geppettoengine

[geppettoengine]

Geppetto 1.0.0 alpha release

New in release 1.0.0-alpha:

Geppetto client factoring out. The web application was split out from the Java backend allowing Geppetto to be used also on other backends. (@rodriguez-facundo )

Initial support for FlexLayout (@ddelpiano)

Refactor Geppetto Demo application to use React declarative instantiation (@ddelpiano)

New menu component (@ddelpiano)

Javascript codebase linting (@rodriguez-facundo)

Typescript support (@ddelpiano)

Volatile simulations support (@jrmartin)

Canvas bug fixes (@jrmartin, @ddelpiano, @Robbie1977)

[geppettoengine]

Geppetto 0.3.6 release

Hello science lovers,

Since the last time we last updated the blog releases 0.3.5 and 0.3.6 went out with some great improvements, as always let’s have a look at what’s new :)

The biggest change has to do with persisting the state of the workspace between sessions. This means that when you reopen your browser you will find all the widgets that you used as you left them. Their state is saved either in the browser local storage or in the database associated to your account if the Geppetto deployment you are using has one.

In Release 0.3.6 we factored out the 3D Canvas to its own component enabling Geppetto to instantiate multiple canvases to visualise different models at the same time.

We added the ability to run experiments in batches, allowing therefore to easily use Geppetto to run computational experiments varying one or many parameters in a programmatic way and comparing the simulation results.

Also by pressing c+click on any visual object inside a canvas it’s now possible to change the centre of rotation of the camera to be the centre of the selected object which makes it handy to explore the topology of complex networks.

A new widget was added to replay videos and audio files in Geppetto, extending the wide range of data types already supported

The NeuroML bundles have also been extended to expose calcium state variables plus the voltage and currents associated with each pulse generator or voltage clamp instance.

For the full list of changes you can check out the release notes.

We are now working on release 0.3.7 which will have some juicy additions like the ability to visualise MRI data and big images so stay tuned for that!

As a reminder we meet every two weeks on Google hangout, if you are currently using Geppetto or would like to find out more about it you are very welcome to join, all meetings are public, this is the link to join the call, every Tuesday at 4pm London Time, 8am Pacific time, 11am Eastern time, 8:30pm India Standard Time. 

A big thanks to all the contributors and groups that have made these releases of Geppetto possible.

Ciao,

Matteo

[geppettoengine]

Geppetto 0.3.4 has arrived. Enjoy!

Hello neuroscience lovers,

Geppetto 0.3.4 has been released this week but since we were busy adding features and didn’t have time to update the blog for release 0.3.3 in January let’s also have a look at what was new there.

The first thing you will probably notice visiting live.geppetto.org is our new plotting widget based on plot.ly. The new widget will allow you to zoom in to take a closer look at your data and to rescale and translate the axis.

The new widget gives you the ability to save your plots as SVG, PNG or JPG, as well as saving the raw data of what’s currently plotted to disk!

A beautiful stack viewer widget was also added and it’s currently used by the version 2.0 of Virtual Fly Brain which is entirely built on Geppetto. The widget gives you the ability to explore an image stack from multiple directions while keeping in synch with the 3D scene.

In this past releases we have also improved how we visualise neuronal connections making it possible, when the data is available, to point to the location of the synapses.

As part of release 0.3.4 we have now also an improved the control panel which makes it easier to visualise all the visual objects, state variables and parameters available in your model and let you perform relevant actions like plotting or setting the value of a parameter in a seamless way. The filter also provides a handy way to explore variables that might have been recorded in other experiments or even in other projects.

For further information on the rest of the features as always you can refer to the release notes. As part of release 0.3.5 we’ll also complete a first release of all the new features that will make it possible to use Geppetto with a Python backend using our own Jupyter Notebook extension, stay tuned!

Again a big thanks to our amazing contributors and as a reminder, if you would like to know more about how you can use Geppetto in your projects or if you would like to help us building it do get in touch!

A presto,

Matteo

[geppettoengine]

Geppetto 0.3.2 release

Geppetto 0.3.2 is finally here packed with many new features to help you on your data exploration and computational modelling adventures!

Of the many additions (check out the full list on the release notes, worth it!), a few major ones stand out:

Query functionality: a lot of work has gone into instrumenting both the frontend and the backend to let users query external datasources (SOLR, Neo4j, AberOWL). This means that data and models can be loaded on demand inside Geppetto after the frontend has previewed their content. Screenshots below show query building and query results displayed to the user while exploring the brain of the Drosophila Melanogaster. A big thanks to Virtual Fly Brain for supporting this work!

Jupiter notebook Geppetto extension (experimental): a jupiter notebook extension acts as Geppetto backend and lets you write your Python straight within Geppetto from an embedded Jupyter console and interact with the Geppetto environment. And guess what? The Javascript and the Python objects are kept in synch so it doesn’t matter where you change them from. This exciting development represents the foundation for a Python based computational playground for Geppetto. In the screenshot below the user interface was built through a sequence of Python commands. A big thanks to the NeuroSim Lab for supporting this work!

Node.js Geppetto backend (experimental): a new light-weight Geppetto backend to facilitate frontend development of widgets/components without having to install anything other than node. 

A big thanks to all who have contributed to this release with their sweat and blood - If you want to join us you can reach out to us via email or GitHub.

Till the next release!

- Geppetto Team

[geppettoengine]

Geppetto 0.3.1 released

Hi all, 

Notably, in this Geppetto release we introduced a lot of performance improvements and fine tunings, a fancy restyling of the connectivity widget and a brand new configurable form component (see screenshot below). 

On the tooling side of things we made available docker images to setup the Geppetto development environment ready to go with eclipse and all the plugins needed - we really hope this will make it even easier for people to contribute to Geppetto.

For detailed release notes see here.

As usual a big thanks to all contributors. If you would also like to contribute you can reach out to us via email or GitHub.

E allora?! :)

- Giovanni

[geppettoengine]

Geppetto 0.3.0 is out!

Hear hear, after many commits, PR and amazing contributions we have finally released a new version of Geppetto!

In this release we have added initial support for the Neurodata Without borders format. We are still doing some work to enable users to explore the entire content of the files and decide which sweep to load at runtime but through the new sample we added you can get a glimpse into how this is all going to work. A big thanks to Nitesh Thali and Rick Gerkin from Arizona State University for this work!

Thanks to Adrian Quintana and the Open Source Brain team Geppetto now also has support to run neuronal simulations using NEURON remotely on the San Diego Supercomputer Center.

Working closely with Robbie Court from Virtual Fly Brain we have started adding support to query remote data sources to load data and models at runtime. This is going to enable the use of Geppetto as a data exploration platform making it possible for the user to load and look at new data and models searching and querying for them directly from the browser.

For the rest of the release notes see here.

Again a big thanks to all our contributors and for the increase support from the academic community. If you would also like to contribute to Geppetto or have any question about our roadmap you can reach out to us via email or GitHub.

A presto,

Matteo

[geppettoengine]

Geppetto 0.2.8 was just released!

For this new version of Geppetto we have done our best to go above and beyond expectations with loads of improvements on stability, performance and usability.

We have rewritten entirely the Geppetto model abstraction using the Eclipse Modelling Framework and we have introduced concepts for types, instances and arrays enabling us to represent the complexity of biological data and models in its entirety.

We have introduced Lightspeed search, available pressing Ctrl+Space, as a way to browse and interact with anything which is inside a project, enabling context based actions that don’t require any Console interactions.

We’ll be releasing some video tutorials and improvements to the documentation to go through some of the details, in the meanwhile check the full release notes on our GitHub release page!

A presto!

[geppettoengine]

Geppetto 0.2.7 was just released

Hail to the units finally appearing also on the plots! 

To checkout the release visit our live demo!

For the full release notes check our GitHub release page.

[geppettoengine]

Installing Geppetto on Debian/Ubuntu Linux - Part 1

This post will provide some tips on installing Geppetto Sources on Debian/Ubuntu Linux. This guide should be treated as an addendum to the guide here: http://docs.geppetto.org/en/latest/osxlinuxsetup.html

1. The default directory to install Virgo Tomcat is /opt. Unpack virgo-tomcat-server-release to this directory.

2. Include the following files in .bashrc in your home directory: 

MVN_HOME=/usr/share/maven/bin export MVN_HOME JAVA_HOME=/usr/lib/jvm/java-1.7.0-openjdk-amd64 export JAVA_HOME export SERVER_HOME=/opt/virgo-tomcat-server-x.x.x.RELEASE

function virgo() {        bash $SERVER_HOME/bin/$1 }

If you are still running into key home errors when attempting to run export SERVER_HOME=/opt/virgo-tomcat-server-x.x.x-RELEASE

3. On Mac OS X you may need to generate a script to switch between different versions of Java. However, for Linux, you can also use the following command to switch between different versions of Geppetto:

sudo update-alternatives --config java

4. Before running mvn install, it is necessary to set permissions on the Virgo Server home directory. Run the following command:

sudo chmod 777 /opt/virgo-tomcat-server-x.x.x-RELEASE/*

5. Proceed to stopping and starting the virgo server. Note that virgo server runs on Port 8080, which is also the same Port that the tcp6 (ipversion 6) service for Linux runs on. To stop this service, run the following command:

sudo netstat -tulpn | grep '8080'

This should show all services running on Port 8080. Kill this service with the following command:

kill - ‘service_number’

[geppettoengine]

How do I install Virgo tooling plugin in Eclipse Luna?

Install Bundlor from the following update site.

Install Eclipse Virgo Utils Feature from the following update site.

Download this archive, unzip it and use it as a local update site in eclipse to install Eclipse Vigo Tools.

Restart your Eclipse, you will now be able to add a Virgo Runtime from Eclipse -> Preferences -> Runtime environments -> Add. 

Virgo Runtime will be inside the EclipseRT folder!

Enjoy!

[geppettoengine]

In the next release 0.2.7 of Geppetto exploring networks of cells will be easier than ever. Also we are now supporting multiple selection!

[geppettoengine]

Data from http://virtualflybrain.org

[geppettoengine]

Set Virgo Server Runtime

Once you have imported your Geppetto repositories from GitHub into Eclipse, you will still need to set your Virgo Server Runtime so all the errors will go away and you can start contributing to Geppetto.

From the Eclipse main menu, click on Preferences > Server > Server Runtime Environment and press Add. Then navigate to the directory where you installed Virgo Server previously (according to these instructions here: http://geppetto.readthedocs.org/en/latest/osxlinuxsetup.html).

Then you need to update Maven to update these changes. Right click one of your projects on the left hand side of Eclipse > Maven > Update Project. Then select the projects you wish to update (all of them most likely) and press Update. This will update the Eclipse project according to Maven settings.

Check the docs and follow this blog for more tips on how on to setup a development environment for Geppetto!