Stable version of the HYBMOD toolbox for hybrid modeling
Demo file "Pichiademo" can be run to train a pichia hybrid model
Associated articles:
Pinto, J.; Ramos, J.R.C.; Costa, R.S.; Oliveira, R. Hybrid Deep Modeling of a GS115 (Mut+) (2023) Pichia pastoris Culture with State–Space Reduction. Fermentation 2023, 9, 643. https://doi.org/10.3390/fermentation9070643
Pinto, J.; Ramos, J.R.C.; Costa, R.S.; Oliveira, R. (2023) A General Hybrid Modeling Framework for Systems Biology Applications: Combining Mechanistic Knowledge with Deep Neural Networks under the SBML Standard. AI, 4, 303-318. https://doi.org/10.3390/ai4010014
José Pinto, Rafael S Costa, Leonardo Alexandre, João Ramos, Rui Oliveira (2023) SBML2HYB: a Python interface for SBML compatible hybrid modeling, Bioinformatics, Volume 39, Issue 1, January, btad044, https://doi.org/10.1093/bioinformatics/btad044
José Pinto, Mykaella Mestre, J. Ramos, Rafael S. Costa, Gerald Striedner, Rui Oliveira (2022) A general deep hybrid model for bioreactor systems: Combining first principles with deep neural networks, Computers & Chemical Engineering, Volume 165, 2022,107952, https://doi.org/10.1016/j.compchemeng.2022.107952
José Pinto, Cristiana Rodrigues de Azevedo, Rui Oliveira, Moritz von Stosch (2019) A bootstrap-aggregated hybrid semi-parametric modeling framework for bioprocess development, Bioprocess and biosystems engineering, 42(11), pp 1853-1865
Rui MC Portela, Moritz von Stosch, Rui Oliveira (2018) Hybrid semiparametric systems for quantitative sequence-activity modeling of synthetic biological parts, Synthetic Biology, 3 (1)
Rodolfo Marques, Moritz von Stosch, Rui MC Portela, Cristiana AV Torres, Sílvia Antunes, Filomena Freitas, Maria AM Reis, Rui Oliveira (2017) Hybrid modeling of microbial exopolysaccharide (EPS) production: The case of Enterobacter A47, Journal of biotechnology, pp 61-70
von Stosch, M, Oliveira, R, Peres, J, de Azevedo, SF (2013) Hybrid semi-parametric modeling in process systems engineering: Past, Present and Future, Comput Chem Eng, 60, pp 86-101
Moritz von Stosch, Jan‐Martijn Hamelink, Rui Oliveira (2016) Toward intensifying design of experiments in upstream bioprocess development: An industrial Escherichia coli feasibility study, Biotechnology progress, 32(5), pp 1343-1352
Ricardo, AR., Oliveira, R., Velizarov, S., Reis, MAM., Crespo, JG (2012) Hybrid modeling of counterion mass transfer in a membrane-supported biofilm reactor, Biochem Eng J, 62, pp 22-33
Von Stosch M, Davy S, Francois K, Galvanauskas V, Hamelink JM, Luebbert A, Mayer M, Oliveira R, O'Kennedy R, Rice P, Glassey J. (2014) Hybrid modeling for quality by design and PAT-benefits and challenges of applications in biopharmaceutical industry. Biotechnol J. 2014 Jun;9(6):719-26. doi: 10.1002/biot.201300385. Epub 2014 May 8. PMID: 24806479
Ferreira, AR, Dias, JML, von Stosch, M, Clemente, J, Cunha, AE, Oliveira, R (2013) Fast development of Pichia pastoris GS115 Mut+ cultures employing batch-to-batch control and hybrid semi-parametric modeling, Bioprocess Biosyst Eng, pp 1-11
von Stosch, M., Oliveira, R., Peres, J., de Azevedo, S.F. A novel identification method for hybrid (N)PLS dynamical systems with application to bioprocesses (2011), Expert Syst Appl, 38(9), pp 10862-10874
von Stosch, M., de Azevedo, S.F., Oliveira, R., Modelling biochemical networks with intrinsic time delays: a hybrid semi-parametric approach (2010), BMC Syst Biol, 4, art. no. 131
von Stosch, M, Oliveira, R., Peres, J., de Azevedo, S.F. A hybrid modeling framework for PAT: Application to Bordetella pertussis cultures (2012) Biotechnol Prog, 28(1), pp 284-91
Carinhas, N., Bernal, V., Teixeira, A.P., Carrondo, M.J.T., Alves, P.M., Oliveira, R. Hybrid metabolic flux analysis: combining stoichiometric and statistical constraints to model the formation of complex recombinant products (2011), BMC Syst Biol, 5, art. no. 34
Peres, J., Oliveira, R., de Azevedo, S.F. Bioprocess hybrid parametric/nonparametric modelling based on the concept of mixture of experts (2008) Biochem Eng J, 39 (1), pp. 190-206.
Teixeira, A.P., Alves, C., Alves, P.M., Carrondo, M.J.T., Oliveira, R. Hybrid elementary flux analysis/nonparametric modeling: Application for bioprocess control (2007) BMC Bioinformatics, 8, art. no. 30
Teixeira, A.P., Carinhas, N., Dias, J.M.L., Cruz, P., Alves, P.M., Carrondo, M.J.T., Oliveira, R. Hybrid semi-parametric mathematical systems: Bridging the gap between systems biology and process engineering (2007) J Biotechnol, 132 (4), pp. 418-425
Teixeira, A.P., Carinhas, N., Dias, J.M.L., Cruz, P., Alves, P.M., Carrondo, M.J.T., Oliveira, R. Hybrid semi-parametric mathematical systems: Bridging the gap between systems biology and process engineering (2007) J Biotechnol, 132 (4), pp. 418-425
Teixeira, A., Cunha, A.E., Clemente, J.J., Moreira, J.L., Cruz, H.J., Alves, P.M., Carrondo, M.J.T., Oliveira, R. Modelling and optimization of a recombinant BHK-21 cultivation process using hybrid grey-box systems (2005) J Biotechnol, 118 (3), pp. 290-303
Oliveira, R. Combining first principles modelling and artificial neural networks: A general framework (2004) Comput Chem Eng, 28 (5), pp. 755-766