Learn MP-GeneticSynth step by step

Step 1. Download MetaPlab-1.3 with MP-GeneticSynth from here (Java JRE 6u45 or later required).

Step 2. Read the Quick Start Guide to learn how to run MP-GeneticSynth.

Step 3. Watch the MP-GeneticSynth Video 1 and MP-GeneticSynth Video 2 to learn how to generate new experiments and to analyse them.

Step 4. Read the Mitotic Case Study Tutorial to test each functionality.

Step 5. Consult the Main Guide to get advanced information.

Step 6. Refer to the Javadoc to learn how the code is implemented.

Models
Download Mitotic oscillator. Mitotic oscillator in early amphibian embryos. This MP model derives from the differential model proposed in 1991 by Goldbeter (reference).
Download Noisy mitotic oscillator. Mitotic oscillator with noisy time series.
Download Predator-prey. Lodka-Volterra model for predator-prey systems (reference).
Download Chaotic logistic map (r=3.9). Synthetic model of the chaotic logistic map. Proposed by May in 1976 and published in Nature (reference) this is a very complex dynamics from which MP-GeneticSynth manages to infer regulation mechanisms.
Download Vega. Synthetic model proposed by Manca (reference) having a complex oscillatory dynamics from that MP-GeneticSynth manages to infer regulation mechanisms.
Experiments and case studies
Download Mitotic oscillator. Test experiments about the mitotic oscillator in early amphibian embryos proposed in 1991 by Goldbeter.
Download Noisy mitotic oscillator. Test experiments about the noisy mitotic oscillator.
Download Predator-prey. Test experiments about the Lodka-Volterra model for predator-prey systems.
Download Chaotic logistic map. Test experiments about the chaotic logistic map proposed by Robert May in 1976.
Download Vega. Test experiments about the Vega model proposed by Vincenzo Manca.
Downloads
Download MetaPlab-1.3 with MP-GeneticSynth. The quickest way to get started with MP-GeneticSynth (Java JRE 6u45 or later required).
Download MP-GeneticSynth source code. NetBeans projects containing the source code of the plugin.
Documentation
Download Quick Start Guide. A quick guide for installing and running MP-GeneticSynth, with references to all other resources (docs, models, exps).
Play MP-GeneticSynth Video 1 A step-by-step video tutorial that explains how generate new experiments by MP-GeneticSynth.
Play MP-GeneticSynth Video 2 A step-by-step video tutorial that explains how to analyse MP-GeneticSynth experiments by the ExpAnalyzer.
Download Mitotic Case Study Tutorial. A step-by-step tutorial that explains how to use MP-GeneticSynth to generate and analyze regulation functions for the case study of the mitotic oscillator in early amphibian embryos.
Download Main Guide. It explains all functionalities and graphical interface elements (buttons, charts, etc.). Moreover, it reports installation procedures and references to other documentation documents.
Download Javadoc. API documentation of MP-GeneticSynth code. All packages, classes and methods are explained.
Selected publications
Download Castellini,A., Zucchelli,M., Busato,M., Manca, V. (2013) From time series to biological network regulations: an evolutionary approach, Molecular BioSystems , 9(2), 225-233.
Download Castellini,A., Manca,V., Zucchelli,M. (2012) Towards an evolutionary procedure for reverse-engineering biological networks. In C. A. Coello Coello et al, editor, Artificial Immune Systems - 11th International Conference, ICARIS 2012, LNCS 7597, pages 271-285. Springer.
Download Manca,V. (2013) Infobiotics: information in biotic systems, Springer.
Download Castellini,A., Franco,G., Pagliarini,R. (2011) Data analysis pipeline from laboratory to MP models. Natural Computing 10(1): 55-76.
Download Castellini,A., Manca,V. (2009) MetaPlab: A computational framework for metabolic P systems, LNCS, 5391, 157-168, Springer-Verlag.