Category: English

Reviewing Paperpile 0.5 beta

January 23, 2011 / / 9 Comments

paperpile logo

Paperpile is a nice software which hit the 0.5 beta version some days ago. It’s been a while that I’m using it and being in the full swing of writing my Thesis, I tend to use it on daily basis, so I decided to review it a bit.

First of all Paperpile is a reference manager, which help to manage, organize, cite and share the collection of scientific papers that you have on your computer. If you do science you know exactly what I’m talking about. If you don’t, imagine you have at least 200 different articles lying on your hard drive, which analyse different but related subjects. When writing a new research article, it’s necessary to cite all the relevant previous work to put you new work in contest. It’s the incremental delta of new information which science uses to evolve (when there is not a quantum leap).

Retrieving, organizing and citing those piece of work is necessary and can be a daunting task, but a good reference manager can help to make your life easier. There are several softwares out there, and I had different experiences, however it seems Paperpile is overcoming anything else and I’m using it productively, making me even to read more papers!

So let’s jump into it.

Paperpile general

General view of Paperpile

This is the general window of paperpile. On the Top left you can see the label Ă  la gmail. More than one label can be added to a paper and different background/foreground colour can be used to personalize it. To add an existing label to a paper just pick and drag it over it. Super easy.

On the Mid right you can add the RSS from journals, which can help you to be updated with the latest articles published. I used to have this RSS in my google reader, however having it directly in paperpile makes super easy to import new papers and collect the pdf.

Bottom right there is a collection of different tool, from being able to search Pubmed to import a directory full of PDF.

Central window is where the meat is. All the paper, ordered by addiction Date (you can change to what you prefer) and the most important feature: the search box. Paperpile implements a search as you type system, so as soon you start to type it it start to search in author title and also abstract.

One very interesting bit is that the search box actually find the article I’m usually looking for, and it’s pretty precise. It really saves me a lot of time. This is a clear edge over Mendeley for example, where the search was a disaster. At least in the version I’ve used so far.

The central window also give you the possibility to add notes to a paper.

On top left there are very useful actions which paperpile can perform for you. Paperpile makes easy to retrieve the article on to the publisher site, either giving you a link to visit the webpage or can automatically fetch the paper for you. Sweet!

Another very useful features, which I used so far at least 3 times, is the automatically generated email, which fire up an already ready to send email to your colleagues with the citation reference.

One last thing that I would like to put under the light is the LaTeX integration. With an easy Ctrl-K the label will be copied in your clipboard ready to be pasted in your LaTeX file. If you need the more standard citation, Ctrl-C will do.

To set up the automatically synch for your bibtex database just click on All Papers, on the top-left and turn it on, choosing the location for the file. After that every new paper you’ll add to your collection is automatically exported in BibTeX and you don’t have to care about it at all 🙂

Paperpile BiBTeX setting

Go and Check it out.

I would like to speak with Salvatore

January 23, 2011 / / 0 Comments

On the guardian there is an article about about Berlusconi, where also Rocco Siffredi is questioned about the RubyGate and the possible effect on the number of votes.

If I get the article correctly it seems that Rocco is saying that Berlusconi will not loose vote for this behaviour. I’m always amazed when people can predict how and what people will behave in an election that is not yet issued, basing their judgement on one fact.

More over, in a youtube video, I remember that Rocco said that Berlusconi is ill and that he can help him. So I don’t know if he changed his opinion or the article is a bit imprecise.

However the number of voters for Berlusconi is a straw argoment.

Berlusconi has a pack of voters whom will vote for him no matter what. This is more like a cult problem than an actually political judgement of what the govern has achieved. This people exist and it will be stupid not to acknowledge that, however this is a fraction of all the voters in Italy.

A third of the country didn’t vote at the last elections. They didn’t vote neither for the right wing or for the left wing. Lack of proper representation it seems to be more the cause of this then not being interested in the politic of the country. What I would like to make clear is that there is a huge pool of possible voters, which could be called to get rid of Berlusconi.

But this is not what I wanted to write about. I would like to comment this sentence:

Salvatore, a blacksmith, said: “I would give my daughter a slap if she went to a party at Berlusconi’s, but I still vote for him since I approve of his politics.”

I really would like to understand what is this politics that he his talking about. The Berlusconi’s politics, in the last 14 years, was only escaping from the law using the power to create new law that will favour him (ad personam), or to change existing law. That’s not politics, that’s tilting the table.

So the number of people that actually vote for Berlusconi are either thinking he is a model or they are convinced he is doing good the job. The last part are completely recoverable because it will be easy to demonstrate that the government is unable to do its own job and its completely stopped.

There is a massive amount of people that could throw away Berlusconi. The only trouble is that the left wing did not yet find the way to organize those people in a coherent way and be able to challenge him.

Several different way are being tried, like http://www.prossimaitalia.it/. We will see.

Appeal for Berlusconi’s Resignation

January 17, 2011 / / 0 Comments

1. Resignation.
We call upon Silvio Berlusconi to resign immediately from his post as Presidente del Consiglio dei Ministri. In no other democratic country would a Prime Minister, faced with such serious legal accusations, remain in office longer than a few hours. All Italian citizens, of whatever political persuasion, must realise that the image of their country is profoundly tainted if Berlusconi remains in office.
2. Attendance in court.
We call upon Silvio Berlusconi not to defend himself on television, using his substantial mediatic power to discredit the magistrates, but to present himself in court and seek to defend himself there, as would any normal citizen. Once in court, he can in any case hope to benefit from the services of the highest paid lawyers in the country. We sincerely hope, for his sake and that of the country, that he is able to demonstrate his innocence. If he and his supporters reply that the judges are irremediably biased against him, we would like to point out that on more than one occasion in the past he has been given the benefit of the doubt by the courts. In the Mondadori case, for example, the court judged in 2001 his position as Head of Government to be part of the ‘extenuating circumstances’ which in his case alone allowed the crime to be prescribed.
3. The role of the President of the Republic
In a situation in which two of the principal powers of the state – the magistracy and the executive – are on a head-on collision course of considerable danger for the future of the Republic, we call upon its President to observe closely the situation and to be prepared to intervene actively, naturally within the limits of the powers ascribed to his office by the Constitution.
4. The opposition parties
We call upon all the parties of the opposition to put aside their differences and to abandon any jockeying for position, uniting instead their voices in a single request of a single word: RESIGNATION.
5. Civil Society
We invite the many associations and the hundreds of thousands of members of civil society to do the same, pooling their resources and joining hands on a single line of action. We would particularly appeal to Catholic civil society to deplore the hesitations and silences of the Vatican on so important an issue of public ethics.
6. The friends of Italy in the world
We have written this appeal in English as well as Italian in order to reach all those abroad who are friends of Italian democracy. Do not despair of Italy! The country needs your solidarity and help.

Gustavo Zagrebelsky, Paul Ginsborg e Sandra Bonsanti per tutta LibertĂ  e Giustizia

I completely agree and I repost it here. Original on the “LibertĂ  e Giustizia” website.

Retroffiting with style:the cinquino elettrico

January 15, 2011 / / 0 Comments

Pietro Cambi is the president of the Eurozev, an association which promotes the conversion from endothermic engine to electric. He converted his own ‘cinquino’ to an electric car, manteining a lot of the original specs (like for example the clutch!)

cinquino picture

Cinquino and the kitegen prototype in the back. At the right side of cinquino Pietro Cambi, at the left side Massimo Ippolito, the kitegen's inventor

 

There is a video on youtube when the cinquino hit the 100 Km/h (the endothermic cinquino was never that fast 🙂

This is pretty cool and I think the way to go.

Profiling python app

January 1, 2011 / / 1 Comment

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..

Crowd power on steroids

December 31, 2010 / / 0 Comments

This is not a news, but I think there is a big shift happening in the society.

I guess the idea of community sharing is becoming bigger. Opensource movement was a precursor in this regard, I think and a loose collaboration is able to get things done.

This will raise with the creation of more peer to peer networks which have a strong focus and an objective. Collaborative consumption will be the next stop.

Another trend which is worth of noticing is increase of collective intelligence. Making data available to people is opening up a lot of possibilities. From opengoverment to opendata to openknowledge.

I still remember the Time cover with You. Next year I bet it will be “we”.

Happy New Year,

I guess it will be full.

Fixing a bug. The power of opensource

December 31, 2010 / / 1 Comment

 

If you used gnome 2.30 and used two screen, cloning the smaller in the bigger one,  you were annoyed by this bug. At least I was really annoyed. Nothing too bad, just the image was not drawn correctly. In my case was drawn twice at different resolution, one on top of the other. However this was a regression from gnome 2.28 where this was not present. The bug was up for a long time and was also reported upstream at gnome side.

I did some research on it and I had nailed down where was the problematic code, however I was unable to propose the solution because C is no my cup of tea.

Yesterday Florent proposed a fix which was tested by Thomas, which was kind enough to give the instruction how to recompile the package, making a deb out of it and install it. Therefore I just give it a try. Finally, I have the desktop fixed!!

The patch it’s already on the gnome bugzilla and everyone will get this back as it supposed to be.

The thing that I want to underline is the anarchic collaboration:

  • somebody open the bug,
  • other people reported it and the bug was confirmed
  • somebody else found which part of code was interest
  • somebody proposed the solution
  • other people tested on different system

This is the beauty of opensource. Just give an hand if you can and enjoy it.

Stand your ground

December 30, 2010 / / 0 Comments

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.

A Trenitalia experience

December 20, 2010 / / 2 Comments

Saturday I was very brave and I had decided  to take the train and go all the way to Turin  from Ancona and back using the amazing trains run by Trenitalia. The Wind Operations Worldwide was having the annual meeting. Good news were announced for the Kitegen project, especially the drawing to a close for the first industrial prototype.

The meeting was starting at 13:30, in Turin so I’ve decided to catch the train from Falconara Marittima @7:50. This train was supposed to arrive @Bologna at 10:37 and then I had to catch the super fast “Alta VelocitĂ ” High speed train at 10:53.

A sad 10 appeared under the delay column in the screen. This delay was really strange because the line was free, others trains from Ancona were arriving on time and the train was supposed to start from a very close station,  just 10 Km away.

At the end the train show up with at least 40min of delay. When I’ve asked on the train what was the cause of the delay the answer was a laconic – “there was a problem with the safety check on the locomotive engine, so it has to be detached and reattached. That took a bit of time.” When I’ve pointed out it that I was risking to loose the coincidence to Turin the ticket collector said he was unable to do anything.

I arrived in Bologna after the other train departed, there were not High Speed train to Turin anymore and the only thing left was to change the ticket for a High Speed train to Milan (which arrived delayed as well) and then to take a low speed train from Milan to Turin, which took 1 hour and 55 min.

I’ve arrived in Turin at 15:27 and I was able to reach the meeting only around 16:00.

For the return I was taking the “Intercity Notte” from 21:05 from Turin, which was scheduled to arrive in Ancona at 2:59. This train is one of the long distance train which connects the country from North to South. Turns out that our carriage, number 6, had a problem with the heating. The indoor temperature was very close to the outdoor, which was 0° C. We were freezing. Badly.

In my compartment there was one child, and there were other children on the same carriage. People were travelling even further than me, all the way south to Lecce, where the train was supposed to arrive around 10 o’clock in the morning.

The ticket controller said he was unable to do anything for us. The train was completely full, also the carriage 11 was experiencing the same problem, and there was no possibility to change the seats. The only thing they were able to do was to give us some blankets at Bologna station, after 4 hours trip. As you can understand, some light blankets didn’t really change the situation. More over there were not enough blankets for all the passengers.

Finally I’ve arrived around 3 o’clock at Ancona station, completely frozen.

Was it bad luck? Was just a set of circumstances, impossible to predict? I don’t think so.  The problems I and the other passengers have encountered were not related to the heavy snow, or the bad weather conditions or any other kind of exceptional situation. Last year it took me 26 hours to get back, everything completely blocked due to the heavy snow. That was something you have to accept and deal with it. This I think was a different case.

My guess is that these problems were completely avoidable with a regular maintenance, which has been shrunk badly. This is not an isolated case. Speaking with regular passengers of the long distance train they said: “you freeze in winter and you sweat in summer. No way out.”

I’ve filled the form to ask the reimbursement . At least I want my money back for a not existing service, the High Speed to Turin, and the money back for the freezing conditions which I had to deal for the return trip.