An Eye to the World, an Eye to the Net
I’ve uploaded my last presentation at the CodeJam4 on slideshare. You can see it also below. (Maybe it doesn’t show up if you use a reader..)
The subject is the integration between Neuronvisio which hit the 0.5.0 release and sumatra.
[slideshare id=4665695&doc=neuronvisiosumatraworkflow-100702055903-phpapp01]
Sumatra is very cool idea which I felt the need from a long time. Andrew started the development of it and released the version 0.1 few days ago. The idea was great: record all the details about your simulation, storing the parameters, why you have launched it, what was the outcome. Tagging on top for categorization as well.
There was only one problem: Sumatra was not supporting git so I was unable to use it. Therefore, giving the fact was opensource I just baked a series of patches which were integrated in the tool and now sumatra has a git support π
If you want to have a feel about it and want to try with git there is an example repository on github which you can use.
This is the results of the webinterface (sumatra stores everything in the django ORM system) showing the tables of the simulations:
If you click on the single record you can access the details of the simulation:
Using sumatra you will be able to:
Storing all this informations is done automatically for you (except the analysis’ results of course), so you can focus more on your science, without worrrying on loosing your results.
Soon I’ll integrate sumatra in Neuronvisio.
P.S.: The patch for git integration (second part) is on its own way and it should be integrated soon in the tree, so you will need to run the bleeding edge and integrate the patch yourself if it’s not yet there (and you can’t wait π )
Have Fun
Today I released Neuronvisio 0.4.4 .
This release fix quite a lot of the doc and change the API to load the sqlite database. There are a lot of changes under the hood.
There is a lot of work going on on the plotting, and if you are interested to have a modularity (so you can plot anykind of variables and integrate is with Neuronvisio just let me know.
Have a look at the plot_vector() method in the Control class
I think it will be possible to refactor the code, creating a Plotter obj where the x and y are for the plot and how to create the legend. Then just pass this object to the plot routine, which will have no idea what is plotting, but is able to extract this info from the plot obj. This need a bit of thinking and use cases
What’s next:
There is an ongoing process to integrate Neuronvisio with sumatra. Sumatra is very handy software however it supports only hg and subversion for now, while I’m really based on git. For this reason there is a patch sent to Andrew to start to work on this. Hopefully Sumatra will support git soon and then I will start to see how to integrate that on Neuronvisio and TimeScale.
One problem I need to solve is how to save the geomtery of the model when I save the results of a simulation.
Using the NEURON ability to export the model in NeuroML and to reload it would be the way to go, but more investigation on this are required.
In the mean time..
.. enjoy Neuronvisio
In ubuntu to install all the reqs for neuronvisio you have to type:
sudo apt-get install python-numpy python-gtk2 python-visual python-matplotlib
and you ready to go. On the other systems, like Mac or windows you have to run for every package by yourself, making your life more complicated.
This is a fact. November 2009.
Today I released the first public release 0.1.0 of NeuronVisio.
NeuronVisio is a GTK2 user interface for NEURON simulator.
NeuronVisio connects with NEURON using the new python NEURON interface.
The code is on github (which I discover create automatically a tarball for you when you tag the package… sweet π )