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  • Tools you use often to work on Mac

    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!

  • #2
    I use emacs + python for my linux system.
    mysql is also very useful.

    Comment


    • #3
      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?

      Comment


      • #4
        -Macports
        -EMBOSS (thru MacPorts)
        -Python + Idle
        -BioPython
        -Inkscape could be alternative to Illustrator

        Comment


        • #5
          Originally posted by cliffbeall View Post
          -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?

          Comment


          • #6
            What I like about IDLE is the way the editor integrates with the interactive shell.

            Comment


            • #7
              Originally posted by cliffbeall View Post
              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..

              Comment


              • #8
                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
                Last edited by CraigJ; 03-22-2013, 10:18 AM.

                Comment


                • #9
                  Originally posted by CraigJ View Post
                  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!

                  Comment


                  • #10
                    Originally posted by gene_x View Post
                    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.

                    Comment


                    • #11
                      Originally posted by CraigJ View Post
                      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.

                      Comment

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