Category: Science

The other way

December 3, 2010 / / 0 Comments

I’m still amazed by the subs of the Phosphorus with Arsenic as found out and report in Science here

So life can have a completely different way for working… It’s also true that the Arsenic sits just under the Phosphorus, so it share a lot of chemical property, but still is the first time we have an example of something living without Phosphorus. Some questions just right off the bat:

  • What’s going on with the Adenosin Three Phosphate (main energy molecule in all cells)?
  • Is that thing using an ATA (Adenosin Three Arsenate) ?
  • Is that stable/does it even exist?
  • Which are the pathways? All the kinase/phosphatase system is just working with ATA? I guess we need to change the phosphatase names if that is the case..
  • Which kind of evolution?
  • Where is on the phylogenetic tree?
  • Is it on the phylogenetic tree?

Time to read the paper.

Symphony of Science

December 1, 2010 / / 0 Comments

Great video about science and a way of thinking.
[youtube http://www.youtube.com/watch?v=1PT90dAA49Q]

Best quotes:

Plait:
Teach a man to reason
And he’ll think for a lifetime

Randi:
Enjoy the fantasy, the fun, the stories
But make sure that there’s a clear sharp line
Drawn on the floor
To do otherwise is to embrace madness

How to use ecell from an ipython console with pylab

October 25, 2010 / / 0 Comments

If you use Ecell simulator sometimes it’s handy to have a way to use it inside an ipython/pylab session to quickly test some features and try some small thing.

For this reason I’ve created a class called quickEcell which takes care to initialize ecell simulator, create the ses object and offer a qcuik way to create loggers and plot the variable.

Below is the minimal to run a model and plot it. All the code is on http://github.com/mattions/QuickEcell

[code]"""Demo method. This should be the skeleton of your simulation"""

qE = QuickEcell(‘simple_ecell_mod.eml’)
variables = [‘S’, ‘P’]
loggers = qE.create_loggers(variables)
qE.run_and_plot(1000, variables, loggers)
plt.title("Test for Michaelis-Menten")
plt.show()[/code]

Research as a way to advance society

October 5, 2010 / / 0 Comments

This morning I had a really interesting conversation with a friend of mine on the bus to work.
Then I read this post from Luca De Biase about the Japanes law of Science and Technology which was in good agreement with my position.

Sometimes Science and Research is seen as a tool to achieve a better handling of technology. That’s a really narrow way to look at it and it’s not the main point.

I think Research regarding both humanistic and scientific topics, is a way to improve society. The better we understand the world and ourself, the better we can live on this planet and have a better society.

Japan has passed in 1995 a law called: “Science and Technology basic law“, this is the first article

Article 1
The objective of this law is to achieve a higher standard of science and technology (hereinafter referred to as “S&T”), to contribute to the development of the economy and society in Japan and to the improvement of the welfare of the nation, as well as to contribute to the progress of S&T in the world and the sustainable development of human society, through prescribing the basic policy requirements for the promotion of S&T (excluding those relevant only to the humanities in this law) and comprehensively and systematically promoting policies for the progress of S&T.

The real deal is to improve society and to create a sustainable way to do it. It is not about the money, is about the vision of the society and about building a better one for the future.

This is way, I signed the petition on science is vital, and I’m going to the rally on Saturday.

People should not be mistaken, this is not scientists calling for more money because they are fearing to loose the job, they can always do another job.

This is scientists calling the whole society to understand that research is a way to build a better society and to build a better future. The rally is happening in UK, but this is a worldwide issue.

The delta. Why we are modelling.

August 7, 2010 / / 0 Comments

Medium Spiny Neuron. 3D representation made using Neuronvisio.

Model of Medium Spiny Neuron. (3D representation made with Neuronvisio)

Disclaimeir: This is a long one. Get a cup of coffee and ten solid mins of your time, otherwise leave now 😉

When I meet new people and I’m asked to introduce what I do, it usually takes at least 3 minutes to give a proper overview. Usually, if the person is interested, I’ll go deeper and deeper, using an onion strategy to explain dive in the details of my subject’s research, going from a very simplified explanation to a more and more precise one.

The interesting thing is the recurrent question which arise at the end of my explanation: Why? What is the reason behind that?

I think this is a very interesting question and I have a personal answer, which I will tell you in no time. However, before that, let me introduce you a bit my research so we are on the same page. Then I will take a risk and try to generalize this to the whole modelling world.

In my Ph.D research I’m modelling the Medium Spiny Neuron of the Basal Ganglia. If you want to know why this is interesting and you want more detailed information about it just go on my academic page, otherwise here let’s just say that I’m investigating how the memory works, trying to shade some lights on the complicated business of memory and learning. In computational neuroscience we have a lot of different data, from physiology spanning to morphology to biochemical pathways. However, all this data usually belongs to quite well defined different area of expertise and they are not integrated. I’m trying to develop a coherent theory which integrate all these areas, which then we can use as a tool to understand the system.

The system I’m studying is not linear, which means a lot of different and concurrent processes influence each other, with different magnitude and at different times dynamics. The network of relations is intricate, and the different delays makes really difficult to have a static representation which can explain the situation.

This is why modelling is useful, and in my case is quantitative modelling. One of the way to try to understand this system is to create a model where we can simulate what’s going on, then run it to try to catch the emergent properties of the system and isolate them. If this approach is successful it will give us the knowledge about how the Medium Spiny Neuron should work in physiological conditions at least about some precise situation.

So what? I heard you said. Well, we have a good representation of what is going on. Which is the main idea of basic research. But there is more, so keep reading.

Let’s say the systems (in this case the Medium Spiny Neuron) can be found in pathological and then in normal conditions.

If we know how to simulate the physiological conditions and the pathological conditions then we have the possibility to understand the difference between the two. This difference or the ? (delta) ? = physiological - pathological, as I like to think about it borrowing a classic mathematical notation, is what differentiate the system in the two conditions.

This can be done also from an experimental point of view. You can replicate the two states using experiments, but given the fact the system is very complex, you can use a lot of different method to force the system into pathological conditions. Usually the system acts like a black box: you know what you put in, you can read what you’re getting out, but you don’t know what’s going on inside the box. In other words you don’t know the ?, or said in another words you don’t know why the two conditions are different.

Therefore the job of the model is try to open the box.

Now, if you know what is the ? and why it exists you have also a good indication of what is going wrong in the pathological conditions, what is missing or what is overproduced or, in more general terms, what is the bit you lack between the two systems. Then you have a starting point where to look to patch it.

I think this doesn’t apply only to computational neuroscience, but to all the models that deals with complex systems.

That’s why I think modelling is important. It will be cool to know what are the thoughts of mine 25 readers if they made up to here. Comments are open, as usual.

Sumatra and git support

April 7, 2010 / / 2 Comments

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 🙂

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:

  • search your simulations’ results
  • describe the results of the simulation on the simulation record itself, keeping everything very compact and ordered.
  • retrieve all the tiny details when you will need (papers hopefully..)

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 🙂 )

Have Fun