematical Programming Bordeaux, France, Jul 1-6, 2018.

• Ding Ma, Ken Judd, Dominique Orban and Michael Saunders (2018), Stabilized Optimization via an NCL Algorithm, 11th US-Mexico Workshop on Optimization and its Applications, Huatulco, Mexico, Jan 8-12, 2018.

• Michael Saunders, with Ron Estrin and Dominique Orban (2017), Error Bounds for CG via SYMMLQ, Householder Symposium XX, Jun 18-23, 2017.

• Michael Saunders, Large-scale linear algebra and its role in optimization, SIAM Conference on Optimization (OP17), Vancouver BC, Canada, May 22-25, 2017.

• Ding Ma and Michael Saunders, The DQQ procedure for multiscale optimization, International Conference on Continuous Optimization (ICCOPT 2016), Tokyo, Japan, Aug 6–11, 2016.

• Ding Ma and Michael Saunders, Experiments with linear and nonlinear optimization using Quad precision, INFORMS Annual Meeting 2014, San Francisco, CA, Nov 9–12, 2014.

• Ding Ma and Michael Saunders, Experiments with quad precision for iterative solvers, SIAM Conference on Optimization, San Diego, CA, May 19–22, 2014.

• Michael Saunders, Santiago Akle, Ding Ma, Yuekai Sun, Ronan Fleming, and Ines Thiele, Numerical linear algebra and optimization tools for bioinformatics, 2013 BMES Annual Meeting, Seattle, WA, Sep 25–28, 2013.

• M. A. Saunders, I. Thiele, R. M. T. Fleming, B. O. Palsson, Y. Ye, S. Akle, O. A. Dalal, J. A. Lerman, Y. Sun, and N. A. Taheri, Satisfying flux balance and mass-action kinetics in a network of biochemical reactions, DOE Genomic Science Awardee Meeting IX, Crystal City, VA, Apr 10–13, 2011.

• S. Akle, O. A. Dalal, R. M. T. Fleming, M. A. Saunders, N. A. Taheri, and Y. Ye, Existence of positive equilibria for mass conserving and mass-action biochemical reaction networks with a single terminal-linkage class, DOE Genomic Science Awardee Meeting IX, Crystal City, VA, Apr 10–13, 2011.

• R. M. T. Fleming, Stoichiometric modelling of biochemistry: A variational approach, Biomedical Engineering Department seminar, University of Texas at Dallas, Mar 11, 2011.

• R. M. T. Fleming, On optimality principles in nonequilibrium biochemical networks, 11th International Conference on Systems Biology, Edinburgh, Oct 2010.

• I. Thiele, Expanding genome-scale metabolic models, Workshop IOMPA, 11th International Conference on Systems Biology, Edinburgh, Oct 2010.

• R. M. T. Fleming, A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks, Para 2010: State of the Art in Scientific and Parallel Computing in Reykjavik, Jun 2010.