Software I Use

First of all, I use Linux (mostly Scientific Linux 4, on desktop machines) and Mac Os X (on my wonderful black MacBook). I use almost exclusively Open Source software.

Please note that I also talk, possibly in more detail, about many of these applications in other pages of the PSI wiki, so make sure you search for them!

On this page... (hide)

  1. 1. Missing:
  2. 2. Writing:
  3. 3. Browsers:
  4. 4. Mail:
  5. 5. Development:
  6. 6. Scientific:
  7. 7. Networking:
  8. 8. Web:
  9. 9. Misc:

1.  Missing:

The software that I would like to have, but is not there...

  • a data analysis tool that
    • is as powerful as Root,
    • is as fast from the command line as PAW,
    • has as good interactive display as the old HistoScope,
    • has the modular design of OpenScientist,
    • has a standard AIDA API
    • has powerful 3D visualization like OpenDX,
    • has support for HBook, Root and HD5 data files.

No, sorry, OpenScientist does not fit the bill, it crashes way too much, and does not support anything but the simplest Root data files.

  • a truly cross platform, open source project planning tool (something MS-Project), with a standard file format.
    But there seems to be no standard file format...
  • an iSync for Palm that does not need the messy PalmSync for OsX
  • a good way to sync Palm with Thunderbird
  • a ToDo app which is cross platform, able to sync to a server for group sharing, and able to work disconnected. And easy to use, of course
  • a cross-platform, networked "sticky notes" application

2.  Writing:

  • see LaTeX
  • OpenOffice (Linux,Windows) / NeoOffice (OsX)
    I enjoy very much the presentation tool.
  • LaTeX - what else would you use to write papers?
  • LyX
    LaTeX without the pain. Well, almost.
    • LyX on Mac
      It really is getting better and better at each revision.
      Integration with the spell checker (aspell) is now pretty good, though I am missing the while-you-type checking. It's nice that it supports well British spelling (just remember to choose it in the document settings)
      I would much appreciate if they added a multiple document interface, instead of reusing the same window...
    • http://www.la.utexas.edu/~tnishino/osx_lyx/
  • TeXniscope (OsX)
    good native DVI viewer
  • Preview (OsX)
    it just works - isn't that great? Plus, it allows adding annotations and marks on PDF files - something that only the non-free version of Acrobat can do.
  • Skim PDF reader
    Preview lets you add notes and marks to a PDF, but they become "fixed" as soon as you save. Skim solves this and much more. It also automatically updates when you recreate the PDF (Preview doesn't) so it's a lifesaver for writing LaTeX. Great!
  • BibDesk
    to manage BibTeX bibliography. Very good - it would be even better if it could "speak" with Aigaion.
  • Aigaion
    to store papers and references, and share them with the rest of the group.
    Pity it needs MySQL - if it could use SQLite, it would be perfect, as I could easily keep a mirror site on my notebook.
  • PmWiki, of course

3.  Browsers:

  • Safari (OsX)
    Nice, easy and fast. I think the weakest point is bookmark management.
    And it would be nice if it could sync with Google Bookmarks like Firefox.
    • SafariPlus - flash blocking etc
    • Sogudi - search and more from the address bar
  • Firefox (Linux,OsX, Windows)
    in the few cases when Safari can't render a page

4.  Mail:

  • Apple Mail
    excellent on connected/disconnected usage,
    lacks setting of mail priority and return receipts, forwarding mails as attachments
    • MailTags 2 - tried it, works well, but maybe it requires too much work
    • Mail_SelectionFix - fix the shift-arrow selection behaviour
    • MailPriority was extremely useful, but it does not work on Tiger, and it's not mantained - that's what you get with non-OpenSource software.
  • Thunderbird (Linux,OsX, Windows)
    when I am on Linux, or in OsX when Mail does not help (see above)

5.  Development:

  • Eclipse (Linux,OsX,Windows)
    Excellent, if you have 1GB of RAM. I wish the C++ refactoring tools were as good as Java..
    I am not happy with the AStyleclipse autoformatting plugin, it's too invasive, and not as good as Emacs.
    • Subclipse is a great plugin for integration with Subversion
  • XEmacs (Linux,OsX)
    My favourite for a long time in Linux. But in OsX I am suffering from the lack of a really good implementation.
    Its autoindent is way better than any other editor I have tried.
    • [[http://aquamacs.org/|Aquamacs] is a good Emacs for OsX, and it gets better and better - pity it is not XEmacs...
  • TextMate (OsX) (shareware)
    One of the few non-free softwares I have. I use it for quick editing when Eclipse wold be overkill, and TextEdit is not enough.
    Unfortunately it can't do autoindent.
    • get Fortran mode bundle
      (you may need to first setup http proxy info for subversion)
      mkdir -p '/Library/Application Support/TextMate/Bundles'
      svn co --username anon --password anon \
       http://macromates.com/svn/Bundles/trunk/Bundles/Fortran.tmbundle \
       '/Library/Application Support/TextMate/Bundles/Fortran.tmbundle'
  • Subversion
    developing without revision control would be like driving without safety belts.
    It's also good for LaTeX, and handles well even binary files (CVS doesn't)
    • svnX (OsX)
      is a reasonably good standalone GUI
    • eSVN (Linux)
      is a reasonably good standalone GUI too
    • TortoiseSVN
      is an excellent GUI that integrates with Windows Explorer. I wish there was something like it for OsX and Linux...
    • Subclipse integrates very nicely with the excellent RCS interface of Eclipse
    • SCPlugin (OsX)
      a Finder plugin :-) I'm trying it now.
  • Doxygen (Linux,OsX)
    JavaDoc style documentation generator.
    Absolutely, insanely great.
    • GraphViz - used for dependency and inheritance graphs

6.  Scientific:

  • Geant4
    • Dawn for publishing-quality 3D
  • Geant3
  • Root (but I wish there was something better)
    • Go4 is a somewhat nicer interface for Root, pity it does not work on OsX
  • PAW
    outdated in many ways, but first love is hard to forget...
  • Octave (Linux, OsX)
    is nice and quick for simple calculations and plots.
    • AquaTerm is wonderful for using it under OsX without having to start X11
  • I have also used Grace in the past, but now I find that Octave is as fast and more flexible for making simple plots.
  • Mathematica
    I'm being a bit lazy here, there are OpenSource alternatives; but Mathematica is just simple and does not get in the way of working
    • FreeMath is not bad, but nowhere nearly as polished as Mathematica
  • CERNLIB
    getting it to work on OsX 4, which uses Gcc 4.x, and therefore no g77, has been non-trivial. Write me if you need instructions. Update: now it's working just fine from FINK.
  • Midas DAQ software
    I use almost only the low level drivers, not the whole infrastructure, which I find kind of overkill for simple, fast DAQ.
  • qucs (Linux,OsX)
    OpenSource circuit emulator, easier than MacSpice
  • ImageJ - Image analysis and editing for those 16bit gray images
  • Janis - excellent tool to access databases of nuclear properties and cross sections
  • digitizers convert an image file showing a graph or map, into numbers
  • Task Spooler very simple batch job queues for standalone PCs.

7.  Networking:

  • OpenSSH
    it might be obvious, but it is 'so' important...
    • puTTY whenever I'm forced to use Windows..
  • I am still looking for a good, opensource graphical SFTP client for Os X. I have tried:
    • CyberDuck
    • Fugu
  • rsync
    fundamental for keeping things in sync, for backups etc
  • BitTorrent
    is wonderful for downloading heavy stuff like whole Linux distributions. Pity that ADSL here in ZA are 640kbps, and capped to 3GB/month, and more expensive than uncapped 2Mbps ADSL in Italy!!
    • Azureus is pretty good, but somewhat heavy
    • Transmission (OsX) is nice and light
  • Skype
    when you live far away from home (~8Mm), you appreciate it even more. And the audio quality is sometimes better than the phone...
    But I really do not like the complete lack of control on the use of your link, which is a very serious problem here: leaving Skype open can easily exaust your 3GB/month cap... Please, give us at list a bandwidth limit setting!
  • dovecot IMAP server
  • postfix SMTP server

8.  Web:

  • Google
  • Google Scholar
    Does a pretty good job at finding scientific papers
  • arXiv
  • La Repubblica
    to keep in touch with what goes on near home
  • Wikipedia
  • CiteULike
    a community for scientific papers - excellent filters to import from publisher's websites, and to export BibTeX
  • GMail
    excellent, but I need my mail with me when there is no network...

9.  Misc:

  • Fink (OsX) - think Debian-like packages for OsX
    absolutely necessary, could not work without it. Not so polished, and I am not enthusiast of the fact that unstable is source only.
  • Parallels (OsX)
    Since I cannot run natively our "standard" SL4 on the MacBook, this is a lifesaver.
  • DesktopManager - virtual desktops under OsX
    I grew so accustomed to virtual desktops in Linux, being able to keep plenty of applications open, that I would be very improductive without. DesktopManager works quite well, but it does crash often when waking up from sleep. I have tried VirtueDesktop, but I did not really like it (or maybe it was incompatible with something??).
    One thing that I miss, compared to Gnome's virtual desktops, is the capability to move windows from one desktop to another by just dragging its image in the miniature display.
  • Midnight Commander - an Orthodox File Manager for Unix/Linux/OsX terminal
  • RemoteBuddy (OsX) (non-free)
    It allows you to configure the behaviour of the small remote control for any application. Simply great for presentations.
  • iStumbler (OsX)
    check WiFi signal levels, and more
  • Strip for storing password on my Palm Zire
  • perl-strip to read Strip DB away from Palm
  • Book Archive
    I never really consider keeping an archive of my books, CDs etc, until I found
    • Delicious Library (OsX) (non-free)
      which is simply impressive, expecially when you use the built-in webcam to get the ISBN from the barcode, and it finds all the info on its own. But almost completely useless, because it does not support any database of Italian books. So I tried
    • Books and
    • BookPedia
  • Google Earth (OsX)
    is amazing. And where it has street information, is also actually useful!
  • iTunes (OsX,Windows)
    it works well, and does almost everything I need. Except for being able to access multiple repositories, to let me store unfrequently used stuff on an external HD.
  • iPhoto (OsX)
    very good for photo archival and basic editing like crop and color balance. It would be even nicer if it had a faster way to add keywords.
  • Gimp (Linux, [[http://gimp-app.sourceforge.net/|OsX], Windows)
    good enough for the little image editing that I happen to have to do. Its multi-window interface in X11 does not fit well in OsX, but it works, anyway.
  • [http://www.inkscape.org/|Inkscape] (OsX,Linux,Windows)
    vector drawing program. Native SVG, support for EPS import (currently in devel version)
  • Dia (Linux)
    diagrams and so on. Also on OsX, but, being in Fink unstable, it requires recompiling the whole world.
  • VLC (OsX,Linux,Windows)
    complements well QuickTime - it can usually play stuff that QT cannot, and viceversa.
  • Flip4Mac WMV, DviX (OsX) - for other media formats
  • CoreDuoTemp (OsX)
    yes, sometimes the MacBook feels so hot that you worry it could melt... so it's comforting to have a look at the temperatures.
  • Nudge (OsX) - force update of directory in Finder
  • coconutBattery (OsX) - check battery status and lifetime
  • DoubleCommand
    now supports independent settings for different keyboards; but this is not yet exposed in the control panel, so you need a script to configure it:
#!/bin/bash
# reconfigure an external keyboard 
# to swap "Command" and "ALT" keys for a mac
# using DoubleCommand
# http://doublecommand.sourceforge.net/
# Default config:
sysctl -w dc.config=0
# Option Key as Command Key = 64
# Command Key as Option Key = 16
# Enter Key as Option Key   =  6
V=84
# Microsoft Natural Ergo4000 keyboard:
sysctl -w dc.keyboard1=40 
sysctl -w dc.config1=$V
# Internal MacBook keyboard:
sysctl -w dc.keyboard2=38 
sysctl -w dc.config2=0
# display configuration
sysctl dc
  • Resistulator (OsX widget)
    cute thingy to find out resistor values from color bands and viceversa.
  • Boinc & Rosetta@home
    help save the world and feel better - don't let your CPU idle!