Scientific Software options for Ubuntu

[MrPok]

Gephi

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

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

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

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

Biological Network analysis: representing patterns of biological data.

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

(www.gephi.org)

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

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

[zampes]

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

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


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

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

ClustalX: For DNA alignment and drawing Phylogenetic Trees

Phylip: is a package of programs for inferring phylogenies (evolutionary trees). also provides source code!


Fungal ITS Extractor: An ITS1/ITS2 extractor for the fungal ITS region. Simple page with download link.


FinchTV: NOT FREE SOFTWARE, although at least it is free of charge and there's a Native Linux Version! It reads Chromatogram viewer, BLAST, reverse complement sequences, etc.

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

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

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

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

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

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

[cwarner7_11]

The CAELinux 2010 distro is built on Ubuntu 10.04, and includes a lot of the packages here (Scilab, Octave, R, Maxima- however, primarily focusing on FEA, including fluid dynamics, stress analysis, dynamic simulation, etc. Very powerful. The primary advantage of the CAELinux distro over picking up these packages independently is the fact that all of the dependencies are already worked out, and everything works out of the box...

[cwarner7_11]

I recently did a summary of various packages available for circuit simulation- you can find it here. You may be interested in the Xcos package included with Scilab, or the original Scicos package.

[juancarlospaco]

Hi
ʘ‿ʘ

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

Try Hot


PyGAS


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

Thanks
^‿^

[hydroxygen]

Does anyone know if there is a open source equivalent of EniG Chemistry Assistant ?

[mJayk]

You neeeed to include jabref in the bibliography section

[Christian Poulsen]

Hi all,

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

[patrick295767]

what about a version based on the console ?
Efficient and reliable

http://ncursespim.scienceontheweb.ne...?p=screenshots

[mohanbylapudi]

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

Thanks in advance....