Category: English

Say hello to NeuronVisio

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.

  • 3D visualization of the model with the possibility to change it runtime
  • Creation of vectors to record any variable present in the section
  • Pylab integration to plot directly the result of the simulation
  • Explore of the timecourse of any variable among time using a color coded scale in the 3d representation
  • the GUI runs in its own thread so it’s possible to use the console to modify/interact with the model.

pyramidal neuron model

The code is on github (which I discover create automatically a tarball for you when you tag the package… sweet πŸ™‚ )

Getting away from some Gtk Warning

If you found a warning like:

GtkWarning: Ignoring the separator setting

when you are playing around with glade and pygtk it is because glade create any dialogue with the “Has separator” set to No, instead Yes.

More info in this #587288

On a side note this solved the first bug/warning on neuronvisio πŸ™‚

HIH someone πŸ™‚

Tracker website and (another) git workflow

Tracker is under a massive refactoring phase for the release of the 0.7.x series and there is a lot of work carried out. So to catch up and to give better info we started to work on the website to update the info over there.

Look at our new shiny development page where you can find the details and how to install tracker from the source with all the packages that you need in a debian based distro. BTW if you know what you have to install in Fedora and friends just let us know and we are going to add them in no time.

Anyway, I started this post to highlight another hint on how to use git (and where to find later when I will forget…)

The good news is Tshepang stated to contribute to the tracker website (source tracker website – if you feel like patches are always welcomed and yes you have to download all the gnomeweb-wml module).

Before today I always used git as a stand alone developer, but now I had to figure out how to track the changes in the master form the other projects, without losing all my work and the patches.

So here is the solution of this riddle.

From the master create your own branch

git checkout -b WIP

apply the patch and work on the branch

git am 0001-super_patch.patch

hack hack hack

git commit -am "A lot of good stuff"

Now you ready to go. You want to put back your changes in the master and then push on the server.

How to do that?

You must rebase your local Work In Progress branch with the local master that track the remote master. eh? yeah. Let’s go through the command:

git checkout master #Back in master

git pull # Grab all the new updates

git checkout WIP # Back in WIP

git rebase master #The Black magic. Commit all you change on top of the master ones

and now you good to go:

git checkout master # Back in master
git merge WIP # It’s gonna be a fast foward merge so no commit message will be created; that is exactly what you want, because the meaningful commits’ messages are in the WIP branch and a commit with the message “merged WIP” is not that interesting.

git push # And we go online. πŸ™‚

On a side note:
gitg is your friend.

gitg screenshot

gitg screenshot

Ustream, they did it

So just two words about the ustream website and my experience for the mortal immortal symposium.

First of all I want to say it worked like a charm. I used a mac and a firewire cable to connect the camera with the computer. For the technical point of view, we took the video from the camera and the audio from the auditorium system and plugged that into the mac.

The quality of the sound it’s really good. The quality of the video is good enough I think.

More over you can watch or download the video from the channel url

We had 60 unique visitors, 88 total viewers with the mean of 19.3. Below the statics.

Mortal Immortal live streaming stats

Mortal Immortal live streaming stats

The Mortal Immortal live streamed!!

If you are around Cambridge this friday and you are interested in science and society I would like to let you know that there is going to be a conference called:

The Mortal Immortal – Scientific and Social Aspects of Ageing

The good news is if you can’t make it you can see the event in live stream on ustream.tv on this link:
http://www.ustream.tv/channel/The-Mortal-Immortal—Scientific-and-Social-Aspect

At the final panel we are going to take questions also from the net, so don’t forget to join the chat and throw your question πŸ™‚

Let the partition be

Yesterday one of my housemate asked me if I was able to make a partition of his hard-disk.

He has a 40 Gb drive and wanted to make two partitions, one only for windows and one only for the data.

To accomplished that I just had to fire up an ubuntu live cd (It was the 7.10 version, the one that I had handy at that time) and I used gparted to do the job.

It worked like a charm.

Open a terminal and then write

sudo gparted

to start it.

We were able to resize the old partion from 38 Gb to 12 Gb, create a new one of 28 Gb and format it with the ntfs filesystem.

Oh yeah, because this friend is still using windows.

Then we boot up in windows and the system recognized the two new partitions (C: and E:) and it was happy to use them.

All this thanks to an Ubuntu Live system. And in 5 mins. πŸ™‚

Git set up a public repository

If you have to set up a public repository with git you can follow the instruction found on the git-core tutorial
(Hint: Search for “Publishing your work”)

Things to keep in mind:

  • Public repository are usually named as project.git and it’s a directory even if you can be mislead to think it’s a file for the extension (.git). Well, it’s not a file.
  • you need to login in the remote host (the one from which you will share your repo) and initialized a local git database:
    • ssh account compulsory
    • git should be in the path and available in the web server
  • You need an ssh account over there.
  • Then you can push your changes to the new shiny repo.

The steps to do that:

  1. login the remote <public-host>
  2. mkdir project.git
  3. GIT_DIR=my-git.git git init
  4. mv project.git/hooks/post-update.sample project.git/hooks/post-update This make sure that after every push the git update-server-info is ran and your repo can be accessed in the public way.
  5. git push <public-host>:/path/to/project.git master