In early 2016 we plan to release as open-source our software for signaling pathway identification, developed in collaboration with the groups of Leonidas Alexopoulos at NTUA and of Julio Saez-Rodriguez.
The software implements the methods in the references below In parallel we are considering improvements and extensions of the formulations with our partners. In particular we aim to provide direct interfaces to cplex and gurobi as well as to the tools in.
If you are interested in using this software please feel free to contact us.
A. Mitsos, I. N. Melas, P. Siminelakis, A. D. Chairakaki, J. SaezRodriguez and L. G.
Alexopoulos. Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data. PLOS Computational Biology, 5(12):e1000591. 2009.
I. N. Melas (equal contributor), A. Mitsos (equal contributor), D. E. Messinis, T. Weiss, and L. G. Alexopoulos. Combined Logical and DataDriven Models for Linking Signaling Pathways to
Cellular Response. BMC Systems Biology, 5:107. 2011.
I. N. Melas (equal contributor), A. Mitsos (equal contributor), J. SaezRodriguez, Thomas Weiss, Dimitris E. Messinis, and Leonidas G. Alexopoulos. Construction of Large Signaling
Pathways using an Adaptive Perturbation Approach with Phosphoproteomic Data. Molecular BioSystems, 8(5):1571–1584. 2012.
A. Mitsos (equal contributor), I. N. Melas (equal contributor), M. K. Moris, J. SaezRodriguez, D. Lauffenburger, and L. G. Alexopoulos. Quantitative modeling of signal transduction pathways via a Non Linear Programming (NLP) formulation on phosphoproteomic data. PLOS One, 7. 11 2012.
I. N. Melas (equal contributor), A. D. Chairakaki (equal contributor), E. I. Chatzopoulou (equal contributor), D. E. Messinis, A. Mitsos, Z. Dailiana, P. Kolia, and L. G. Alexopoulos. Modeling signaling pathways in chondrocytes based on phosphoproteomic and cytokine release data. Osteoarthritis and Cartilage, 22(3):509–518. 2014.