Scientific Software options for Ubuntu [Archive]

akniss

March 25th, 2006, 08:01 PM

At MIPS suggestion:
A place to tell others about software that you have found to be useful in scientific fields. Feel free to post your useful scientific software packages, and I will try to keep this first post up to date with your suggestions.

Statistics:
R
http://www.r-project.org/
sudo aptitude install r-recommended

LaTeX editors:
Lyx
http://www.lyx.org/
sudo aptitude install lyx
Kile
http://kile.sourceforge.net/
sudo aptitude install kile
TeXmaker
http://www.xm1math.net/texmaker/
sudo aptitude install texmaker

Bibtex:
Pybliographer
http://sourceforge.net/projects/pybliographer/
sudo aptitude install pybliographer

Bibliographic Database:
Bibus
http://bibus-biblio.sourceforge.net/wiki/index.php/Main_Page
Installation instructions (http://bibus-biblio.sourceforge.net/wiki/index.php/Installation#Debian_and_Ubuntu)

Spreadsheet:
Gnumeric
http://www.gnome.org/projects/gnumeric/
sudo aptitude install gnumeric

Desktop Publishing:
Scribus
http://www.scribus.net/
sudo aptitude install scribus

GIS:
GRASS
http://grass.itc.it/
sudo aptitude install grass

QGIS
http://qgis.org/
sudo aptitude install qgis

Mathematics:
Scilab
http://www.scilab.org/
sudo aptitude install scilab
Some users have had issues with text showing up only in Hindi when installing scilab from the Ubuntu repos. There is a binary version available on the scilab website. Just unpack it and read the README_Unix file.

Maxima
http://maxima.sourceforge.net/
sudo aptitude install maxima

Octave
http://www.gnu.org/software/octave/
sudo aptitude install octave

Barrakketh

March 25th, 2006, 08:07 PM

You could consider giving Kile a try for LaTeX. It's rather nice.

ssam

March 25th, 2006, 08:10 PM

there is also some good info on https://wiki.ubuntu.com/UbuntuScientists

i am looking forward to having a science forum :-)

towsonu2003

March 25th, 2006, 08:31 PM

I would (unfortunately) add qemu for those who have no time to learn a new program and need solution right away (thus using Windows)... again, unfortunately.

PS. SPSS => R != GUI => qemu + keku + SPSS

LadyDoor

March 25th, 2006, 08:40 PM

Hey! None of you Ubuntu scientists would happen to be social scientists, would you? And if you are (or not) would you happen to know how to get the latest version of PSPP from CVS? When I do the first step described in their instructions (make -f Smake) it works for a while, then prints out a lot of commented "include" statements, and then the following:

Don't forget to
- add "gl/Makefile" to AC_CONFIG_FILES in ./configure.ac,
- mention "gl" in SUBDIRS in Makefile.am,
- mention "-I gl/m4" in ACLOCAL_AMFLAGS in Makefile.am,
- invoke gl_EARLY in ./configure.ac, right after AC_PROG_CC,
- invoke gl_INIT in ./configure.ac.
autoreconf --install
aclocal: configure.ac: 12: macro `AM_PROG_CC_C_O' not found in library
autoreconf: aclocal failed with exit status: 1
make: *** [all] Error 1

Does anybody know how to fix this problem with what could be very good scientific software?

neoflight

March 25th, 2006, 09:09 PM

You could consider giving Kile a try for LaTeX. It's rather nice.

a how to for texmaker and kile with texlive in my signature.... :mrgreen:
even some instructions on getting kile from source without tetex ....:KS

akniss

March 26th, 2006, 02:51 AM

I just got Bibus working also by following the howto at this thread:
http://www.ubuntuforums.org/showthread.php?t=122841&highlight=bibus

derjames

April 6th, 2006, 03:12 AM

Hi there,
For those interested in physical/chemical modelling I did find an open source multiphysics package similar to COMSOL (formerly FEMLAB), I haven't compiled yet, however I will work on this shortly, The name of the package is ELMER, developed by a Finnish institute, there are binaries for download for Win32, Linux RPM, Mac, etc... the source code is available to download as well.

Hope this helps

http://www.csc.fi/elmer/index.phtml

akniss

April 9th, 2006, 11:28 AM

Has anyone used or tried the ChemicalInventory package listed on the Science Wiki? Just curious if it is functional enough to warrant giving it a try...

mips

April 10th, 2006, 01:08 PM

People, have a look at this:

http://www.openchannelfoundation.org/
http://www.openchannelfoundation.org/cosmic/

Please note that the above is NOT free but could prove valuable to some people.

ericsp

April 26th, 2006, 11:51 AM

Re: Akniss and the R-project.

I see the power of the R-project, but the interface is horrible. Is there anyone working on a good interface?

akniss

April 26th, 2006, 12:17 PM

Re: Akniss and the R-project.

I see the power of the R-project, but the interface is horrible. Is there anyone working on a good interface?

I suppose that really depends on what you are used to. In my field, SAS is the standard. This makes the switch to R rather easy, as they both have a command-line programming language feel to them. Most people who feel as you do typically come from Minitab or SPSS or... Excel *shudder*. The learning curve is steep; however coming from SAS I've really enjoyed the transtition. I can make a plot in R with two or three lines of code that would take me a page and a half of code in SAS. However, two or three lines of code is two or three too many for those used to pointing and clicking their way around Minitab or SigmaPlot.

The true "power of the R-project" really comes from the fact that it is a full progamming language. We are not limited to a set of default analysis methods which may or may not be appropriate for the data. I have written a few functions in R that allow me to create detailed diagnostic plots with a one-line command. This sort of thing is just not possible with 95% of commercial gui-based statistical packages. It can be cumbersome at times when one only wants to perform simple analyses or transformations on a data set; but if this is all you want out of a statistical package, then R is probably not for you anyway. Any attempt at simplifying the interface to point and click will necessarily take away functionality, as there is no way to incorporate all the functionality of R into a few context menus.

With all that being said, there are a few projects out there that have put a gui interface on top of R. Rcmdr is available in the Ubuntu repos and does an ok job. The one that looks the most exciting in my opinion is JGR (pronounced Jaguar). It is java based and so platform independent. I have not personally tried it but have heard good things.

Kyle-

April 26th, 2006, 12:29 PM

Re: Akniss and the R-project.

I see the power of the R-project, but the interface is horrible. Is there anyone working on a good interface?

This is by far the most promising thing I've seen. http://kde-apps.org/content/show.php?content=14880

You can also install a GUI called Rcmdr within R. Just connect to an R reposititory, install the package, and at the input prompt type

library(Rcmdr)

It's not the prettiest thing in the world, but it's stable.

One other thing. I've recently begun experimenting with using DOSbox to run an old DOS version of Kwikstat. It works well after some fiddling with the install (edit a script so it Kwikstat doesn't look for a printer on install). This might be an option for those of you who are still using older software. I find Kwikstat quite satisfactory for most things.

Aside from statistics, I use CXoffice to run Endnote. I just cant switch. There is a Linux version of Maple, so no problem there. Maxima is also a decent free computer algebra system.

I really wish someone could get a recent versionn of SPSS working in Linux with a GUI.

towsonu2003

April 26th, 2006, 12:30 PM

I see the power of the R-project, but the interface is horrible.
check out this: https://stat.ethz.ch/pipermail/r-devel/2006-March/036728.html

This is a bug (or, rather, a feature request) I filed a while ago. You will find your response in devels' replies to my bug report / feature request......

claudine

April 26th, 2006, 08:26 PM

I'm forced to use Stata at work but I'd like to learn R. Do you think going from Stata to R would require a huge mental leap?

akniss

May 3rd, 2006, 09:11 AM

I'm forced to use Stata at work but I'd like to learn R. Do you think going from Stata to R would require a huge mental leap?

I don't know much about Stata... From looking at their website, it looks like it is predominantly a command based package as well. (I'm actually kind of interested in playing around with Stata now!) I think the switch to R is much easier for those of us who are already used to typing in commands to get means, regressions, and box plots.

However, learning any new language is frustrating at times. It took me a couple years to learn SAS to the point that I was reasonably proficient, and it was difficult to transition from the proc ****; world over to the function() world. I gave up a few times, but eventually got the hang of it and am now much more efficient in R.

akniss

May 3rd, 2006, 09:13 AM

This is by far the most promising thing I've seen. http://kde-apps.org/content/show.php?content=14880

Kyle, that looks fantastic! I hadn't heard of it yet. I suppose the chances of it getting into the Dapper repos are null...

towsonu2003

May 3rd, 2006, 09:23 AM

Kyle, that looks fantastic! I hadn't heard of it yet. I suppose the chances of it getting into the Dapper repos are null...
try suggesting it to the backports (there is a forum section for that). Let us know of the thread link so we can support.

claudine

May 3rd, 2006, 10:40 PM

I don't know much about Stata... From looking at their website, it looks like it is predominantly a command based package as well. (I'm actually kind of interested in playing around with Stata now!) I think the switch to R is much easier for those of us who are already used to typing in commands to get means, regressions, and box plots.

However, learning any new language is frustrating at times. It took me a couple years to learn SAS to the point that I was reasonably proficient, and it was difficult to transition from the proc ****; world over to the function() world. I gave up a few times, but eventually got the hang of it and am now much more efficient in R.

Yes, Stata is very much command-driven. I'm writing Stata scripts in Emacs with ESS mode. Stata mostly does what I need, but it's not free (my philosophical objection). And all the statisticians at work use it and seem to think R is too "difficult". It seems the main issues with R are its object-oriented nature and syntax.

akniss

May 3rd, 2006, 11:52 PM

Yes, Stata is very much command-driven. I'm writing Stata scripts in Emacs with ESS mode. Stata mostly does what I need, but it's not free (my philosophical objection). And all the statisticians at work use it and seem to think R is too "difficult". It seems the main issues with R are its object-oriented nature and syntax.

R certainly does have a cryptic syntax... however, I would argue that there is nothing more cryptic than Emacs ](*,) , so if you've mastered that... ESS is also able to interface with R, so I think it wouldn't be too terrible a transition for you. I gave ESS a whirl a few months ago and just coulnd't get hooked. I thought it was ok, but decided KDE's kate editor was better suited for my needs. I guess there's only one way to find out: install it and give it a try. Just take it slow and don't think you'll be able to master it the first few times. If you're anything like me, it will take a while to 'unlearn' your other language (It took me about a month to stop putting a semi-colon at the end of each line). Good luck, and if you have trouble getting started there are pretty good books, online help, and documentation available. And I'm sure there are a few R junkies on this forum besides myself as well!

akniss

September 12th, 2006, 10:58 PM

I've just installed scilab and am starting to play around with it. Does anyone know of a good noob-level tutorial for scilab?

akniss

September 26th, 2006, 12:20 PM

I've just installed scilab and am starting to play around with it. Does anyone know of a good noob-level tutorial for scilab?

To answer my own question, here is one quick and dirty tutorial that has gotten me started.
http://www.scilab.org/doc/intro/node7.html

I was quite happy to learn that the Emacs commands work at the scilab command line! All that time spent learning ESS has finally paid off!

philyer

November 6th, 2006, 05:00 AM

Maxima
A powerful symbolic caculation tool, like Mathematica.

adamkane

November 9th, 2006, 03:01 AM

Lyx and Maxima can be combined to create a very good report writer and equation solver:

Lyx + Maxima
http://www.jstatsoft.org/v17/s01/v17s01.pdf

Steve Pullman

November 17th, 2006, 11:29 AM

Zhu3D is a very nice opengl surface plotter

http://www.kde-apps.org/content/show.php?content=43071

I had to compile it (it isn't in the repository), but it wasn't troublesome.

abarth

November 28th, 2006, 11:18 AM

Octave is very well suited for numerical computations. Its syntax is quite easy to learn and it is mostly compatible with Matlab.

http://www.octave.org

adamkane

November 30th, 2006, 12:05 AM

Can anyone describe how they got octave-workshop installed on Ubuntu?

http://www.math.mcgill.ca/loisel/octave-workshop/
http://www.math.mcgill.ca/loisel/octave-workshop/octave-workshop-0.7/doc/install.html

slimdog360

November 30th, 2006, 04:55 AM

You may want to add the octave-forge package to that list.

adamkane

December 2nd, 2006, 04:34 AM

I downloaded octave-workshop:
http://www.math.mcgill.ca/loisel/octave-workshop/octave-workshop-0.10.tar.gz

octave is already installed.

octave-workshop requires QT4.1, so you need to install QT4, then install QT4.1 from source:
https://help.ubuntu.com/community/BuildingQuantumGisPoint8FromSource
http://openmodeller.cria.org.br/wikis/omgui/LinuxBuildInstructions

QT4:

sudo apt-get install libqt4-core libqt4-debug libqt4-debug-dev libqt4-dev libqt4-gui libqt4-qt3support libqt4-sql lsb-qt4 qt4-designer qt4-dev-tools qt4-doc qt4-qtconfig uim-qt gcc libapt-pkg-perl resolvconf
QT4.1:

sudo apt-get install libxrender-dev libxrandr-dev libxcursor-dev libxinerama-dev libfontconfig-dev libxext-dev libx11-dev libxi-dev libsm-dev libx11-dev

mkdir -p $HOME/installers
cd ~/installers
wget ftp://ftp.trolltech.com/qt/source/qt-x11-opensource-src-4.1.0.tar.gz
tar xfz ~/installers/qt-x11-opensource-src-4.1.0.tar.gz
cd qt-x11-opensource-src-4.1.0

/configure -prefix /usr/local/Trolltech/Qt-4.1.0
make
sudo make install
I then tried to install octave-workshop from source, but I got this error:

checking whether we can build a liboctave program... configure: error: Cannot link against liboctave
I don't think there is a solution to this error without recompiling octave-workshop, which is beyond my ability.

QT4.1 is installed, so we can try another method. Convert the RPM file to a DEB file.

I downloaded the octave-workshop RPM to my desktop:
http://webpages.charter.net/qspencer/rpm/

I converted the RPM to a DEB:

cd ~/Desktop
sudo alien -d octave-workshop-0.10-1.i386.rpm
The RPM file uses termcap, but the DEB file requires ncurses:
http://directory.fedora.redhat.com/wiki/Howto: DebianUbuntu (http://ubuntuforums.org/%22http://directory.fedora.redhat.com/wiki/Howto:DebianUbuntu%22)

so you need to download these old breezy DEB files to install octave-workshop in dapper:

termcap-compat
http://packages.ubuntu.com/cgi-bin/download.pl?arch=i386&file=pool%2Funiverse%2Ft%2Ftermcap-compat%2Ftermcap-compat_1.2.3_i386.deb&md5sum=65eaae25cd8382a193b416428617bc79&arch=i386&type=main

libc5
http://packages.ubuntu.com/cgi-bin/download.pl?arch=i386&file=pool%2Funiverse%2Flibc%2Flibc%2Flibc5_5.4.46-15_i386.deb&md5sum=e8fffc5b3bfb9b1d716a93e764547baa&arch=i386&type=main

ldso
http://packages.ubuntu.com/cgi-bin/download.pl?arch=i386&file=pool%2Funiverse%2Fl%2Fld.so%2Fldso_1.9.11-15_i386.deb&md5sum=53caec6628874f687137d242a6adbc42&arch=i386&type=main

You then need to create a link for libhdf5.so.0:

cd /usr/lib
sudo ln -s libhdf5-1.6.4.so.0 libhdf5.so.0
I then get this error when I ran octave-workshop:

*** glibc detected *** free(): invalid pointer: 0x08c90cb0 ***
Aborted
That's as far as I got.

I then uninstalled the breezy DEB files, and removed the libhdf5.so.0 link:

cd /usr/lib
sudo rm libhdf5.so.0

maystar

December 5th, 2006, 05:10 AM

hello just trying out ubuntu forums!!

Toufik

January 9th, 2007, 09:21 AM

I went further with less step :D

Install QT4
$ sudo apt-get install libqt4-core lib-qt4-dev

Download RPM
$ wget http://webpages.charter.net/qspencer/rpm/octave-workshop-0.10-1.i386.rpm

Convert into .deb
$ sudo dpkg -d octave-workshop-0.10-1.i386.rpm

Install it
$ sudo dpkg -i octave-workshop-0.10-1.i386.deb

Then try it:
$ octave-workshop

You get libtermcap error --> search for it ($ locate libtermcap) --> it only changes name so make a symbolic link
$ sudo ln -s /usr/lib/libtermcap.so /usr/lib/libtermcap.so.2

Now, I'm stuck with liboctinterp.so
octave-workshop: error while loading shared libraries: liboctinterp.so: cannot open shared object file: No such file or directory

But I've of course the liboctinterp.so in /usr/lib/octave-2.1.73/liboctinterp.so I guess the binary is looking at th wrong place... don't know how to correct this. I've put symbolic link everywhere... nope

Pffff

cuonght

January 9th, 2007, 09:35 AM

I am very interested in IFEFFIT software, but I don't know how to install this soft ware in my computer. Here is a link for this
http://cars9.uchicago.edu/ifeffit/download.html

Can someone help me to install it? thanks a lot!

Toufik

January 9th, 2007, 11:34 AM

Just follow the instructions here :
http://cars9.uchicago.edu/ifeffit/src/INSTALL

Rmq: You'll need that first
$ sudo apt-get install build-essential

Basically, when you get source in .tar.gz format:
1) decompress the archive and enter the new directory
$ tar -xzvf xxxx.tar.gz
$ cd xxxx
2) configure the building and installation
$ ./configure
You should get messages telling if it is OK or not. In that last case, look at the problem and try to correct it by installing the missing software via apt-get. For instance, if it tells you that yyyyy is missing, then look for it:
$ apt-cache search yyyyy
You'll get some answer(s) (if not then look in the forum), let's say abcdef. Then install it via
$ sudo apt-get install abcdef
and start point 2 again.

3) When it finished ok, you can build the program:
$ make
Here also, you'll get a lot of messages, if there is a problem, look in the forum. At the end, you'll get a binary

4) Install the binary
$ sudo make install
And everything should be working and located at the right place (you can safely remove xxxx.tar.gz and the directory xxxx). To execute, type the name of the program.

Rmq: there is always (at least) one problem when installing from source... always look for a .deb first

cuonght

January 10th, 2007, 11:08 AM

thanks for your instruction. But I still got a problem, that is, after configure, it informs an error as following:
===
=== ifeffit 1.2.8 Configuration Results:
=== linking to PGPLOT with: /home/htcuong/Desktop/ifeffit-1.2.8/src/pgstub/libnopgplot.a
===
=== could not find TERMCAP Libraries : 'make' will fail.
===
=== Please set TERMCAP_LIB in src/cmdline/Makefile or use the
=== --termcap-link argument before running make

Do you know what it is? thanks

Toufik

January 11th, 2007, 03:53 AM

termcap is now replaced by ncurses but I don't know which packages exactly. Try to install some packages containing ncurses (probably ncurses-base, ncurses-bin and ncurses-term)

If you experience problem with an installation: open a new forum! You'll get more help with a precise title!

olejorgen

January 15th, 2007, 03:28 AM

Zhu3D is a very nice opengl surface plotter

http://www.kde-apps.org/content/show.php?content=43071

I had to compile it (it isn't in the repository), but it wasn't troublesome.
Does anyone know of a program like this (that support implict 3d plots) for gnome?

sureinlux

February 21st, 2007, 03:11 AM

RLPLot (http://rlplot.sourceforge.net) is a great WYSIWYG plotting software with a shallow learning curve. Available in the repos and great for publication quality graphs.

slaanco

February 21st, 2007, 12:50 PM

many astronomical codes that can be run on ubuntu can be found here (http://en.wikiversity.org/wiki/Astrophysics_Source_Code_Library)

Timtro

March 12th, 2007, 11:17 PM

You could consider giving Kile a try for LaTeX. It's rather nice.

TeXmaker is nice too. I hear it's from the guy who started the Kile project. There are some differences, but Texmaker loads a--lot--faster.

Cellular

March 28th, 2007, 07:05 AM

tomasz2006

April 12th, 2007, 05:31 PM

gretl is a great package for econometrics and time series analysis. It also has some simple tools for finding p-values and doing elementary t-tests etc. It has a very easy-to-use GUI as well as a command line interface, it is easy (from what i've heard) to extend with scripts, and it can send it's data to R.

It produces plots with Gnuplot, and you can get it's output in latex format.

http://gretl.sourceforge.net/

I agree with the above, the main strength of gretl is its easy-to-use and friendly interface. Also, the export of output to LaTeX might be of interest.

I add a little ``installing gretl HOWTO'' which I wish had existed when I tried to install it. gretl has some `non-standard' dependencies but luckily the following command helps a lot (worked perfectly on Edgy Eft):

apt-get build-dep gretl

Then, download the source package from

http://gretl.sourceforge.net/

Decompress the archive and enter the new directory. Then, execute, one by one, the following:

./configure
make
sudo make install

Hopefully, everything goes smoothly and gretl is installed. In case you wonder, the above procedure did NOT work with the checkinstall. I hope this helps.

vinx

April 20th, 2007, 09:42 AM

It is easier to compile Octave Workshop for Actave 2.9 on Fiesty, since the newest QT4-libs are included. You'll need to make one edit before compiling.

Install the following packages (and dependecies):

qt4-dev-tools
octave2.9-headers
libreadline5-dev

Just download the tar.gz from http://www.math.mcgill.ca/loisel/octave-workshop/ , unpack and add the following as line 11 to the file 'editwindow.cpp':
#include <assert.h>

Now it's time for a './configure' , which should give no errors.
now do a 'make'. If you did not make the edit to editwindow.cpp, it complains about 'assert' not being defined.

Few moments later you have a 3.4mb bunch of working code. Don't forget to install gnuplot and to start the workshop from the shell to see some usefull crash-output.

--
Vincent

kikuhi

May 2nd, 2007, 11:04 AM

For quick plotting, check out "gnuplot". It is quite handy and versatile. If anybody know other open source plot tools?

Cheers,
KiKuHi

abarth

May 4th, 2007, 10:54 PM

For quick plotting, check out "gnuplot". It is quite handy and versatile. If anybody know other open source plot tools?

Cheers,
KiKuHi

The python package matplotlib is quite powerful too. Its interface is modeled after the plotting commands of matlab.

Cheers,
alex

guano

June 23rd, 2007, 10:43 AM

For thos interested in using the latest stable versions of GIS software (GRASS, GDAL, QGIS), use this repo:

deb http://les-ejk.cz/ubuntu edgy multiverse
deb-src http://les-ejk.cz/ubuntu edgy multiverse
or
deb http://les-ejk.cz/ubuntu feisty multiverse
deb-src http://les-ejk.cz/ubuntu feisty multiverse

the versions in the official repos are a bit outdated.

As for the Kile x Texmaker, Texmaker loads faster, but Kile has word completion (and tex commands too).

As Reference manager, I use JabRef. Is Java based and very good. I found a .deb somewhere...

If you go to http://www.getdeb.net, you can fin a tool called Extrema, for graphs creation. Sounds good.

seobeglobal

June 25th, 2007, 03:00 AM

thank you for the shared information

hardyn

July 7th, 2007, 02:14 AM

I got octave workshop to compile under feisty...

you must use all the QT 4.1 libs as noted previous in this post (synaptic)
you must install the readline-dev libs (synaptic)
you must intstall the octave-headers (synaptic)
you must edit the "editwindow.cpp" file and add "#include <assert.h>" to the includes, compile error without
then compile using ./config and make
(way too much work)

cheers.

dannemil

July 9th, 2007, 12:44 PM

RLPLot (http://rlplot.sourceforge.net) is a great WYSIWYG plotting software with a shallow learning curve. Available in the repos and great for publication quality graphs.

Outstanding! I have been looking for a good open-source, easy to use, gui plotting package for years. RLPlot (http://rlplot.sourceforge.net/) is it! Thanks for the suggestion.

Jim

Schoappied

July 12th, 2007, 07:15 AM

akniss

July 12th, 2007, 10:00 AM

Hi,

I study Psychology and I work a lot with SPSS. What is the best program in Ubuntu to work with statistics and have the same possibilities which SPSS has?
The program must be able to open SPSS-files if possible...

Sounds like you might want to take a look at PSPP. (http://www.gnu.org/software/pspp/) It might not have the functionality you are looking for yet, but the goal is to have an SPSS-like program eventually. I think its your best bet for opening SPSS files. However, if you want a truly powerful statistical program for linux, you should look into R. (http://www.r-project.org/)

Schoappied

July 12th, 2007, 02:48 PM

Thanks, I think PSPP can not really compare to SPSS. Tell me if I'm wrong...
I will try R-project...

ibbuntu

August 15th, 2007, 03:59 AM

I like JabRef for managing my references. It's in the repos and can be used with a whole host of different editors. Saves its files in BibTex format and can import many other different reference file formats. It's a Java application, so will run on any operating system too.

kiranbhaskar

August 30th, 2007, 02:47 AM

Dear akniss nice post :)

glee

September 9th, 2007, 09:21 PM

Emacs + ESS (http://ess.r-project.org/) (Emacs Speaks Statistics) is a great interface when using R!!

jjvenkit@uwaterloo.ca

November 21st, 2007, 09:58 PM

Can anyone recommend an alternative to NVivo?

thanks,
jason.

zasf

December 10th, 2007, 02:24 AM

I use geany with great pleasure for programming (ruby and python) and latex. Altough not fancy it is very quick and powerful.

I previously tried bluefish for latex editing but, altough it provides some useful shortcuts, it had worst higlight support than geany.

slimdog360

December 26th, 2007, 12:10 AM

I dont know if its been mentioned yet but you should put in FreeMat http://freemat.sourceforge.net/wiki/index.php/Main _Page

myle

January 17th, 2008, 12:38 PM

TeXmaker is nice too. I hear it's from the guy who started the Kile project. There are some differences, but Texmaker loads a--lot--faster.

I agree with you. Even if Kile has a better reputation, I think if you ise Gnome, it's better to use TeXmaker.

Xtrmi

January 30th, 2008, 11:41 AM

towsonu2003

January 30th, 2008, 01:04 PM

I need to be able to plot equations in implicit form on my eeepc. Does anybody have any suggestions. Installed Scilab to to what it would do but I dont have the time to figure it out cuz I got to much HW. Also this doesn't belong here but could someone quickly mention a messenger program that works with the camera. Thanks for any help u can provide. Even a web version of the graphing program would work for me. if you know of one. Thanks.

I don't know what 'implicit form' is, but you can use gnuplot to plot equations, get the output in some image format, and put it in your HW.
http://www.gnuplot.info/
http://mathewpeet.org/computing/gnuplot/

olejorgen

January 30th, 2008, 05:45 PM

Implicit form: x^2 + y^2 = 1

I don't think gnuplot can do this out of the box, but I think I've seen some triks you can do. Can't remember where I saw it though.

Xtrmi

January 30th, 2008, 10:44 PM

Installed it throuh the consol and i can't find it. any hints on where it might be?

marrabld

March 4th, 2008, 07:18 AM

Use Octave to plot your implicit function. <google for help> it will pass you solution to GNUplot.

And on that point can anyone tell me how to change the background colour of plots when using Octave. For some reason the ubuntu version is set to grey, I need to put my plots into documents and grey is horrible.

I have looked far and wide on the net and cannot find help on this. I really need to solve it soon or ill be forced to install Octave into windows and i dont want to do that.

Cheers

Moonlit Knight

March 6th, 2008, 06:27 AM

Turn it into parametrics and you can plot it quite well with gnuplot just put:

set parametrics on

That function is a circle just do g(x,y) = (cos u, sen u)
There it is

rjmoerland

March 6th, 2008, 06:38 AM

I love the combination of jabref (mentioned already in this thread) with subversion. I use subversion a lot to version control my articles, but what I find truely useful is that I can use a single bib file for all my articles, using the 'external' property of subversion. This way, if I edit any checked out copy of the bib file, all the other onces are updated as well. Moreover subversion makes it incredibly easy to work at home and at work on the same text, just commit changes at work, go home, update working copy and continue.

My 2 cts.

qgfreire

May 6th, 2008, 05:42 PM

OpenFoam FoamX
http://www.opencfd.co.uk/openfoam
The OpenFOAM (Open Field Operation and Manipulation) CFD Toolbox can simulate anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics, electromagnetics and the pricing of financial options. OpenFOAM is produced by OpenCFD Ltd, is freely available and open source, licensed under the GNU General Public Licence.

It's a must for a free version os CFD.
Great forum. But ....

dbulnes

May 30th, 2008, 01:16 AM

dbulnes

May 30th, 2008, 01:25 AM

jjgomera

May 30th, 2008, 06:00 AM

Is there Anybody out there using Chimera from UCSF, They have a linux version, but me being new on linux/ubuntu havent been able to make it work. If someone has, please let me know how you did. Thanks a lot!

open a terminal

download program:
wget https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=linux/chimera-1.2470-linux.exe

make it executable:
chmod -x chimera-1.2470-linux.exe

run it as root
sudo ./chimera-1.2470-linux.exe

it asks install directory, you can let by default /usr/local/chimera/

It's autoinstall program, so it installs all its dependences

Finally for run program: sh /usr/local/chimera/bin/chimera

If you use 64bits architecture use https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=linux_x86_64/chimera-1.2470-linux_x86_64.exe

PD: thanks for info, i dont know that program, and it looks good:)