CellNetOptimizer (CellNOpt, also known as CNO) was originally a matlab toolbox for creating logic-based models of signal transduction networks, and training them against high-throughput biochemical data using various logic formalisms. The development of CellNOpt is now mostly around the R version (see www.cellnopt.org), but you can download the version 2.1 in the page download page.
Q2LM: Querying Quantitative Logic Models
Q2LM is a MATLAB library that uses constrained fuzzy logic models based on prior knowledge networks to address two questions about a biological system: (i) What perturbation results in a specified downstream effect?; (ii) In what environments do those perturbations produce that effect?.
Q2LM is a tool developed by Melody Morris and Doug Lauffenburger. © Copyright 2011,2012 Massachusetts Institute of Technology. You can download the version 2.1 in the page download page.
- For the CellNOpt MATLAB toolbox:
M. K. Morris, I. Melas, J. Saez-Rodriguez. Construction of cell type-specific logic models of signaling networks using CellNetOptimizer. to appear in Methods in Molecular Biology:Computational Toxicology, Ed. B. Reisfeld and A. Mayeno, Humana Press. Preprint
- For the Q2LM toolbox:
M. K. Morris, Z. Shriver, R. Sasisekharan, D. A. Lauffenburger. 2012.
Querying quantitative logic models (Q2LM) to study intracellular signaling networks and cell-cytokine interactions.
Biotech. J. 7.
CellNOpt and Q2LM are free software: you can redistribute them and/or modify it under the terms of the GNU General Public License version 2 as published by the Free Software Foundation. Q2LM is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License at http://www.gnu.org/licenses/old-licenses/gpl-2.0.html for more details