Category: Science

Cesium contamination projections

As you know there was a massive Earthquake (and there are still some going on) in Japan followed up by a massive nuclear accident at Fukushima I which has been evaluated 7 on the INES scale grade accident.

Now there are some prediction made by the University of Cologne about how the Cesium will spread around the world.

In the case it does rain

Cesium spreading Wet scenario

and it doesn’t look good.

And in the case it doesn’t rain

Cesium spreading Dry scenario

And it doesn’t look good at all.

Via Crisis

Opensource philosophy to science?

Lately there has been a clear movement to move science towards a more open way to make research.

I’m not talking about Open Acess Publishing, which is still important, but to the real art and sweat to do science.

Science has always been very collaborative, however the dimension of this collaborative effort has always been restricted to a small group. This is not the case when general problems seems to be tackle.

For example, when the problem is the definition of a standard, like NeuroML or SBML, the development of it is a community driven project, where the community works as a whole to achieve a standard which is backed by the biggest number of people interested, so can be easily adopted.

The beneficial impact of standard is not the topic of this post, and for the sake of brevity I just want to point out that a well-coded model in a well-recognised standard gives the possibility to share the work of a modeller (in this instance) and make the model be re-used by other people.

On the same line OpenWetWare wanted to share the protocols used in the lab as soon they were established, and actually even before that as ‘Work in progress’.

The ability of a scientist to be a part of a community is not taken in account at all, due to the Publish or Perish system which is right now up and running. This model does not encourage collaboration, and actually create groups of people which are competing on the same topic to scoop each other. This is a broken system.

It’s so broken that some people even decide to leave academia, and that is only one of the cases. A lot of letters are also available in Nature and this article from the Economist got quite famous as well.

Therefore I watched with a lot of interest the new way proposed by Dall’Olio  which consist in collaborative editing of papers.

So far, if I didn’t miss any, at least two papers with this approach have been written, which is very interesting and shed a bright light for the future.

Still the number of places available in academia and the way the recruitment is organized uses the current model, which does not fit the market, and it’s prone to discard talented people very easily. There should be at least a live debate on how to fix this problem, and move science to a super collaborative discipline.

Happier scientists and better science sounds good to me.

We’ve got tips

Writing the Thesis is a big deal, however right tools makes the experience a little bit easier..

I’m using Gedit on steroids, which is quite easy to achieve.

Just get the LaTeX plugin, and the to get all your files up and running in no time, try to gedit manager plugin.

Then use Classic thesis.

One more tip about screenshoots. Long story short, your video resolution will be always a bit short for the rendering in printing, so if you can’t use svg (made with Inkscape) or pdf or anything that is not a vectorial format you have to rescale (up) the png picture, which is tricky.. ’cause you’re trying to make more info from less.

However if you take the picture at top resolution you can use gimp scale tool to make a decent work.

To do that open the image (png, jpeg or what you’ve got) with gimp and then increase the resolution to 300×300 dpi and then change the canvas to a decent dimensions and scale it up.

This should make you rolling. Hopefully 🙂

Being a little gear

Sul fattoquotidiano c’è un canale seguito da Andrea Valdambrini sui cervelli in fuga, dove si raccontano le storie di esuli italiani fuggiti dall’Italia, molte volte non per scelta, ma per necessità.

Molti di questi sono scienziati, la cui capacità non vengono valutate secondo criteri meritocratici, ma secondo criteri di conoscenze e parentele. Ok, same old story fino a qui.
L’unica cosa interessante è che di queste cose bisogna parlarne e siccome è appena uscito un articolo che proviene da Cambridge, dove momentaneamente risiedo, e visto che il contatto tra Chiara ed Andrea sono stato io, pensavo che era interessante linkarlo.

Lo trovate qui.

Come ha scritto un commentatore sul fatto, questa non è una storia isolata, ma un’atteggiamento sistematico del sistema Italico verso persone brave e competenti, che vengono scartate a favore di qualcuno che invece non è capace di fare quel lavoro. O a favore di un depauperamento della ricerca, chiudendo i finanziamenti alla ricerca di base che è appunto di base, e senza la quale la famosa applicata non esisterebbe.

Profiling python app

If you have to profile application, in python for example, it’s good to read this blog post which I found very useful information.

The profile is used to compare pytables, a python imlementation of HDF5 and pickle, which is a classic choice which you ran into if you are dealing with saving big files on the harddrive.

The best tool so far seems to be the massif profiler, which comes with the valgrind suite. How valgrind works:

This will run the script through valgrind

valgrind --tool=massif python test_scal.py

This produces a “massif.out.?????” file which is a text file, but not in a very readable format. To get a more human-readable file, use ms_print

ms_print massif.out.????? > profile.txt

So I’ve run some test to check the scalability of HDF5.

[sourcecode language=”python”]
import tables
import numpy as np

h5file = tables.openFile(‘test4.h5′, mode=’w’, title="Test Array")
array_len = 10000000
arrays = np.arange(1)

for x in arrays:
x_a = np.zeros(array_len, dtype=float)
h5file.createArray(h5file.root, "test" + str(x), x_a)

h5file.close()
[/sourcecode]

This is the memory used for one array

 

profile_one_array

Profiling one numpy array

This is for two arrays

profile_two_arrays

Profiling two numpy arrays

Four arrays

profiling_four_arrays

Profiling four numpy arrays

And this is for fifty

profile_fifty_arrays

Profiling fifty numpy arrays

As soon you enter the loop the efficiency is preserved in a really nice way
Summing up:

  • one ~ 87 Mb
  • two ~ 163 Mb
  • four ~ 163 Mb
  • fifty ~ 163 Mb

So the problem is not on pytables, but it lies somewhere else..

Stand your ground

The story, picked up also by the guardian here is rather interesting. In few words, a student @Darwin College at the University of Cambridge has published, on his personal website a MPhil thesis about how to construct a device which shows a flaw on the credit card system, which makes possible to make a transaction with a stolen card using any PIN.

The bankers has asked to take this information down. Now think about it for a moment. Instead to fix it, they asked to take it down.

I can foresee your objection.. They should give them time to act and then disclose the flaw. They actually did, because the problem was reported in 2009 (yes, last year) as said on this letter.

In the letter they also write why they will not take it down:

you seem to think that we might censor a student’s thesis, which is lawful and already in the public domain, simply because a powerful interest finds it inconvenient. This shows a deep misconception of what universities are and how we work. Cambridge is the University of Erasmus, of Newton, and of Darwin; censoring writings that offend the powerful is offensive to our deepest values.

This the right way to go. Full disclosure. Fix the problem, don’t hide it. It was also the position expressed @ the Moka Olografix. (An Italian camping about security which I went ages ago).

Hat tip to Ross Anderson and Omar Choudary.

Too much phosphorus

It seems the big paper about the Arsenic which I’ve talked briefly on the previous post lacks a lot of precision and that the impurities presents in the medium will give room to the possibility that actually the bateria is not using arsenate, but still phosphate.

We were not really convinced at lunch discussion and then it seems we are not the only ones.

More info here. Especially interesting these criticisms . ).3 µM of Phospate is quite a lot in a P-/As+ medium.

I guess there is room to have another look at this bacteria.

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