A detailed description of the format used to specify the benchmark problems: format.pdf.
Parser written in C for the benchmark problems: keywordReader.c
Gennemark and Wedelin, Benchmarks for identification of ordinary differential equations from time series data, Bioinformatics 25(6):780-6. This is the original publication presenting the collection of benchmark problems on this site.
Gennemark P. and Wedelin D. (2007) Efficient algorithms for ordinary differential equation
model identification of biological systems IET
Syst Biol. 1(2):120-9.
Submitted manuscript
and supplement.
This is the algorithm we have used to find solutions to the benchmark problems.
Gennemark, P. and Wedelin, D. 2009. Improved Parameter Estimation for Completely Observed Ordinary Differential Equations with Application to Biological Systems. In Computational methods in systems biology, LNCS 5688, 205-217. ISBN 978-3-642-03844-0. An improvement of the original parameter estimation, together with some new problems. arameter estimation problems are presented.
Dieck Kattas G., Gennemark P. and Wedelin D. 2010. Structural identification of GMA models: algorithm and model comparison. Proceedings of the 8th International Conference on Computational Methods in Systems Biology, 107-113. ISBN:978-1-4503-0068-1. An algorithm for identification of GMA models and related identification problems are presented.
Detailed references to each source system/model can be found via links in the benchmark problem table. A summary is also given below.
Cho,D.Y., Cho,K.H.,Zhang,B.T. (2006) Identification of biochemical networks by S-tree based genetic programming. Bioinformatics, 22, 1631-40. PMID:16585066 (Problems: ss_5genes6 and ss_sosrepair1)
Daisuke,T.,Horton,P. (2006) Inference of scale-free networks from gene expression time series. J Bioinform Comput Biol., 4, 503-14. PMID:16819798 (Problems: ss_5genes5 and ss_clock1 )
Gennemark,P.,Wedelin,D. (2007) Efficient algorithms for ordinary differential equation model identification of biological systems. IET Syst Biol., 1, 120-9. PMID:17441553 (Problems: metabol1, metabol2, metabol3, ss_5genes2 and ss_5genes3)
Gonzalez,O.R., Küper,C., Jung,K., Naval,P.C.Jr., Mendoza,E. (2007) Parameter estimation using Simulated Annealing for S-system models of biochemical networks. Bioinformatics, 23, 480-6. PMID:17038344 (Problems: ss_branch6 and ss_cadBA1)
Karnaukhov,A.V., Karnaukhova,E.V., Williamson,J.R. (2007) Numerical Matrices Method for nonlinear system identification and description of dynamics of biochemical reaction networks. Biophys J., 92, 3459-73. PMID:17350997 (Problem: osc2)
Kikuchi,S., Tominaga,D., Arita,M., Takahashi,K., Tomita,M. (2003) Dynamic modeling of genetic networks using genetic algorithm and S-system, Bioinformatics, 19, 643-50. PMID:12651723 (Problem: ss_5genes1)
Kimura,S., Ide,K., Kashihara,A., Kano,M., Hatakeyama,M., Masui,R., Nakagawa,N., Yokoyama,S., Kuramitsu,S., Konagaya,A. (2005) Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinformatics, 21, 1154-63. PMID:15514004 (Problems: ss_5genes4 and ss_30genes2)
Kutalik,Z., Tucker,W., Moulton,V. (2007) S-system parameter estimation for noisy metabolic profiles using newton-flow analysis. IET Syst Biol., 1, 174-80. PMID:17591176 (Problems: ss_branch4 aned ss_branch5)
Liu,P.K., Wang,F.S. (2008) Inference of biochemical network models in S-system using multiobjective optimization approach. Bioinformatics, 24, 1085-92. PMID:18321886 (Problems: ss_5genes8, ss_30genes3 and ss_ethanolferm1)
Marino,S., Voit,E.O. (2006) An automated procedure for the extraction of metabolic network information from time series data. J Bioinform Comput Biol., 4, 665-91. PMID:16960969 (Problem: ss_branch2)
McKinney,B.A., Crowe, J.E.Jr., Voss,H.U., Crooke,P.S., Barney,N., Moore,J.H. (2006) Hybrid grammar-based approach to nonlinear dynamical system identification from biological time series. Phys Rev E Stat Nonlin Soft Matter Phys., 73, (2 Pt 1). PMID:16605367 (Problems: simpleFb4 and cytokine1)
Moles,C.G., Mendes,P.,Banga,J.R. (2003) Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res., 13, 2467-74. PMID:14559783 (Problem 3genes1 inspired by this reference)
Tsai,K.Y., Wang,F.S. (2005) Evolutionary optimization with data collocation for reverse engineering of biological networks. Bioinformatics, 21, 1180-8. PMID:15513993 (Problems: ss_cascade1 and ss_5genes8)
Tucker,W.,Moulton,V. (2006) Parameter reconstruction for biochemical networks using interval analysis, Reliable Computing, 12, 389-402. http://www.springerlink.com/content/r5252637515v1qq3/ (Problems: ss_branch3 and ss_5genes7)
Voit,E.O.,Almeida,J. (2004) Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinformatics, 20, 1670-81. PMID:14988125 (Problem: ss_branch1)