diff --git a/README.md b/README.md new file mode 100644 index 0000000..266b7b8 --- /dev/null +++ b/README.md @@ -0,0 +1,90 @@ +# 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/](http://www.gnu.org/licenses/). + +--- + +## DISCLAIMER + +This is a lab development, intended for use only in experiments and not for full distribution. Familiarity with UNIX-like systems (Linux, Mac, etc.) command line operation is required for its use. An improved, more user-friendly version for this software is in development. + +--- + +## TOOL + +A Machine Learning Method for the Prediction of Receptor Activation in the Simulation of Synapses + +--- + +## AUTHORS + +- J. Montes +- E. Gomez +- A. Merchán-Pérez +- J. DeFelipe +- J. M. Peña + +--- + +## VERSION + +1.0 alpha (pre-release) + +--- + +## DESCRIPTION + +This is an implmentation of our machine-learning-based AMPA receptor activation prediction model. + +--- + +## SYSTEM REQUIREMENTS + +- UNIX-like command line environment (Linux, MacOS X or similar). Windows is not directly supported. This software could be executed in Windows using cygwin, or other tool capable of creating a Linux-like environment. +- Java 1.6 or higher. +- The R statistical tool ([http://www.r-project.org/](http://www.r-project.org/)). This is used during the curve-fitting process. Previous versions of this software used MATLAB for this task, but we have replaced it with R, which produces the same result with improved performance. In addition, R is free, like the rest of this program requirements. + +--- + +## COMPONENTS + +- **ML-AMPA.sh:** This is the main program file. It is a bash shell script that performs the basic curve prediction tasks. +- **AMPA.O_model_M5P.bin:** This is the machine-learning model. It has been previously trained using a synapse dataset including 1000 different synapse configurations. +- **weka.jar:** The machine learning library. +- **src and bin directories:** They contain the Java source code and binary files of the AMPA receptor activation prediction model. + +--- + +## CONFIGURATION + +Before using this software, it has to be properly configured. To do so, the ML-AMPA.sh file must be edited. More specifically, the R_HOME variable inside this script has to be correctly set to the system path where R is installed. Without R the program cannot perform the final curve-fitting stage of the AMPA receptor activation prediction. + +--- + +## USAGE + +To use this software, just change into the directory where the component files are and run the ML-AMPA.sh script. This script requires a set of 5 arguments to operate. These are the values of the synapse parameters: + +- **[AMPA]:** AMPA concentration, in molecules per square micron. +- **[T]:** Transporter concentration, in molecules per square micron. +- **Ls:** Synapse length, in nm. +- **Hc:** Synapse height, in nm. +- **E:** Side of total apposition length, relative factor to Ls + +For example, running the following command: + +$ ./ML-AMPA.sh 2000 1600 500 16 1.5 + +Would predict the AMPA receptor activation curve of a synapse with 2000 AMPA receptors per square micron, 1600 transporters per square micron, 500 nm of synaptic length, 16 nm of synaptic height and a total apposition length of 1.5 times Ls, that is 750 nm in total. + +Running this script will generate a csv file containing the predicted AMPA activation curve, sampled in 0.05 ms intervals. The results file is called result.csv. + +--- + +2025-07-09: Converted README to Markdown. \ No newline at end of file diff --git a/README.txt b/README.txt deleted file mode 100644 index 7a56eb8..0000000 --- a/README.txt +++ /dev/null @@ -1,127 +0,0 @@ -******************************************************************************* -* -* 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 . -* -******************************************************************************* - -DISCLAIMER: - -This is a lab development, intended for use only in experiments and not -for full distribution. Familiarity with UNIX-like systems (Linux, Mac, -etc.) command line operation is required for its use. An improved, more -user-friendly version fot his software is in development. - - -******************************************************************************* - -TOOL: - -A Machine Learning Method for the Prediction of Receptor Activation in the -Simulation of Synapses - -******************************************************************************* - -AUTHORS: - -- J. Montes -- E. Gomez -- A. Merchán-Perez -- J. DeFelipe -- J. M. Peña - -******************************************************************************* - -VERSION: - -1.0 alpha (pre-release) - -******************************************************************************* - -DESCRIPTION: - -This is an implmentation of our machine-learning-based AMPA receptor -activation prediction model. - -******************************************************************************* - -SYSTEM REQUIREMENTS: - -- UNIX-like command line environment (Linux, MacOS X or similar). - Windows is not directly supported. This software could be executed - in Windows using cygwin, or other tool capable of creating a - Linux-like environment. -- Java 1.6 or higher. -- The R statistical tool (http://www.r-project.org/). This is used during - the curve-fitting process. Previous verisons of this software used MATLAB - for this task, but we have replace it with R, which produces the same result - with improved performance. In adittion, R is free, like the rest of this - program requirements. - -******************************************************************************* - -COMPONENTS: - -- ML-AMPA.sh: This is the main program file. It is a bash - shell script that performs the basic curve prediction tasks. -- AMPA.O_model_M5P.bin: This is the machine-learning model. It has been - previously trained using a synapse dataset including 1000 different - synapse configurations. -- weka.jar: The machine learning libary. -- src and bin directories: They contain the Java sorice code and binary files - of the AMPA receptor activation prediction model. - -******************************************************************************* - -CONFIGURATION: - -Before using this software, it has to be properly configured. To do so, -the ML-AMPA.sh file must be edited. More specifically, the R_HOME variable -inside this script has to be correctly set to the system path where R is -installed. Without R the program cannot perform the final curve-fitting stage -of the AMPA receptor activation prediction. - -******************************************************************************* - -USAGE: - -To user this software, just change into the directory where the component files -are and run the ML-AMPA.sh script. This script requires a set of 5 arguments to -operate. These are the values of the synapse parameters: - -- [AMPA]: AMPA concentration, in molecues per square micron. -- [T] : Transporter concentration, in molecues per square micron. -- Ls : Synapse length, in nm. -- Hc : Synapse height, in nm. -- E : Side of total apposition lenght, relative factor to Ls - -Fo example, running the following command: - -$ ./ML-AMPA.sh 2000 1600 500 16 1.5 - -Would predict the AMPA receptor activation curve of a syanpse with 2000 AMPA -receptors per square micrion, 1600 transporters per square micron, 500 nm of -synaptic length, 16 nm of synaptic height and a total apposition lenght of 1.5 -times Ls, that is 750 nm in total. - -Running this script will generate a csv file containing the predicted AMPA -activation curve, sampled in 0.05 ms intervals. The results file is called -result.csv. - -******************************************************************************* -*******************************************************************************