Tools you use often to work on Mac

[gene_x]

I searched around trying to find some useful tools people use often in work related to genomics/bioinformatics. I think it may be a good idea to create a post and gather some inputs from you guys!

To start, I'll list some tools I find very useful or use often:

Text editor: TextWrangler, free and powerful
FTP: Fugu, easy to use
R: Rstudio
Adobe Illustrator to edit phd or other images
Papers for organizing papers
Excel, Cluster 3.0+ Java TreeView

I'd love to hear from you and try some cool new tools!

[crazyhottommy]

I use emacs + python for my linux system.
mysql is also very useful.

[gene_x]

i heard emacs is very powerful once you got used to it.. i still use vi at this moment..

yes, mysql also, do you mean command-line mysql or you use a GUI?

[cliffbeall]

-Macports
-EMBOSS (thru MacPorts)
-Python + Idle
-BioPython
-Inkscape could be alternative to Illustrator

[gene_x]

-Macports
-EMBOSS (thru MacPorts)
-Python + Idle
-BioPython
-Inkscape could be alternative to Illustrator

I heard of Inkscape.

Macports and EMBOSS are pretty new to me..
What's most special abou python IDLE? I think it's basically a text editor, am I right?

[cliffbeall]

What I like about IDLE is the way the editor integrates with the interactive shell.

[gene_x]

What I like about IDLE is the way the editor integrates with the interactive shell.

Yeah, that's a nice feature to test programs I guess. Somehow python IDLE is very slow on my computer..

[CraigJ]

TextWrangler - Text editor
RStudio - R IDE
PyCharm - python IDE (sometimes Editra for a more lightweight python ide)
Cyberduck - FTP client
iTerm2 - improved terminal for ssh'ing, etc
IGV - integrative genomics viewer from broad institute
Sequel Pro - great mysql database management
Zotero - research/references & citations tool
Adobe Photoshop - for making some figures
Google Chrome - I like it better than safari
Texmaker - LaTeX development environment
VirtualBox - if I need to run a virtual machine
FastQC - sequencing quality control reports

[gene_x]

TextWrangler - Text editor
RStudio - R IDE
PyCharm - python IDE (sometimes Editra for a more lightweight python ide)
Cyberduck - FTP client
iTerm - improved terminal for ssh'ing, etc
IGV - integrative genomics viewer from broad institute
Sequel Pro - great mysql database management
Zotero - research/references & citations tool
Adobe Photoshop - for making some figures
Google Chrome - I like it better than safari
Texmaker - LaTeX development environment
VirtualBox - if I need to run a virtual machine
FastQC - sequencing quality control reports

iTerm seems really interesting!

[CraigJ]

iTerm seems really interesting!

Oh, I forgot to put that its iTerm2. The original iTerm isn't developed anymore I don't think, but iTerm2 is actively developed. I like it a lot as you can easily save many different profiles, and I have a different profile for each server I ssh to. 1 click and I'm ssh'd in and ready to go.

http://www.iterm2.com/#/section/home

[gene_x]

Oh, I forgot to put that its iTerm2. The original iTerm isn't developed anymore I don't think, but iTerm2 is actively developed. I like it a lot as you can easily save many different profiles, and I have a different profile for each server I ssh to. 1 click and I'm ssh'd in and ready to go.
http://www.iterm2.com/#/section/home

Yeah, I saw iTerm2 and realized that.