Most of my favorites were already mentioned:

- Linux (in my case its Debian to which I've been faithful since 1999!),

- BASH,

- LaTeX (with Beamer class for presentations and lecture notes and TikZ for diagrams)

- GNUPlot for plotting,

- python with numpy and scipy for scripting and small applications,

- FORTRAN and occasionally C with BLAS and LAPACK libraries for CPU intense applications,

- Zotero for a bibliographic database (nowadays I can't imagine working without it). It supports bibtex exports but works with MS Word and OpenOffice as well.

- VIM, the best editor ever!

Microcal Origin / Windows.

Graphs, fit, small calculations etc.

eclipse - win/linux/mac - one of the most powerful IDEs ever.

citavi - win - for handling the daily lit.rev. and paper repository

git - win/linux/mac - perfect for collaboration on code as well as writing

R - linux - a powerful statistical and multidimensional data processing environment

minc tools - linux - advanced multimodal medical image processing software package

fsl - linux - brain image processing utilities

perl python, bash - linux - scripting for data manipulation, administration

SGE - linux - running scripts and complex utilities under parallel uenvironment

lyx/tex -linux - documentation system, combined with R : effective report generator

g++, gsl, boost - linux - c++ development environment for scientists

m3i - linux -MultiModal Medical Imgae processing sw. developement environment

Operating System : Windows 7

Tool : C#.NET Using Visual Studio , Microsoft Office Word and Outlook

To summarize .....Microsoft Corporation rocks

Mendeley

R

citavi

texnic/latex

dropbox

LaTeX/Kile (editing documents), git + meld (collaborative work and version control), Screen sharing (e.g. Skype), R (statistical analysis, visualization), the Follow-up plugin of Thunderbird mail (tracking deadlines of emails), Audacity (to record voice messages), the ScrapBook plugin of Firefox browser (save and organise web pages)

I prefer to use Mac OS because it doesn't need any antivirus and the things become so faster...

R/Matlab : statistical softwares on Linux

Google Drive/Drop box

Microsoft Office

Good i.e. fast Internet explorer like Firefox or crome

photo viewer

there are many required programs but depend on individuals need...

I am working with MacOSX at work, but when I'm working at home I prefer Windows 7.

For collaboration purposes Google Docs turned out to be very useful in multi-national projects or in the paper writing process. Other tools I really appreciate are: Dropbox/GoogleDrive, Mendeley, RescueTime (for monitoring my routines), MS Office, Skype, MaxQDA (for qualitative data analysis), doodle (for scheduling meetings) and sometimes Adobe Photoshop.

Mac OSX:

R - statistical programming & data visualization

LyX & LaTeX - writing documents & presentations

BibDesk - handling references

Eclipse - programming environment for C/C++/Java

Chrome - web browsing

Outlook - communication

arRsync - backup

Win 7 Pro : OS

MiTeX + TexnicCenter : for text editing

Eclipse + Visual Studio : Programming

Adobe PDF solutions + Office 2010 : for documents managements

i hope to buy a Mac Book Pro soon :)

I use mainly Linux (arch) with the following:

* Eclipse for Java/Python programming

* TexWorks/Texlipse for LaTex - publication production

* Pylab/Matplotlib/python rather extensively for analysis and plotting of results

* I combine Java and Python for data manipulation (including even direct manipulation from raw data to tables and graphs for the use with LaTex)

* to deal with large amount of data, sometimes I store them in a MySQL database

* CVS - a must!

* Unison/Rsync to keep stuffs at a remote safe place

* Virtualbox with Windows if I need to produce MS Office documents

Hope this helps :)

Linux is best for all type of research related job personally i am using Linux since 2 years

I'm also using Linux (Debian & Fedora), but some of the following programs are available for Windows too, don't know about Mac OS X:

- Basket: Taking & organising notes

- Jabref: Managing references (Windows also)

- Kile: LaTeX editor

- LaTeX (Windows also)

- rsync

- Unison: Two-Way sync of files and directories (Windows also)

- Kate: Texteditor (great Windows alternative: Notepad++)

- Freemind: Mind-mapping program (Windows also)

Matlab (The only reason to switch to windows!),

For most other programs I use Ubuntu 12:

Eclipse for Python,

kile for latex,

jabref for organizing my pdf files and generating bibliographies,

Google Drive and Chrome

For QM purposes, TURBOMOLE suite of programs, absolutely. MOLEKEL and MOLDEN for wavefunction analyses and molecular orbital displaying and also for graphics purposes. MOE is also a useful tool for classical force field based methods

@Imene Bensalem: you mentioned "todo list and time tracking: Time coach". I could not find this with Google. Can you please give an URL as well?

I use Wunderlist for Todo...

Most of my favorites were already mentioned:

- Linux (in my case its Debian to which I've been faithful since 1999!),

- BASH,

- LaTeX (with Beamer class for presentations and lecture notes and TikZ for diagrams)

- GNUPlot for plotting,

- python with numpy and scipy for scripting and small applications,

- FORTRAN and occasionally C with BLAS and LAPACK libraries for CPU intense applications,

- Zotero for a bibliographic database (nowadays I can't imagine working without it). It supports bibtex exports but works with MS Word and OpenOffice as well.

- VIM, the best editor ever!

Mathematica (under any OS), LaTeX

Not windows. I am trying to move away from Windows to Linux just because it is an open source software. The tool i am working with : R, LaTEX et. (both open source). They can be downloaded freely.

I'm a Mac user (been that way for years). In no particular order, these are the software I use daily:

- Sublime Text 2: for editing any kind of text, be that LaTeX, JavaScript, Python, HTML, etc. I prefer to do it all in one program, and ST2 is my current choice.

- Sparrow Mail: for email, best I've found so far.

- Chrome/Firefox: I use both everyday.

- Evernote: perfect for notes, since it syncs well between my laptop and a (growing) set of mobile devices.

- SugarSync: for backups and syncing files between my work and home computers.

- 1Password: storing my infinite (and still growing!) number of passwords for various websites (including this one). Syncs the passwords to my mobile devices as well.

Others in almost daily use: XCode & iOS Simulator for mobile development, Timing for time tracking, Anvil for "server" file access, iCal for calendar, VirtualBox for the occasional need to use of Linux/Windows in virtual machines.

Linux as OS (before linux came I used Unix). Bash shell which is the best shell ever. Vi (now Vim) as text editor - it has plenty of unique options if you know how to use it properly. Latex (since 1991 i.e. my M.Sc.). Quantum chemistry software: Molpro (I am Molpro developer), occasionally I use other software, as Dalton, G03, SAPT. I started to use Gabedit recently (mostly for plotting densities). Other programs used from time to time: Molden, wxMaxima, Gnuplot....

I'm a long-time Windows user who has been shifting to mac in the past year, so I use tools which are common to both Windows 7 and OSX. Most of the time I can seamlessly transfer my files between both systems.

Anyway, my main tools are:

Programming: GNU C/C++ (MinGW under Windows) - I used to use MS Visual C++, but I don't do GUIs anymore, and working with gcc makes my code more portable.

IDE: Code::Blocks under Windows, XCode under OSX - Love Code::Blocks but it doesn't work well in OSX, so I also use XCode.

Most used libraries: OpenCV, FFTW

Math work / algorithm design: Octave - I used R a lot during my PhD but once I learned Octave, I started using it for everything, even statistical work.

Scientific writing: LaTeX (and sometimes Word)

LaTeX editors: WinEdt under Windows, TeXworks under OSX

Office tools: Microsoft Office

PDF Reading/Annotations: Adobe Acrobat

Web browsing: Google Chrome

Image editor: GIMP

linux system.

eclipse, code::blocks and qtcreator for programming,

Kile and gedit for documentation,

qtiplot for graphing,

wxmaxima for algebra.

The reason why I am using Mathematica is that I do not need a special program for graphics and image editing, another one for presentation, another one for numerical calculations (statistics, diff eqs etc.), another one for symbolic calculations, another one writing programs (even in C, even for parallel elaboration and using graphic cards), another one for chemistry or linguistics or engineering etc. Go here: http://demonstrations.wolfram.com/ and it will be really hard for you to leave the page :)

I'm using mostly Ubuntu, but almost all of the following are multi-platform programs I found very helpful.

Reading/Writing

Mendeley: to easily handle and annotate my pdf database

Google drive: access my project notes from every computer and share with my collaborators

LyX: A "what you see has the structure of what you get" latex base document processor. Especially useful for two things: 1/ writing beamer presentations: you see directly the pictures of your document and the structure is very clear, 2/ writing mathematical research notes and early drafts: visualize equations as you type them. Latex import and export is easy.

Inkscape: handle all vector graphics with a lot of import/export formats+latex equations supported.

Coding

spyder: nice interactive python development environment, you can execute and test parts of a script as you write

Computing

byobu (unix): enhancement for screen. To attach/detach multiple interactive shells, very useful to access the same interactive processes (say matlab sessions) both locally and remotely

svn: synchronize code between different computers

meld: compare different versions of a file

just a side discussion - have anyone noticed the trend - majority/many of the answers here use linux and/or open source software. Is this the current trend? or users of research gate are mainly open source-friendly?

Why not Windows? I use Windows 8, and I am developing applications for C, C++, and C#, in Visual Studio 2012 (which is an awesome IDE) with ReSharper (which is a fantastic tool).

I occasionally use IntelliJ IDEA for Java and for everything else, Notepad2-mod.

For other *nix things, I do it on Backtrack. Cygwin when using *nix tools for Windows.

GitHub works best for SC.

Browser? Probably the alpha versions of Firefox (Aurora), and Google Chrome Dev. IE10 comes in handy at times.

Also, Mendeley! Thank you guys for mentioning it.

I used routinely following programs

SVM_light " Implementing Support vector machine

SNNS : for neural network

Apache : Launching web sites

PERL for routine programming

MySQL for database management

PHP web site development

Linux for OS

clustalw multiple sequence alignment

Weka for data mining techniques

CDK for descriptor calculation for developing QSAR model

PADEL descriptor calculation

Regarding the OS choice, for me it has always been an issue. There are many good programs on all platforms, but from the point of view of productivity, I mostly used unix because:

- I can use a terminal easily

- I can install latex easily

- I can setup ssh clients AND servers easily

- I'm able to attach/detach interactive sessions easily

I did not check the recent progress, but all that used to be way too complicated to do/install on windows. A good Cygwin setup can fix some of the issues, I agree. But if you have to change machine frequently, everything just works directly on unix and not on windows.

However, Windows has some advantages:

- Word and Powerpoint are still superior to their free alternatives (LibreOffice). Especially, grammatical correction and revision functions are really great on Word. Also if you have to collaborate, they are the dominant programs among biologists for example.

- copy-pasting vector graphics from Matlab to Powerpoint or equivalent is still only working on windows (maybe mac?), and it saves a lot of time!

@Sian Lun Lau:

I've chosen to go with open source software for a reason so that my students can use exactly the same software I'm using without having to spend any money or use pirated software. But just like Michel Besserve said, Microsoft Office is the exception, mostly because they are the standard for collaborations, but also because anything else I've tried is not as powerful or does not work so well.

In MS Office, there are a few things that even work better under Windows than under OSX: equation editing being one of them, copying and pasting of images being another one.

I'm the kind of researcher who now travels a lot and actually doesn't do that much science directly any more - instead I work with my geographically distributed team to do it collaboratively. Therefore most of my picks are to do with how you share work around.

I use Mac laptops along with an iPhone, Windows virtual machines, cloud IaaS and a smattering of UNIX boxes.

Simplenote (and the Simplenote IOS app / Notational Velocity on Mac) - the best synchronised notetaker if you want just the text. Evernote always seemed to be too functional for my needs.

Trac - most of what we're working on is recorded in Trac using the ticketing system, it allows people to provide updates that can be read by others at their leisure.

SVN - we use this to share documents, although increasingly we're Google Drive.

StarCluster - I use this to create ad hoc compute clusters for running simulations on Amazon EC2

Mendeley - used as my reference manager

Skype - out primary means of communication, particularly Skype chat. We also have an XMPP based chatroom. Often we use a combination of Skype and shared Google Docs to collaboratively work on things during a day.

Finally, a big shout out to TripIt - if you travel a lot to conferences, this tool is invaluable.

I often use the following (mostly freely available) tools:

- LaTeX for creating documents, along with various tools like pdftk, ghostview, etc.

- Python and Matlab for developing small software projects and for testing numerical methods,

- C++ for advanced software projects,

- CMAKE for handling the build processes, in a platform-independent way

- SVN for source versioning, using TortoiseSVN as a client

- ParaView for large dataset visualization

- Irrlicht3D for real-time visualization

- POVray for batch high-quality visualization of postprocessed data

- KiCAD for PCB electronic design

- OpenCascade library for c++ projects involving 3D models

- my own Chrono::Engine software for mechanical simulations

- JabRef for handling the bibliography (it interfaces with Bibtex)

- Eclipse as source editor (but I am using VisualStudio for C++)

- Notepad++ for quick ascii editing

I wold add the R software for statistical analysis: firstly with Rcmdr Library of R, and then, once you are familiarized with it, follow with R and Eclipse environment.

Windows 7 as operating system, SSH Secure Client to communicate with Unix/Linux servers, Outlook for emails, both MS Word and MikTex for writing papers, MS PowerPoint for presentations, Paint for basic image edition, EndNote as Bibliography Manager (should I be using Mendeley?), Origin for graphics, Mathematica for testing algorithms. Within Unix I mainly use vi for editing files and bash for scripts, and Fortran compilers to create distributable code.

Linux (any distribution with a recent KDE)

Konsole (for all my terminal needs)

Kate/vim for programing

A fortran compiler (either intel or gcc)

Kile (for latex)

Kbibtex (for bibliography management)

cb2bib (for bibliography extraction)

inkscape (for posters/diagrams/cartoon science)

GMT (for mapping)

gnuplot (for plots)

opendx (for visualisation of data)

okular (pdf reading)

acrobat reader (pdf annotations not supported by okular)

akregator (news/jobs/science feeds)

kmail (mail)

korganizer (keep organized)

owncloud (backup/share of data)

Generally I use the following software tools:

>> Windows/Linux (for OS)

>> Chrome/Mizilla (Web access)

>> Mendley (for reference managemnet)

>> Matlab (for programming and simulation)

>> Java (for program writing)

>> OriginLab (for plotting)

>> SmartDraw (for drawing)

>> MS Visio (for various kind of drawing)

>> NeuroSolution (for machine learning)

>> GPDotNet (for genetic programming simulation)

>> Cytoscape (for network construction)

>> GNA (for network analysis)

>> Cluster (for data clustering)

>> MEGA (for phylogenetic analysis)

>> ClusterW (for multiple sequence alignment)

>> DaliLite (For secondary structure prediction)

>> RasMol (for protein 3D structure visualization)

>> Weka and Rapid Miner (for classifiers and data mining)

>> PHP, Apache & MySQL (for web development & hosting)

>> DreamWeaver (for programming IDE)

>> Apache Tomcat (for J2EE Web Container)

>> MS-Office (for documentation, presentation, etc.)

>> Skype (for Video Calling)

>> Nimbuzz (for IM)

>> VNC and TeamViewer (for accessing remote desktop)

>> IPMessenger (for messaging and content sharing on LAN)

>> Many more ...

I am working with both, Linux and Windows, whereas one of these I am more or less forced to, guess which ;)

*XUbuntu/Win7

*OpenOffice

*Mozilla/Opera

*Thunderbird (Mail, Tasks and Calendar)

*Latex (TeXMaker/TexnicCenter) for scientific writing if I am allowed to....

*JabRef for References

*yEd/Dia for simple Diagrams

*Gimp for image editing

*Foxit Reader 4.3 (still free at those days) for pdf viewing and annotation

*gedit/nano for text file editing

*KeePassX for secure passwords

*F4(Commercial)/Folker for audio transcriptions

*Atlas.ti(Commercial) for qualitative analysis

Well, and of course all those sweet tools a linux distributions comes along with.

For an overview of software for the social science research process pls have a look at http://www.sosciso.de.

http://www.sosciso.de

I would add Freeplane, a fork of MindMap, for mindmapping.

@Robert Gora +1

In addition to that, R together with R-Studio for data analysis and NX-server & OpenNX client for remote controlling GUI machines.

GNU/Linux as OS;

LaTeX to do documents (articles, tutorials, ...);

GCC to compile C/C++ code;

Mendeley for references;

Git to work with colleagues (code and papers);

Lua for script Programming;

Geany to write Code and papers;

Hello, I am the founder of Docear which is a free and open source literature management software for Windows, Mac, and Linux and it's definitely a very powerful tool in a researcher's daily routine :-). Docear has a unique concept that helps you organizing, creating and discovering academic literature with a strong focus on the management of PDFs and annotations.

If that sounds interesting to you, have a look at http://www.docear.org/2013/10/17/docear-1-0-stable-a-new-video-new-manual-new-homepage-new-details-page/

And you might also be interested in this article which is discussing some aspects of how to (not) chose a reference manager http://www.docear.org/2013/10/14/what-makes-a-really-really-bad-reference-manager/

Perl