Introducing xmgrace
created: 21 Mar 2010 18:54
tags: plotting xmgrace
xmgrace is, like gnuplot, a nice piece of software to create scientific plots. As opposite to gnuplot, xmgrace has a graphical interface and can generate only 2D plots. To the other hands, it allows for quite sofisticate analysis, such as autocorrelation, fourier transformation, interpolations, non linear fitting, regression, convolution and so on.
The user guide is here.
Install xmgrace in linux is quite straightforward, since is included in the repositories of all the major linux distribution, as for gnuplot.
Soon I will write a page dedicated to xmgrace.
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Gnuplot cheatsheet
created: 21 Mar 2010 17:49
tags: cheatsheet gnuplot plotting
Gnuplot is, along with xmgrace, my program of choice to plot data. I even make a script to plot data on the fly, directly from bash.
From the official website:
Gnuplot is a portable command-line driven graphing utility for linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986.
Gnuplot supports many types of plots in either 2D and 3D. It can draw using lines, points, boxes, contours, vector fields, surfaces, and various associated text. It also supports various specialized plot types. Demos here.
Gnuplot supports many different types of output: interactive screen terminals (with mouse and hotkey input), direct output to pen plotters or modern printers, and output to many file formats (eps, fig, jpeg, LaTeX, metafont, pbm, pdf, png, postscript, svg, …). Gnuplot is easily extensible to include new output modes. Recent additions include an interactive terminal based on wxWidgets and the creation of mousable graphs for web display using the HTML5 canvas element.
You can easily install gnuplot in linux, since is in the repository of all the main distro.
I encourage my students to use gnuplot and to help them, I made a cheatsheet.
This cheatsheet is far to be complete, but just time gnuplot in google and you will have tons of results, tutorials, guides, examples… An amazingly useful link for gnuplot is this.
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Leeenux 2.0 the best linux for your eeepc 701
created: 17 Mar 2010 18:47
tags: eeepc leeenux
Being a geek, sometime is really a pain in the ass neck, and my relation with my eeepc 701 g4 has always been a mix of love and hate.
It is nice, because is small, light and resistant to shocks, humidity, … : perfect for people like me, that commute every day from home to work. The problem was that I never found a decent linux distribution that was really working out of the box, and that allows me to transform the small eeepc in a perfect lab buddy. The best distro I tried out were:
- crunchee, based on ubuntu 8.10
- fluxflux
and.. that's it. Then Asus put an end to the production of the little 701 and linux distro followed the market: netbook with big screens, huge standard hard drives (bye bye solid state hard drives). So, my little friend was sitting, unused, in a lab drawer.
On monday, I was using train+folding bike to go to work, so I left the macbook pro at home: of course, an unexpected visitor came in the lab and I used the eeepc again. With the usual problems. So I surf the web to see if there was some new distro that could have perform better than crunchee. And, joy oh joy, I have found it, the perfect distro:
Based on ubuntu Jaunty, comes with a iso of less than 500MB. It has a nice graphical interface based on gnome, it boots fast, everything really work out of the box (yes, also suspend/resume, functions keys Fn+Fsomething, wireless strong enough, webcam (B/W only for me when using cheese), sound, microphone, … ) and the windows are, by default, maximized and adapted to the small screen.
Quoting from the web site, some good reasons to use Leenux:
- Don't throw away your old Asus eee netbook, because it can gain usability once again with Leeenux.
- Leeenux is a linux distribution made mainly for Asus eee with 7" screen, but other netbooks can use it as well. It is lightweight, and in every new release it uses less resources. Current ISO contains only 460MB. It can be installed on eee with 2GB of SSD, and on 4GB eee you will have planty of room to spare. Installed, it takes up only 1.2GB.
- It is the best distribution for this widely distributed netbooks.
- Everything works Out of Box, unlike Ubuntu UNR.
- It is made using remastersys from easypeasy 1.1, which was made from Ubuntu UNR 8.04. In order to be as much lightweight and fast, in May 2010 it will be made only from Ubuntu UNR 10.04.
- It is FREE! Liberty means a lot, and there is no proprietary software nor drivers included in this distribution. EasyPeasy is not free. Its only free of charge, but contains lots of propriatery software. Why propriatery software is BAD, you can find out on many websites.
- Unlike many other distros which try to be as complex as possible, Leeenux is trying to reduce Bloating. Thus many things are not installed by default, the things for which there is 99.9% you wont need. If you still need them, they can be installed via Synaptic.
- Propriatery software can be installed, if needed.
- It is licenced under GPLv3, so anyone can redistribute or change it if they like.
And, I could not agree more.
With only 1.2gb used, it leaves plenty of room to install scientific software:
- latex
- compilers
- python/perl libraries
- shells csh, ipython, tkcon
- Mendeley desktop for organize papers
- gromacs
- tinker
- gnuplot
- vmd
- pymol
- xmgrace
- chemistry software like chemdraw and openbabel
- gimp
- graphical utiles like imagemagik
- wine (so to use portable apps such as open office etc.)
and much more…
A list of the default applications is here
Now, having 1gb free and all I need installed and fully working, is time to show some screenshots:
The graphical interface (fully customizable)
The terminal: nice and big thanks to the default maximization… come on… I know you use it too ;)
VMD (unmaximized), with the window set to 400x400 pixels
You can see how nice is the feeling with the small screen of the 701: not a problem anymore. To make the long story short:
best out-of-the-box experience ever
If you, like me, are looking for give a new life to your old 701, this is the distro for you. And if also you are appreciate the work of the Leeenux team (which is not connected in anyway with me or this site), you may want to offer them a beer.
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