A Method for Prediction of Receptor Activation in the Simulation of Synapses (Montes et al. 2013)

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Accession:150207
A machine-learning based method that can accurately predict relevant aspects of the behavior of synapses, such as the activation of synaptic receptors, at very low computational cost. The method is designed to learn patterns and general principles from previous Monte Carlo simulations and to predict synapse behavior from them. The resulting procedure is accurate, automatic and can predict synapse behavior under experimental conditions that are different to the ones used during the learning phase. Since our method efficiently reduces the computational costs, it is suitable for the simulation of the vast number of synapses that occur in the mammalian brain.
Reference:
1 . Montes J, Gomez E, Merchán-Pérez A, Defelipe J, Peña JM (2013) A machine learning method for the prediction of receptor activation in the simulation of synapses. PLoS One 8:e68888 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Synapse;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s): AMPA;
Gene(s):
Transmitter(s): Glutamate;
Simulation Environment: Java; R;
Model Concept(s): Simplified Models;
Implementer(s): Montes, Jesus [jmontes at cesvima.upm.es];
Search NeuronDB for information about:  AMPA; Glutamate;
#!/bin/bash
# *******************************************************************************
# *
# *  A Machine Learning Method for the Prediction of Receptor
# *  Activation in the Simulation of Synapses
# *  Copyright (C) 2013 J. Montes, E. Gomez, A. Merchan-Perez, J. DeFelipe,
# *                     J. M. Peña
# *
# *  This program is free software: you can redistribute it and/or modify
# *  it under the terms of the GNU Lesser General Public License as published
# *  by the Free Software Foundation, either version 3 of the License, or
# *  (at your option) any later version.
# *
# *  This program 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 Lesser General Public License for more details.
# *
# *  You should have received a copy of the GNU Lesser General Public License
# *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
# *
# *******************************************************************************

# CONFIGURATION VARS
# These must be properly for the program to work

# Directory path to the R instalation. This MUST be set prperly.
R_HOME=/opt/local/lib/R

# Directory path to the rJava extension. This can usually work with the default value.
RJAVA_PATH=${R_HOME}/library/rJava/jri/

# *******************************************************************************

if [ $# -lt 5 ]
then
    echo "use $0: <[AMPA]> <[T]> <Ls> <Hc> <E>"
    exit 1
fi

RJAVA_CLASSPATH=${RJAVA_PATH}/JRI.jar
export R_HOME

java -Djava.library.path=${RJAVA_PATH} -cp ./bin:./weka.jar:${RJAVA_CLASSPATH} Predictor AMPA.O_model_M5P_all.bin $1 $2 $3 $4 $5