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Merge pull request #589 from openworm/development
Release 0.3.9
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‎README.md‎

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<p align="center">
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<img src="https://github.com/tarelli/bucket/blob/master/geppetto%20logo.png?raw=true" alt="Geppetto logo"/>
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<img src="https://raw.githubusercontent.com/tarelli/bucket/master/geppetto%20logo.png" alt="Geppetto logo"/>
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</p>
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# [Geppetto](http://www.geppetto.org/)
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[![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/openworm/org.geppetto?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
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[![Stories in Ready](https://badge.waffle.io/openworm/org.geppetto.png?label=ready&title=Ready)](https://waffle.io/openworm/org.geppetto)
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[![StackShare](http://img.shields.io/badge/tech-stack-0690fa.svg?style=flat)](http://stackshare.io/tarelli/geppetto)
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#### [Website](http://www.geppetto.org/) | [Documentation](http://docs.geppetto.org/) | [Releases](https://github.com/openworm/org.geppetto/releases/)
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#### [Contribution guidelines](http://docs.geppetto.org/en/latest/contribute.html#how-to-contribute-code-to-geppetto) | [Development progress](https://waffle.io/openworm/org.geppetto)
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**Geppetto is a web-based platform to visualise and simulate biological models.**
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**Geppetto is an open-source platform to build web-based applications to visualize and simulate neuroscience data and models.**
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Although Geppetto was designed with neuroscience and biology in mind, Geppetto can be used anywhere there is need to rely on a backend to perform any kind of simulation and allow the user to interact with it through a web application.
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**If you just want to play with a demo Geppetto deployment you don't need to install anything, just visit <https://live.geppetto.org>.**
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**If you just want to play with a sample Geppetto deployment you don't need to install anything, just visit <https://live.geppetto.org>.**
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If you want to setup your own Geppetto deployment from sources use our [Setup Instructions](http://docs.geppetto.org/en/latest/osxlinuxsetup.html). If you need help building a neuroscience application using Geppetto or if you want to join the project as a contributor you can [send an email](mailto:matteo@geppetto.org) or just interact with us through GitHub!
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If you want to setup your own Geppetto deployment from sources use our [Setup Instructions](http://docs.geppetto.org/en/latest/osxlinuxsetup.html). If you need help designing your own custom Geppetto deployment or want to join the project as a contributor you can [send an email](mailto:matteo@geppetto.org) or just interact with us through GitHub!
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This is the umbrella project that keeps together all the different modules currently available:
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This is the umbrella project that keeps together all the different Geppetto modules currently available:
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#### Java backend
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The Java backend is used in client-server deployments of Geppetto. The Java backend is modular allowing each deployment to be customised only with the relevant bundles.
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* [org.geppetto.persistence](https://github.com/openworm/org.geppetto.persistence) [![Build Status](https://travis-ci.org/openworm/org.geppetto.persistence.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.persistence)
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* [org.geppetto.datasources](https://github.com/openworm/org.geppetto.datasources) [![Build Status](https://travis-ci.org/openworm/org.geppetto.datasources.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.datasources)
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* Domain Specific
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* Neuroscience
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* [org.geppetto.model.neuroml](https://github.com/openworm/org.geppetto.model.neuroml) [![Build Status](https://travis-ci.org/openworm/org.geppetto.model.neuroml.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.model.neuroml)
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* [org.geppetto.simulator.external](https://github.com/openworm/org.geppetto.simulator.external) [![Build Status](https://travis-ci.org/openworm/org.geppetto.simulator.external.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.simulator.external)
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* [org.geppetto.model.swc](https://github.com/openworm/org.geppetto.model.swc) [![Build Status](https://travis-ci.org/openworm/org.geppetto.model.swc.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.model.swc)
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* [org.geppetto.model.nwb](https://github.com/openworm/org.geppetto.model.nwb) [![Build Status](https://travis-ci.org/openworm/org.geppetto.model.nwb.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.model.nwb)
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* Previous releases (not currently supported)
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* Neuroscience
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* [org.geppetto.simulator.jlems](https://github.com/openworm/org.geppetto.simulator.jlems) [![Build Status](https://travis-ci.org/openworm/org.geppetto.simulator.jlems.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.simulator.jlems)
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* Fluid mechanics
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* [org.geppetto.model.sph](https://github.com/openworm/org.geppetto.model.sph) [![Build Status](https://travis-ci.org/openworm/org.geppetto.model.sph.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.model.sph)
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* [org.geppetto.solver.sph](https://github.com/openworm/org.geppetto.solver.sph) [![Build Status](https://travis-ci.org/openworm/org.geppetto.solver.sph.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.solver.sph)
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* [org.geppetto.simulator.sph](https://github.com/openworm/org.geppetto.simulator.sph) [![Build Status](https://travis-ci.org/openworm/org.geppetto.simulator.sph.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.simulator.sph)
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#### Python Backend (prototype)
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* Neuroscience
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* [org.geppetto.model.neuroml](https://github.com/openworm/org.geppetto.model.neuroml) [![Build Status](https://travis-ci.org/openworm/org.geppetto.model.neuroml.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.model.neuroml)
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* [org.geppetto.simulator.external](https://github.com/openworm/org.geppetto.simulator.external) [![Build Status](https://travis-ci.org/openworm/org.geppetto.simulator.external.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.simulator.external)
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* [org.geppetto.model.swc](https://github.com/openworm/org.geppetto.model.swc) [![Build Status](https://travis-ci.org/openworm/org.geppetto.model.swc.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.model.swc)
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* [org.geppetto.model.nwb](https://github.com/openworm/org.geppetto.model.nwb) [![Build Status](https://travis-ci.org/openworm/org.geppetto.model.nwb.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.model.nwb)
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* Fluid mechanics (Currently in development)
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* [org.geppetto.sibernetic](https://github.com/openworm/org.geppetto.sibernetic) [![Build Status](https://travis-ci.org/openworm/org.geppetto.sibernetic.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.sibernetic)
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#### Python Backend (prototype, in development)
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The Python backend is based on a Geppetto Jupyter extension which allows the user to interact with the Geppetto frontend from Python. This deployment makes it ideal to use Geppetto as a visualization/computational local playground.
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* [org.geppetto.frontend.jupyter](https://github.com/openworm/org.geppetto.frontend.jupyter) [![Build Status](https://travis-ci.org/openworm/org.geppetto.frontend.jupyter.png?branch=master)](https://travis-ci.org/openworm/org.geppetto.frontend.jupyter)
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* [pyGeppetto](https://github.com/openworm/pygeppetto)
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Geppetto is released under the [MIT](http://opensource.org/licenses/MIT) license.
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<p align="center">
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<img src="http://www.geppetto.org/images/geppetto.png" alt="Geppetto"/>
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</p>

‎geppetto.plan‎

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http://www.springsource.org/schema/dm-server/plan/springsource-dm-server-plan.xsd">
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<artifact type="bundle" name="org.geppetto.model" version="0.3.8"/>
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<artifact type="bundle" name="org.geppetto.core" version="0.3.8"/>
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<artifact type="bundle" name="org.geppetto.model.neuroml" version="0.3.8"/>
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<artifact type="bundle" name="org.geppetto.simulation" version="0.3.8"/>
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<artifact type="bundle" name="org.geppetto.frontend" version="0.3.8"/>
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<artifact type="bundle" name="org.geppetto.model" version="0.3.9"/>
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<artifact type="bundle" name="org.geppetto.core" version="0.3.9"/>
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<artifact type="bundle" name="org.geppetto.model.neuroml" version="0.3.9"/>
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<artifact type="bundle" name="org.geppetto.simulation" version="0.3.9"/>
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<artifact type="bundle" name="org.geppetto.frontend" version="0.3.9"/>
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</plan>

‎pom.xml‎

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<groupId>org.geppetto</groupId>
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<artifactId>org.geppetto</artifactId>
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<name>Geppetto</name>
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<version>0.3.8</version>
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<version>0.3.9</version>
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<packaging>pom</packaging>
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<modules>
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<module>../org.geppetto.model</module>

‎utilities/docker/geppetto-persistence/Dockerfile‎

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ENV aKey=${aKey}
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ARG sKey
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ENV sKey=${sKey}
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ARG persistenceBranch=development
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ENV persistenceBranch=${persistenceBranch}
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ARG frontendBranch=development
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ENV frontendBranch=${frontendBranch}
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RUN echo "$frontendBranch";
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RUN echo "$persistenceBranch";
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ARG persistenceBranch
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ENV persistenceBranch=${persistenceBranch:-development}
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ARG frontendBranch
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ENV frontendBranch=${frontendBranch:-development}
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RUN echo $frontendBranch;
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RUN echo $persistenceBranch;
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RUN apt-get update && apt-get install -qq -y sudo
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#VIRGO INSTALL
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USER root
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RUN apt-get update && apt-get install -y -qq curl bsdtar
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RUN apt-get update && apt-get install -qq -y curl bsdtar locate
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USER developer
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RUN mkdir -p /home/developer/virgo
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RUN curl -L 'http://www.eclipse.org/downloads/download.php?file=/virgo/release/VP/3.6.4.RELEASE/virgo-tomcat-server-3.6.4.RELEASE.zip&mirror_id=580&r=1' | bsdtar --strip-components 1 -C /home/developer/virgo -xzf -
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ADD dmk.sh /home/developer/virgo/bin/
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USER root
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RUN chown developer /home/developer/virgo/bin/dmk.sh
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USER developer
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ENV SERVER_HOME /home/developer/virgo
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#VOLUME /home/developer/virgo
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RUN sudo chmod -R 777 workspace;

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