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akniss
March 26th, 2006, 02:01 AM
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 26th, 2006, 02:07 AM
You could consider giving Kile a try for LaTeX. It's rather nice.

ssam
March 26th, 2006, 02:10 AM
there is also some good info on https://wiki.ubuntu.com/UbuntuScientists

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

towsonu2003
March 26th, 2006, 02:31 AM
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 26th, 2006, 02:40 AM
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 26th, 2006, 03:09 AM
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, 07:51 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, 08:12 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, 04:28 PM
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, 06:08 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, 04:51 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?

akniss
April 26th, 2006, 05:17 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, 05:29 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, 05:30 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 27th, 2006, 01:26 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?

akniss
May 3rd, 2006, 02:11 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?

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, 02:13 PM
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, 02:23 PM
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 4th, 2006, 03:40 AM
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 4th, 2006, 04:52 AM
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 13th, 2006, 03:58 AM
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, 05:20 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, 11:00 AM
Maxima
A powerful symbolic caculation tool, like Mathematica.

adamkane
November 9th, 2006, 09:01 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, 05:29 PM
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, 05:18 PM
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, 06:05 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, 10:55 AM
You may want to add the octave-forge package to that list.

adamkane
December 2nd, 2006, 10:34 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, 11:10 AM
hello just trying out ubuntu forums!!

Toufik
January 9th, 2007, 03:21 PM
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, 03:35 PM
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, 05:34 PM
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, 05:08 PM
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, 09:53 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, 09:28 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, 09:11 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, 06:50 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 13th, 2007, 05:17 AM
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, 12:05 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/

tomasz2006
April 12th, 2007, 10:31 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, 02:42 PM
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, 04:04 PM
For quick plotting, check out "gnuplot". It is quite handy and versatile. If anybody know other open source plot tools?

Cheers,
KiKuHi

abarth
May 5th, 2007, 03:54 AM
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, 03:43 PM
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.

hardyn
July 7th, 2007, 07:14 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, 05:44 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, 12:15 PM
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...

akniss
July 12th, 2007, 03:00 PM
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, 07:48 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, 08:59 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, 07:47 AM
Dear akniss nice post :)

glee
September 10th, 2007, 02:21 AM
Emacs + ESS (http://ess.r-project.org/) (Emacs Speaks Statistics) is a great interface when using R!!

jjvenkit@uwaterloo.ca
November 22nd, 2007, 03:58 AM
Can anyone recommend an alternative to NVivo?

thanks,
jason.

zasf
December 10th, 2007, 08:24 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, 06:10 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, 06:38 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, 05:41 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.

towsonu2003
January 30th, 2008, 07:04 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, 11:45 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 31st, 2008, 04:44 AM
Installed it throuh the consol and i can't find it. any hints on where it might be?

marrabld
March 4th, 2008, 01:18 PM
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, 12:27 PM
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, 12:38 PM
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, 10:42 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, 06:16 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!

dbulnes
May 30th, 2008, 06:25 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!

jjgomera
May 30th, 2008, 11:00 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:)

UbuWu
May 31st, 2008, 11:14 PM
Rkward
(http://rkward.sourceforge.net/) is a great alternative to spss.

Also there is a more comprehensive list on the wiki:
https://help.ubuntu.com/community/UbuntuScience

Guillex
September 9th, 2008, 09:22 PM
Perdon que no escriba en ingles.

Se llama librarian

http://www.bioinformatics.org/librarian/index.php

Para todo aquel que investigue... recomiendo que vean el link

no lo he probado aun.

mips
September 10th, 2008, 07:26 PM
Perdon que no escriba en ingles.

Se llama librarian

http://www.bioinformatics.org/librarian/index.php

Para todo aquel que investigue... recomiendo que vean el link

no lo he probado aun.

Google Translate:

Perdon not write in English.

It's called librarian

http://www.bioinformatics.org/librarian/index.php

For anyone who investigate ... I recommend them to see the link

I have not tried yet.

garba
September 25th, 2008, 01:14 AM
engauge and gnuplot

jotacebusta
October 18th, 2008, 01:33 AM
There is also TeXmacs. It's really great, though it's not completely stable and some how hard to use.

It is a WYSYWYG document processor tha allows to obtain (and see) LaTeX quality documents. But it also can be used as an interface to R, SciLab, Octave, Maxima, and others. I really love it, even if there are still some few things I can't do.

Also, TeXmacs developers are already working on version 1.0.7, but the one in the repos is very old (1.0.6.11, I think, and there is at leart a 1.0.6.15 version...)

Does anyone know about something like Scientific Workplace? Besides TeXmacs, I know the linux version of Lyx can evaluate some expressions by using maxima. Other ideas?

neoflight
October 31st, 2008, 03:08 PM
I agree with you. Even if Kile has a better reputation, I think if you ise Gnome, it's better to use TeXmaker.

I concur.

neoflight
October 31st, 2008, 03:10 PM
anyone installed abaqus in linux? i have the steps CAE Journal (http://www.caejournal.com/).

I am having some trouble getting ansys multiphysics working. if anyone got it working please write a howto there in the link above?

Spike the Dingo
December 4th, 2008, 01:14 AM
SAGE... I'm an R geek and I just discovered SAGE. It's positively wonderful! I hope it gets in the Ubuntu repository soon! It doesn't get enough press!

http://www.sagemath.org/index.html

I think it's going to be big!




...(R is still the best for stats)

windhair
December 11th, 2008, 12:55 AM
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.



It is restricted to US citizens.

Functional_Fooled
March 11th, 2009, 03:02 AM
To repeat what I know a number of others have already said, R for statistics is very useful. I taught myself how to use it while taking my graduate level statistics classes (trying out homework and redoing labs done in SAS in R to re-enforce my understanding). I then used it for the statistical computations in my thesis and the generation of all graphs. There may be better ways of making professional graphs or plots, but I liked having a test file of the commands I could tweak and play with until I got the look I wanted.

cholericfun
March 21st, 2009, 04:18 PM
as a matlab person i quiet like octave,
just thought to mention that its well capable of a few things that recurrently are mentioned here: stats and graphs.

and if you need some specific packages theres no harm looking at the matlab file exchange for scripts that do what you need to get done.
its also a nice "front end" to gnuplot (if you have some matlab experience) - i think with all or most of the functionality of the plotting commands in matlab i.e. setting grids/color,linetypes and whatnot.


by way of plotting:
grace is a rather click-around based plotting tool,
which makes quiet good graphs

grinias
March 26th, 2009, 07:55 PM
See also post #583 of this (http://ubuntuforums.org/showthread.php?t=29919&highlight=beta&page=59)...

parktownprawn
March 27th, 2009, 01:38 PM
I just learned about Scubuntu (http://scubuntu.meraka.org.za/wiki/Home) who aim to develop a flavour of Ubuntu Linux for use by scientists. Looks promising.

grinias
March 27th, 2009, 06:14 PM
I just learned about Scubuntu (http://scubuntu.meraka.org.za/wiki/Home) who aim to develop a flavour of Ubuntu Linux for use by scientists. Looks promising.

thanx for this :KS

skotos
May 18th, 2009, 10:14 AM
http://geogebra.org

It is truly cross platform: GNU/Linux with Ubuntu specific package, Windows, Mac OSX and Java VM.

dchandan
August 16th, 2009, 03:03 AM
I mostly use python for scientific progrmming. It is very powerful, has a lot of useful packages available and is very easy and quick to program. A lot of universities are switching over to python for teaching undergrads scientific programming. I would suggest getting Python 2.6 at the moment and not 3.0, because a lot of important packages have not been ported over to 3.0.

Some useful pyhton packages/add-ons:
Numpy - A general-purpose array-processing package designed to efficiently manipulate large multi-dimensional arrays of arbitrary records.

Scipy - Python libraries for mathematics, science, and engineering.

ScientificPython - A Python library for common tasks in scientific computing. Useful for people in atmospheric physics, oceanography, geophysics.

Mayavi - Mayavi includes two related packages for 3-dimensionali visualization: Mayavi which is a tool for easy and interactive visualization of data; and TVTK which is a wrapper for the popular, open-source, visualization library known as VTK.

HDF4 - HDF is a physical file format for storing scientific data.

Cython - A language for writing C extensions for Python, based on Pyrex, but with more cutting edge functionality and optimizations.

PIL - Python Imaging Library provides powerful image processing and graphics capabilities.

Chaco - Chaco is a Python plotting application toolkit that facilitates writing plotting applications at all levels of complexity, from simple scripts with hard-coded data to large plotting programs with complex data interrelationships and a multitude of interactive tools.

A good list of useful packages can be found on this page - http://www.enthought.com/products/epdlibraries.php .

You should also download these:

Paraview - ParaView is an open-source, multi-platform data analysis and visualization application. http://www.paraview.org/

Fenics - FEniCS is free software for automated solution of differential equations. We provide software tools for working with computational meshes, finite element variational formulations of PDEs, ODE solvers and linear algebra. http://www.fenics.org/wiki/FEniCS_Project

marako
September 3rd, 2009, 10:27 PM
Could I teach myself any of this? I really like biology.... Ive been watching a bunch of ttc's on it ad just broke the spine to my new book, the ancestors tale. Id like to contribute to science... but I lack the money to get the degree.

frenchn00b
September 9th, 2009, 06:19 PM
QtiPlot

Description:
Data analysis and scientific plotting.
Free clone of Origin.


http://www.kde-apps.org/content/show.php?content=14826

LabPlot

Description:
LabPlot is a KDE application for data plotting and function analysis. It support both 2D and 3D plots and tries to emulate most of the functions supported by programs like Microcal Origin or SPSS Sigmaplot.

http://www.kde-apps.org/content/show.php?content=9881

But I cannot say, if these programmes offer the complete functionality of Origin. I used Origin at university, but never the mentionend freeware alternatives.

_________________
Kanotix-Manual (pdf):
http://linux.kopporama.de/km_downloads.html

Kanotix-Manual (html):
http://linux.kopporama.de/de/Kanotix_HB.html
http://linux.kopporama.de/en/kanotix_manual.html

D. Venu Gopal
September 13th, 2009, 11:49 AM
Thanks for the Scubuntu link. Like edubuntu can it be available as an iso image? If it is available as an iso then it will be easier to install for novices like me.

I like the following to be included in Scubuntu :

GNU Octave
GNU Plot
Asymptote
TeX/LaTeX
R
Kile

Otherwise in the edubuntu CD there is so much space available (about 300 MB). So except TeX/LaTeX all others can be accommodated on edubuntu CD.

Can any body give a consideration for this?

D. Venu Gopal
September 13th, 2009, 11:58 AM
Just seen the scubuntu!! A huge repository 2.2 GB ISO image!!

Better it may be devided into various categories so that it can fit onto different CDs. Because I don't have a DVD drive in my computer, only CD drive. The other thing is it is easy to down load CDs than DVDs.

asdir
October 14th, 2009, 12:38 PM
As for referencing and bibliography, you might want to replace bibus with Zotero. Though not Linux-specific, it is OSS and runs under Ubuntu. I find it much more comfortable than bibus. Most of my institute colleagues switched instantly, and they even had EndNote (which I still consider to be better than bibus).

Also, I think ESS in Emacs deserves to be mentioned in connection with R. It might not be Tinn-R, but it certainly is more helpful than just having a naked R in a terminal.

baniasad
November 29th, 2009, 05:49 PM
Replace Windows Warez?

Open Source Ubuntu!
Clo$$ed $$ource Windows 7


Open Source R
http://www.r-project.org/
clo$ed source spss or excel

open source DownthemAll (extension of mozilla firefox)
https://addons.mozilla.org/en-US/firefox/addon/201
clo$ed $ource Internet download manager

Open Source Scrapbook (extension of mozilla firefox)
https://addons.mozilla.org/en-US/firefox/addon/427
Clo$ed $ource meta product off line explorer

Open source Jabref Or mendeley
http://www.mendeley.com/
jabref.sourceforge.net (http://ubuntuforums.org/jabref.sourceforge.net)
Clo$ed Source Endnote X3

Open source mid (extension of mozilla firefox)
https://addons.mozilla.org/en-US/firefox/addon/524
clo$ed $ource Babylon

samden
November 30th, 2009, 04:01 AM
Mendeley is closed source.

And drop all the dollar signs. Most of us are professionals and know you have to pay for stuff sometimes, it's not like money is evil or anything. Even open source developers have to be paid by someone somewhere along the line for something, or they'd starve.

You sound like a teenager who's just discovered open source software and are temporarily enthusiastic about it being the best thing ever in the whole wide world, while everything else is brewed from the faeces of Satan. But next month you'll forget it and be on to a new fad, maybe genetic engineering or nuclear power or something.

Teenagers.

bondmatt
December 22nd, 2009, 01:37 AM
www.caelinux.com

The latest release is 64bit Ubuntu (8.04 LTS). The focus for this package is mechanical/civil engineering. I think there is essentially one person responsible for this package. There are quite a few little tools included to make it easy to use.

It does look like ubuntusci would give this a run for its money but if your an engineer I think CAELinux is a little more interesting.

Janneman27
January 7th, 2010, 05:17 PM
I am used to using Matlab on Windows Systems at work, but only have ubuntu systems at home. I need an alternative to matlab and have used Octave before (Windows version).

What is the most like Matlab, QtOctave or Scilab?

Any comments on usability?

barnex
January 11th, 2010, 07:54 PM
I am used to using Matlab on Windows Systems at work, but only have ubuntu systems at home.

Matlab does run on linux (if you have the licence, that is). Otherwise, I personally like octave.

bondmatt
January 23rd, 2010, 03:15 AM
I think Scilab is a completely different program whereas Octave and Matlab and nearly identical (I think they both have very similar programming). QtOctave or XOctave are very similar to Matlab. Octave through a plain terminal can be a bit shocking at first. The standard text editor that comes with Ubuntu has Octave highlighting capabilities built in which is very nice. I really like that text editor.

Best regards,
- Matt Bondy

Raamanaur
March 2nd, 2010, 01:42 PM
What about considering the package gedit-latex-plugin as a LaTeX editor? I didn't go through all the thread so I'm sorry if someone already commented about it, but since I didn't see it in the first post I assume that's not the case. I'm currently using this editor and I think it's a great option for Gnome users since it weights only 2MB compared to almost 200MB for Lyx and around 650MB for Kile.

kordenal
March 11th, 2010, 01:34 PM
Hello Gurus.
Can anybody help me - how to re-calculate all Maxima's formulas in TexMacs document?

Thanx...

superarthur
March 11th, 2010, 03:14 PM
Well, many scientists who are willing to share their software share them in source code and linux binary only.
One example is HMMER, a sequence homology search software using Hidden Markov Model
http://hmmer.janelia.org/

Azrael3000
April 8th, 2010, 04:28 PM
What about considering the package gedit-latex-plugin as a LaTeX editor? I didn't go through all the thread so I'm sorry if someone already commented about it, but since I didn't see it in the first post I assume that's not the case. I'm currently using this editor and I think it's a great option for Gnome users since it weights only 2MB compared to almost 200MB for Lyx and around 650MB for Kile.

seconded.

Another good bib tool is JabRef. Can be found in the repos and is based on Java.

rajn
May 10th, 2010, 04:58 PM
Python especially - its scientific packages Scipy, Numpy. There are options to integrate it with C++ or Fortran.

Even better: SAGE integrates python, and other software which also includes symbolic math alternatives.

manzdagratiano
May 25th, 2010, 05:03 AM
SAGE... I'm an R geek and I just discovered SAGE. It's positively wonderful! I hope it gets in the Ubuntu repository soon! It doesn't get enough press!

http://www.sagemath.org/index.html

I think it's going to be big!




...(R is still the best for stats)

SAGE is indeed phenomenal!!! It contains R and Maxima, and much more... I have completely discarded Mathematica in favor of SAGE.

manzdagratiano
May 25th, 2010, 05:11 AM
And the best deal is, aside from it being open-source, it is written in Python!!! The author, William Stein, is a Professor of Mathematics at the University of Washington. His blog:

http://sagemath.blogspot.com/

is quite compelling - especially the history of SAGE:

http://sagemath.blogspot.com/2009/12/mathematical-software-and-me-very.html

READ it pray!

attila82
July 6th, 2010, 05:00 PM
- matplotlib 2D, graphs & more
http://matplotlib.sourceforge.net/f

- mendeleydesktop - to organize documents, papers...
http://www.mendeley.com/

tonyt3
August 29th, 2010, 10:55 PM
One of the best packages I have seen is Matlab. It is not open source -- a proprietary version of which Octave is available as open; available for all OS. a huge percentage of people in the earth sciences use it. extensible, interpreted. www.mathsoft.com

zhangtudou
November 23rd, 2010, 01:56 AM
Is any physicist using ROOT (http://root.cern.ch/drupal/)?
http://root.cern.ch/drupal/
It is powerful on data analysing, based on C++, gets a lot of open source classes.

sudo apt-get install root-system

ibsys2562
December 5th, 2010, 06:14 AM
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
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:

kokoshmusun
December 5th, 2010, 02:01 PM
I am a social scientist, but have never used PSPP. I could use it on some tests, but normally I need a lot more options than PSPP offers at the time. I've been thinking about switching to R, but haven't found the time. If you're interested in learning it together, we could team up to give each other encouragement.

Love-computers
January 5th, 2011, 06:13 PM
I use free pascal :)

johny28
January 12th, 2011, 05:16 AM
i use matplotlib 2D its great tools

mlamorey
January 14th, 2011, 12:37 AM
I'm looking for a circuit / field simulator.
Very little to do with silicon or cmos more along the lines of relays and MEMS. Any thoughts / experience?

Also, I' a heavy Matlab user at work and based upon input from this forum I'm going to go with Octave rather than buying Matlab for Linux at home.

MrPok
March 3rd, 2011, 11:04 AM
Gephi

"Gephi is an interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs."

Exploratory Data Analysis: intuition-oriented analysis by networks manipulations in real time.

Link Analysis: revealing the underlying structures of associations between objects, in particular in scale-free networks.

Social Network Analysis: easy creation of social data connectors to map community organizations and small-world networks.

Biological Network analysis: representing patterns of biological data.

Poster creation: scientific work promotion with hi-quality printable maps.

(www.gephi.org)



It has decent poster-size pdf output for poster presentations and such.. nice for academia.

http://gephi.org/users/download/
http://gephi.org/users/install/#linux
(after unzipping, you can for example mv your folder to /opt/)

zampes
March 9th, 2011, 04:09 PM
Resources for scientists working with DNA Sequencing
During the last couple of months I've been working on acquiring software to work on different aspects of DNA sequencing, DNA sequence cleaning, Phylogenetic tree drawing, Blasting, DNA Database look-up and matching, ITS Extracting, and Statistical Analysis.

The following is a list of packages you can download via Synaptic in Ubuntu, or whatever method you use. You can also search for these packages online, in case they are not available through synaptic... and some aren't, sadly. These are all *free software*, unless otherwise indicated. I hope this saves future M.Sc. students some time and effort (God knows it took me forever to find all these tinhgs! ;) )
I'm sorry I had to include non-free software; I also hope this will show us all what there's still to be done in our community!


SeaView: Multiple Sequence Alignment editor, reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick)

RKWard: R project for Statistical Analysis, in this case with an incredibly useful graphic user interface (GUI) (uses KDE libraries, but will work fine in gnome, xfce, etc., you don't have to switch to KDE to use it.)

ClustalX: For DNA alignment and drawing Phylogenetic Trees

Phylip (http://evolution.genetics.washington.edu/phylip.html): is a package of programs for inferring phylogenies (evolutionary trees). also provides source code!


Fungal ITS Extractor (http://www.emerencia.org/FungalITSextractor.html): An ITS1/ITS2 extractor for the fungal ITS region. Simple page with download link.


FinchTV (http://www.geospiza.com/Products/finchtv.shtml): NOT FREE SOFTWARE, although at least it is free of charge and there's a Native Linux Version! It reads Chromatogram viewer, BLAST, reverse complement sequences, etc.

EstimateS: NOT FREE SOFTWARE, windows executable ONLY. Version 8.2. DOES NOT work under WinE (no matter the version), so use version 7.5. which does run perfectly well under WinE. However, most of the things you can do with EstimateS, you can do better with R Project, which IS Free Software.

DNA Baser: NOT FREE SOFTWARE, windows executable ONLY. It runs very well on WinE. Sequence alignment and automatic cleaning of DNA sequence, with will save you a lot of time. DOWNSIDE: trial period is 5 hours... you read that right: 5 (five) hours...

Geneious (http://www.geneious.com/): NOT FREE SOFTWARE, although at least it is free of charge and there's a Native Linux Version (although it is a hassle to install it, and requires the proprietary version of Java, does not support OpenJDK)!

For a list of free software packages available for bioinformatics, see: http://packages.gentoo.org/category/sci-biology?full_cat

In case you are looking for a complete suite of programs all bundled in one distro, all free software, no-hassle, check out

BioPuppy Linux (http://biopuppy.org/features.html): http://biopuppy.org/features.html
DNALinux (http://www.dnalinux.com/): http://www.dnalinux.com/
BioLinux (http://nebc.nerc.ac.uk/tools/bio-linux-5/bio-linux-5.0): http://nebc.nerc.ac.uk/tools/bio-linux-5/bio-linux-5.0

cwarner7_11
April 24th, 2011, 04:31 PM
The CAELinux 2010 (http://www.caelinux.com/CMS/) distro is built on Ubuntu 10.04, and includes a lot of the packages here (Scilab, Octave, R, Maxima- however, primarily focusing on FEA, including fluid dynamics, stress analysis, dynamic simulation, etc. Very powerful. The primary advantage of the CAELinux distro over picking up these packages independently is the fact that all of the dependencies are already worked out, and everything works out of the box...

cwarner7_11
April 24th, 2011, 05:55 PM
I recently did a summary of various packages available for circuit simulation- you can find it here (https://files.one.ubuntu.com/biRojnEQQU-X3l5TiIJhIA). You may be interested in the Xcos package included with Scilab (http://www.scilab.org/products/xcos/features), or the original Scicos (http://www-rocq.inria.fr/scicos/) package.

juancarlospaco
May 20th, 2011, 01:12 AM
Hi
ʘ‿ʘ

By random browsing this forum i ended here, and read the kind of software listed,
im a Python developer that make some Chemistry related software for my LoCo and
i think that it can be useful for someone here, and want to share the GPL apps,
the software is done via specifications of a person that teach Chemistry using Ubuntu,
i never traduced the apps because i never find someone interested, all are .DEB packed,
you can extract the .deb's and read the source, all are plain text files (with .py extension)
its on Spanish ...but its open source, and easy to traduce or use.

Try Hot
https://lh3.googleusercontent.com/_aWHwXiftflE/TXlgWErhomI/AAAAAAAAAOM/0dfuf37UcnU/tryhot.jpg (http://tecnicoslinux.com.ar/livecd/tryhot_0.5_all.deb)

PyGAS
https://lh5.googleusercontent.com/_aWHwXiftflE/TXlfVbMmodI/AAAAAAAAAN8/gnWq4_nc-0c/pygas.jpg (http://goo.gl/4emlU)

Im writing more apps all the time, you can search for more here:
https://wiki.ubuntu.com/juancarlospaco

Thanks
^‿^

hydroxygen
June 1st, 2011, 08:01 PM
Does anyone know if there is a open source equivalent of EniG Chemistry Assistant ?

mJayk
December 16th, 2012, 01:16 AM
You neeeed to include jabref in the bibliography section :)

Christian Poulsen
April 17th, 2013, 02:41 PM
Hi all,

I am looking for freeware that can do the same thing as dedoose.com.
That is allow learners to make annotations from documents, videos or audio.
Can anyone give me some direction where to look?

patrick295767
May 27th, 2013, 04:57 PM
what about a version based on the console ?
Efficient and reliable

http://ncursespim.scienceontheweb.net/nframe-os.htm?p=screenshots

mohanbylapudi
May 17th, 2014, 11:12 AM
Hi, I am mohan bylapui a basic linux user. I am very enthusiastic towards the linux system level programming, So i would like to request any one of u kindly tell me the concepts i have to be very clear and suggest me any system level project.

Thanks in advance....

qpanas
October 27th, 2014, 10:33 AM
Not exactly on topic, but strongly associated with it. I am looking for the best hardware configuration for use with scientific software for mathematics / statistics. I currently have two configurations that I take into consideration. It is described here:
http://ubuntuforums.org/showthread.php?t=2250111
I have written here, because I think here will be people who are related to academic work. Sorry if I should not have.

Ric_Helm
October 28th, 2014, 03:46 AM
Does "scientific" include electrical engineering?
I have been trying to use Multmeter, LCR, and Hand Scope software through WINE to work.

I suspect that I just do not know how to install drivers through WINE, however using search terms for multimeter or DMM only pull up threads that were quickly closed..
FYI, the Test Equipment is as follows, an Amprobe DMM via Serial to USB adaptor, A Velleman Hand Scobe also via Serial to USB adaptor, two Uni-T DMM's directly to USB.
Plus the Arduino IDE

martin-d-hurst
February 10th, 2015, 11:32 PM
There has been no mention of wxMaxima, which I've found to be a really useful for mathematical computing as an alternative to Maple or Mathematica. Check out http://maxima.sourceforge.net/.
Given that I've posted this twice (here and a different thread), and they are my first two posts, I feel I should point out that I am not associated with this software ;)