Merry Christmas and Happy New Year….
ghostbusters
Wondering?
๐
Have fun and Happy Holidays
P.S.: mattions@triton:~$ cowsay -f ghostbusters Ops! We did it again!
Merry Xmas
Category: English
Google is becoming evil? No (or not yet?)
When I saw this news on an italian journal about “Google approaching major cable and phone companies that carry Internet traffic with a proposal to create a fast lane for its own content” I was kind of skeptical. It looks really odd to me that google, people who know internet really well, were thinking that was an action to take.
So I hit slashdot (yes, there you want to go for this type of information) and the story starts to be more clear.
It seems the news appeared on the Wall Street Journal but the way they reported was a little bit confused. The clarification of Google came from their policy blog where they reaffermed they support net neutrality.
The Net neutrality is one of the key attribute to have a lively and healthy network and I’m really happy there is a general agreement on this idea.
Is it pretty amazing the agile blog answer given by the google folks about this story. Is not that common for a big company…
The importance to have a VCS..
…Or as Bazaar just saved me the day
In bioinformatics the Good Programming Practices are always seen as a “too big solution for a too small problem”.
BioinfoBlog is not of this advise and I totally agree.
For example the use of a Version Control System is always seen as an overdue for our project (classical objection: my project is just a bunch of scripts… yeah.. sure….).
Let me try to convince you with a real life example and why today bazaar save my day (or at least a lot of time).
Scenario: I was running a custom simulation of this model available from Biomodels database when I saw that something that before was working it wasn’t anymore!
The model encodes the really complex series of biochemical reactions that permits DARPP-32 (a protein present in the spine of the Medium Spiny Neuron) to integrate different stimuli (Glutamate and Dopamine releases) and to respond accordingly.
for the brave biologist or interested scientists between you I promise I will speak about this later on….
To better understand the model and simulate different input today (ok, the simulation started yesterday night..) I was running a simulation using a stochastic simulator. The expected result would be to have different output due to the stochastic variability but still quite similar.
Bear in mind that I will show you 4 copies of the same simulation that should diverge only for the stochastic effect; this means you should expect 4 curves that will be more or less of the same shape.
Doh!
In this image you can see the time courses of the molecules of DARPP-32 (D) in the not phosporilated state; there is a dramatic drop of this form of the protein because the input of Calcium activate several kinases that are going to phosphorilate DARPP-32. The input of Calcium is applied (technically is a train of Calcium) at 100s
The discrepancy between the four trajectories is too big and cannot be addressed to the stochastic variability only, but it looks like in three of the iterations there is the lack of the input (No Calcium applied at all).
So I took a look to the trajectory of Calcium to see if it was missing:
Calcium input 4 different iteration
Eureka! The Calcium is not applied in the 3 of the four iterations.
If you thinking where is bazaar and why it saved my day… don’t worry! I’m getting there… It just takes time…
So I know:
- which is the reason of the Bug
- I know that I refactored the code some time ago to have the possibilities to ran different kind of simulations and I very likely introduced the BUG
- I know the simulation was working before this point
I fired up olive and try to understand where and when I’ve changed this bit
Olive GTK screenshot
The selected revision is the one where I refactored the code and added the new Experiment class to better shape my inputs, and the one where most likely I’ve introduced the BUG.
Rewieving the changes that I made I found out that I don’t create a new list of inputs for each iterations, but only for the first one, so when the other iterations check for the input to apply, they don’t find anything!
So I fixed the BUG, and I re-run the simulation and I’ve got the right results.
4 iterations DARPP-32 BUG fixed
If I didn’t have bazaar installed or I didn’t use any VCS, I had to spend a lot of time to debug my code this morning with no clear idea where to look and what to change. More over there would be also the frustration to get something to work again when it was working before.
So if you are in bioinformatics or you like/have to program think about to use a VCS. I’m using bazaar because it’s easy, it’s distributed and it has also a really good svn-bridge-plugin, so I can push all my code to the svn of my group ๐
Python 3.0 . Here it comes…
Python 3.0 is out. Has been released yesterday and the first production stable release is ready to be grabbed. This release breaks the compabilities with the 2.x series. Nothing will work anymore ๐
Things that I would like to to underline:
- The print statment becomes a function (so you need the brackets)
print "Hello World"becomesprint("Hello Wolrd") - dict.keys() or dict.values() give a view that is a “lazy” list read-only. It’s an iterator and you cannot pop stuff out of it. If you need a proper list you have to force it with list(dict.values())
So take a look on the documentation to have a proper idea of what’s going on, read this small paper to know why there was the need to do this change and before start screaming around check this blog post too that give a clear answer to the question: “What to do about the python 3.0?”
Have fun with the new python….
I mean HH ๐
TuxGuitar rock!
Long time ago, when I was still a user of windows (yeah… the original sin …) I was really happy with a music program powertab.
Now a lot of things has changed, first of all I don’t use windows anymore (my last win sys was win 2000 NT …) but I use Linux (ehm.. GNU/Linux), in Ubuntu flavor with GNOME as my main Desktop Enviroment.
Guess what… Powertab editor is a windows only program.
Today one of my friend sent me a two ptb (Powertab original format) files and I was already wondering how to retrieve the program and if it will work emulated with wine..
Then I thought it was impossible nobody has written a cool tab editor for linux. And Indeed I was right!
tuxguitar smoke on the water
TuxGuitar is able to import the .ptb files, it has a midi player and it’s pretty amazing!
So, if you enjoy music and need a professional tab editor with a lot of features, give it a shoot!
Keep on rockin…
P.S.: Rock midi file are horrible to listen ๐
RessearchGate, the scientific facebook?
The social networks is new direction of the web. Different kind of social networks create different kind of possible relationship. For example the network that I have on facebook has a small overlap with the network that I have in linkedin.
An email suggestion pointed me to a new kind of social network called researchgate.
Research gate logo
for my usage this will hold the network that I have in linkedin, but as for all the social network, it has to grow to become a meaningful resource.
On the technical side I saw that it’s possible to import your library but right now the format accepted is only XML. I hope they are going to implement also the support for a BibTeX import, so I can test the semantic engine and take a look to the papers it’s proposing.
The wave 2
This is a tiny blog that use several languages and has a kind of stable number of readers that I would like to thank.
So everytime there is a massive increase of the number of visits it’s always cool to try to find the reason.
This time this is what happened:
From 30ish average readers on daily base to a peak of 496!
I was wondering why that happened when I figure it out:
Yes, YANNB was the first hit on this google search .
It matters to be first on google, also if it is only for one really particular problem. And I’ve received one of the most rewarding comment till now. ๐
It seems everytime I share a solution there is a lot of interest on that bit and it’s useful for some of the people out there like this one , in how to layout the partition on your harddrive (link in italian… if there is interest I can translate and post it again.)
However this post has been read not in one burst but during a long period (and ok, it’s also quite old so this can be biased).
This time was the second time there was a burst.
The first time happened when pollycoke linked me and all that traffic had clicked the link.
Skype and Ubuntu 8.10
If you wondering why Skype is not anymore working with your new shiny Intrepid Ibex 8.10 you’re not alone.
It seems pulseaudio is somehow responsible for this bad behaviour. To bring back everything to the normal situation:
killall pulseaudio
sudo apt-get remove pulseaudio
sudo apt-get install pulseaudio ubuntu-desktop
This should solve the problem. It worked here at least. ๐
Update: I found out that only the command
killall pulseaudio
is enough.
After that you have to launch skype and it should work.
The annoying bit is that you required to do that every time you want to use skype…
OpenEverything London – Live Blogging
9.35: Ok, I’m at the OpenEverything in London. I’ll try to do some live blogging.
Let’s see how it goes.
10:16: First presentation from Glynn Moody. Everything was Open and we lost it. Intelectual Property is a monopoly that stop innovations
11:15: Speed GeeK:
Late night: So it turns out the live blogging was impossible, too much stuff to follow, a lot of really interesting conversation.
Just pointing two projects that are really interesting:
- www.open.ac.uk/openlearn – Open University. Well establish running and alive.
- themis project — How to run a community and which way is the best to take collective decision. (Pre- alpha. No site yet, I will keep you informed)
Publishing system
from Nothing Shocking
Sequential publishing.
In the case is the normal process all that guys come over you all together….