Are there any scientists-biologists out there using Ubuntu?

[Campitor]

Hello:

I'm a population ecologist/genticist and I was wondering if there are other biologist-ecolofreaks-molecular biologist-nature people out there using ubuntu. Maybe we can start a little Ubuntu-Science discussions I believe Linux will be the OS of the academic world, and the more we promote it, know about it...the better.

Hope you're out there

Campitor

[defkewl]

Well I'm a scientist :P A computer scientist and computer science is under faculty of science in my uni.

[ssam]

does a physics student count?

i use latex for labreports and octave for maths stuff.

a science forum would be nice

sam

[greenwom]

I believe Linux will be the OS of the academic world, and the more we promote it, know about it...the better.

Campitor

I'm in school picking up some lower level classes I never took for my BS (few to go :-P )

In this English class I'm in I have to write an argumentative (sp) paper on something, I was thinking Linux.

Any sujestions to published works that would provide some good material?

As a newbee it'd be fun to research a little linux history, trends, and performance.
Maybe even the ethics and amazing progress made through open-source software development...

Let me know,

I'd also love science explored more in a conversation online.

[kanem]

does a physics student count?

i use latex for labreports and octave for maths stuff.

a science forum would be nice

sam
I'm also a physics student, soon to be physicist. I've finally grown to like Lyx for latex writing and am using it for my thesis. But am still booting into windows for kaleidagraph. The last damn program in windows that I need. Grrr. Maybe I'll make another effort to use Octave or Scigraphica.

One thing that would be useful for a thread like this is if the scientists could say what programs they use for their field and why. There are lots of scientific programs for linux, but they often aren't publicized enough so no one knows about them.

There's a distro that specializes in scientific software called Quantian (Knoppix based). I once installed it just to see what programs it had and what they were like. Most of them I had never heard of, but almost all of them were in Ubuntu's repositories. There was a maple clone which would be useful, except that I just got Mathematica5 for Linux. Which is pretty nice. It's closed source of course though. The only difference I've noticed between it and It's windows version is the look. Some kind of gtk1 or something.

There's also a KDE app that aims to be an Origin clone called qtiplot. It's seems pretty good, although I haven't tested it's fitting capabilities.

[minio]

Does biology student count? I won't be student for long anyway (10 days to deadline for finishing my thesis :/ ), but i doing cell physiology :).
I am not sure about linux in academic world, because almost every device I used required specific version of windows (from 3.11 to XP) and not speaking about some of grant agencies sending forms in .doc format...

[Campitor]

One thing that would be useful for a thread like this is if the scientists could say what programs they use for their field and why. There are lots of scientific programs for linux, but they often aren't publicized enough so no one knows about them.



I agree with you...it would be really important to centralize the availabillity of software for scientific computing. it takes a lot of google time to find a piece of software that does what I need, specially if I need to find a Windoze substitute.

I do believe it will take some effort for Linux to become mainstream in academia...I know many new pieces of equipment come already hardwired to Windows...nothing you can do there. But many new applications, specially those that are extremly computer-intensive are mostly being developed for Unix/Linux plataforms. One needs stability to run a model for two straight months...try that with windows and you'll see a nice blue-screen.

WHen I've asked collegues why they haven't switched to Linux...the main response is: I don't know if I'll find software that does XXX (fill in the blanks). They are all sick of windows (Mac people love their macs), but they do not know if they will find the specific software they need. Complexity is never an issue (I know two collegues who still use MS-DOS and SMart-Word processor to write papers...talk about complexity). Lack of information, is the key factor detering many good people from Linux in science.

kanem: Have you tried gnuplot and python together (with numeric), that made me get rid of Scigraphica and Octave all together. ANd BTW, Lyx is really cool. I wish I could submit papers in Lyx format..that would be cool.

[Alexander Kirillov]

To add to the mix, I am a mathematician (SUNY at Stony Brook, NY ,USA). ANd, of course, all mathematicians around have been uisng Linux for the last 5 years - our dept. now has a mix of Red Hats and Ubuntu's.

Most used software: latex (I use Kile as frontend).

[tkiesel]

Got my Physics degree (and a Philosophy degree too!) a little more than a year ago at Purdue University (http://www.purdue.edu/). After some research assistantship work, and my future wife's time as an aide to an engineering professor I decided that the life of a physicist in academia wasn't my cup of tea for lots of reasons.

Now I'm teaching junior high and loving it. I still maintain a very active interest in physics and philosophy, and my training and study allow me to be a bit more conversant with the subjects than your average layman. ;) I'd love being involved in any kind of Ubuntu science sub-community.

[Kimm]

I'm a schience student for Pysics maths chemistry and biology and I use ubuntu, usualy Open Office for formulas and reports

[kanem]

kanem: Have you tried gnuplot and python together (with numeric), that made me get rid of Scigraphica and Octave all together. ANd BTW, Lyx is really cool. I wish I could submit papers in Lyx format..that would be cool.

Nope, I never tried that, but I've now installed it and have looked at a few of the example files. You can do curve fitting and stats analysis with it?

[Tobias Pistohl]

Actually, I am a biologist. But I'm working in (computational) neuroscience. At the university we use Suse, mostly with Matlab. Ubuntu is just my private/home distribution, where I have the freedom of choice.

[larry]

I am interested in scientific software as well.
I installed Octave, R and Gnuplot.
I used to do pretty basic stuff with them, but now I want to learn to do more.
I only have a concern: is the scientific software in Ubuntu reasonably up do date?
Does in come from Debian unstable?
I think it would be nice if some scientific package was to be included in the main repository.
Regards

Larry

[minio]

I think all of you would agree with me if I say, that we REALLY need alternative to Endnote with all of it's features (click to cite, searching in databases etc.). Everything I found has some of those features but never all of them.

[Campitor]

Nope, I never tried that, but I've now installed it and have looked at a few of the example files. You can do curve fitting and stats analysis with it?


Hi:

I know you can do curve-fitting (kinda') with gnuplot if you have an equation and need to fit parameters to that equation. Then you can plot observed and fitted parameters to get an estimate of fit. The best thing to do is to download the entire gnuplot manual, and go through it. A good web-page for a quick into is:

Not so FAQ gnuplot (http://http://t16web.lanl.gov/Kawano/gnuplot/index-e.html)

In terms of python and scientific computing, I recomend doing a google search, but a few interesting links:
http://www.python9.org/p9-jones.ppt
http://www.llnl.gov/computing/tutorials/python/sci_python.pdf

In terms of a substitute for Endnote...I agree..lInux defenitely needs one. The best solution I've found so far are the following: Use JabRef (http://jabref.sourceforge.net/) to manage your references...you can't do database searches from it, but you can do searches in WebofScience and download all references into JabRef. JabRef can then pipe citations into LyX for writting. The only problem I've run into is trying to format bibliographies to match the journals requirements. If the bst style file doesn't exist, you can try to make your own with the makebst program (located in CTAN) but it is really tedious and complicated. The other solution is to write your paper in Lyx, including the citations in the text and then export to a tex file. Use the aux file produced to create a sub-database in JabRef, and export the citations in the right format using Html code. I know is complicated and rough, but it beats the hell of writting your own bibliographies by hand. I know, that if more people email the JabRef developers, they might include new features into the program. In my mind, is developing to be a really god Endnote substitute.

IMHO this thread (and any future forum within ubuntu) for scientific computing would reach more people in different areas, by focusing on a place to discuss software developed for scientific analysis which runs in Ubuntu-Linux (or platform independent). Additionally, people with more experience in using specific software, may give pointers as how to achieve specific goals, redirect to relevant texts or info. As well as posting new software created by scientist which may need testing or improving.

I don't see why we shouldn't also leave the possibility for discussing interesting questions such as: Physics; how does blackhole and local universe bulge mass correlation aid in the study of the evolution of galaxies? Chemestry: The inclusion of instantaneous spatial correlations among electrons to achieve a more accurate description of atomic and molecular electronic structure? Evolution: The importance of genetic preadaptation in cultivated crops. Ecology: The creation of many small or few large reservers vfor the conservation of species?

Campitor

[Stormy Eyes]

Hello:

I'm a population ecologist/genticist and I was wondering if there are other biologist-ecolofreaks-molecular biologist-nature people out there using ubuntu. Maybe we can start a little Ubuntu-Science discussions I believe Linux will be the OS of the academic world, and the more we promote it, know about it...the better.

Being a tradesman (programmer) and not an academic or a scientist, I thought Linux was already the de facto OS of the academic world, primarily because of LaTeX.

[Alexander Kirillov]

Being a tradesman (programmer) and not an academic or a scientist, I thought Linux was already the de facto OS of the academic world, primarily because of LaTeX.
In Math/Physics, this is definitely so. In biology - no: most molecular biology labs I've seen use Macs.

[Campitor]

In Math/Physics, this is definitely so. In biology - no: most molecular biology labs I've seen use Macs.

That is true...most still use macs. But the new breed of bioinformatics and molecular biologist are changing quickly to Linux mainly because of perl and python. Many new applications run smoother when both interpreted languages are run under Linux. I've already lured four evolutionary biologists into Ubuntu...and they love it. It will take some time though for more people to put down Macs, specially with the stability of the new OS. We'll see

[kanem]

In Math/Physics, this is definitely so. In biology - no: most molecular biology labs I've seen use Macs.
Many of the theorists in our physics department run some form of Linux, but us experimentalists need our computers to run our equipment. Our proprietary equipment with their proprietary drivers so you can guess what OS we have to use.

[kehan]

I'm a Botanist, and while I'm stuck with windoze at work I am advocating Ubuntu like mad, and do feel it will be the way forward - just need to convince collaborators to use it as well :)

I'd like to use Ubuntu to do major statistical analyses and also as a database system but need to get my head around the basics of those before I can stop relying on M$.

Let me know if you need to do some rallying around and getting publicity going.

[Daz]

Hi!

I'm a student studying Bioinformatics in the UK. In our department here, the only version of Linux we use is Ubuntu, we've just found it to be super stable, reliable and full of bleeding edge packages (which we need!) and damn easy to set-up and administer!

I think Linux is going to be the way forward in Scientific applications, (it already is for most Bioinformatics / Computational Biology set-ups) and yep - somewhere to chat about scientific-specific things would be great!

In response to larry's question:

I am interested in scientific software as well.
I installed Octave, R and Gnuplot.
I used to do pretty basic stuff with them, but now I want to learn to do more.
I only have a concern: is the scientific software in Ubuntu reasonably up do date?
Does in come from Debian unstable?
I think it would be nice if some scientific package was to be included in the main repository.
The software in the main Ubuntu repo's are pretty up-to-date, but if you want to make sure you have the latest packages etc. (or at least one of the more recent versions), you could try adding the repo's mentioned here (http://www.ubuntuforums.org/showthread.php?t=17542) as they have some pretty specialised scientific apps on there - originally built for debian, but i've been using them since the release of Warty on Ubuntu and they haven't caused me any troubles yet...

[ssam]

I thought i'd try and kick start some stuff in the wiki

https://www.ubuntulinux.org/wiki/UbuntuScientists

please add your favourite science applications to it, and anything else you think is useful.

[Daan]

Hi, my name is Daan, and I am studying for my MSc in biology (ecology and evolution) at the University of Amsterdam. I got Linux/Ubuntu only yesterday. I have been programming in C++ a little before, and now I hope to alter/moderate Cellular, a cellular automata program. I coudn't get it to work under MS Windows, and the computer geeks I know would only help me if I used Linux. ;-) But I still have a lot to learn...

Here's the adress of the Cellular webpage: http://staff.vbi.vt.edu/dana/ca/cellular.shtml

[henriette_holm]

Hi.
I'm Henriette and I have a MSc in chemical engineering – now I'm working on a ph.d. in computational chemistry. Since all the programs I need for work run only in linux the choice was easy – though I'm still forced to dual boot with Windows XP since I need the following programs:

Reference Manager
ChemOffice
SciFinder
MDL Crossfire Beilstein

Any suggestions for linux versions of the above?

-Henriette

[Jurgen]

Hi!

I'm a Physics student right now at RIT, personally I prefer Mac OS X for doing my physics work =) but right now I gave my ibook to a relative so all I have is my PC and here I am trying out ubuntu linux.

ok a few questions, are there any linux programs that will run matlab code?(I only have the windows version of matlab) If not, anything like matlab? Or should I just stick with good old c/c++ code.

Also, any good reccomendations for programs to run? Some good math programs would be awesome! I already have gnuplot and xephem.

Thanks.

[desdinova]

I'm halfway through my M.Phys in Astrophysics, and I love using stuff such as Octave, GnuPlot, Maxima (which is great for checking calculus!), OO.org for reports and Intel's Fortran 95......

[desdinova]

Hi!

I'm a Physics student right now at RIT, personally I prefer Mac OS X for doing my physics work =) but right now I gave my ibook to a relative so all I have is my PC and here I am trying out ubuntu linux.

ok a few questions, are there any linux programs that will run matlab code?(I only have the windows version of matlab) If not, anything like matlab? Or should I just stick with good old c/c++ code.

Also, any good reccomendations for programs to run? Some good math programs would be awesome! I already have gnuplot and xephem.

Thanks.
You can register for a free copy of Intel's Fortan at their website.. although Matlab is also available for Linux btw. I heartily recommend Maxima/Xmaxima - utterly indispensible for checking your integrals and stuff like that ;-)

[Jurgen]

cool, thanks!

Although I don't know any fortran yet, the only computational physics class ive taken so far is an intro class and it delt with matlab. Apparently Octave can run .m files so im installing that right now =)

[desdinova]

cool, thanks!

Although I don't know any fortran yet, the only computational physics class ive taken so far is an intro class and it delt with matlab. Apparently Octave can run .m files so im installing that right now =)
We did a year of Fortran - besides, I have the advantage of being a Mature Student - for 12 years before this I worked as a sysadmin ;-0

[Jurgen]

cool, octave is ok. Although it doesn't plot the same way as matlab and I dunno yet how to change colors of each line, but it did work with my 3 body orbit program perfectly fine except for a few changes I needed to make with regard to plotting. Not to mention it didn't have the memory problems that matlab has for me under windows, ie matlab cant do more then 35000 iterations of my 3body program, if I set it to that many it just hangs. Octave ran 50000 iterations fine =)

Thanks again!

[desdinova]

cool, octave is ok. Although it doesn't plot the same way as matlab and I dunno yet how to change colors of each line, but it did work with my 3 body orbit program perfectly fine except for a few changes I needed to make with regard to plotting. Not to mention it didn't have the memory problems that matlab has for me under windows, ie matlab cant do more then 35000 iterations of my 3body program, if I set it to that many it just hangs. Octave ran 50000 iterations fine =)

Thanks again!
Octave uses GnuPlot (http://www.gnuplot.info/) for plotting - you may find these links useful

http://www.phy.uct.ac.za/courses/phy205h/gnufit/node1.html
http://www.duke.edu/%7Ehpgavin/gnuplot.html
http://camden-www.rutgers.edu/HELP/Documentation/Unix/S50-1501_Gnuplot_and_Snapshot.html

You can get some quite professional graphs and fitting done with it - I'm doing Spacetime Metrics for a Black Hole for my year 3 project so I hope to get more au fait with some of this stuff ;-)

[Jurgen]

Thanks a lot!

Ill probablly have to get used to gnuplot =) Even though im going to be buying a new ibook/powerbook next summer(once the x86 ones are released) and using matlab for OS X, ill still be using gnuplot probablly.

[desdinova]

Thanks a lot!

Ill probablly have to get used to gnuplot =) Even though im going to be buying a new ibook/powerbook next summer(once the x86 ones are released) and using matlab for OS X, ill still be using gnuplot probablly.
GnuPlot rocks... It takes a little work with it to get the best out of it, but it is worth it - ditto maxima

[phen]

Hi!

I am an aerospace engineering student, and i would love to use linux for the rest of my studies. Our University is using Debian for the student's computers (and in some offices). But there are only compilers installed, and hence i have no clue which program i could use to replace matlab or mathcad for example. I think the wiki or a forum is a good idea!

For me, a big problem will be to find a CAD/CAE program for linux. Any ideas? We get free copies of a windows CAD system from the university, and i don't even know if there are linux programs on the market (except CATIA perhaps, which costs 300€/year for the students edition - totally crazy.... :)

Answers to these questions would give me additional ammunition for my linux advertisement and convincing of my colleagues :-)

have a good time,

cheers,
kai

[desdinova]

Hi!

I am an aerospace engineering student, and i would love to use linux for the rest of my studies. Our University is using Debian for the student's computers (and in some offices). But there are only compilers installed, and hence i have no clue which program i could use to replace matlab or mathcad for example. I think the wiki or a forum is a good idea!

For me, a big problem will be to find a CAD/CAE program for linux. Any ideas? We get free copies of a windows CAD system from the university, and i don't even know if there are linux programs on the market (except CATIA perhaps, which costs 300€/year for the students edition - totally crazy.... :)

Answers to these questions would give me additional ammunition for my linux advertisement and convincing of my colleagues :-)

have a good time,

cheers,
kai
http://www.ribbonsoft.com/qcad.html - QCAD Open Source Cad

Matlab is available for Linux, and I find Mathcad unwieldy and awkward - check out maxima/xmaxima, octave, gnuplot and possibly even R

[Jurgen]

you might be able to run some of the cad apps your uni gives out with crossover.

[kb00heda]

What is your favourite editor for writing MATLAB and Fortran code? I left MATLABs own editor for emacs, but recently began using Kate instead.

The reason for choosing Kate was, in some part, due to Kile, which is quite similar in style (both being KDE applications). Also, I have tweaked --- at least for me --- the syntax highlightening somewhat (for MATLAB that is), by adding more commands/functions to it.

gedit was no good at syntax highlightening (the ' symbol had apparent drawbacks), but otherwise I liked it, and it seems to be lighter than Kate.

emacs works pretty much for everything, also being the least resource demanding in the group, but I found myself working more effectively, e.g., when using command and keyboard shortcuts, under Kile and Kate.

BTW, I'm a swedish bioengineering and math student, working on my thesis. :)

[wirjo]

I didn't know there are so many scientists in this forum.. O.o

[kleeman]

I am a mathematician/atmospheric scientist and use Fortran all the time (the oldies are the goodies besides which c sucks in terms of readibility and scientific libraries). I also use Kate because of the source highlighting but mainly because the kde networking is really good so I can remote edit on several machines very seamlessly. I have found development environments like kdevelop or photran (an eclipse plugin) are overkill for what I do (play with large atmospheric numerical models).

[desdinova]

What is your favourite editor for writing MATLAB and Fortran code? I left MATLABs own editor for emacs, but recently began using Kate instead.

The reason for choosing Kate was, in some part, due to Kile, which is quite similar in style (both being KDE applications). Also, I have tweaked --- at least for me --- the syntax highlightening somewhat (for MATLAB that is), by adding more commands/functions to it.

gedit was no good at syntax highlightening (the ' symbol had apparent drawbacks), but otherwise I liked it, and it seems to be lighter than Kate.

emacs works pretty much for everything, also being the least resource demanding in the group, but I found myself working more effectively, e.g., when using command and keyboard shortcuts, under Kile and Kate.

BTW, I'm a swedish bioengineering and math student, working on my thesis. :)
Pico ;-)


Nah I use Kate and or Gedit.

[Optimal Aurora]

I wouldn't call myself a scientist but I am an amatuer astronomer and that is what I usually use ubuntu for especially since it is directly link to my computer...

[kanem]

GnuPlot rocks... It takes a little work with it to get the best out of it, but it is worth it - ditto maxima
GnuPlot does rock. I found that out recently. After spending days trying to get either Maple, Mathematica or Matlab to make a 3-D plot of my data in cylindrical coordinates. They all sucked. some sort of did it, but not good enough. Finally I tried GnuPlot as a last resort and got great results in a relatively short amount of time.

And I thought I was over being biased towards GUI programs, but considering the amount of time I refused to even try GnuPlot shows I wasn't.

[desdinova]

GnuPlot does rock. I found that out recently. After spending days trying to get either Maple, Mathematica or Matlab to make a 3-D plot of my data in cylindrical coordinates. They all sucked. some sort of did it, but not good enough. Finally I tried GnuPlot as a last resort and got great results in a relatively short amount of time.

And I thought I was over being biased towards GUI programs, but considering the amount of time I refused to even try GnuPlot shows I wasn't.
GnuPlot is one of those apps that really grows on you quickly - I love its fitting ability, which helps when trying to work out things - combine it with Maxima's ability to solve calculus problems for you and one could get really lazy ;-)

[Campitor]

Hello All...

It's so nice to see so many people responding to this thread. I moved back to Costa Rica and haven't accessed the forums in about a month and was very happy to see all the comments.


I do agree...gnuplot is the best program. Here{s an interesting webpage for quick help
Not so frequently asked questions about gnuplot (http://t16web.lanl.gov/Kawano/gnuplot/index-e.html)

For Matlab code, Octave is the best substitute. The only problem I've found with ocatve is that it does not work with three dimensional arrays (I dont know if recent versions have fixed this). And although I liked octave, I've switch completely to python with the numeric module. Python, can also plot through gnuplot, and the computation skills required for programming in python are not as d3emanding as octave.

Someone mentioned that for scientific computing we need a good reference manager. The best I've found so far is JabRef (http://jabref.sourceforge.net/) although a bit slow because its Java, it works on any platform. It interacts perfectly with PubMed and will import/export to Endnote. It only interacts with LyX and TeX at the moment, but work is underway to make it work with O.O. I believe a word of encouragment from many users will gear this program to a fantastic opensource reference manager

Camp

[Spleenie]

I would also like to throw my hat into the mix.

I am a Physicist and Mathematician (at least thats what the degree says ;) ) and I am an avid Ubuntu user.

I would love to join any Ubuntu Science sub-group that pops into existance. I have been trying fruitlessly to encourage open source in my work environment but to no avail at this stage...too many MCSE hacks praising M$.

Cheers, Spleenie

[poster_nutbag]

I am a computer scientist/evolutionist who uses Ubuntu - you can see some of my work at http://www.unac.org.uk/

[Campitor]

Does anybody have a good suggestion for statistics in Ubuntu? I use to use MacAnova on F.C.1, and due to time, age and plain stubourness I really dont want to learn R.

Anybody has any suggestions, or maybe some program we can beg the Ubuntu gurus to include in the repositories?


Camp

[ramkiraman]

I am a physicist and have been using linux for my work and home the past three years - I am now beginning a move to ubuntu. I agree that a concerted effort needs to be made to identify key software for scientific environments.
LIke a few others, I have completely migrated out of windows because of the usual stability, economic and usecurity reasons. However, applications like Lyx, gimp, imageJ, openoffice, pybliographer, octave, are enough reasons to use linux.
National instruments provides significant linux support for its hardware and this is a growing trend.
My one peeve still is that kaleidagraph is still the best graphic software around and just for that I have had to run a windows emulator like win4lin. I have note been successfull at getting it to run usiong codeweaver. While gnuplot is excellent, I find command line programs a big barrier in todays GUI era. However, things like swish-e (a file indexing utility) still make it worthwhile using commmand line programs.

RK

[kanem]

My one peeve still is that kaleidagraph is still the best graphic software around and just for that I have had to run a windows emulator like win4lin.
Every couple of months I get desperate and search the web for any small sign that Kaleidagraph is coming to Linux.

Have you seen QtiPlot? It's supposed to be an Origin clone. The last time I tried it was nearly a year and several versions ago when it first came out. And it was already useful then. Should be better now.
http://soft.proindependent.com/qtiplot.html

[ramkiraman]

thanks for the suggestion kanen.
Like you I also periodically try out various software without much luck. I have looked at qti a while ago - I will check it again shortly. Also. one which was very good is called Grace and it has improved considerably over the last year

RK

[desdinova]

My one peeve still is that kaleidagraph is still the best graphic software around and just for that I have had to run a windows emulator like win4lin. I have note been successfull at getting it to run usiong codeweaver. While gnuplot is excellent, I find command line programs a big barrier in todays GUI era. However, things like swish-e (a file indexing utility) still make it worthwhile using commmand line programs.

RK

Now I'm the opposite - unfortunately too many times I find the GUI gets in the way, whereas GnuPlot Just Works

[parktownprawn]

grace (http://plasma-gate.weizmann.ac.il/Grace/) is a nice WYSIWYG plotting tool - easier to use than gnuplot and its in the ubuntu repositories (universe i think)

[bkristan]

Late to the party - I've been using Linux for about four years, and just switched to Ubuntu yesterday (from Mandrake). I'm an ecologist.

I'll put in a good word for Grace. It has an ugly, somewhat non-intuitive user interface, and only handles 2-d graphics. It's very flexible, though. I even figured out a way to pipe eps output from grace through a couple of filters to create an Openoffice.org draw file. If anyone's interested in the details I'd be happy to share...

I also like R quite a lot. The list of contributed packages is growing fast, and includes several packages that are very useful to biologists. It's hard to learn, but rewards your devotion.

[LaserJock]

Hi all!
I am a PhD student in Physical Chemistry. My group uses linux almost exclusively (1 postdoc like Windows 2000). My advisor can't use Windows to save his life (Where's emacs?). We use Gentoo, Fedora, and I use Ubuntu (dual-boot with whatever other distro I take a fancy to).
For programs we use Gnuplot a lot, lots of Fortran (although I am trying to shift things to Python), PGPLOT (awsome for plotting if you like Fortran), LaTeX for just about all of our dissertation, report, presentation creation. Our university also has Maple, Mathematica, ChemDraw, and Scifinder set up via a Citrix server. All I have to do is download the ICA client and I can run them on my linux box. I can even run IE (ugghh!). We also use GPIB data aquisition cards and write our own data aquisition programs (no LabView here :roll: ).
Anyway, I am very interested in what other scientists are using in their research.

-LaserJock

[yarri]

Hi!

I am PhD. student in Plant physiology. I have started my adventure with linux (and Ubuntu just couple of weeks ago). And I must say I am happy. It looks like there are only two things that I need from windows - games and... Endnote. I was trying to work with Lyx, but it is a little bit frustrating. Especially when you consider that there is no way to convert Lyx into .rtf or .doc - and I am the only person in the Institute using Linux. I am not used to CLI and documentation of Gnuplot is a little bit scary for me - but I am stubborn sort of fellow.

Cheers, Yarri

[minio]

It looks like there are only two things that I need from windows - games and... Endnote. I got word and endnote working under wine. Maybe you should give it a try.

[parktownprawn]

Especially when you consider that there is no way to convert Lyx into .rtf or .doc - and I am the only person in the Institute using Linux. I am not used to CLI


its not to hard to convert lyx documents to .rtf with latex2rtf.

1. install latex2rtf (you may have to enable extra repositories (http://ubuntuguide.org/#extrarepositories) ):
sudo apt-get install latex2rtf

2. export your lyx file as latex (file->export->latex)

3. in a terminal type

latex2rft your_file.lyx

which should produce a file called your_file.rtf

you can also export your files to html and convert the html to a .doc using openoffice (thats a bit tedious :( though )

to export to html:

1. install latex2html:
sudo apt-get install latex2rtf
2. reconfigure lyx (edit->reconfigure)
3. restart lyx
4. convert lyx doc to html (file->export->html)

actually for some reason lyx doesn't seem to export formulas properly to html
but viewing your file as html (view->html) and then saving it in your browser seems to work.

[kanem]

Hi all!
I am a PhD student in Physical Chemistry. My group uses linux almost exclusively (1 postdoc like Windows 2000). My advisor can't use Windows to save his life (Where's emacs?). We use Gentoo, Fedora, and I use Ubuntu (dual-boot with whatever other distro I take a fancy to).
For programs we use Gnuplot a lot, lots of Fortran (although I am trying to shift things to Python), PGPLOT (awsome for plotting if you like Fortran), LaTeX for just about all of our dissertation, report, presentation creation. Our university also has Maple, Mathematica, ChemDraw, and Scifinder set up via a Citrix server. All I have to do is download the ICA client and I can run them on my linux box. I can even run IE (ugghh!). We also use GPIB data aquisition cards and write our own data aquisition programs (no LabView here :roll: ).
Anyway, I am very interested in what other scientists are using in their research.

-LaserJock

Wow, that's awsome. Especially the writing programs for your GPIB cards. I've never even considered straying from LabView.

Can I ask what school you're at?

@parktownprawn:
very useful info. thanks. I was facing the prospect of writing my cv in tex and then having to do it over again in html for my webpage.

[parktownprawn]

Hi

I'm a theoretical physicist so my computing need are not that intensive.

I use lyx for producing papers. when my collaborators mangle the latex code beyond lyx's understanding i use emacs with preview-latex.

otherwise i use mathematica and maple a lot. i'm trying to wean myself off these and use maxima which is free and OS.

btw wxMaxima (http://wxmaxima.sourceforge.net/) is quite a nice front end for maxima. i installed the deb from their site but it looked crappy (something to do with gtk1 vs gtk2 - i dont care) so i compiled it from source and not it looks just like their nice screen shots :D

[LaserJock]

Wow, that's awsome. Especially the writing programs for your GPIB cards. I've never even considered straying from LabView.

Can I ask what school you're at?

I'm at the University of Nevada, Reno. We primary use our programs (written in C) to get data from an oscillascope (and do calculations on the results), but we also use them to time our experiments ( we run Nd:YAG lasers at 10Hz) and scan the wavelength on our dye lasers. Right now we use the free National Instruments GPIB driver.
Sometimes its hard to tell whether it is worth the effort. The advantages are that you can make a program that does exactly what you want with minimal resources (nothing extra), and of course it's free (in terms of money). However, I have to spend time programming (instead of research) to get it done. ](*,)

[cinnabar]

I'm a PhD hydrogeologist but I primarily do environmental geochemistry and atmospheric chemistry work (read: I'm a funding whore). Just in case anyone is new to linux (or even if they are not), here are some scientific programs I've that may be useful to some people. FYI, I don't plot equations or do much calculaus so I'll leave those programs to the mathematicians and physicists. For LaTex, I primarily tried Lyx and Kile but often use a work processor just as much.

All of the program names below are linked to their homepage for your shopping convenience.

Data Plotting Software:
Qtiplot (http://soft.proindependent.com/qtiplot.html)
One of my favorites. It's made a lot of headway in the last few months. Reminds me a lot of Sigmaplot but it has some rough spots.

LabPlot (http://labplot.sourceforge.net/)
Very similar to qtiplot but the interface seems to be a little more clumsy. It seems to take about twice as long to make the same plot in LabPlot as in Qtiplot.

Grace (http://plasma-gate.weizmann.ac.il/Grace/)
I've only used this program a little bit but it seems very comprehensive but may take a long time to master.

Gnuplot (http://www.gnuplot.info/)
Used by many hydrologists and geophysicists I know but I've never used it. I will say that I've never seen a gnuplot graph that I thought was nice enough to publish. Maybe somebody will post one. ;)

Generic Mapping Tools (GMT) (http://gmt.soest.hawaii.edu/)
Seems like primarily a mapping program but I have a friend who uses to make all of his graphs and swears by it. It sure does make some attractive figures.

Statistical Software:
R (http://cran.r-project.org/)
The defacto linux stats package. The basic version has no GUI nd I find it rather cumbersome. Great scripting capabilities. THere are also several GUI's available (PMG and R_Commander, for example). Lots of extra modules and extremely well documented. Steep learning curve though.

Vista (http://forrest.psych.unc.edu/research/)
A great EDA-oriented stats package. However, the Windows version is much more up to date (and better) version. :sad:

OOoStatistics (http://www.ooomacros.org/user.php#106652)
A statistics macro for openoffice calc.

I hope this helps someone out in the future.

[DirtDawg]

I'm a graphic-designer/cartoonist/loser.
Does that count?
:wink:

[drizek]

Vista (http://forrest.psych.unc.edu/research/)
A great EDA-oriented stats package.


*cough*lawsuit*cough*

[xmastree]

I'm a graphic-designer/cartoonist/loser.
Does that count?Only if you learn to spell ... [-X

[kanem]

Gnuplot (http://www.gnuplot.info/)
Used by many hydrologists and geophysicists I know but I've never used it. I will say that I've never seen a gnuplot graph that I thought was nice enough to publish. Maybe somebody will post one. ;)Here's a couple. Although since the paper hasn't officially been accepted yet I guess this doesn't prove the graphs are publishible. The referee reports looked promising though.....

I have some colour ones also, but don't know where they are at the moment.

[macgyver2]

Those look nice, kanem.

I'll have to ask my girlfriend what she used for the paper she just submitted. There's a chance it may have been gnuplot, but it was probably supermongo (non-free :-x). And they were made on Mandrake because someone else set everything up for her a while back, before we were dating. I'll probably be able to convince her to switch to Ubuntu after she finishes the master's segment of her degree.

She's in grad school for astrophysics. We both have astrophysics bachelors. I'm thinking about going back to school for a grad degree in meteorology next year (climate modelling).

It's nice to see so many scientists in these forums! :)

[cinnabar]

Thanks Kanem. Those are nice. I think a lot of why I haven't been impressed with gnuplot's graphs are that the default font that everyone seems to use makes it look so 1990. Good luck with getting the manuscript accepted.

I'm starting a new job in a couple of months and trying to decide what software to use. I'm also concerned with Ubuntu because the version of R they use is 2.0 but almost all of the libraries require 2.1 Even Debian-testing is uses R 2.1 so I may have to switch distros, which is really too bad.

[DirtDawg]

Only if you learn to spell ... [-X
lol! Oops.

[kanem]

I think a lot of why I haven't been impressed with gnuplot's graphs are that the default font that everyone seems to use makes it look so 1990.Ok I have a confession. After I posted I remembered that those axis titles were a cheat. I wrote out the equations in Lyx, exported to pdf, then copied and pasted onto the graphs. Those fonts in Gnuplot are pretty nasty. Although I haven't tried making them better.

In related news there's a neat app called eqe (http://www.gnomefiles.org/app.php?soft_id=1040) that lets you write equations in Latex and easily get it into other applications by just dragging it over. If I had had it a couple of months ago I wouldn't have needed that convoluted process described above to get those pretty axis titles onto that graph.

[cinnabar]

Busted!!! I knew that looked too good for Gnuplot. Just kidding.

I ran across a couple more plotting programs:

Veusz (http://home.gna.org/veusz/)
It's only been around a short time. I used it to make some x-y plots that were set up in a column. It worked very well for that; I was pulling my teeth out trying to do the same thing with Qtiplot. One note was that I had a very difficult time getting data with several X and Y variables into the program. I ended up hacking an example data file that was supplied with the program. The other thing about the program (be it good or bad is debatable), is that everything is adjusted through a series of dialogs that are opened via a flow graph element layout (sorry, bad description) rather than clicking on the graph itself. Last thing is that you can't draw lines or shapes on graphs as far as I could figure out. Definitely worth checking out though.

SciGraphica (http://scigraphica.sourceforge.net/)
This has been around for a while but hadn't been updated for years until recently. No debs available and I decided not to compile it myself. Perhaps someone will get a chance to play around with it.

On a last note, has anyone used stata on linux (not an open program)? I'm considering buying it but have only run it in Windows.

[Managarmr]

Evolutionary Ecologist here.
So far mostly using Windoofs (also due to Endnote, statistic programs Statistica, SPSS, Anosim) or part time Mac (wild mixture at the institute),
but a course for R recently did wake up interest for ubuntu, which i have running now (64bit), but still not using regularly (lacking time). This week I will visit a LateX introduction (being annoyed by Words often-times unexpected popping up problems in things which were working one week before), let's see.

[Campitor]

Does anybody know where the OO.org bibliography project stands?

I've seen that JabRef exports in a format which should be recognizable to OO.org. But as of now, I still don't know if this project is working well enough to actually use OO-Write to make manuscripts and have a workable reference list.

I've seen that a better version of the reference database should be available for OO.org version 3, but that is still a long wait.

Any infor would help a lot of us.

Camp.

[Tinuz]

A bit late, but i never spotted this thread.
I hope to be admitted to a MSc next year, so not really a scientist, just aspiring to be one.
I'm hoping to be admitted to Computational Bio- and Physical Geography(in short: CBPG). And the main focus is the modelling of mostly everything except for the really specialized things other than physical geography and biogeography.
The entire department uses windows because of ESRI ArcGIS which is windows only and the industry standard. The ArcGIS software is horrid, all people who have ever used it will know that it has its own will. Sometimes it works, sometimes it doesn't for no apparent reason. I suspect the constellation of stars at the moment is to blame. ;-)

Currently i am a Nature and Landscape engineer(A mix of pratical ecology and geography)(almost graduated) and we use windows, mostly because of GIS but also because most of my fellow students are allergic to computers.

By the way, what kind of programming languages do you use? I'm thinking of specializing in C++ and Perl. C++ because of its speed in calculations. And Perl because it is very good in parsing things and has a huge community(Or so i am told...).

And now i have to get back to math, i haven't had it for the last 4 years and i have to get it up to an undergrad level(for someone who did have math) by myself(its not really hard, but alot of work especially getting to the point where it has become a second nature).

[parktownprawn]

I'm hoping to be admitted to Computational Bio- and Physical Geography(in short: CBPG). And the main focus is the modelling of mostly everything except for the really specialized things other than physical geography and biogeography.
The entire department uses windows because of ESRI ArcGIS which is windows only and the industry standard. The ArcGIS software is horrid, all people who have ever used it will know that it has its own will. Sometimes it works, sometimes it doesn't for no apparent reason. I suspect the constellation of stars at the moment is to blame.

you may find ubuntuGIS (https://wiki.ubuntu.com/UbuntuGIS) has some useful info

[Paul Bramscher]

I work as a professional programmer in a Big-10 academic research library (http://www.tc.umn.edu/~brams006/). It's mostly Solaris for servers, and Windows on the public workstations (neither choice was mine).

I use linux for LAMP development, and put Ubuntu on my newest box.

There's some strange battles that one must fight, at times I frankly wonder whether some large institutions of learning aren't overly used primarily as vehicles to transfer public/student wealth to corporate vendors.... ](*,)

[Tinuz]

I work as a professional programmer in a Big-10 academic research library (http://www.tc.umn.edu/~brams006/). It's mostly Solaris for servers, and Windows on the public workstations (neither choice was mine).

I use linux for LAMP development, and put Ubuntu on my newest box.

There's some strange battles that one must fight, at times I frankly wonder whether some large institutions of learning aren't overly used primarily as vehicles to transfer public/student wealth to corporate vendors.... ](*,)

I must agree, sometimes there are some strange things going on. A while ago my university bought some new computers, which were exactly the same(except for some minor changes and a different monitor, but still) as the old ones.... :-# . Now i heard this is because of some weird regulations cutting their budget if they dont spend it fully, but buying 'new' computers simply because of this is absurd.

[y_farkash]

Hi.

I am a Biochemistry student (4th year undergrag). I am just starting to explore the Linux world through Ubuntu.

I would be very interested in a science oriented Ubuntu forum, especally for the purpose of learning about what software is available out there. At the moment I don't use any specific scientific software on Ububtu, but I believe ImageJ (powerfull Java based image processing software) would work on Ubuntu - this is usefull for microscopy work.

Maybe we can start a thread or maintain some document which lists differest software which would run under Ubuntu with a short description of their capabilities and links to the download page.

Cheers,

Yoav.

[alancaerdydd]

Hi,
i'm a research biochemist. i'm a very heavy computer user but no formal training, I have to pick stuff up as I go along and think a scientific discussion group would be a brilliant idea. I use Unix, macs and have used several linux distros. I rarely use windows these days and even then running under VMware on a linux box. Just joined the forum today having installed Ubuntu (it's the preferred disto in my new university).

Liked the initial install. Over the next few days I'll be installing a lot of software (molecular modelling, docking, phylogenetics and protein analysis stuff) most of which I've run (with varying degrees of success) on other distros and it would be great to have others to share info with.

alan O:)

[cinnabar]

Now i heard this is because of some weird regulations cutting their budget if they dont spend it fully

I'm not sure about other countries but if you work for any organization tied to the US government, this is the standard game. My boss-to-be just ordered me a 20" flat screen monitor because of this (had to spend all his money by the end of the fiscal year).

especally for the purpose of learning about what software is available out there

If you look back a page or two I put together a couple lists and links to several statistical and plotting packages. You can also try www.kde-apps.org under the scientific programs category (down on the left hand side) and openscience.org for links to other scientific linux programs.

[parktownprawn]

Maybe we can start a thread or maintain some document which lists differest software which would run under Ubuntu with a short description of their capabilities and links to the download page

the wiki page UbuntuScientists (http://wiki.ubuntu.com/UbuntuScientists) does that to a certain extent. anyone who has any additions to make should add to the page.

[bogoliubov]

Hello. I've been a PhD in Theoretical Physics since january. At work we mainly use Solaris, but some are switching to various Linux distros. I use Ubuntu on my computer at home. I've been trying out some computational programs on my Ubuntu-machine; mostly to see how much longer time it takes to run as compared to a supercomputer (quite a bit longer, I tell you! :) ).

Whenenever I work from home, I do 'ssh -X' so I can run the programs I need from ove of the servers at the university. This requires a rather fast intenet connection though...


I'd love to see some scientific software packages for Ubuntu. However, my main concern is that I can't even install MatLab (R14) so at the moment I'm kinda disappointed with Ubuntu. As a worst case scenario, I'd be forced to switch to some other distro. I'd hate that, since I really like Ubuntu...

[phen]

did you do a search on that topic? I think i've seen threads about it - maybe there's a solution somewhere on the forums? if you find a solution you could post it to the ubuntuwiki!
https://wiki.ubuntu.com/UbuntuScientists

cheers

[bogoliubov]

did you do a search on that topic? I think i've seen threads about it - maybe there's a solution somewhere on the forums? if you find a solution you could post it to the ubuntuwiki!
https://wiki.ubuntu.com/UbuntuScientists

cheers

Yeah, I've made some searches for a solution; but none of the posts concerning MatLab R14 had the same cause as mine I think. But I'll have a look every now and then...

[phen]

a second thought: when mathworks releases a linux version, they should provide their users with installation instructions, shouldn't they? maybe you can ask for known problems.. thats the good thing about prop. software: you can blame the creator :-)

[bogoliubov]

I kinda got the thing working now; so I'm happy

[petunia_volubilis]

Hi,
I am a biologist in a french University. I teach electrophysiology and cell biology. I heavily use ubuntu hoary on my laptop, mainly for writing stuff for my students (OOo and lyx), classes (OOo) and labs.
I also give all the html pages for our web site (here, but sorry it's in french ! http://www.unicaen.fr/ufr/ibfa/) to the computer techs. I use gedit/firefox to edit them without any formating and they apply our university style sheets to publish them.
However, all the research is done with specific equipment and none of the data acquisition and analysis softs are developped for linux environments.

I have to say that my colleagues are quite reluctant to switch to linux, mainly because it does not work strait out of the box !

[labs_bane]

I'm a 3rd year biochemistry student,


although almost all the resarchers and tutors have macs, us students are stuck with windoze to work with in the department, pity

[bogoliubov]

Hi,
I have to say that my colleagues are quite reluctant to switch to linux, mainly because it does not work strait out of the box !

That's the usual complaint, but I must say that I've never ever gotten Windoze to work straight out of the box either.
Anyway, isn't that what one has the tech support for?

At my department (physics) we don't "fix" anything ourselves; the computer support takes care of everything. This works since we use Sunary thin clients, so the support guys don't have to run around the entire building. Many want to switch to PCs with Linux though; since Sun stuff is rather expensive.

You should bring your colleagues to visit the physics or maths department where probably many use linux/unix... :)

[petunia_volubilis]

That's the usual complaint, but I must say that I've never ever gotten Windoze to work straight out of the box either.
Anyway, isn't that what one has the tech support for?

Yes, I agree. What about rebooting 10 times a day because libs and drivers mess around ? But habits, fear of the unknown, "my stuff works anyway, why to change" and specific equipment and softs do the rest. I have swithched to linux 3 years ago and still get some "oh your file stuck my computer, I had to reinstall excell" ! This takes lots of time to explain that no, my file exported to the ms format did not do anything as nobody else that received the file had that problem. I do my presentations in classes or in meetings with OOo, students are more ready to the idea of switching than my biology colleagues. They can be so conservative, who would have expected that from scientists ?


At my department (physics) we don't "fix" anything ourselves; the computer support takes care of everything. This works since we use Sunary thin clients, so the support guys don't have to run around the entire building. Many want to switch to PCs with Linux though; since Sun stuff is rather expensive.

You should bring your colleagues to visit the physics or maths department where probably many use linux/unix... :)

Tech support is present only for network and I have to say that we are all on our own for the rest (but we do not hire computer people in our biology department either ! pity). Hard science and computer department mostly use linux/unix as you say. Our intranet and web site are all designed on linux/unix machines. And fortunately to me there is that nice tech in the network department that has allways helped me when I was lost in setting up my laptop and when information on forum or specific mailing lists was like a foreign langage to me.
I guess I am an epiphenomenon to that regard (the staff is around 120 people in our department), mostly for intellectual reasons (no more contribution to the big company monopole, hope that international communities can exist and survive and will save us all :grin: )

[avelldiroll]

Every couple of months I get desperate and search the web for any small sign that Kaleidagraph is coming to Linux.

Have you seen QtiPlot? It's supposed to be an Origin clone. The last time I tried it was nearly a year and several versions ago when it first came out. And it was already useful then. Should be better now.
http://soft.proindependent.com/qtiplot.html
Qtiplot is working great, although I prefer using GNUplot or Grace (once you start you cannot come back). A year ago or so I tried to pull myself into DX but I must have been too lazy to persevere ... Ah procastination

I would say that Qtiplot (0.6.4) is as functionnal as Origin v6 (It lacks the scripting capabilities of v7 - I was told ... I never used it myself ...).

[avelldiroll]

I always thought *nix were the OS of tthe academic world.
I am a phd student in computational chemistry and biology, and in the labs I've been working in, every irix/aix/solaris is changed to linux. I even have a few sgi around my desk to run some legacy proprietary softwares.
I know some of the data visualization softwares I use have been ported to windows but most of the calculations are handled on clusters now, and I never saw a windows one ...

Also for the equipment recently bought by the labs at my uni, the interface is developped for unix most of the time (nmr, mass spectroscopy, x-ray diffraction, ...).

The only people I see using m$ products are the ones who use a computer only to write reports and publications (and who have been tied with endnote for so long that it took their bibliography in hostage).

[rsankuratri]

Hello:

I'm a population ecologist/genticist and I was wondering if there are other biologist-ecolofreaks-molecular biologist-nature people out there using ubuntu. Maybe we can start a little Ubuntu-Science discussions I believe Linux will be the OS of the academic world, and the more we promote it, know about it...the better.

Hope you're out there

Campitor

Lets not forget the chemists... Organic Chemists particularly, who are computer geeks also. :)

I was going back and forth between Windows XP and various distributions of linux for the past 4 years. Finally, finally I got introduced to Ubuntu and I am extremely impressed by this dist. I have a Dell Inspiron 9100 working (wireless networking and all)... So finally I have found stability and will not have to go back to Windows. Cool huh! \\:D/

[greenpenguin]

I always thought *nix were the OS of tthe academic world.

Yep :)

Quote from New Scientist (the most popular scientific mag in the UK):

"For Gardiner, a theoretician, independence only became possible when Linux, the standard scientific operating system, became readily available on PCs, doing away with the need to have a specialist in scientific computing around."

:grin: :grin: :grin:

The article is here (http://www.newscientist.com/article.ns?id=mg18725082.600).

I smiled all day when i read that :)

[kingsidy]

i am an electrical engineering student. i run matlab r14 for linux, qucs circuit simulator, i also use open office for reports and things. The linux version of matlab is faster and takes less space than its windows counterpart.

[kleeman]

Yep :)

Quote from New Scientist (the most popular scientific mag in the UK):

"For Gardiner, a theoretician, independence only became possible when Linux, the standard scientific operating system, became readily available on PCs, doing away with the need to have a specialist in scientific computing around."

:grin: :grin: :grin:

The article is here (http://www.newscientist.com/article.ns?id=mg18725082.600).

I smiled all day when i read that :)

I can confirm the reality of that article. Last year I bought a linux cluster (24 node opterons) for about $30K which I pretty much administer myself using self acquired linux sysadmin skills. I have never been more productive scientifically (20 papers in the last 2 years). The sysadmin chores are actually fun (!) and I am more productive because I don't need to rely on anyone else at all plus the cluster has the compute power of a supercomputer. In addition a fast broadband link means all this can be done from the comfort of my home office and commuting is not needed for science at least. Applied Math/Physics/Numerical Modelling nirvana really! Thanks Linus!

[alastair lewis]

I am an academic surgeon. I have got into Lyx for paper writing recently. I am using pybliographic for reference collection and .bib file preparation. I have a .bst file that produces reference lists in British Journal of Surgery format. If any one want's it e-mail me.

[aev]

hi,

i am a physicist and a hardcore FORTRAN programmer. New to Linux though. My biggest concern is if I can get that Intel FORTRAN running under Ubuntu. Intel gives it in rpms. I really need a good debugger. Seems that a lot of programming in physics goes under FORTRAN and it would be nice to have that problem solved for Ubuntu. I found some help but was not satisfied with the results. For visualization programs I use sometimes OpenDx (Or just DX). Cool stuff. Easier to learn (IMO) than VTK, although VTK provides better multi-processor operation, but do you really need it ? :) . So far appears that DX and VTK share the 1st place for scientific viz tool.

[LaserJock]

Intel gives it in rpms. I really need a good debugger.
I usually use alien to convert rpms to debs. You can get it via apt-get or synaptic. You then just run:alien "file".rpm where "file" is the name of your rpm. If you didn't already know, there are FORTRAN compilers that come with Ubuntu (g77 being the most common one).
Sorry if this is all old news to you.

-LaserJock

[earlycj5]

The entire department uses windows because of ESRI ArcGIS which is windows only and the industry standard. The ArcGIS software is horrid, all people who have ever used it will know that it has its own will. Sometimes it works, sometimes it doesn't for no apparent reason. I suspect the constellation of stars at the moment is to blame. ;-)

Currently i am a Nature and Landscape engineer(A mix of pratical ecology and geography)(almost graduated) and we use windows, mostly because of GIS but also because most of my fellow students are allergic to computers.



Nothing like being really late to the party, but I didnt' start using Ubuntu until last month sometime I reckon. Slackware before that.

I'm a PhD student in Plant Pathology. I'm doing a disease forecasting modeling project that involves GIS. Which means even though there is QGIS I'm still tied to Windows for ESRI ArcGIS, which I don't find to be as bad as Tinuz does apparently. I don't care for the Windows aspect but the program is by far more robust than any OS program I've found and admittedly my GIS and Cartography classes and training have been ESRI centered.

Using Kile/Latex to write most of my papers and tex2rtf to submit grant proposals in a Word DOC format. :rolleyes: Seems like a final document should be a PDF, but I digress.

It's nice to see other scientific folks around using Linux. In our department several folks are switching due to the Biometrics programs available. Our tech support installs/supports SUSE. Which I've never quite developed a liking for. I hate that it does everything graphically for you. :)

[nsa_767]

Hi there,

WOW, what a pleasant surprise to see the sheer volume of posts on this thread!

OK, I'm not a scientist as such, I'm an economics student who loves maths and stats... I make use of the following in my studies:

Kile, for typing out mathematical proofs and the like.
Maxima, with the wxMaxima front-end, for symbolic computing
R, for stats.... or at least I'm trying to use it!


I really feel that there should be a sub-forum for the scientific and academic use of Ubuntu... This might also be useful in getting some of the many useful apps, not currently in the repos, added to official repositories. (I have made mention of this, in the following thread: http://www.ubuntuforums.org/showthread.php?t=72606)

Even for those applications already in the repositories, there is the problem that it seems to take forever for new versions to filter down into the Ubuntu repositories.

[kanem]

As someone who has had to use Windows in their lab I'm kind of jealous of all the folks here who get to use GNU/Linux as their research tools as well. I do use mine to do work, just not run the experiments. Also, I'm surrounded by Windows users.

So when I went to this place (http://www.triumf.info/) last week to try and get a job I was quite pleased to see that almost all the computers I saw ran either Red Hat or Fedora. It's the first time I've seen a whole work/lab environment where GNU/Linux was just used as a tool by people to do their work (and not people like us who play with computers for fun and read /. everyday).

I gave a presentation which I had prepared in OO. I always take the precaution of making sure everything looks right in Windows. Happily, this time, I didn't have to.

[GrumpyBob]

I'm a molecular geneticist in the UK. I use Ubuntu on the home PCs, at work Win2k.

The biggest problem I have is the lack of a simply installable bibliography database for OOo. I managed to set up Bibus when I was running Mandrake, never managed to do so for Ubuntu 5.04, or now 5.10. (It's relatively easy to do so for Win2k!

Just off to evaluate Sixpack and pybliographer.

Robert

[chemgoode]

Hi.
I'm Henriette and I have a MSc in chemical engineering – now I'm working on a ph.d. in computational chemistry. Since all the programs I need for work run only in linux the choice was easy – though I'm still forced to dual boot with Windows XP since I need the following programs:

Reference Manager
ChemOffice
SciFinder
MDL Crossfire Beilstein

Any suggestions for linux versions of the above?

-Henriette

Henriette (and everyone else too),
I have been able to get both ChemOffice 2002 and SciFinder 2006 to run under wine on Ubuntu 5.10. ChemDraw is a little finiky though, some issues with drawing the tools on the screen. Chem3D appears to mostly work, but I have more limited success with ChemFinder.
On the other hand, SciFinder Scholar 2006 is running perfectly on my system. It is nice to get at least one research tool running because MDL Crossfire Beilstein will not work, and I have tried many times with different versions.
As far as a reference manager, I have heard that EndNote will run under wine, but I have no experience with this. Instead, I have another suggestion: RefWorks (http://www.refworks.com). It is completely controlled through a web browser, so it is platform independent. Check it out sometime.
Just to fill everyone in, I am a chemical biology graduate student and have been using Ubuntu on my work system for about 6 months. I still dual boot every now and then when I need to use the right tool for the right job.

Happy ubuntuing,
-chemgoode

[santorini]

Hi there,
I really feel that there should be a sub-forum for the scientific and academic use of Ubuntu... This might also be useful in getting some of the many useful apps, not currently in the repos, added to official repositories. (I have made mention of this, in the following thread: http://www.ubuntuforums.org/showthread.php?t=72606)

Even for those applications already in the repositories, there is the problem that it seems to take forever for new versions to filter down into the Ubuntu repositories.

yea, agree~

I'm a math student preparing for postgraduate studies. Currently using Gentoo, Suse and Ubuntu plus the waiting-to-be-ditched WinXP. I recently logged into windows, and the desktop looked unfamiliar now.

[Greyfoxwolf]

Chemical engineer here!...well student atleast :)
i use ubuntu (with kde) @ home, anyone here ever tried running Aspen and Polymath with wine???

[DrBubba]

I'm a mathematician at Penn State Altoona. I've been using Linux for the last 8 years - various distributions (Caldera Open Linux, RedHat, Debian and now Ubuntu). I mostly use TeX/LaTeX (Xemacs as a front end), Perl, maxima and am playing around with R for some assessment stuff regarding freshman placement exams. Many, many, many years ago I used to know FORTRAN (f77 was bleeding edge then). Glad to know there are some other scientific users out there.

[LaserJock]

I really feel that there should be a sub-forum for the scientific and academic use of Ubuntu... This might also be useful in getting some of the many useful apps, not currently in the repos, added to official repositories. (I have made mention of this, in the following thread: http://www.ubuntuforums.org/showthread.php?t=72606)

Even for those applications already in the repositories, there is the problem that it seems to take forever for new versions to filter down into the Ubuntu repositories.


I have been trying to work on this for a little while. The essential problems are that most of the developers are more Computer Science oriented (programmers, IT, network admins, etc.) so they work more on their particular interests and they have to also look at the popularity of packages they want to spend time on. For instance, a package called popularity-contest (or popcon) is installed on every ubuntu install. I tracks what applications are installed and how often they are used. By default this is turned off (we're not Microsoft remember). However, if you turn it on by: sudo dpkg-reconfigure popularity-contest the information will be sent to the developers on a weekly basis. Results for Universe packages (where a lot of science packages reside) can be at http://popcon.ubuntu.com/universe/by_inst The developers/maintainers use these results when they want to prioritize their work. There are about 20-30 Masters of the Universe (MOTU) as they are called for around 15000 packages. In the last few days before Breezy was released all of the MOTU (and MOTU wannabes) were workin like mad (very little, if any, sleep) just to make sure that stuff like xemacs, python, beep-media-player, etc. were building OK. I was trying to do my best to get some of the science stuff included (python-scipy, pyx, gdis, ghemical) but there was soo much to do. If we want to get more work done on science packages the MOTU have to know about it and they need help doing it.

The best way to help is to get on the wiki http://wiki.ubuntu.com/MOTU and take a look around and see where help is needed. Also, do some background before you make a request. See if the package you want is in Debian (http://packages.debian.org). It is much easier to just sync from Debian than to try to do it from scratch. Talk to the maintainers of the program you want and see if anybody is working on a Debian/Ubuntu package. If nobody is working on packaging the program you want, try to do it yourself. The MOTU wiki has some good packaging tips at http://wiki.ubuntu.com/MOTUWannabeTips. If you want to help at all it is highly recommended that you head on over to the MOTU IRC channel (#ubuntu-motu) on irc.freenode.net. Most of the MOTU are usually there at some time of the day. If you are polite they will help you with just about anything. Something like: "Hi! A new version of xyz just came out and it has some big improvements over the old version. Is it possible to get one of you to make a package, or at least point me in the right direction to make it myself. Thanks. " The MOTU also have teams set up to organize their activities. They have a MOTUPython team, a MOTUDesktop team, and many others. It would be really cool if we could get a MOTUScience team formed.

I really like the idea of having a subforum on science/academic use of Ubuntu, both using Ubuntu as a computational tool and as a research/academic desktop (journal article and dissertation writing, presentations, teaching tools, etc.). I think it would make the science/academic community more noticable within the Ubuntu community. One thing to keep in mind, however, is that the developers (for the most part) don't read the forums very much. They mostly use the wiki (http://wiki.ubuntu.com) and now Launchpad (http://www.launchpad.net) for bugs. Posting a message on the forums saying you want an updated package will virtually fall on deaf ears. If you post a bug, or ask on #ubuntu-motu, you will have much better chances. For instance, we really need to do more on the UbuntuScientists (http://wiki.ubuntu.com/UbuntuScientists) wiki page. This would help us organize and would be more noticable to the developers/maintainers.

[Rohan]

I'm a Bio major... at USC. So you got me on your side against all the math/physics/comp sci majors

Speaking of which... anyone wanna help me get a research job?

[NikoC]

I got my master degree in Biology 2 years ago and last year I optained another one in Biochemistry. For the moment I'm working as a PhD student, just bought a new laptop on which i have to install Ubuntu. But on my previous one it worked just fine for basic tasks like office applications. Now i'm planning to use it for more statistical applications.

[Ced22]

I'm a Student of Molecular Biology in Basel, Switzerland.
I use Linux for my personal writing needs, but plan to use it in my later work as a scientist; if possible.

[Campitor]

we really need to do more on the UbuntuScientists (http://wiki.ubuntu.com/UbuntuScientists) wiki page. This would help us organize and would be more noticable to the developers/maintainers.

I agree...and have added a couple of new programs to the wiki. I'm in the field and my internet connection is not very fast, I will add more programs later next week.

A quick question...does any body know how to log-out from the wiki? Or the lack of logout botton is just a quirk of my slow internet connection?

See you in the forums...

CAmp

[Crod]

To add to the mix, I am a mathematician (SUNY at Stony Brook, NY ,USA). ANd, of course, all mathematicians around have been uisng Linux for the last 5 years - our dept. now has a mix of Red Hats and Ubuntu's.

Most used software: latex (I use Kile as frontend).

Another mathematician here!

I am an Emacs priest.... I have Ubuntu in my laptop BUT I can't install Ubuntu in the PC in my office.... I get "segmentation fault" when I run the installer from VMware.... What can I do??????

[Campitor]

A quick question...does any body know how to log-out from the wiki?
CAmp

Nevermind...found it. How many scientist do you need to logout from a wiki page:rolleyes: ...hehehe

[a212359]

Hello all - nice thread. I am a physics/astronomy masters student (and a linux newbie) so this is all very helpful. I just started school again and was working at another university before where I had a workstation with mathematica/matlab/idl etc, but now I am 'on my own' and trying to set up my laptop to do everything I need....

I also have a few questions, if anyone can help:

1) I have maxima working, and I tried to install wxmaxima by downloading the deb file but the following happens:
sudo dpkg -i downloads/wxmaxima_0.6.2-4_i386.deb

Selecting previously deselected package wxmaxima.
(Reading database ... 67735 files and directories currently installed.)
Unpacking wxmaxima (from .../wxmaxima_0.6.2-4_i386.deb) ...
dpkg: dependency problems prevent configuration of wxmaxima:
wxmaxima depends on libstdc++6 (>= 4.0.2); however:
Version of libstdc++6 on system is 4.0.1-4ubuntu9.
wxmaxima depends on libwxgtk2.6-0 (>= 2.6.1.2); however:
Package libwxgtk2.6-0 is not installed.
dpkg: error processing wxmaxima (--install):
dependency problems - leaving unconfigured
Errors were encountered while processing:
wxmaxima


In synaptic there is not I higher version of libstdc++6 than 4.0.1-4 ...I guess I could get the .deb for the newer version from the debian site, but I am afraid of screwing up my machine. Does anyone have wxmaxima working under breezy?

2) Does anyone who is familiar with IDL know of any free (speech or beer) alternatives, or similar programs? There are so many good programs (espcially for astronomy) people have made for IDL I doubt I could do without it, but for now I only have access to it at another institution, so the connection is very very slow. I am wondering if there are languges/programs with similar structure that I could put on my computer just to have to play with and make simple plots etc, in the type of way you would using ".pro" files in IDL?

Thanks!

[ow50]

1) I have maxima working, and I tried to install wxmaxima by downloading the deb file but the following happens:
sudo dpkg -i downloads/wxmaxima_0.6.2-4_i386.deb
...
As far as I know there's no wxMaxima package for Ubuntu Breezy. You apparently tried to install either the Ubuntu Dapper or the Debian Sid package. Breezy has different versions of some libraries, so the dependencies don't match. You need a package built for Breezy.

I have a Breezy package made for my own use. I could upload it my unofficial repository if you want. Alternatively you could request it from Ubuntu Backports, but that might take a while. And, you can always build from source (the ./configure && make && sudo make install).

[cardador]

Hello

I am PhD student in Chemical Engineering. I only use Linux to do my work, mainly Octave for numerical calculations, OpenFOAM for Computational Fluid Dynamics, Kile to write papers, reports and make presentations (beamer package) and Gnumeric.

It is nice to know that there are so many scientists out there that use Ubuntu!

In the scientists wiki someone referred Scicraft and Scigraphica, but until now I was not able to compile them, or install the Debian packages that I found. Was anyone able to accomplish this?

[Joey French]

I am a marine sciences student. Currently I use only Ubuntu to do my work, and am trying to expand on that by getting into data acquisition and such. The lab that I work in has moved to Linux, mainly because they didn't have anyone in there before who really knew anything about Linux.
This is kinda neat, though... I have a friend that is a PhD student in the Physics department, 5 floor up from my lab in the same building. I have known him for a few years, and some time ago we got on the subject of linux, and ubuntu in particular. At the time he had Fedora on his box at home, but never really fiddled with it. So, I said he should give Ubuntu a try, cause I was using and liking it. He installed and loved it. Then, he started running it on his box in the lab. Then, when it came time to get the other boxes in the lab up to snuff, he went with ubuntu on all of them (32). So, the other day, I head over to his lab to see what he's up to and he shows me their new setup (this 2 terrabyte server thingy that is all crazy and I don't event have a clue what kinda physicsy stuff it does) running ubuntu. Kinda cool.
So then he tells me to come check out his other new toys. So, I go to his office, and he's got these two new giant flatpanels, with some crazy ultra high resolution displays. I was like wow, those things made xterm and emacs look good!:lol:

[a212359]

As far as I know there's no wxMaxima package for Ubuntu Breezy. You apparently tried to install either the Ubuntu Dapper or the Debian Sid package. Breezy has different versions of some libraries, so the dependencies don't match. You need a package built for Breezy.

I have a Breezy package made for my own use. I could upload it my unofficial repository if you want. Alternatively you could request it from Ubuntu Backports, but that might take a while. And, you can always build from source (the ./configure && make && sudo make install).

Yes, I tried to install the Debian Sid package before...now I have followed your advice and tried from source. This time everything seems to work, but when I start wxMaxima, the terminal I start it in begins displaying this error message every 2 seconds or so:

** (wxmaxima:11057): WARNING **: IPP request failed with status 1030
**(wxmaxima:11057): WARNING **: IPP request failed with status 1030
** (wxmaxima:11057): WARNING **: IPP request failed with status 1030


Can you put a link to the .deb file you built so I can give that a try and see if the error goes away? Thanks!

[ow50]

Can you put a link to the .deb file you built so I can give that a try and see if the error goes away? Thanks!
http://koti.mbnet.fi/~ots/ubuntu/breezy/

[jsmidt]

I am a physics major at BYU and will continue into graduate school.

[a212359]

http://koti.mbnet.fi/~ots/ubuntu/breezy/

Thanks - I installed your .deb and I get the exact same problem...so its some problem on my system. Maybe because I have the i686 kernel and gcc4 ? I'm not sure...for now I guess I will stick to texmacs which works fine, and perhaps make another post in the help forum to try to get this sorted out.

[parktownprawn]

Thanks - I installed your .deb and I get the exact same problem...so its some problem on my system. Maybe because I have the i686 kernel and gcc4 ? I'm not sure...for now I guess I will stick to texmacs which works fine, and perhaps make another post in the help forum to try to get this sorted out.

you could try compile wxmaxima yourself:

1) Install some dependancies:

sudo apt-get install build-essential libwxgtk2.6-dev libxml2-dev

2) download the source (http://wxmaxima.sourceforge.net/), untar it and do the usual:

./configure
make
sudo make install

if you want to make a .deb, install checkinstall and replace the last line with sudo checkinstall

----------------------------

another nice front end to maxima is imaxima which embeds a maxima session in emacs and produces output using latex

http://members3.jcom.home.ne.jp/imaxima/

(try ignore the fact that the installation instructions are for cygwin not linux - they work fine)

a pretty picture of imaxima running in emacs:
http://maxima.sourceforge.net/screenshots/imaxima.png

[jasplund]

I am a PhD-student in lichen-ecophysiology at the Norwegian University of Life Sciences in Ås, Norway. I am working on the chemical herbivory defense of lichens.


Johan

[david_finlayson]

I'm a marine geologist PhD Candidate (almost done!).

I'm a GIS / Remote Sensing guy along with some light numerical modeling and a lot of statistical analysis. Here's a list of great OS GIS software:

Hard-core GIS and Remote Sensing:

GRASS (http://grass.itc.it) Very competative with ArcInfo
GMT (http://gmt.soest.hawaii.edu) Beautiful figures with this
Proj4 (http://proj.maptools.org) Map projections

There is a lot more GIS and terrain analysis software (as well as mapserver, etc) at freegis.org (http://freegis.org)

Statistics and Data Analysis

R (http://www.r-project.org/) Great plotting abilities and first-rate statistics packages (including a geo-statistics link with GRASS). Can be difficult to learn.

Scripting and light-weight programming

Python (http://www.python.org) (Lot's of scientific packages available)
Pysco (http://psyco.sourceforge.net/) This is a byte compiler for Python that requires adding only 1 line of code to your program. I've seen significant speed increases in some of my scripts.

Also, with python, don't forget about Numeric and SciPy which have nice NetCDF readers and other goodies.

[Roptaty]

Veterinarian student here, with a BS in Electrical Engineering...

[nsa_767]

Hi there,

I'm using Hoary and wxmaxima version 0.6.1 works, I installed it via a .deb I downloaded from their site a while back. Just see if they don't have that version still, it should work.

[akniss]

PhD student / Research Scientist in Agroecology here.

I am an avid fan of the R statistical package. Still looking for a Linux replacement for my Tinn-R in Windows.

I would also be curious about bibliography managment packages that anyone has found useful in Linux. (Not a big fan of BibView; have not yet tried to install Bibus) Why no Bibus in any of the Ubuntu repos?

[earlycj5]

PhD student / Research Scientist in Agroecology here.

I am an avid fan of the R statistical package. Still looking for a Linux replacement for my Tinn-R in Windows.

I would also be curious about bibliography managment packages that anyone has found useful in Linux. (Not a big fan of BibView; have not yet tried to install Bibus) Why no Bibus in any of the Ubuntu repos?

I've used Kbibtex and been quite satisified with it and Kile but I'm using Kubuntu.

I had used JabRef prior to this, http://freshmeat.net/projects/jabref/

[cowboycamilo]

Hi u all... I'm a population Getntist from Colombia, great idea of getting this on the go.
I really think that in Biology, Windows has nothing to do.. 95% of the software for biology, genetics, etc etc runs unders Linux.... and I'm happy its that way... linux is just the best!!!

[parktownprawn]

PhD student / Research Scientist in Agroecology here.

I am an avid fan of the R statistical package. Still looking for a Linux replacement for my Tinn-R in Windows.

I would also be curious about bibliography managment packages that anyone has found useful in Linux. (Not a big fan of BibView; have not yet tried to install Bibus) Why no Bibus in any of the Ubuntu repos?

pybliographic is quite nice and in the ubuntu repos.

there are .debs for bibus on http://bibus-biblio.sourceforge.net but i don't know how well they work with ubuntu

[akniss]

Thanks for the tips earlycf5 and parktownprawn. Haven't tried any of the KDE packages... I installed pybliographic last night and played around. I really like the interface, but its probably going to take me a while to figure out. Entry is pretty simple... that's a good thing. And I've heard that BibTex is pretty powerful. Do you use it with LyX? That's another program I've not tried, but would like to...

[parktownprawn]

Thanks for the tips earlycf5 and parktownprawn. Haven't tried any of the KDE packages... I installed pybliographic last night and played around. I really like the interface, but its probably going to take me a while to figure out. Entry is pretty simple... that's a good thing. And I've heard that BibTex is pretty powerful. Do you use it with LyX? That's another program I've not tried, but would like to...

I really like using bibtex with lyx - its very convinient

[akniss]

I really like using bibtex with lyx - its very convinient

I installed LyX today. I typed an article in it to try it out... problem is that once I got it typed, I couln't figure out how to get it into an electronic reviewable format to send to my co-authors... I was rather frantic. I finally figured out I could export is as a TeX file, then installed latex2rtf to convert it to rich text to email to a colleague for review... I should know better than to experiment on a deadline by now...

How do you get your LyX files to a format that others can edit... or do you only use LyX when you know that won't be an issue?

PS... I think once I learn how to use it, I will like the pybliographic/LyX setup. thanks for the tip!

[parktownprawn]

How do you get your LyX files to a format that others can edit... or do you only use LyX when you know that won't be an issue?


Unless those you are working with know how to edit LaTeX or have LyX its not such a good option for collaboration.

[david_finlayson]

Unless those you are working with know how to edit LaTeX or have LyX its not such a good option for collaboration.

LaTeX might be the only document processor that can properly render ancient Greek, but for 99% of the world it might as well BE ancient Greek. It's simply not possible to collaborate with the vast majority of users using this technology. Sure, there are a few academic circles where LaTeX is popular (math, cs, physics), but who else uses it?

I wrote a beautiful, long, complicated report that was wonderfully rendered in LaTeX (pdflatex and hyperef are amazingly cool tools!) only to be told point blank that if I wanted it published to resubmit the entire manuscript in MS Word. It doesn't matter how wonderful latex is if no one will be able read what you've written in it.

[parktownprawn]

Sure, there are a few academic circles where LaTeX is popular (math, cs, physics), but who else uses it?


Conversely in the theoretical physics community its a pretty good bet that an article written in MS word was authored by a crackpot.

Perhaps you would like to start a new thread to discuss the relative merits and demerits of Latex.

[david_finlayson]

Conversely in the theoretical physics community its a pretty good bet that an article written in MS word was authored by a crackpot.

Perhaps you would like to start a new thread to discuss the relative merits and demerits of Latex.

It's not surprising that LaTeX is king in theoretical physics. But lets be honest, LaTeX hasn't made your papers any easier to read! ;)

It sounds like you use Lyx enough to answer a question of mine...

My university publishes a custom class file for dissertations. It has all the boiler plate frontmatter as well as some special formating for fullpage figures and captions. How difficult would it be to bring this customized class file into Lyx?

I looked at the Lyx FAQ and it seemed quite difficult to use a custom style. To date, I have just been using Auxtex in emacs. It works, but I wouldn't mind simplifying the compile-write-edit-comple cycle.

[parktownprawn]

well its pretty easy to use a custom class with lyx.

go to Layout>Document>Preamble

You can cut and paste the formating instructions into the Preamble.

If the formating comes as a file called custom.sty file just put

\usepackage{custom}

in the preamble

You would also have to install the custom style - see http://wiki.ubuntu.com/Latex for instructions

how well it will work and how easy it will be to use is another question.
Lyx also inserts some of its own formating stuff which may conflict.

[kleeman]

It's not surprising that LaTeX is king in theoretical physics. But lets be honest, LaTeX hasn't made your papers any easier to read! ;)

It sounds like you use Lyx enough to answer a question of mine...

My university publishes a custom class file for dissertations. It has all the boiler plate frontmatter as well as some special formating for fullpage figures and captions. How difficult would it be to bring this customized class file into Lyx?

I looked at the Lyx FAQ and it seemed quite difficult to use a custom style. To date, I have just been using Auxtex in emacs. It works, but I wouldn't mind simplifying the compile-write-edit-comple cycle.

Have a look at this Lyx Wiki entry:

http://wiki.lyx.org/Layouts/CreatingLayouts

The Wiki for Lyx is excellent btw.

[akniss]

Perhaps you would like to start a new thread to discuss the relative merits and demerits of Latex.

Excellent idea. Lets try it!
http://www.ubuntuforums.org/showthread.php?p=538843#post538843

[madmaxx]

I am an avid fan of the R statistical package. Still looking for a Linux replacement for my Tinn-R in Windows.

Hi, haven't read the entire thread because searching for the string "R" is.. uhm.. not possible. ;)

Anyway, I learned today from a java-based app which helps R users quite a bit, although it is not a real GUI (IMHO). It is called JGR (http://www.rosuda.org/JGR/index.shtml) (pronounce: Jaguar).

The problem is that these guys do not really focus on the Linux side of it with the result that after 1.5yrs you can get v1.3 as .dmg or .exe -- but Linux packages are only available as source!

Now, I have no idea how complicated it would be to a) compile that thing (they say, it -needs- Sun's JDK1.5) and b) to make an ubuntu .deb package, but i am absolutely sure that this would be a huge boost for pushing ubuntu at the science front (and perhaps even among linux distros scientists use...).

I found MOTUScience (https://wiki.ubuntu.com/MOTUScience) on the ubuntu wiki but could not find a possiblity to suggest this package for integration. Can someone do this or show me how to do it?

Thanks!
madmaxx

[LaserJock]

madmaxx,
It might be hard to get JGR into Ubuntu because of it's dependency on Sun's JDK. Sun's JDK can't be shipped with Ubuntu right now because of it's license. However, if JGR could be compiled with a free Java compiler then it would have a good chance of getting it in. If it can then the place to put it would be http://wiki.ubuntu.com/UniverseCandidates .

Thanks for bringing MOTUScience (http://wiki.ubuntu.com/MOTUScience) up. I have wanted to talk about it on this thread but have been too busy/lazy to do so.

I created the MOTU Science team to help spur growth of science in Ubuntu. It is mainly for people wanting to become Universe maintainers (Masters Of The Universe), however, anybody is welcome to contribute. The MOTUs are pretty good about teaching new people how to package and get started. I would really encourage anybody who is interested in getting science packages into Ubuntu or science package development in Ubuntu in general to join the MOTUScience mailing list (ubuntu-science (http://tauware.de/cgi-bin/mailman/listinfo/ubuntu-science))

If you have anymore questions please post here or email the ubuntu-science list.

[Robocoastie]

amature astronomy here. Although when I'm out observing i use winXP laptop because of power management issues. (linux eats the battery up too fast).

[tigerstripedcat]

I cant remember If I posted in her or not. But I am a physics graduate student. We all use linux. I use Ubuntu in particular. Just so much more powerful and convenient.

I use it exclusively.

[akniss]

Hi, haven't read the entire thread because searching for the string "R" is.. uhm.. not possible. ;)


:confused: Yeah... I've run into the same issue... they may have thought it was cute when they named it, but they certainly weren't thinking of search engines!

Thanks for the tip on JGR... i may cruise on over to the wiki and check it out.

[professor_chaos]

MEG (magnetoencephalogy) psychiatric brain research. I use linux and unix. Free your mind and the brain will follow.

[Ugeek]

I am a grad student in physics. I use ubuntu. Our department is only-linux based. have a mixture of fedora and ubuntu. I find labplot is quite usable as a replacement for origin. I dont think we should keep away from windows softwares, as most experimental setup is bundled with a windows one, so we can use cxoffice(professinal version is much better) for that.

[Campitor]

C'mon everybody...we need to keep adding stuff to the wiki. https://wiki.ubuntu.com/UbuntuScientists

I've been away from a termnal, and haven't been able to add new stuff, but we'll remedy that soon. The more stuff we add, more scientists will choose Ubuntu as their OS.

see you all on the wiki!!!

Camp...

[tonderai]

I have been trying to find some image processing software to do some color thresholding to determine canopy cover for an ecology project.

In addition to ImageJ (http://rsb.info.nih.gov/ij/) (mentioned previously), I found VIPS (http://www.vips.ecs.soton.ac.uk/index.php) - and its in the repositories too! (sudo apt-get install nip2).

I will add both of these to the wiki.

[David Valentine]

Glad to see another ecologist on here! I'm interested in the SciGraphica package, which on SourceForge is up to version 2.1.0 but in the Ubuntu and Debian repositories is only up to 0.8. I'd request a backport, but as I'm a newbie to Linux, I'm not yet up to the building effort the backport folks want us to try first.

[agapito]

I'm a Chemist and I'm taking a PhD in Physical-Chemistry, more specifically in Computational Chemistry. I use linux every day (Ubuntu when I'm working at home). All my computers are Wind0w$ free. ;)

[quazar]

Hi there, I'm a molecular/molecular biologist working om my PhD. Unfortunately my university is almost 100% Linux-free, which is a shame! Thats why I've still got Windows in my dual boot setup :(

[bkristan]

Hi David,

Glad to see another ecologist on here! I'm interested in the SciGraphica package, which on SourceForge is up to version 2.1.0 but in the Ubuntu and Debian repositories is only up to 0.8. I'd request a backport, but as I'm a newbie to Linux, I'm not yet up to the building effort the backport folks want us to try first.

I can't remember anymore whether I've gotten SciGraphica working on Ubuntu, but I know that I've never had any luck with it on Mandriva. The 2.1.0 release still crashed constantly for me.

The alternatives that I've used more successfully are Grace, which is great for 2D graphs, and LabPlot, which can also do 3D. Neither of them has a particularly intuitive GUI (at least they don't match my intuition well at all). I've used Grace more, but am trying to learn LabPlot because its data handling is better for me (for example, you can label columns in LabPlot, but you can't in Grace).

I don't mean to discourage you from trying SciGraphica out, but it has developed very slowly and has never been as stable as either Grace or LabPlot, so unless you really have a burning desire to give SciGraphica a try I'd recommend another option.

[LaserJock]

Glad to see another ecologist on here! I'm interested in the SciGraphica package, which on SourceForge is up to version 2.1.0 but in the Ubuntu and Debian repositories is only up to 0.8. I'd request a backport, but as I'm a newbie to Linux, I'm not yet up to the building effort the backport folks want us to try first.

I've also been interested in getting Scigraphica 2.1.0 in Debian/Ubuntu. There is a Debian wishlist bug: http://bugs.debian.org/314241
but it is over 6 months old and I haven't seen any movement. It is a fairly major packaging project however since it actually involves packaging GTKExtra and the Scigraphica source has been split into a library and the main program :( . I might try to contact the Debian maintainer by email to see if he is working on it. If not I might have a go at it and see if we can it in Debian at least. It probably wouldn't make it into Dapper since we are in a Version Freeze state at this point and only allow new upstream version by exception.

In other science related developer news, the MOTU Science (http://wiki.ubuntu.com/MOTUScience) team recently got Texmaker (yeah!), plotdrop (gnome frontend for Gnuplot), and EasyChem (yet another chemical structure drawing program) into Universe for Dapper. We have until Feb. 23rd to get new (never been in Debian/Ubuntu) packages into Dapper so if there are some apps that the scientific community really wants the MOTU Science team might be able squeeze them in.

LaserJock