tag:blogger.com,1999:blog-87037604197677829192024-03-13T12:30:05.479+01:00Let's Follow the White RabbitA blog about Free Open Source SoftwareLucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.comBlogger31125tag:blogger.com,1999:blog-8703760419767782919.post-63456601144341744392020-07-21T08:53:00.000+02:002020-07-21T08:53:13.019+02:00Launching Kdenlive TutorialsMany years ago I started writing a number of tutorials about Kdenlive, describing how to achieve visual effects similar to what you can get from commercial software (like the Adobe suite). But I didn't have time to translate my writings in English and format them with HTML. That was, until the last couple of weeks.<br />
Now, I'm ready to release the website <a href="https://www.kdenlivetutorials.com/"><b><span style="font-size: large;">kdenlivetutorials.com</span></b></a>.<br />
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<a href="https://1.bp.blogspot.com/-LpFRoYk_ZnQ/XxXPcUl0oXI/AAAAAAAAMAw/2Saya97--vMUOlTynuQ7mOGsBQLUVC9OQCLcBGAsYHQ/s1600/homepage.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" data-original-height="669" data-original-width="1366" height="195" src="https://1.bp.blogspot.com/-LpFRoYk_ZnQ/XxXPcUl0oXI/AAAAAAAAMAw/2Saya97--vMUOlTynuQ7mOGsBQLUVC9OQCLcBGAsYHQ/s400/homepage.png" width="400" /></span></a></div>
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<a name='more'></a>All the contents you'll find on Kdenlive Tutorials are released under Creative Commons Attribution Non Commercial.<br />
At this moment there are 48 different tutorials, I'm working on other two because I like multiples of ten.<br />
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<a href="https://1.bp.blogspot.com/-HC8dg6nMbo8/XxXQYAHkhMI/AAAAAAAAMA8/aqPiW7sqTHAUjoHnXlaiA-QNwv-YnJbVQCLcBGAsYHQ/s1600/newarticle.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" data-original-height="596" data-original-width="1345" height="141" src="https://1.bp.blogspot.com/-HC8dg6nMbo8/XxXQYAHkhMI/AAAAAAAAMA8/aqPiW7sqTHAUjoHnXlaiA-QNwv-YnJbVQCLcBGAsYHQ/s320/newarticle.png" width="320" /></span></a></div>
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All this work has been done in my spare time: I've been using automatic translation, performing some fast manual fixes. The result should be understandable, in the next months I'll fix the text to make it sound better.<br />
I also know that Kdenlive's interface has changed a lot in this years: the functions I use in these tutorials are still available, they might just have a slightly different name or might be placed in a different spot of the GUI. If enough people are interested, I'll consider taking new snapshots and adapting the tutorials to the last version of Kdenlive.<br />
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<a href="https://1.bp.blogspot.com/-xvl_5EQAgsY/XxXQiXvoOXI/AAAAAAAAMBA/IGJsfGP8P38oOXycJVy9x-KrIpBK8KkHACLcBGAsYHQ/s1600/tutorials.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" data-original-height="598" data-original-width="1349" height="141" src="https://1.bp.blogspot.com/-xvl_5EQAgsY/XxXQiXvoOXI/AAAAAAAAMBA/IGJsfGP8P38oOXycJVy9x-KrIpBK8KkHACLcBGAsYHQ/s320/tutorials.png" width="320" /></span></a></div>
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The website's layout is simple, and every screenshot can be zoomed on. Every tutorial comes with a video that shows the results of the procedure. Videos are often raw: they have been made quickly, just to show what could be done in a couple of minutes. Anyway, every tutorial explains also how to improve the result, if you wanna spend more time on it.LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com4tag:blogger.com,1999:blog-8703760419767782919.post-18337596214069815832020-03-08T13:47:00.000+01:002020-03-08T13:47:52.710+01:00Women in the IT industry (interview from Akademy)<span style="font-family: "roboto" , "noto" , sans-serif; font-size: 15px; white-space: pre-wrap;"><span style="color: white;">There's a clear gender gap in computer science, beginning with education: women in schools and colleges tend to approach computer studies less frequently than men. And we should also consider the usual obstacles for occupation every woman encounters in her work life in every field. So, it's not surprising that the majority of computer science workers are men. </span></span><br />
<span style="font-family: "roboto" , "noto" , sans-serif; font-size: 15px; white-space: pre-wrap;"><span style="color: white;">And, at the same time, the Free Open Source Software world is made of many kinds of communities. Some are quite closed and unfriendly for new developers, expecially if they are women. Others, instead, commit to welcome everyone, without discrimination based on gender, nationality, or any other parameter. </span></span><br />
<span style="font-family: "roboto" , "noto" , sans-serif; font-size: 15px; white-space: pre-wrap;"><span style="color: white;">At Akademy 2019 in Milan, as editor for GNU/Linux Magazine Italy, I've had the opportunity to discuss this issue with Lydia Pintscher, president of KDE e.V., and Lays Rodrigues, developer for KDE software.</span></span><br />
<iframe allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/36SQiwY5j1U" width="560"></iframe>
<span style="background-color: black; font-family: "roboto" , "noto" , sans-serif; font-size: 15px; white-space: pre-wrap;"><span style="color: white;"><br /></span></span>LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com0tag:blogger.com,1999:blog-8703760419767782919.post-340886493510093102019-01-28T21:29:00.000+01:002019-01-28T21:30:22.329+01:00PySide2 on Raspberry Pi 3b+ with Raspbian BusterPySide2, or Qt for Python, is becoming more usable: since it has landed on PyPi, it is easy to install on almost every PC. Unfortunately, this does not apply to the RaspberryPis. Actually, there are only wheels for 64 bit x86 (and 32bit on Windows), not ARM. And there's a reason for this: the actual Raspbian Stretch has way too old packages for PySide2 to work. To get PySide2 on a RaspberryPi, you'll need Rasbpian Buster, which has not been released (even though there are repositoryes for an upgrade). Then, you can use the packages already compiled for Debian armhf (which are not in the Raspbian repository, at this moment). This is not straightforward, expecially for beginners. So I made an image, ready to be written on a (at least 16GB) microSD card. This image has Raspbian Buster with the main Qt5 and PySide2 modules. I've also switched the desktop environment from LxDE to LxQt.<br />
You can find the image here:<br />
<a href="https://www.codice-sorgente.it/raspbian-buster-pyside2-lxqt/#English">https://www.codice-sorgente.it/raspbian-buster-pyside2-lxqt/#English</a><br />
In that page you'll find also links to the Debian Qt5 and PySide2 packages for armhf, if you want to install them on another distro. This image works on a RaspberryPi 3B+, because that's the one I have, but should work also at least on version 3 and 2.<br />
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I also wrote an article (actually only in Italian) to demonstrate what could be built with PySide2 on a RaspberryPi: <a href="https://www.codice-sorgente.it/2019/01/un-termostato-touchscreen-con-raspberrypi/">https://www.codice-sorgente.it/2019/01/un-termostato-touchscreen-con-raspberrypi/</a>. The project behind this article is a simple touchscreen thermostat, so it's a multithread Qt MainWindow used in "kiosk mode" on the PiTFT3.5 with a temperature sensor and a relay. If you just want to look at the code, here it is: <a href="https://codice-sorgente.it/cgit/termostato-raspberry.git/tree/">https://codice-sorgente.it/cgit/termostato-raspberry.git/tree/</a>, but please take note that this code has been written to show different features of PySide2, so it's not really elegant. If someone wants to translate the article in English, I'll be happy.LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com2tag:blogger.com,1999:blog-8703760419767782919.post-74617337402942251402015-08-12T09:30:00.001+02:002015-08-12T09:30:52.143+02:00Kartesio 1.0: free best fitting for science labs is now stableI'm finally able to release the first stable version of Kartesio, Kartesio 1.0. There are lots of new features, and I feel the program is now ready for everyday use.<br />
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<!--StartFragment-->Kartesio is a program I wrote in 2011 for calculating best fit curves from a set of points. Kartesio uses QCustomPlot widget to plot data, and Maxima to solve expressions. The icons used in Kartesio have been designed by KDE Oxygen team. Kartesio also uses ZorbaNeuralNetwork to recognize the best fit curve. ZorbaNeuralNetwork is a library for easy neural networks construction I started writing in 2006, and supports training with both Widrow-Hoff algoritm and genetic algorithm.<br />
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<tr><td style="text-align: center;"><a href="http://www.zorbaproject.org/kartesio/handbook-1.0/kartesio1.0-1.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://www.zorbaproject.org/kartesio/handbook-1.0/kartesio1.0-1.png" height="179" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Using the neural network you can choose the function prototype from a combo box</td></tr>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://www.zorbaproject.org/kartesio/handbook-1.0/kartesio1.0-2.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://www.zorbaproject.org/kartesio/handbook-1.0/kartesio1.0-2.png" height="179" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Using the regression algorithm you can write your own function prototype (the only rule is that it must be in the form "y=...")</td></tr>
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Kartesio is not based on KDElibs anymore. I made this choice basically for two reasons: the main one is that I wanted Kartesio to run easily also on Windows, and KDElibs building is way too much complex for my taste. The second reason is that KDE developers seemed not particularly interested in Kartesio: maybe that's because this program is designed for science laboratories (in high schools and universities, for example) and this is a way too limited set of users for KDE Edu. Obiously, it's still a program meant to be used on KDE when possible (I'm using Oxigen icons to give that wonderful KDE feeling). But if you really want to use it without KDE, it's not a problem anymore.<br />
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Now, Kartesio is only based on Qt, and can be built everywhere you can install QtCreator just loading the "kartesio.pro" file and pressing the "build" button. That's how easy I wanted it to be. It would be cool to make an Android version of Kartesio, but maybe this is quite too complex. For now, I prepared some binary packages for Windows and Debian/Ubuntu (you can download them from <a href="https://github.com/zorbaproject/kartesio-build">https://github.com/zorbaproject/kartesio-build</a>).<br />
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And here is the source code:<br />
<a href="https://github.com/zorbaproject/kartesio">https://github.com/zorbaproject/kartesio</a><br />
Of course, in this repository you'll find the source code of both Kartesio and ZorbaNN, since this one is just a couple of C++ files. In case you want to use ZorbaNN in a program of yours, just copy the files "neuralnet.ccp" and "neuralnet.h" in your program directory. And you'll find also a working copy of QCustomPlot. To compile Kartesio you will need QtCore, QtGui, and QtScript. On a Ubuntu system you just need to install these two packages: qt-sdk qtscript5-dev. On Windows you just need to install the QtSDK with QtCreator, it's already complete.<br />
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I added a feature called "Automatic recognize shape": it uses the neural network to find out which shape fits best the experimental points. The fun part is that the program shows you the neural network in real time: while the automatic recognition is running, a little window appears. This little window represents the structure of the neural network: every I is an input neuron, and the O is the output neuron. Every input is linked to the output neuron via a weight, which is written just under the I character. This way you can understand how a neural network works. For me it's particularly interesting when the neural network runs with only the genetic algorithm, cause you can see how the evolution works.<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://www.zorbaproject.org/kartesio/handbook-1.0/kartesio1.0-5.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://www.zorbaproject.org/kartesio/handbook-1.0/kartesio1.0-5.png" height="179" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Watch the neural network structure in real time</td></tr>
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I don't have too much time to work on this program (I'm a journalist, not a programmer), and if anybody else wants to contibute to Kartesio or just fork it and play with the code, I'll be very happy. I started writing this program when I was a chemistry student, becaused I needed a best fitting program and I couldn't find one good enough for my taste. Hope this can be useful also for someone else.<br />
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I may write a handbook in the next months, if I'll have some spare time. But, again, if someone wants to write a handbook for Kartesio I'll be very happy.<br />
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BUG:<br />
There is a bug I'm already aware of: the program crashes sometimes when the plot is painting. This is not really a bug in Kartesio, but in QCustomPlot, and I did not understand its cause. In fact, this problem presents rarely and in different situations. Should not be a real problem: if you correctly saved your data you can just reopen Kartesio after the crash and then load your table and function.LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com12tag:blogger.com,1999:blog-8703760419767782919.post-26514084885888178122014-04-01T12:33:00.000+02:002014-04-01T12:33:22.031+02:00Microsoft's going to release source code of Windows PhoneAs you all may know, Windows 8 Phone (codename Apollo) has not been the great "Android replacer" that Microsoft hoped. Developers do not like this OS, and neither users: too much complex, too slow. Given that it's not worth spending resources on Windows Phone 8, Redmond decided that the support for this system <a href="http://techcrunch.com/2013/03/18/microsoft-says-windows-phone-8-support-ends-july-2014-still-no-official-successor-announced/">will end on July 2014</a>.<div>
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So, trying to go for broke, Microsoft decided to publicly release the source code. The day of the public release is not yet decided: the code needs to be cleaned and organized first, so it will happen probably after July. Redmond hopes to attract, in particular, people who are disappointed by the <b>NSA</b> scandals.</div>
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Microsoft declared that all the source code of Windows Phone will be released, including the NT kernel.</div>
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Obiously, the NT kernel used for Windows Phone is not exactly the same that runs in personal computer's Windows editions.</div>
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The Phone NT kernel is called, by codename, "<b>April fool</b>".</div>
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By the way, if you are really looking for a "open source Windows" you may choose ReactOS. And if you want free software (not only open source), you should think about trying GNU/Linux distros like Debian (or Ubuntu, but it's not properly free software "out of the box" these days).</div>
LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com1tag:blogger.com,1999:blog-8703760419767782919.post-80164263268633279452013-12-31T16:06:00.000+01:002013-12-31T16:07:15.560+01:00SteamOs: the good, the bad, or the ugly?You may have heard that Valve, one of the major videogames companies, is going to release its own operating system: SteamOs. It is based on Debian: basically, it's just a Debian GNU/Linux distro with GNOME, that comes with Steam preinstalled and ready for use. If you want to try it, I have prepared a VDI image for Virtualbox (you will need to create a Debian VM, with 3D enabled):<br />
<a href="http://www.zorbaproject.org/steamos/Steamos-vdi.zip">www.zorbaproject.org/steamos/Steamos-vdi.zip</a><br />
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<a name='more'></a>I think SteamOs will be another Android, for the GNU/Linux world: it will demonstrate to non-GNU/Linux users that Free Open Source operating systems are easy to use.<br />
The facts are these: just a couple of years ago the majority of users thought that "linux is too much complex to use". Just because uncle Bill (Gates) told them so. But then Google released Android, and a lot of users tried it: this way they discovered that it is based on Free Open Source Software and it's easy to use. You may like Android or not, but it's undeniable that it has taken away the fear of FOSS from users that have been using only Windows before. Today, every day, a lot of people try GNU/Linux distros for their first time, and they have been encouraged to do this by using an Android system (maybe also by the loss of Microsoft's software quality).<br />
Also RaspberryPi helped, but it's still a too little project, since the majority of users will never use a Raspberry.<br />
Now think about SteamOs: an open source game console system. And it's a real GNU/Linux system, it does not try to hide its FOSS roots (like, instead, Android does). If SteamOs will be appreciated by gamers (and considering the power of Valve I think it will) it could finally show to all World's users that GNU/Linux is easy to use, and more powerful than proprietary solutions.<br />
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Will Valve be able to solve Canonical's first bug (<a href="https://bugs.launchpad.net/ubuntu/+bug/1">https://bugs.launchpad.net/ubuntu/+bug/1</a>)? Maybe not. But it will surely help a lot.<br />
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Off topic:</div>
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Someone may have noticed that I've not written anything in the last six months. I just have been too much busy with my work. Some people asked me when will I release a new stable version of Kartesio: I hope I'll be able to do the last changes in January.</div>
LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com0tag:blogger.com,1999:blog-8703760419767782919.post-86886558562786822372013-06-23T22:25:00.000+02:002013-06-23T22:25:47.635+02:00Kartesio: best fit curves with experimental pointsI finally had the time to build a simple website for Kartesio. This is a program I wrote about two years ago for my phisycal chemistry laboratory: I needed to calculate best fit curves for some experimental points I got from the refractometer and the regression algorithms available in the common office suites were not so good. But I also wanted something really simple: why sould I use "R" if I just want to best fit some points?
So I decided to create a program which does this operation and only this one, but does it well.
Kartesio is able to best fit curves using a regression algorithm or a neural network.<br />
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<a name='more'></a><br />
This is the website:
<a href="http://www.zorbaproject.org/kartesio/">http://www.zorbaproject.org/kartesio/</a><br />
there is also the official handbook:<br />
<a href="http://www.zorbaproject.org/kartesio/handbook/kartesio-handbook.html">http://www.zorbaproject.org/kartesio/handbook/kartesio-handbook.html</a>
so if you need some help to figure out how the program works you should find all the answers there.<br />
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If you use a Debian system you can install Kartesio from this package:
<a href="http://www.zorbaproject.org/kartesio/binary-packages/kartesio_0.2-1_i386.deb">http://www.zorbaproject.org/kartesio/binary-packages/kartesio_0.2-1_i386.deb</a>
If you want a Rpm package here it is:
<a href="http://www.zorbaproject.org/kartesio/binary-packages/kartesio_0.2-1_i386.rpm">http://www.zorbaproject.org/kartesio/binary-packages/kartesio_0.2-1_i386.rpm</a><br />
You can also get the latest source code from git:<br />
<span style="font-family: Courier New, Courier, monospace;">git clone git@git.kde.org:kartesio</span><br />
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It is also needed to install ZorbaNeural (which is another project of mine, a neural network library). You can find packages here:<br />
<a href="https://www.gitorious.org/zorbaneural/zorbaneural/trees/master/binary-packages/libzorbaneural-0.1">https://www.gitorious.org/zorbaneural/zorbaneural/trees/master/binary-packages/libzorbaneural-0.1</a><br />
To make the regression algorithm work Maxima is needed: I'm sure you can find it in your distro's repository.<br />
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If you have some trouble you can obiously write me, but please be sure that you have followed the guide before (for installation and use of the program).<br />
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The program is very simple, but it works fine.
There are a few thing I will work on in the next months for Kartesio:<br />
-Add a window for editing points table (sort Xaxis, import and export from/to CSV, add or remove lines to/from the table)<br />
-Button for automatically fitting plot to experimental points (calculating xmin-max and ymin-max)<br />
-Use a QtTemporaryFile instead of a prefixed temporary file.<br />
-Check at program loading if maxima is correctly installed<br />
-Change the layout, so the user can reduce the area covered by the table<br />
-Try to use a library for algorithm regression instead of maxima executable<br />
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<br />LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com2tag:blogger.com,1999:blog-8703760419767782919.post-37793772559014457252012-12-14T19:32:00.001+01:002012-12-14T19:32:06.372+01:00Free software at the CERN, or: how did FOSS help the discovery of Higgs bosonWhat are the main fields in which FOSS is really important, and had given big successes in these years? Research is, probably, one of the most important. And when you talk about research, scientific research, you must speak about the CERN.<br />
In the GNU/Linux Magazine Italy number of January, you will find an interview I did to two researchers about this topic: Sebastien Ponce is the head of CASTOR, the CERN's data storage system (based on GNU/Linux) and Brian Bockelman is an american physicist that works with CERN software to analyse data from ATLAS and CMS experiments (those who found the existence of Higgs particle).<br />
I think you will find their answers really interesting.<br />
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<b>Se leggete GNU/Linux Magazine Italia troverete nel numero di gennaio 2013 (in edicola già la prossima settimana) la traduzione in italiano dell'intera intervista, con una breve introduzione.</b><br />
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I would like to thank both Brian and Sebastien, for the time they spent answering me, but also Melissa Gaillard from the CERN press office for all the work she did.<br />
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Among other things, at the end of this page, there is an off-topic image.<br />
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Here's is the interview:<br />
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-First of all, please tell us something about you... </b><br />
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<b>Sebastien Ponce:</b>
I am a computer scientist, specialized in development of large software frameworks for data analysis and in mass storage.
I am currently the head of the development of CERN's mass storage's system (CASTOR) that is storing and managing most of the data produced at CERN (85 PB right now, growing at a rate of 1PB/week).
I started using free open source software at school in the 90s with debian 2.0 and am mainly using FOSS since then (still under debian).
All the software I've been writing in the last 15 years is free and open source, be it for CERN or outside. </div>
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<b>Brian Bockelman:
</b>I work for the University of Nebraska-Lincoln as a postdoc and work for the Open Science Grid (OSG) and the Compact Muon Solenoid, one of the experiments on the Large Hadron Collider (LHC) at CERN.
At Nebraska, we have one of the Tier-2 computing sites dedicated to CMS, this got me started with large scale storage systems as a graduate student. I've been using Linux since the late 90's - I've played with several different distributions, but almost always end up on either Fedora or RedHat. </div>
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<b> -We know that at the CERN you use GNU/Linux systems. Do you use a common distribution (Debian, Fedora,...) or have you developed a your own distro? </b></div>
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<b>Sebastien Ponce:</b>
CERN is indeed using mainly GNU/Linux systems for data storage and analysis. A dedicated distribution has been developed together with FermiLab and various other labs and universities around the world.
It is called Scientific Linux or SL and its primary purpose is to reduce duplicated effort of the labs participating in the CERN's related projects, and to have a common install base for the various experimenters.
The base SL distribution is Enterprise Linux, recompiled from source. </div>
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<b>Brian Bockelman:</b>
At Nebraska, we also use Scientific Linux 6.3. The CMS experiment has about 50 computing sites throughout the world and all use some variant of RedHat Enterprise Linux - be it RHEL licenses, CentOS, ROCKS, or Scientific Linux.<br />
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<b>-Why did you choose Free Open Source Software? Do you also use some proprietary tools? </b></div>
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<b>Sebastien Ponce:</b>
Open access in general has a strong tradition at CERN. In 1953, the Convention for the establishment of CERN already stated :
"the results of its experimental and theoretical work shall be published or otherwise made generally available".
This still holds today in all fields where CERN is involved including computer science. For example, it's worth mentioning two initiatives outside software in this domain: the open hardware initiative with its Open hardware license and the Sponsoring Consortium for Open Access Publishing in Particle Physics.
So when talking about software, CERN is naturally releasing its code under free open source licenses and makes heavy use of free open source software.
Having said that, we also use non free open source software, and proprietary tools in specific domains like civil engineering, databases or tape storage.<br />
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<b>-How does the distribution of data works? (Or: Can you explain briefly Castor and the "tiers" mechanism?)
</b></div>
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<b>Brian Bockelman:
</b>We primarily have two types of data: simulated event data, and data read from the detector. The detector data starts off underground at CERN, where it is transferred to the CERN data center. A first quick transformation of the data (called "reconstruction") is done there, written to tape in Castor, and transferred to multiple "Tier-1" sites around the world.
At the Tier-1 sites, a second copy is written to tape and another processing pass is done. The data, now in a format appropriate for physicists to use in their work, is copied to one of forty CMS Tier-2 sites like Nebraska. Compared to the Tier-1s, which are fully utilized by centrally-planned processing, the Tier-2s are somewhat chaotic. Each user will be analyzing a different set of data with a different application; the analysis may have to work at ten different sites to complete.
The distributed nature of our work has led to quite a bit of middleware development - we have to distribute petabytes of data to multiple sites and make it so the user has transparent access to all of them.<br />
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<b>-What is Apache Hadoop, and why do you use it? </b></div>
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<b>Brian Bockelman:</b>
CERN writes its data in Castor and the Tier-1 sites write data into various niche systems which integrate directly with tape. However, at the Tier-2s, we have more flexibility in selecting the storage system.
A storage system needs to be able to stitch together multiple disk servers (there's about 2.5 petabytes of raw disk at Nebraska), provide a uniform namespace, be quite reliable, and have sufficiently high-performance. We need to be able to layer grid components for cross-site data access. Finally, this all needs to be easy to administer: the whole of our Tier-2 has two sysadmins, and we cannot afford to dedicate one solely to filesystem issues.
In late 2008, I began examining the Hadoop Distributed File System (HDFS) from the Apache Software Foundation. HDFS is implemented in Java and shares many design characteristics with the Google File System. The services run in userspace and layer on top of the disk server's filesystem. There are two basic node types, the namenode and the datanode (there is a third, the secondary namenode, which can be ignored for now). The namenode manages the namespace and orchestrates access to data for user processes; the namespace metadata is kept in-memory, allowing for incredibly fast read-access. It also breaks the files into fixed-size blocks (we use 128MB) and selects the datanode to host each block. It keeps track of each block's location and makes sure there is a sufficient number of replicas (we require two replicas for each block).
Because of the replication, HDFS is a breeze to manage. The death of an entire datanode is not a critical event: the namenode will simply create another replica of all the data it held. In fact, we don't even bother returning dead hard drives until we have at least a box full of dead ones. The only host we have to keep an close eye on is the namenode; it's a lot easier to have only one critical system compared to dozens.
While other systems may have similar or better performance characteristics, the reliability and ease-of-management is really why we selected HDFS in the end. It's also quite comforting to know that we won't ever be the largest user of HDFS; it's nice to have someone else work out scale issues.
We converted the site to HDFS in early 2009; since our initial success, six other Tier-2 sites in the US have also converted. We have been happily using HDFS since then, but I try to keep an eye on the alternates. The systems which are closest to HDFS are Ceph and Gluster, but we're not planning a switch anytime soon. </div>
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<b>-In particular, how the analysis of ATLAS and CMS data have been done? </b></div>
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<b>Brian Bockelman:
</b>Readers familiar with Hadoop notice that I only described the filesystem, but skipped the distribution of the Map/Reduce component.
This is because we actually don't use Map/Reduce: the resources CMS uses overlaps with those used by other LHC experiments on the grid. The entire grid is about 140 computing sites; getting everyone to agree on a single technology implementation is nearly impossible. Instead, we make sure we have interoperability between sites' technology using platforms from organizations like the Open Science Grid or the European Middleware Initiative.
Our analyses are based on breaking large tasks into many batch system jobs which are distributed about the planet; they read data directly from the sites' storage system. Conceptually, it's close to Map/Reduce: we are often either transforming data to different formats and filtering out data not relevant to the individual's work. This is done in several passes, each one having smaller, more-specialized data than the last. Finally, we end up with something which the physicist can move off the grid and onto his laptop for some final work using techniques like neural networks and multi-variate analysis. </div>
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<b>-Is there something you think is still missing in FOSS for research (physic research)? </b></div>
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<b>Brian Bockelman:
</b>As mentioned by Sebastien, the field of High Energy Physics (HEP) has a long history of collaboration, leading to its natural fit with FOSS. Accordingly, basically all the tools used in research are open source. It adds up to a huge amount of software - the core physics software of CMS alone amounts to about 6 million lines of code.
Nothing strikes me as "missing", but there are always things we could do better. I work closely with sysadmins running university clusters, so I always hear their pain:
- Package management on RHEL still has rough spots. It's nearly impossible to roll-back from a significant upgrade; in the end, we typically just have to scratch the host and let Cobbler/Puppet rebuild it. We also have poor tools for userspace installs: a user often has to resort to compiling tens of software packages from source if they want to install something in their home directory without sysadmin help, yet they may not want the responsibilities of running their own VM (and maintaining a safe, fully-patched configuration). The amount of work necessary for a non-admin user to install their favorite python module for personal use is striking when compared to how easy it is for the sysadmin.
- We tend to configure software a single piece at a time, yet complex services may involve a dozen pieces of software and scattered system configuration. There don't seem to be many "best-practices" available for configuring many pieces of software that don't involve editing dozens of configuration files.
The progress made since I've started is indeed striking; for example, I'm incredibly excited to roll out systemd at work. I've had enough of poorly-written init scripts for my lifetime.
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<b>-What do you think about the future of computer aided analysis, and which role FOSS can have in it? </b></div>
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<b>Sebastien Ponce:</b>
Computer aided analysis has imposed itself as the main tool for scientific researchers and I believe it will stay so for long.
FOSS has an essential role to play there as it is the most efficient approach to software for this community, that is spread, heterogeneous and where users have a high level of education.
As CERN has proven in the last 58 years, collaborating is the key to success in such a context, and FOSS is making it happen in the computer science field.
So I see FOSS as a key player of computer aided analysis in the future (and already now), that may structure all the software in the domain.
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<b>-Can you give us your personal opinion about the use of FOSS in university and research institutes?<br />Brian Bockelman: </b>I personally think that the use of open source software (and free open source software in particular) in universities and research institutes is fundamental and I see two main reasons for this.<br />
First because of the nature of research institutes and universities : they usually have a small budget, but very skilled and talented people. This usually makes the payment of licenses associated with non free software an heavy constraint while the skills needed to support and maintain open source software are often available.<br />
So free open source software matches well here, next to non free open source software when support and/or maintenance are outsourced. The second reason is that open source software in general (free or not) allows university and research communities to build extremely large and heterogeneous systems (like the LHC computing grid(5)). It would be extremely difficult to agree on a unique set of proprietary tools for such systems across 100s of laboratories with different constraints and strategies. With open source software, one can adapt more easily existing tools so that different solutions cooperate. This was a key ingredient in the success of the grid.<br />
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<b>-Is there something you would like to add for our readers? </b></div>
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<b>Sebastien Ponce:</b>
If you are interested in knowing more about CERN and our research there (including in computer science), have a look at our web site (http://cern.ch) or come and visit us in Geneva.
It's free and our computer center can be part of the tour. You may also be interested in CERN's job offers, there are all available on our web site.<br />
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Ok this is, basically, the interview. Before concluding this post, even if it's off topic, I would like to thank Jonathan Riddell for sending me a Kubuntu polo shirt. I received it just some days ago, and I wanted to wear it immediately. Even if in those days it snowed, and it was quite cold (about 4°C). Worth it:<br />
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LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com2tag:blogger.com,1999:blog-8703760419767782919.post-67368969349958972882012-12-04T15:39:00.001+01:002012-12-04T15:39:21.289+01:00Pengpod's GNU/Linux tablets are coming. Also in Italy.I just read the news that Pengpod is going to release a couple of tablets with a GNU/Linux system (not with Android).<br />
I got the news from ANSA, the main italian agency (<a href="http://www.ansa.it/web/notizie/rubriche/tecnologia/2012/12/04/gennaio-tablet-Linux-sfida-Android-Apple_7899132.html">http://www.ansa.it/web/notizie/rubriche/tecnologia/2012/12/04/gennaio-tablet-Linux-sfida-Android-Apple_7899132.html</a>) and the title of the article is "In January a Linux tablet will challenge Android and Apple".<br />
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The news is beautiful for two reasons. First: a new tablet with GNU/Linux, hurray. Second: an italian press agency (the most important, inter alia) mentioned Linux. Ok, I know it's GNU/Linux and not "Linux" but don't demand too much: it's incredible that someone in our press world recognized just the existence of GNU/Linux. In Italy, basically, it's unusual to read about GNU/Linux on a newspaper. At maximum you will hear about "Open Source" the word "free" is not even mentioned. And, "GNU/Linux" and "Linux" are often considered synonyms. The title itself of the the article recognizes GNU/Linux as a character of the mobile challenge.<br />
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Talking about the tablets, they seems to be good products, expecially for their price. Personally, I can't wait to see them running Plasma Active.<br />
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So it's a good period for Italy in freedom of software: today we hear this news, and some weeks ago our parliament has issued a law that forces public administration to choose Free Open Source Software every time it is possible (and buy proprietary programs only if there is no FOSS alternative). This is the base for a mentality change: if everything goes well, in less than ten years FOSS will not be just "an alternative", but it will be "the normality".LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com1tag:blogger.com,1999:blog-8703760419767782919.post-52129598014286862562012-10-15T14:08:00.000+02:002012-10-15T14:08:09.220+02:00Progetto Archimede: energy for everyoneComputers, obiously, need energy to work. And so do all the other machines: the problem of power sources is becoming bigger every day, since we don't have a renewable energy source that could really replace fossil fuels. Or do we?<br />
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Some months ago I wrote an article for BBC Science Italy, about the "Progetto Archimede" (Archimedes Project) built from the ENEA based on an idea of Carlo Rubbia (an italian Nobel prize winner for physics). Because of some troubles in the layout of the magazine, we decided to not publish the article. For this reason I would like to publish at least the interview I did at the italian minister of environment Corrado Clini (and former director of ENEA).<br />
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Just for those who don't know what we are talking about, Progetto Archimede is a new kind of power plant based on solar thermodynamic that works both in day and night: according to Rubbia's calculations, a power plant of this type large about 2000 Km<small><sup>2</sup></small> (this is nothing in terms of desertic areas) can give energy to the whole Europe. Forever.<br />
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Here's the interview:<br />
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<iframe allowfullscreen="allowfullscreen" frameborder="0" height="315" src="http://www.youtube.com/embed/L_9senwonK8" width="560"></iframe>LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com0tag:blogger.com,1999:blog-8703760419767782919.post-75672662966668738932012-09-03T18:26:00.003+02:002012-09-03T18:26:37.625+02:00Social networks: the new major mediaA few days ago, I got an email from Sarah Wenger, with an infographic she developed about the power of online people. There is a line that says "Social media is becoming the new major media". This is basically right, I think we are all aware that Facebook and Twitter (for example) are the main way for the diffusion of news. Is this good or bad? This question, obiously, is stupid. Tecnology is not good and not bad: tecnology is just an instrument. The use people do of tecnology can be positive or negative.<br />
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<a name='more'></a>The problem is that social networks does not have an "editorial staff" that checks news. This is the reason of many fake news (in italian we call them "bufale", like the mozzarella). Sure, also newspaper and televisions are not "super partes", but usually they are a little more reliable. Basically, an ill-intentioned person could use social networks to spread news to control what people think. In Italy, we seen something like this some months ago, when Facebook was filled with fake news about new incredible taxes (I remember a "tax on dogs"): those news were made to put the public against new laws the Government made to fight tax evasion.<br />
The freedom of internet can be used to control people. And there is no tecnical solution, since the problem does not came from the tecnology: free software can not help in this situation. The only solution is that people must use the brain.<br />
This is the reason for which I think in the primary school children should be taught to understand what is true and what is not, without believing at anything they read on the internet.<br />
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By the way, you can find the full infographic at the address: <a href="http://open-site.org/blog/power-to-the-online-people/">http://open-site.org/blog/power-to-the-online-people/</a>LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com3tag:blogger.com,1999:blog-8703760419767782919.post-34393487072140189962012-08-25T22:07:00.000+02:002012-08-25T22:07:07.854+02:00In memoriamI just read on the italian main press agency that Neil Armstrong, the first man that walked on the moon, died. This blog talks about tecnology, and I thought it's important to remember that the Apollo XI mission is the simbol itself of what the human kind can do using science, tecnology, and all the amazing power of our brain. Basically, in less than a century we came from a situation where flying was just a mere dream, to seeing a man walking out of Earth atmosphere and over the Moon.<br />
Sometimes I ask myself if cavemen would have ever been able to imagine that in the future someone would be able to touch the very surface of Moon.<br />
Fellini, in a movie, talked about some mad people that wanted to take the Moon and bring it here, on the Earth. Armstrong, Aldrin, and all the other men of Apollo program are maybe the people who went as near as possible to this dream.<br />
In conclusion, thank you Neil, since you demonstrated what we are able to do with science (and also a little bit of courage).LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com4tag:blogger.com,1999:blog-8703760419767782919.post-29471207885887241432012-06-29T14:36:00.000+02:002012-06-30T12:45:47.869+02:00KDE on the Raspberry PiAs you may know, there is no Kubuntu for Raspberry, due to the incompatibility of Kubuntu ARM version with the little computer. I wanted to create an image for raspberry most similar as possible to Kubuntu, so I basically took the original Debian release and add some packages to have the entire Plasma Desktop. The result is quite nice, I think, and the system itself uses about 100-110 MB of the total RAM (there is also some swap on the card image). It's also quite speddy: the only problem could be that when you launch a new program, for some seconds the CPU load is 100%. You just need to wait a little and then eveything returns fine. The image can be downloaded from this link:<br />
<a href="http://www.zorbaproject.org/raspberry/debian-raspberry-kde.img">http://www.zorbaproject.org/raspberry/debian-raspberry-kde.img</a><br />
and you can dd it on a 4GB SD card with the command:<br />
<span style="font-family: 'Courier New', Courier, monospace;">dd bs=1M if=~/debian-raspberry-kde.img of=/dev/sdd</span><br />
<span style="font-family: inherit;">if your SD card is /dev/sdd, obiously.</span><br />
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Just a note: the username is "pi" and the password is "raspberry".<br />
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Have fun hacking with Raspberry and KDE.<br />
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EDIT: Now with screenshots:<br />
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I decided to shot photos with a camera, because it shows that there is no "trick" and what you are seeing is really KDE on a RaspberryPi.<br />
If you want to look at other shots, here they are: <a href="https://picasaweb.google.com/109718345247929494628/KDEOnRaspberryPi">https://picasaweb.google.com/109718345247929494628/KDEOnRaspberryPi</a>LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com41tag:blogger.com,1999:blog-8703760419767782919.post-83328739361177556112012-06-02T22:27:00.000+02:002012-06-02T22:27:34.755+02:00Raspberry Pis have arrivedJust writing to say that my RaspberryPi from Farnell and the one from RS Component have arrived yesterday.<br />
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I'm playing with them a little, doing some experiments, and actually they seems quite good, expecially for the price. The official Debian GN/Linux distro runs fast and without troubles. Actually, I'm trying to prepare a Kubuntu version for the RaspberryPi, but it will take some time, I think, to make it work smoothly.<br />
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If you want to give a look at them, you will find all the pictures in my gallery:<br />
<a href="https://picasaweb.google.com/109718345247929494628/RaspberryPi">https://picasaweb.google.com/109718345247929494628/RaspberryPi</a>LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com2tag:blogger.com,1999:blog-8703760419767782919.post-19343695525983705592012-04-21T19:34:00.000+02:002012-10-24T10:21:01.683+02:00Internet ruining brains?A reader send me an email, because he wanted to know what I think about an image he prepared. The graphic has an explicit title "Internet ruining your brain" (by the way: the image can be found at the address http://www.forensicpsychology.net/internet-ruining-your-brain/). Now, what to say about this work?<br />
I can agree with the informations (and the graphic is nice), but I absolutely disagree about the opinion expressed:<br />
sure, the internet is reducing our use of memory. But this is not a bad thing.<br />
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It's obious that, for someone, internet is still a new thing, and as every news it could be considered scary. For example, the legend says that when writing have been invented, many people believed it would kill the memory skills of men. But where would we be, now, without writing? Everything in our life is based on the possibility to write. The fact is that, every time we reduce the use of memory, we have the chance to improve our intelligence.<br />
In many countries, expecially countries with a culture based on academic knowledge like Italy, memory is often confused with intelligence. Many people think that remembering a large number of things means to be smart, like Pico della Mirandola (<a href="http://en.wikipedia.org/wiki/Pico_della_Mirandola">http://en.wikipedia.org/wiki/Pico_della_Mirandola</a>). Really, intelligence is the ability to link different pieces of knowledge together to solve a problem. Obiously, you may need some informations, but you don't need to remeber them. You just need to know how to get them. For example, it's completely unuseful to remeber the Van Der Vaals equation of gasses: you just need to know that it can be found on Wikipedia, and then you can use it to calculate the pressure of a certain quantity of gas in a box.<br />
The fact is that a person can study for the whole life: he/she will never be able to remeber or to know everything. But the internet can. Just wikipedia have a quantity of knowledge a hundred higher than what a single man can ever know. what does this mena, that the server hosting Wiki is smarter than a man? No. It just means that the server can remember a lot of things more, but it is not able to use them to solve a problem. Instead, a person who does not remember some equations, but knows how them work, is a smart person.<br />
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<b>Internet is not ruining our memory skills, it is just changing the way we remember things.</b> We don't remember concepts anymore, we remember where to find a concept. This means we need to store in our memory a lower number of things, because many concepts can be found in the same place. And this means, also, that we are practically able to work with a higher number of concepts than people who don't use internet. Because, in pratice, internet in just an extension of our brain.LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com8tag:blogger.com,1999:blog-8703760419767782919.post-49357788023207124942012-03-12T12:17:00.001+01:002012-03-12T12:17:26.426+01:00Meet the new Windows 8Usually, if you say "linux" people think about a very hard to use OS. But is it true? Is Kubuntu really an OS for developers and nerds? I'm going to present "common people" Kubuntu, saying it's the new version of Windows 8: let's see what they think about it without any prejudice. And, since I'm a serious person, I'm filming it.<br />
By the way: I got the idea because KDE has been awarded as best desktop environment of the year.<br />
So, here is the result of my "investigation":<br />
<div>
<iframe allowfullscreen="" frameborder="0" height="315" src="http://www.youtube.com/embed/D_nBBoekkdI" width="560"></iframe>
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<br />
The result is that, on 14 interviewed people only one already knew Ubuntu, but everybody said that KDE is better than Windows (the medium vote reached is 8/10).<br />
Well done, KDE.</div>LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com8tag:blogger.com,1999:blog-8703760419767782919.post-20602436334392423162012-03-01T14:08:00.000+01:002012-03-01T14:08:26.064+01:00KDE on Diaspora... why not?Just a little ago, I thought about a question: KDE is free software. Diaspora is free software. So, why not share KDE related posts on Diaspora? Doing this is quite easy, and I'm gonna tell you how. Every one of you (everyone that have a blog) can <b>follow these instructions to let people share blog posts on Diaspora</b>.<br />
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By the way, if you don't know what I'm talking about, Diaspora is a free social network, built in an interesting way that allows you to have always control on you datas. For more info have a look at <a href="http://www.whatisdiaspora.com/">www.whatisdiaspora.com</a> and register on <a href="http://joindiaspora.com/">joindiaspora.com</a>.<br />
A little info: on the official diaspora pod is not possibile, acutally, to create groups of users. It is, anyway, possible on another pod: <a href="https://diasp0ra.ca/">https://diasp0ra.ca/</a>. Also, on joindiaspora you can't simply register, since the number of users is limited. But on other pods the registration is immedate.<br />
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Some KDE developers are already on Diaspora, and there is also the official <b>Krita</b> account (<a href="https://joindiaspora.com/u/krita">https://joindiaspora.com/u/krita</a>). But we could also create a KDE-offical account, and use it to share official announcements.<br />
Another idea: it would be nice to put a little button "share on diaspora" in the posts of <b>dot.kde.org</b>.<br />
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<a name='more'></a><br />
If you have a <b>wordpress</b> blog, there is a dedicated add-on. If your blog uses another platform, wee, have a look at the official site to see what is better for you (<a href="http://diasporial.com/articles/share-on-diaspora-the-requirements">http://diasporial.com/articles/share-on-diaspora-the-requirements</a>). Basically, just use this code:<br />
<span style="font-family: 'Courier New', Courier, monospace;"><img src="http://iliketoast.net/img/diasporaWebBadge80x15_3.png" border="0" onClick="dshare();"> </span><div>
<span style="font-family: 'Courier New', Courier, monospace;"><script type="text/javascript"> </span></div>
<div>
<span style="font-family: 'Courier New', Courier, monospace;">function dshare() { </span></div>
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<span style="font-family: 'Courier New', Courier, monospace;">var url = window.location.href; </span></div>
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<span style="font-family: 'Courier New', Courier, monospace;">var title = document.title; window.open('http://iliketoast.net/dshare.html?url='+encodeURIComponent(url)+'&title='+encodeURIComponent(title),'dshare','location=no,links=no,scrollbars=no,toolbar=no,width=620,height=400'); </span></div>
<div>
<span style="font-family: 'Courier New', Courier, monospace;">return false; </span></div>
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<span style="font-family: 'Courier New', Courier, monospace;">} </span></div>
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<span style="font-family: 'Courier New', Courier, monospace;"></script></span>But hey: if you use <b>blogspot</b>, then just follow reading this little tutorial I have made this morning:<br />
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<a href="http://4.bp.blogspot.com/-fyuKHH3RgS8/T09il9xAg0I/AAAAAAAABIY/rlB85hfiFC8/s1600/share-diaspora1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="http://4.bp.blogspot.com/-fyuKHH3RgS8/T09il9xAg0I/AAAAAAAABIY/rlB85hfiFC8/s320/share-diaspora1.png" width="320" /></a></div>
Ok, first of all enter the "Model" tab on your blog's settings and click on the button "Edit HTML".<br />
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<a href="http://1.bp.blogspot.com/-C2arEZycxl4/T09ingLWh9I/AAAAAAAABIg/6SsORqppbFY/s1600/share-diaspora2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="http://1.bp.blogspot.com/-C2arEZycxl4/T09ingLWh9I/AAAAAAAABIg/6SsORqppbFY/s320/share-diaspora2.png" width="320" /></a></div>
Blogger will tell you that it's dangerous to edit directly the html structure of your blog's model, and ask you if you are sure to do this. Since you are a cool guy/girl you don't care about this alert. So, click on "Proceed".<br />
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<a href="http://1.bp.blogspot.com/-Y-z9QzvBE50/T09iq3Dj2kI/AAAAAAAABIo/vepnNEGOcmY/s1600/share-diaspora3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="http://1.bp.blogspot.com/-Y-z9QzvBE50/T09iq3Dj2kI/AAAAAAAABIo/vepnNEGOcmY/s320/share-diaspora3.png" width="320" /></a></div>
Now look at the HTML. Nice, right? We will need to see all the code, so click on the checkbox "Expand Widget Templates".<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://4.bp.blogspot.com/-FrojIIpwt-o/T09islLY1RI/AAAAAAAABIw/zhaMcK7d5vg/s1600/share-diaspora4.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="http://4.bp.blogspot.com/-FrojIIpwt-o/T09islLY1RI/AAAAAAAABIw/zhaMcK7d5vg/s320/share-diaspora4.png" width="320" /></a></div>
What we are looking for is the "shareButton" section, so press Ctrl+F and search for "<b:includable id='shareButtons' var='post'>".<br />
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<a href="http://3.bp.blogspot.com/-TspEtFtm_ic/T09iuaJgrsI/AAAAAAAABI4/F5mdrTaOKtc/s1600/share-diaspora5.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="http://3.bp.blogspot.com/-TspEtFtm_ic/T09iuaJgrsI/AAAAAAAABI4/F5mdrTaOKtc/s320/share-diaspora5.png" width="320" /></a></div>
Just after this line, we need to insert this code:<br />
<span style="font-family: 'Courier New', Courier, monospace;"><a expr:href='"http://iliketoast.net/dshare.html?url=" + data:post.url + "&amp;title=" + data:post.title' target='_blank' title='Share on Diaspora'><img src='http://joindiaspora.com/favicon.png' style='width:16px; height:16px; padding:0; border:0; vertical-align:top;'/></a></span><br />
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Then just save the code, and look at your blog.<span style="text-align: center;"> </span></div>
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<a href="http://3.bp.blogspot.com/-As9lj04gYA0/T09iyWyqjqI/AAAAAAAABJI/A4PdqyrjPmw/s1600/share-diaspora7.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="http://3.bp.blogspot.com/-As9lj04gYA0/T09iyWyqjqI/AAAAAAAABJI/A4PdqyrjPmw/s320/share-diaspora7.png" width="320" /></a></div>
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Under every post you will see the usual share buttons, but there's also the little Diaspora asterisk.</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://1.bp.blogspot.com/-6R4p2kXvD0o/T09iv8_C6iI/AAAAAAAABJA/10LgajDMKTc/s1600/share-diaspora6.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="http://1.bp.blogspot.com/-6R4p2kXvD0o/T09iv8_C6iI/AAAAAAAABJA/10LgajDMKTc/s320/share-diaspora6.png" width="320" /></a></div>
So, if you click on that simbol, will be opened another tab that allows you to choose the message to post, and the "aspects" to share with. After the last update of the Diaspora code, this interface is a little broken, but it sitll works.<br />
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Obiously, don't forget to use the button, once you placed it into your blog.</div>LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com5tag:blogger.com,1999:blog-8703760419767782919.post-24968780273357836572012-02-22T12:26:00.000+01:002012-02-22T12:26:09.814+01:00Ubuntu for Android... and Plasma Active?So, it's news of the day that Canonical presented Unity for Android devices (<a href="http://www.ubuntu.com/devices/android">http://www.ubuntu.com/devices/android</a>). As I seen the video I thought: well, also Plasma Active can do this. The problem is that there is no porting of Plasma Active for Android platform. So I'm asking: wich are the main techincal problems we could encounter in transforming Plasma Active in an app for this system (it's not rhetorical, I'm really asking it because I don't know)?<br />
Talking about the ethical question, sure, Android is not really FOSS. But it's the most used quasi-free system, and having Plasma Active for this system could only improve the freedom of users. It would also became a big "advertisement" for the whole KDE software compilation.<br />
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By the way, here's a video of Unity for Android in action:<br />
<iframe allowfullscreen="" frameborder="0" height="315" src="http://www.youtube.com/embed/ZQozs5tXxwY" width="560"></iframe>LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com10tag:blogger.com,1999:blog-8703760419767782919.post-49744681778191465452012-02-15T18:33:00.000+01:002012-02-15T18:33:56.802+01:00The "raspberry" that wants to change computer scienceSome months ago, the project RaspberryPi has been announced. Its purpose is very ambitious: creating a good computer at a very low price, so it will be possible to reduce the "digital divide". In January, models A and B have been presented (<a href="http://www.raspberrypi.org/faqs"><b>http://www.raspberrypi.org/faqs</b></a>), and they will be available <b>after February 20th</b>. The B model will cost <b>25 euros</b>.<br />
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The "flow rate" of this thing is enormous: having a computer, perfectly working, at about 25 euros, means that we will be able to computerize a lot of things: used with Arduino, RaspberryPi will make possible the low cost domotics.<br />
<br />
I asked some questions to Eben Upton, and I have managed to undestand a little bit more about what they are going to do.<br />
<b></b><br />
<a name='more'></a>First of all the name: they have choosen "Raspberry" because there are many computer industries with fruit names (e.g.: Apple, Blackberry,...) and Pi because, originally, they thought to use only Python (at least to let childs learn to write programs for this computer). Obiously, now is possible to use every language you want (it just needs to run on GNU/Linux sistems with ARM processors).<br />
RaspberryPi is a complete computer, so it can be used for every operation you usually do with a normal computer, but its low price has been the most important feature for Raspberry's creators: in fact, they thought as an educational instrument for childs, to learn them how to program a computer. Personally, I think that primary and secondary schools should teach programming to the kids. In fact, we are running into a world where everything works with a computer, and if you know how to control the computer, you will be able to manage your life. And, programming is really important for improving child's logic skills. I don't know how the rest of the world is, but in Italy our schools are mainly based on memory. They does not teach you to understand what you are doing, what you are reading: they only ask you to be able to repeat some phrases written by someone else before. Teaching computer programming will encourage childs to ratiocinate.<br />
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The recommended systems, for RaspberryPi are GNU/Linux distros, like Debian and Fedora. And, as you can see down here, Qt libraries work very good:<br />
<span style="text-align: center;"> </span><iframe allowfullscreen="" frameborder="0" height="295" src="http://www.youtube.com/embed/A-vBbqamNBU" style="text-align: center;" width="500"></iframe><br />
In a near future, a lot of companies will probably use Raspberry in their products, but actually RaspberryPi creators have no plan about this.<br />
I also asked Eben about the possibility of delivering another model of RaspberryPi with a wi-fi network card integrated, that could be a lot easyier (so you don't have to connect every computer with a cable, that is a little confusing in a classroom of 20 students). But, unfortunately, they don't have any official plan about wi-fi, actually (but I know they are thinking about it).<br />
There will be also a certain number of local shop points, so you won't need to get the computer shipped from the United Kingdom. Actually, anyway, there are no reliable informations.<br />
<br />
<b>Ok, dreams time</b>: now, just think about a mediacenter built with a RaspberryPi and a GNU/Linux distro with Plasma Mediacenter (I know it's not ready to be used, but I'm dreaming). With less than 100 euros you can have a complete Full HD mediacenter, usable to control some areas of your house (with the help of Arduino). For example, turn on a light with a console command, maybe from a remote ssh console.<br />
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A conclusive note: obiously, Eben Upton recommends you to follow the official site <b>www.raspberrypi.org</b> and consider buying a computer, when they will be available (after February 20th).LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com1tag:blogger.com,1999:blog-8703760419767782919.post-9509417030459082162012-02-07T19:00:00.000+01:002012-02-09T00:33:19.455+01:00Interviewing Ton Roosendaal: will it blend?Yes, I could not resist to associate Blender with "will it blend" my favourite way to use an iPhone (check out this video <a href="http://www.youtube.com/watch?v=_S8sxpK4_iA">http://www.youtube.com/watch?v=_S8sxpK4_iA</a>).<br />
<div>
<br />
Some days ago, I asked some questions to Ton Roosendaal and he, really nicely, found the time to answer. As you all may know, he is the creator of Blender and the head of the Blender Institute. Anyway, for me, the most important idea he developed is the "open movie" project. It introduces a completely new concept of creating an artistic opera, where the public can be an active part during the production and expecially after it, possibly improving the opera itself or creating another version (if it's a movie, you can create your own final). Basically, it's the power of free open source software ported to art, expecially cinematographic art.</div>
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Tra l'altro: se siete italiani, potrete leggere una traduzione dell'intervista con presentazione nel prossimo numero di GNU/Linux Magazine Italia.<br />
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<a name='more'></a><b>-So, this will be the first Blender "open movie" with real actors: is there a particular reason for which you decided this or it's just a director's choice?</b><br />
Each time I've picked a main theme connected to technical targets for Blender. The whole concept of our open movies is to get focus for a longer period on bigger targets, and have these targets well tested and validated immediate. That mimics the process how most (bigger) animation studios work with their in-house software. If there's one thing we stand out among the competition it's Blender's open source nature, which really makes it your own in-house software!<br />
After doing one game project and three animation films, doing a vfx based project was a very obvious choice. Modern film making happens with 3d software you know!<br /><br />
<b>-Can you tell us, briefly, the plot of Mango (obiously without spoilering)?</b><br />
In the distant future they find out that the nearing destruction of the World has been caused by a break-up in Amsterdam long ago. They then desperately send a fleet of space ships and robots back to the past to prevent this break-up to happen.<br />
(Also see blog post about this on <a href="http://mango.blender.org/">mango.blender.org</a> + Ian's reaction)<br /><br />
<b>-Since the open movie is also a way to let developers improve some Blender features, collaborating with the artists, the Mango team wrote some "development targets". Can you explain us, practically, what those targets are?</b><br />
Just 2 days ago we posted a very long article on our blog about the development targets. It's actually quite a too long list now, we will need to narrow it down still.<br />
Some techniques are impossible to avoid though; and the main one is camera tracking. That's an artist's tool in Blender that allows you to extract the 3D camera position, orientation and motion from shots. With that info you can then seamlessly merge artificial 3d rendered objects with the real footage. You can even take it steps further and use it to track bodies, faces or even do full motion capture of humans. All in Blender - without need of special equipment.<br />
Basic but good quality camera tracking is Blender already, released last month.<br /><br />
<b>-Now a technical question: do you use GNU/Linux distributions for producing this movie? Which free open source programs do you use, mainly, for the production?</b><br />
In the studio we use Ubuntu for the workstations and Debian for the render farm nodes. Exclusively free/open source tools are being used for the complete visual pipeline here. Apart from Blender that's of course the GIMP, MyPaint, Krita and Inkscape.<br />
An exception is for example the camera data itself - files from Red Epic cartridges require closed software to convert to regular readable image files. Also the sound editing and mix we don't do ourselves, we just accept the best offer from a composer or sound studio.<br /><br />
<b>-Italy has been, from the beginning of the 20th century, a very active country in cinematographic art, and the public is really interested in new movie ideas. Do you think to present Mango also in Italy, for example at the Venice festival (september 2012, it's about when you plan to complete your movie)?</b><br />
Yep, I'm a big fan of Italian cinema! But we make a humble short low-budget film, just 5-7 minutes, I don't think that would be a big event for the Venice festival. For sure I'll try to get it in of course :) We have two Italian artists working here on Mango, they would love to see this happen!<br /><br />
<b>-Which features would you like to see in a future version of Blender?</b><br />
For next year and later? I don't think we need so much new features specifically, what we need mostly is quality and good maintenance of features. With Blender being compared to the big commercial programs, we somehow have to organize our developer community to keep improving too. The only way to keep growing is to organize small/medium studios to get involved with development as well; to hire people to work on Blender and together work on a tool we all can use far more efficiently than any closed program.<br />
Once that's done we obviously have to make a big feature film together. And then add loads of new features again!</div>
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<i>Post Scriptum:</i> If you don't know what camera tracking is, watch this:<br />
<div style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="225" mozallowfullscreen="" src="http://player.vimeo.com/video/34442645?title=0&byline=0&portrait=0&color=ff9e54" webkitallowfullscreen="" width="400"></iframe></div>
<div style="text-align: center;">
<a href="http://vimeo.com/34442645">Digital Makeup in Blender</a> from <a href="http://vimeo.com/sebastiankoenig">Sebastian König</a> on <a href="http://vimeo.com/">Vimeo</a>.<br />
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<b>Edit:</b> Ton suggested me to put here some pictures from mango authors, so I have choosen these (click to see them bigger):</div>
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<a href="http://mango.blender.org/wp-content/gallery/movie-concept-art-01/brainCloud-and-scientist_mango_concept-art_04_net.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="160" src="http://mango.blender.org/wp-content/gallery/movie-concept-art-01/brainCloud-and-scientist_mango_concept-art_04_net.jpg" width="320" /></a></div>
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<a href="http://mango.blender.org/wp-content/gallery/movie-concept-art-01/genghis-jones-pod-active_mango_concept-art_02_net.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="150" src="http://mango.blender.org/wp-content/gallery/movie-concept-art-01/genghis-jones-pod-active_mango_concept-art_02_net.jpg" width="320" /></a></div>
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<a href="http://mango.blender.org/wp-content/gallery/movie-concept-art-01/thom-and-amsertdam_mango_concept-art_01_net.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="160" src="http://mango.blender.org/wp-content/gallery/movie-concept-art-01/thom-and-amsertdam_mango_concept-art_01_net.jpg" width="320" /></a></div>
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<a href="http://mango.blender.org/wp-content/gallery/team-artwork/chasing.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="180" src="http://mango.blender.org/wp-content/gallery/team-artwork/chasing.png" width="320" /></a></div>
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<a href="http://mango.blender.org/wp-content/gallery/team-artwork/underholes.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="180" src="http://mango.blender.org/wp-content/gallery/team-artwork/underholes.png" width="320" /></a></div>
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</div>LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com1tag:blogger.com,1999:blog-8703760419767782919.post-2334955820326626102012-01-14T10:28:00.000+01:002012-01-14T10:28:00.784+01:00Free the research #3<div style="margin-bottom: 0cm;">
<span class="Apple-style-span" style="font-family: inherit;">So this is the last part of the article I'm publishing as a serial. And I will talk about chemistry. In particular, I'm going to show you something about Avogadro, a very powerful program. By the way, did you know that this program takes its name from the italian chemist/physicist Amedeo Avogadro (http://en.wikipedia.org/wiki/Amedeo_Avogadro), best known for the definition of the "mole" concept with his follower Stanislao Cannizzaro? Basically, the mole is a unit to describe the number of objects you have. For example, having a mole of molecules means you have 6,022*10^23 molecules. And having a mole of books means you have 6,022*10^23 books. This number is now called "the Avogadro number", in honour to the scientist.</span></div>
<span class="Apple-style-span" style="font-family: inherit;"><br /></span><br />
<b style="font-size: large;"><span class="Apple-style-span" style="font-family: inherit;">Add a dimension to chemistry</span></b><br />
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<i><span class="Apple-style-span" style="font-family: inherit;">Website: <a href="http://avogadro.openmolecules.net/">http://avogadro.openmolecules.net/</a></span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;">Avogadro is one of the best programs to draw molecules in three dimensions. This program, anyway, can do a lot more: it has handy tools to build complex molecules, and gives you some informations about what you have drawn. There is another interesting program (that I will not describe since it's very easy to use): Kalzium. This one is very useful for its "calculators": these are some little tools allowing us to do some simple calculations (concentration of a soluzion, mass of a compound, etc...). There is also a wonderful chemical equation solver, and a "reader" of risk and security phrases. If you are just starting to learn chemistry, there is also a good glossay, that will show you the main laboratory tools and explain some practices.</span><br />
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<span class="Apple-style-span" style="font-family: inherit;">Okay, the following part is written in tutorial-style.</span></div>
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<span style="font-family: inherit;"><a href="http://4.bp.blogspot.com/-FbmVNEO2a_E/Tqq69_wgomI/AAAAAAAAAc8/tmu9Ag19pqM/s1600/avogadro1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="http://4.bp.blogspot.com/-FbmVNEO2a_E/Tqq69_wgomI/AAAAAAAAAc8/tmu9Ag19pqM/s320/avogadro1.png" width="320" /></a></span></div>
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<span class="Apple-style-span" style="font-family: inherit;"><b style="text-align: -webkit-auto;">THE FIRST SKETCH –</b> Pressing the F8 key we enter into the "draw" view: the <b style="text-align: -webkit-auto;">Draw settings</b><span class="Apple-style-span" style="text-align: -webkit-auto;"> tab allows us to choose wich atom draw and with wich kind of bond link it to another one (the link can be built clicking on an atom and then arriving to the other keeping the left mouse button pressed).</span></span></div>
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<span style="font-family: inherit;"><a href="http://4.bp.blogspot.com/-8yROCKEXJHU/Tqq6-rUXgJI/AAAAAAAAAdE/OqMSy43h5J4/s1600/avogadro2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="http://4.bp.blogspot.com/-8yROCKEXJHU/Tqq6-rUXgJI/AAAAAAAAAdE/OqMSy43h5J4/s320/avogadro2.png" width="320" /></a></span></div>
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<span class="Apple-style-span" style="font-family: inherit;"><b style="text-align: -webkit-auto;">IMPROVE IT –</b> We can improve the drawing with the menù <b style="text-align: -webkit-auto;">Extensions</b><span class="Apple-style-span" style="text-align: -webkit-auto;"> (the first one on the left) and choosing </span><b style="text-align: -webkit-auto;">Optimize geometry</b><span class="Apple-style-span" style="text-align: -webkit-auto;">. Automatically, the program will move the atoms to reach the best geometry, based on the dimension of bonds and steric hindrance.</span></span></div>
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<span style="font-family: inherit;"><a href="http://4.bp.blogspot.com/-gd7zEZNBRfY/Tqq6_qqmrSI/AAAAAAAAAdM/UMqu97Cq7MY/s1600/avogadro3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="http://4.bp.blogspot.com/-gd7zEZNBRfY/Tqq6_qqmrSI/AAAAAAAAAdM/UMqu97Cq7MY/s320/avogadro3.png" width="320" /></a></span></div>
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<span class="Apple-style-span" style="font-family: inherit;"><b>A BETTER VIEW</b> – Pressing the F9 key we enter the navigation view: holding the left mouse button we can rotate the view, while using the right button it's possible to translate it. The central button controls the zoom. If you want to save the image, use <b>File/Export</b> menù.</span></div>
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<b><span class="Apple-style-span" style="font-family: inherit;">Have a look to conformers, the energy, and some other things</span></b><br />
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<span style="font-family: inherit;"><a href="http://4.bp.blogspot.com/-mOGI_J0YLUU/Tqq7Aj2YFlI/AAAAAAAAAdU/oileNi_W-S8/s1600/avogadro4.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="http://4.bp.blogspot.com/-mOGI_J0YLUU/Tqq7Aj2YFlI/AAAAAAAAAdU/oileNi_W-S8/s320/avogadro4.png" width="320" /></a></span></div>
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<span class="Apple-style-span" style="font-family: inherit;"><b style="text-align: -webkit-auto;">CONFORMERS –</b> In the second menù <b style="text-align: -webkit-auto;">Extensions</b><span class="Apple-style-span" style="text-align: -webkit-auto;">, is present the voice </span><b style="text-align: -webkit-auto;">Molecular Mechanics/Find conformers</b><span class="Apple-style-span" style="text-align: -webkit-auto;">: this way the program will give us a list of all the possible conformers (you can see the list using <b>View/Properties/Conformation properties</b>).</span></span></div>
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<span style="font-family: inherit;"><a href="http://4.bp.blogspot.com/-yYjr4bfDTd8/Tqq7BScSQfI/AAAAAAAAAdc/34Uw_w9N9hU/s1600/avogadro5.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="http://4.bp.blogspot.com/-yYjr4bfDTd8/Tqq7BScSQfI/AAAAAAAAAdc/34Uw_w9N9hU/s320/avogadro5.png" width="320" /></a></span></div>
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<span class="Apple-style-span" style="font-family: inherit;"><b style="text-align: -webkit-auto;">PROTEINS –</b> It could also be useful to build a peptide: just click on <b style="text-align: -webkit-auto;">Compile/Insert/Peptide</b><span class="Apple-style-span" style="text-align: -webkit-auto;"> and then choose the amino acids with wich we want to build the proteine. You can also choose the stereochemistry of the molecule and the initial/final terms.</span></span></div>
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<span style="font-family: inherit;"><a href="http://2.bp.blogspot.com/-Dr90rjcHhgc/Tqq7CM8Pk2I/AAAAAAAAAdk/mP83p2rYqb4/s1600/avogadro6.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="http://2.bp.blogspot.com/-Dr90rjcHhgc/Tqq7CM8Pk2I/AAAAAAAAAdk/mP83p2rYqb4/s320/avogadro6.png" width="320" /></a></span></div>
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<span class="Apple-style-span" style="font-family: inherit;"><b style="text-align: -webkit-auto;">ATOMS</b> – The menù <b style="text-align: -webkit-auto;">View/Properties/Atom</b><span class="Apple-style-span" style="text-align: -webkit-auto;"> allows us to see informations about every atom present in the molecule: for example, the valence value and the partial charge. Obiously, if the molecule is not an ion, the partial charge will always be zero.</span></span></div>
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<span class="Apple-style-span" style="font-family: 'Times New Roman', serif;"><i><br /></i></span></div>LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com8tag:blogger.com,1999:blog-8703760419767782919.post-63430919416720040642011-12-16T17:55:00.000+01:002011-12-16T17:55:42.668+01:00Kubuntu should not use KDE only software (or should it?)<br />
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The last week, on the kubuntu-devel mailing list, we discussed the idea to distribute Kubuntu not only with the traditional CD, but also in a DVD containing all the software the user can need. Ok, codecs could have licence problems, but there are some interesting Dolphin service menu, some plasmoids, and software like the wonderful Kdenlive that could be included without troubles... It has also been proposed to release the system directly with Firefox installed. The proposal came from Felix Geyger, and immediately many people said it's a good idea (me too). Other developers, anyway, didn't liked it. Some of them said that Kubuntu must deliver only KDE software.<br />
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Personally, I don't like religious wars between KDE/GTK software (I don't like religious wars at all). Seems to me that "fragmentation" is one of the biggest problems of the FOSS world. This means that wonderful forces are practically wasted creating three similar programs working quite good, instead of creating only one that works very good.<br />
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In Italian, there's a good phrase to describe this situation (it's a little rude): "è come pisciare contro vento". That in English sounds "it's like pissing upwind". In fact, you are creating a problem bigger than the one you're trying to solve.<br />
Some KDE programs are wonderful, never found anything better. But some of them are not so good: one of these is Rekonq. Using only KDE software on Kubuntu means it will became a distribution for "nerds" (it is not intended in an offensive way). I think that, if we want Kubuntu to be a real alternative for proprietary systems, we need to help the users that actually use Windows or MacOS to join our platform. The main way to do this is to let them use the maximum possible number of programs they already use. Actually, Firefox is used <br />
by the 40% of the total users, Rekonq by less then 1%. What does this tell to you? Plus, remember that a Windows user or a MacOs user probably use Firefox, but he/she sure does not use Rekonq. Having the same applications they used to work with, on GNU/Linux systems, is the main request I get by the people I "drive" to <br />
Kubuntu.</div>
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So I'm asking: what do you think about it?</div>LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com57tag:blogger.com,1999:blog-8703760419767782919.post-45445734157888880842011-11-07T19:22:00.000+01:002011-11-07T20:14:48.967+01:00Free the research #0<span class="Apple-style-span" style="font-family: inherit;">I decided to publish here, in serial form, the translation of an article I wrote for GNU/Linux Magazine Italy some months ago. Please take note that this post, as all the content of this blog, is released under Creative Commons Attribution 3.0 There will be 4 parts, dedicated to RKWard, Maxima, Kile, and Avogadro+Kalzium. Ok, let's start...</span><br />
<span class="Apple-style-span" style="font-family: inherit;"><br /></span><br />
<span class="Apple-style-span" style="font-family: inherit;">The work of the researcher has changed a lot in the last years, and it's still changing: we heavily use computers. If some time ago we used to draw plot by hand, now we use computer programs, articles and reports were written with a writing machine, and now they are written and shared digitally (for example in PDF). The biggest calculations are made by computers, not by humans. This means that a lot of computer tools are needed, and everybody knows that their price is not always low.</span><br />
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<a name='more'></a>In this situation, the free software can be a very interesting choice, because of it's more stupid meaning ("free" as in "free beer"). Obioulsy free software should be used by researchers also because the knowledge must be accessible by everyone, and it should not have barriers obstructing the freedom to read something written by another person. Also free hardware could be interesting, but there are not so much projects (Arduino could be wonderful, in the future).<br />
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<span class="Apple-style-span" style="font-family: inherit;">Free software programs are actually able to replace proprietary software, and that's what I'm going to show in this article. </span></div>
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<a href="http://4.bp.blogspot.com/-uSEjBPiFxz8/Tqq7FmeNC1I/AAAAAAAAAd8/yLNvnNuvWQ0/s1600/rkward.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span class="Apple-style-span" style="color: black; font-family: inherit;"><img border="0" height="250" src="http://4.bp.blogspot.com/-uSEjBPiFxz8/Tqq7FmeNC1I/AAAAAAAAAd8/yLNvnNuvWQ0/s400/rkward.png" width="400" /></span></a></div>
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<span style="font-family: inherit; font-size: medium;"><b>RKWard</b></span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">Website: <a href="http://rkward.sourceforge.net/">http://rkward.sourceforge.net/</a></span></i><br />
<span class="Apple-style-span" style="font-family: inherit;">R is a powerful language for data analisys, completely free, and it has a CLI (Command Line Interface) interpreter. To make its use easyer, anyway, there are many GUIs (Graphic User Interface): one of the better developed is RKWard. Starting RKWard, the program will ask us what we want to do: for example, we could choose to create a new table. We will see a two-part view: in the upper section it's possible to manage the variables (they will represent the table's columns) specifying name and format. In the lower part of that view, instead, there is the table itself: the columns, obiously, are those we created in the upper section. Now, please remember that, for doing some particular tasks, R may need some packages to be included in the project: to install them, there is a simple package manager integrated directly into RKWard. The only problem is that the installation is not possible if you have no root privileges. This means you will have to save your work, close the program then reopen it with </span><br />
<span class="Apple-style-span" style="font-family: 'Courier New', Courier, monospace;"><i>kdesudo rkward</i></span><br />
<span class="Apple-style-span" style="font-family: inherit;">It's also possible to write this command directly into KRunner, pressing <b>Alt+F2</b>, and no need to open a console.</span><br />
<span class="Apple-style-span" style="font-family: inherit;">To save the project simply follow the menu <b>Workarea/Save workarea</b>.</span><br />
<span class="Apple-style-span" style="font-family: inherit;">After we have inserted our datas into the table, it's possible to start working on them: the menù <b>Plot</b> contains various kind of plots. If you want to obtain the classical dispersion plot, just use <b>GenericPlot</b>: the "Plot Options" button allows you to configure the plot in every characteristic. To make another example, <b>BoxPlot</b> shows the deviation of a variable's values: in its options, we can choose to see the mean or the standard deviation (SD).</span><br />
<span class="Apple-style-span" style="font-family: inherit;">Using the R console (accessible from one of the buttons in the lower part of the window) it's possible to write directly in R language. For example, the command:</span></div>
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<i><span class="Apple-style-span" style="font-family: 'Courier New', Courier, monospace;">model<-lm(formula
= my.data[["Y-axis"]] ~ my.data[["X-axis"]]) </span></i>
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<span class="Apple-style-span" style="font-family: inherit;">allow us to build a model (that is called "model"... original, isn't it?) in which we study the relation between the variable we called Y-axis and the one called X-axis. It would be, then, a good idea to check that the linear regression makes sense, with the Students test:</span><br />
<i><span class="Apple-style-span" style="font-family: 'Courier New', Courier, monospace;">errors<-residuals(model)</span></i></div>
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<i><span class="Apple-style-span" style="font-family: 'Courier New', Courier, monospace;">t.test(errors)</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;">The program will write a report that ends with the "mean of x": if this value is near to zero, this means that the linear regression we used really works. If this is the case, we would like to obtain a plot. Just use the command:</span></div>
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<i><span class="Apple-style-span" style="font-family: 'Courier New', Courier, monospace;">plot(model)</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;">R will give us many different kind of plots (after drawing one, we have to press "Enter") and, at the end, we can use the buttons <b>previous plot</b> and <b>next plot</b> to see them all.</span></div>LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com0tag:blogger.com,1999:blog-8703760419767782919.post-10187669359051771842011-11-07T13:23:00.000+01:002011-12-22T15:06:56.323+01:00Free the research #2<div style="margin-bottom: 0cm;">
Ok, this is the third part of the serie about doing scientific research with GNU/Linux, and we are gonna talk about Latex (not the material.... ok, stop laughing now).</div>
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<a href="http://2.bp.blogspot.com/-yTFLkYpewaU/Tqq7EhNWO5I/AAAAAAAAAd0/2Jzc-snhzVo/s1600/relazione.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span class="Apple-style-span" style="font-family: inherit;"><img border="0" height="274" src="http://2.bp.blogspot.com/-yTFLkYpewaU/Tqq7EhNWO5I/AAAAAAAAAd0/2Jzc-snhzVo/s320/relazione.png" width="320" /></span></a></div>
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<span style="font-family: inherit; font-size: medium;"><b>Reports? Use Latex</b></span></div>
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<span class="Apple-style-span" style="font-family: inherit;">Website: http://kile.sourceforge.net/</span><br />
<span class="Apple-style-span" style="font-family: inherit;">What is Latex (<b>http://en.wikipedia.org/wiki/LaTeX</b>)? It's a
metalanguage, like html, and helps us to paginate our documents. Basically, we say to Latex what we want to write, wich images or tables should be inserted into the document, and it will prepare the layout automatically, using common sense. Since an example is better than a thousand words, let's see one immediately. </span><br />
<a name='more'></a><span class="Apple-style-span" style="font-family: inherit;">First of all we need to install an editor for Latex: one of the best choices is Kile (at least the version 2.1). Anyway, every other editor is fine. So, open your editor and create a new document: in Kile, there is a wizard that helps you choosing the main settings. Once you have a document ready, try writing these lines:</span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">\documentclass[a4paper,10pt]{article}</span></i></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">\usepackage{graphicx}</span></i></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">\usepackage[italian]{babel}</span></i></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">\usepackage[utf8]{inputenc}</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;"><i>\title{</i><i>Synthesis of</i><i> Ala-Leu-OMe}</i></span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">\author{Tringali
Luca}</span></i></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">\begin{document}</span></i></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">\maketitle</span></i></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">\begin{abstract}</span></i></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">Reaction between Boc-L-Ala-OH and Leu-OMe to obtain Ala-Leu-OMe</span></i></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">\end{abstract}</span></i></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">\section{Mechanism of reaction}</span></i></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">\includegraphics[width=130mm]{meccanismo.png}</span></i></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">\section{Experimental procedure}</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;"><i>First of all, in a flask for 100 ml, insert 0.5 g of Boc-L-Ala-OH and 10
ml of CH$_{2}$Cl (suitable for synthesis of peptides) saturating the flask</i><i> with Argon. Bla bla bla... At the end of the reaction, register the $^{13}$C NMR spectrum.</i></span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">\end{document}</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;">Please note that, before trying to compile the document, you will need to put a file called "meccanismo.png" in the same folder of the .tex file (Latex documents have ".tex" extension). You can take the image from here, if you want: <a href="https://picasaweb.google.com/109718345247929494628/Varie?authkey=Gv1sRgCKiUi4a9jZCcYA#5688945887642836658">https://picasaweb.google.com/109718345247929494628/Varie?authkey=Gv1sRgCKiUi4a9jZCcYA#5688945887642836658</a>.</span><br />
<span class="Apple-style-span" style="font-family: inherit;">Now, give a look at the Latex code: the first line specifies that we are going to write an article, with A4 pages, and a font size of 10 points. The package "graphicx" allows you to include graphical objects, like images. The two following lines, instead, load a complete set of characters (useful if you are writing in italian, for example, and you need accented letters). The "title" tag specifies the title of the document (who would have thought?), while the "author" tag contains the naem of the author(s). Then, the document begins, and we immediately ask Latex to prepare the title. Under the title we put the abstract: it's a phrase that should sum up the purpose of the document. It's possible to create sections, useful to organize the document in a better way. An image can be included using the tag "includegraphics", and we can also specify the dimensions between brackets. Obiusly, the image should stay into the same folder of the document (if it's in another place we must specify the whole path).</span><br />
<span class="Apple-style-span" style="font-family: inherit;">Maybe you need to write some text in superscript or subscript: simply use the ^ or the _ simbol. Anyway, it's considered "mathematical notation", so you need to include the whole super/subscript part in $ (and the text should be clsoed into braces). For example, "$_{2}$" means that we will have the number 2 written as subscript. And "$x^{1-n}$" will write the "1-n" text as superscript. In GNU/Linux you can simply write braces using the composition button of you keyboard (usually it's "Alt Gr", on the right of the spacebar) and the number 7 or 0. It's better if you don't use the numeric keypad.</span><br />
<b><span class="Apple-style-span" style="font-family: inherit;"><br /></span></b><br />
<b><span class="Apple-style-span" style="font-family: inherit;">Kile makes it easy</span></b><br />
<span class="Apple-style-span" style="font-family: inherit;">Obiously, the purpose of Kile is to make easy the use of Latex, so you don't need to remember the language syntax. For example, if we want to add an image, just click on the menù <b>Latex/ImageInsertion</b>. It's also possible to use toolbars, and set them to have al the things we can need handy (menù <b>Settings/Toolbars shown</b>, or <b>Settings/Configure Toolbars</b>). Using the button <b>QuickBuild</b> we will obtain a PDF file, but it's also possible to save the file in other formats. </span><br />
<span class="Apple-style-span" style="font-family: inherit;">If we want to prepare images to insert in the document (for example schemes), there's a program called Cirkuit (<b>http://wwwu.uni-klu.ac.at/magostin/cirkuit.html</b>) very useful to draw professional images.</span><br />
<span class="Apple-style-span" style="font-family: inherit;">Obiously, if we are not writing for the Nobel commission, we can also use the good old Inkscape to draw everything we want, and maybe add some notes over photos (for example, add some texts to describe the photo of an instrument tool).</span></div>LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com5tag:blogger.com,1999:blog-8703760419767782919.post-24749735465071445522011-11-07T13:22:00.000+01:002011-11-18T08:44:28.080+01:00Free the research #1<div style="margin-bottom: 0cm;">
<span class="Apple-style-span" style="font-family: inherit;">So this is the "second episode" of my article about Free Open Source tools for doing research, and we are going to talk about Maxima. It's just a collection of the main commands you will use.</span><br />
<a href="http://1.bp.blogspot.com/-Jc1xxbRjzPk/Tqq7DjeEJhI/AAAAAAAAAds/gNZGFoG0ilE/s1600/maxima.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span class="Apple-style-span" style="color: black; font-family: inherit;"><img border="0" height="200" src="http://1.bp.blogspot.com/-Jc1xxbRjzPk/Tqq7DjeEJhI/AAAAAAAAAds/gNZGFoG0ilE/s320/maxima.png" width="320" /></span></a></div>
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<span style="font-family: inherit; font-size: medium;"><b>Maxima</b></span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">Website: <a href="http://maxima.sourceforge.net/">http://maxima.sourceforge.net/</a></span></i><br />
<span class="Apple-style-span" style="font-family: inherit;">Maxima is a program similar to the more famous Derive. Really, Maxima is a CLI (Command Line Interface) application, but we can use wxMaxima: this is a GUI (Graphic User Interface) that makes the use of Maxima and its language very easy.</span><br />
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<a name='more'></a>For example, the command <b>solve</b> (from the menu <b>Equations/Solve</b>) allows you to solve an equation in one variable (this means that the other characthers will be taken as constants):</div>
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<i><span class="Apple-style-span" style="font-family: inherit;">solve([4*x^2-3*x+6=0],
[x]);</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;">This will solve the equation<span style="font-style: normal;"> </span><span style="font-style: normal;">4*x^2-3*x+6=0 using x as variable.</span></span></div>
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<span class="Apple-style-span" style="font-family: inherit;"><span style="font-style: normal;">In a similar way, the command <b>linsolve</b> tries to solve a system of linear equations (</span><span style="font-style: normal;"><b>Equations/Solve
Linear System</b></span><span style="font-style: normal;">):</span></span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">linsolve([3*x+4*y+6*z,
x/2+y+5*z, x^2+7*y+z], [x,y,z]);</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;"><span style="font-style: normal;">as you can see the comma is used to separate both equations and variables. And these are all easy tasks. But Maxima can do a lot more: the command </span><span style="font-style: normal;"><b>ode2</b></span><span style="font-style: normal;">
(</span><span style="font-style: normal;"><b>Equations/Solve
ODE</b></span><span style="font-style: normal;">)
finds the solution of differential equations. For example, we can look for the value of y function with the variable x:</span></span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">ode2('diff(y,x,2)
- y = 1, y,x);</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;"><span style="font-style: normal;">here, </span><span style="font-style: normal;"><b>'diff(y,x,2)</b></span><span style="font-style: normal;"> means the second derivate of y in function of x. The apostrophe is used to tell Maxima that we don't need the numeric value of the y derivate, but only the "concept".</span></span></div>
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<span class="Apple-style-span" style="font-family: inherit;"><span style="font-style: normal;">In fact, obiously, it's also possibile to execute derivates (</span><span style="font-style: normal;"><b>Calculus/Differentiate</b></span><span style="font-style: normal;">)
and integrals (</span><span style="font-style: normal;"><b>Calcolo/Integrate</b></span><span style="font-style: normal;">).</span></span></div>
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<span class="Apple-style-span" style="font-family: inherit;">This is an undefined integral in x:</span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">integrate(4*sin(x^2),
x);</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;">Wheter this is a defined integral in x from 0 to 1:</span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">integrate(4*sin(x^2),
x, 0, 1);</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;">And this is a second derivate in x (please take note that, this time, we don't use the apostrophe, because we want the numeric value):</span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">diff(4*sin(x^2),x,2);</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;">There is a bunch of useful commands, like <b>ratsimp</b>,that rationalizes decimal numbers:</span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">ratsimp(0.25);</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;">or the functions <b>trigsimp</b> e <b>trigexpand</b>, that simplifiy or expand a trigonometric expression:</span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">trigexpand(sin(2*x)+cos(2*x));</span></i></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">trigsimp(2*cos(x)^2
+ sin(x)^2);</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;">The function <b>factor</b>, if applied to a number returns its factorization in prime numbers, while if it's applied to an expression it factorizes polinomials.</span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">factor(30!);</span></i></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">factor(x^2
+ x -6);</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;">If we want to obtain the result directly in Latex format, just use the <b>tex</b> function:</span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">tex(x^2-1)/(x+1));</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;">Obiously, there are the main constants: %e is the Neper number, %pi is <i>π</i>, %i is the <b>immaginary number</b>, %phi is the <b>golden ratio</b>, inf is the <b>infinity</b>
(real), minf is the <b>negative infinity </b>(real), and infinity is the complex infinity.</span></div>
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<span class="Apple-style-span" style="font-family: inherit;">You can also draw plots in 2 or 3 dimensions with the functions wxplot2d (<b>Draw/Plot2D</b>) and wxplot3d (<b>Draw/Plot3D</b>):</span></div>
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<i><span class="Apple-style-span" style="font-family: inherit;">wxplot2d([x^2+3*x+2],
[x,-5,5]);</span></i></div>
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<span class="Apple-style-span" style="font-family: inherit;">this will draw the plot putting the x variable as abscissa, making it change from -5 to +5. Plots con be saved as images (click on them with the right button of the mouse).</span><br />
<span class="Apple-style-span" style="font-family: inherit;">Last, but not the least, the menù <b>Algebra</b> allow us to work with matrix (no, this time I'm not talking about Neo and Morpheus) and find autovalues, determinant.</span></div>LucaTringalihttp://www.blogger.com/profile/08103748660321285979noreply@blogger.com9