We explore and try different tools and softwares, which enhances our productivity significantly. It will be useful for the community if we share our favorite/recommended tools/software's here.
Recommendations can be shared in the following format:
Name-Use-Link-Personal Rating (out of 5)-Pros and Cons
Example:
Zotero - Bibliography Manager - https://www.zotero.org/ - 4.5/5 - Free, saves references directly while browsing, offline standalone version is also available, comparable to end note.
R -statistical language and environment-http://www.r-project.org-5/5-Free (and open source). This very powerful statistical language (and environment) is perhaps the most comprehensive statistics package available. In addition to it's core functionality, it allows researchers and statisticians to upload their own libraries, extending R's basic functionality. It is also a very versatile language as well (at least in comparison to other statistical DSLs, such as those associated with SAS or SPSS). Perhaps the only cost of this package is that it does not have the friendly front end of Stata, SPSS or S-plus. It would probably not take that much work to develop one, but as free software, there is probably limited motivation for anyone to do this.
R is tailored more for those who do a decent amount of statistical analysis and want/need to use state-of-the-art methods. It also has very powerful graphics. Those wanting to do occasional and/or 'off-the-shelf' analyses are probably better sticking with Stata, S-plus or SAS, as R does involve some investment in time to gain proficiency (especially for those not used to programming).
Qiqqa - Document library annotater, Expedition themes finder, auto & manual tagging, full-text full-library filtering & searching results in context, Brainstormer, citation Sniffer - http://www.qiqqa.com/70557 - 5/5 - Free - cloud syncing. Windows.
Mendeley - Reference Manager and academic social network - http://www.mendeley.com/ - 4/5 - Free - cloud sync, multiple platforms.
Evernote - Multimedia note taking, planning and collecting things from multiple sources - https://evernote.com/evernote/ - 5/5 - Free/Paid - sync, multiple platforms.
Publish or Perish- Reference search- harzing.com-5/5-free
Mendeley- Document management-mendeley.com-5/5-free
clippick- cloud clipboard- clippick.com-5/5-free
Docear, the academic literature suite - (http://www.docear.org) - 5/5 - Software based on freeplane (mindmap manager) and JabRef (reference management that uses BibTeX). It combines many useful features like pdf management, reference management and mind mapping tool. It is ideal for exploring ideas and organizing pdf library. It is possible to take annotations in a pdf document and import directly to Docear. Free and opensource.
R -statistical language and environment-http://www.r-project.org-5/5-Free (and open source). This very powerful statistical language (and environment) is perhaps the most comprehensive statistics package available. In addition to it's core functionality, it allows researchers and statisticians to upload their own libraries, extending R's basic functionality. It is also a very versatile language as well (at least in comparison to other statistical DSLs, such as those associated with SAS or SPSS). Perhaps the only cost of this package is that it does not have the friendly front end of Stata, SPSS or S-plus. It would probably not take that much work to develop one, but as free software, there is probably limited motivation for anyone to do this.
R is tailored more for those who do a decent amount of statistical analysis and want/need to use state-of-the-art methods. It also has very powerful graphics. Those wanting to do occasional and/or 'off-the-shelf' analyses are probably better sticking with Stata, S-plus or SAS, as R does involve some investment in time to gain proficiency (especially for those not used to programming).
You might consider the following:
Org-mode (Emacs) - an Emacs Mode for Notes, Planning, and Authoring-http://orgmode.org-5/5 - Free - most os
Emacs - Text Editor - http://www.gnu.org/software/emacs/ - 5/5 - Free - most os
R - statistical language and environment - http://www.r-project.org - 5/5 - Free - most os
Skim - PDF reader and note-taker for OS X - http://skim-app.sourceforge.net - 4.5/5 - mac os x
GAMS - http://www.gams.com - 5/5 - commercial, offers special prices for academics
With GAMS you can simply write LP, MILP and MINLP models within one environment. To solve this models you can use commercial and open-source solvers like GUROBI, CPLEX, XPRESS, COIN-OR or SCIP and many others.
I totally agree with Rene.
R studio makes life with R much easier, and I would suggest anyone starting out in R to use R-studio. It also helps making your R output look much better (see the Sweave and knitR features in R-studio). Note Sweave and KnitR are not unique to RStudio, but RStudio makes them MUCH easier to use. Sweave is particularly useful for those who use LaTeX as it allows you to integrate (and automatically change) your results within you manuscripts or presentations. However, a word of warning. I wouldn't touch Sweave until you are familiar with both R and LaTeX. KnitR is much easier to use and generally generates/formats your code and output in a nice document (html, Rmd among others).
As with R, R-studio is available for Windows, Macs and Linux
LaTeX - latex-project.org/ftp.html - 5/5 - free
I feel a bit sneaky identifying LaTeX which is so widely used and has been around a long time, but this software is wonderful. LaTeX has traditionally been used by the more 'Mathsy' disciplines (mathematicians, engineers, computer scientists and statisticians). The main reason is is EXCELLENT type setting of mathematical fonts (when you compare a equation generated using MS-Word with one in LaTeX you will know what I mean)
It is excellent for generating your manuscripts, reports or presentations (slides). LateX generated documents look great. The main cost is the (initially) steep learning curve. This can avoided (somewhat) through your choice of LaTeX editor (I use TeX studio), but dye-in-the-wool LaTeX users seem to prefer editors like Vim (trickier to learn). LaTeX includes a lot of third party libraries (see CTAN) and can pretty much do anything. From what I have seen is the only area it has not kept up in is the 'dynamic' bells and whistles that are (somewhat annoyingly) used in MS-Powerpoint and Mac's Keynote. I hope don't offend anyone when I say that I find these fancy-shmacy slide transitions a little 'undergraduate' anyway.
The most commonly used TeX (and LaTeX) typesetting system used in windows is MikTeX, and for mac it is MacTeX. You will have to download this type setting system before you download your editor (I would suggest TeXmaker or TeXstudio for the beginner. There is HEAPS of help on the internet for those starting out (or even the 'intermediate user such as myself), including WIkibooks, Youtube stuff, dedicated Q&A sites.
My last piece of advice is that LaTeX seems heavy to start with, but stick with it. Most converts never look back.
Name-Use-Link-Personal Rating (out of 5)-Pros and Cons
AWK - basic data exploration and management - https://www.gnu.org/software/gawk/ -5 -
Pros:
-the first approach to exploring any plain text data file
-search on patterns, checks, conditions, and reformat, or elaborate complex reports
-there is no file large enough...
-it may even allow for poor man's SQL on two linkable files
Cons:
-command line interfaced
-be aware that this is in fact a minimalist programming language
example:
on a dat.txt file with two columns, id and measure:
awk '{l[$2]++};END{for(i in l)print i,l[i]}' dat.txt
yields a list of value-frequency pairs that, if sorted, plots a PDF
Yes with With GAMS you can simply write LP, MILP and MINLP models within one environment. To solve this models you can use commercial and open-source solvers like GUROBI, CPLEX, XPRESS, COIN-OR or SCIP and many others.
I am a PhD student so most of my tools are aimed at keeping track of my research:
Manic Time - Time tracking - 4.5/5.0 Free - and Commercial. www.manictime.com
Pocket - Bookmark tool- 5.0/5.0 - Free -Good for when I see an article that interests me but I am on my android device so I can't use Zotero or Mendeley (well, not in such a convenient manner, at least).https://getpocket.com/a/
Git - Version Control Software - 5.0/5.0 - Free. Helps you keep track of your writings and code in an easy manner.
Mind42 - Mindmapping , web-based, 4.0/5.0 - Free.
FreeMind - Mindmapping, for desktop, 4.0/5.0 - Free
and a few others for those days when concentration just does not abound (Fences, Joe's goals, Redbooth(formerly Teambox). I wrote a longer post about this on my blog, feel free to visit if you like: http://therandomlinguist.blogspot.com.es/2014/02/free-tools-to-help-you-on-your-phd.html
I would like to suggest JAB REF as an alternative to traditional reference managers, have been using for years,
The web page description follows, "
JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format. JabRef runs on the Java VM (version 1.6 or newer), and should work equally well on Windows, Linux and Mac OS X"
http://jabref.sourceforge.net/
Another software very very easy Frontier, DEAP de Coelly. Try from the internet
Best wishes
I a gee with Dr .Maria José Palma Lampreia Dos-Santos.
best regard
I am grateful for your answers. For me this is useful information.
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