software-i-use.html

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layout: default
title: "Charles Sutton: Software I Use"
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<h1>Recommended Software</h1>

<p>What I like most about the Mac is that there is this enormous subculture
    of nifty productivity software.  These programs tend to be more numerous, easier to use, and of better quality
    than those I have seen for other platforms.  These days there are a lot of useful Web applications
around as well.  People have also started asking me <a href="#ipad">what iPad apps</a> I use. <span class="paren">(OK they haven't, really, but I was just
looking for a modest-sounding reason for why I'm going to tell you about what I like anyway.)</span>
</p>

<p>I enjoy trying out new software, so I'll try to keep this page
regularly updated as I learn about new software and also about
which shiny new programs I actually end up using
day in and day out. <em>Last update: 27 December 2016</em></p>

<p>Here is a list of software that I recommend.  None of these are very expensive; many are free. Except where indicated, everything on this list
is software that I use regularly.</p>

<h2>Mac Applications</h2>

<div class="software">
<p>
  For keeping research notes, I've gone through a bunch of different
  apps, but I have settled on <a href="http://www.evernote.com/">Evernote</a>.
 It is well suited for short notes that you want organized
   by date and by tag.
  It has an email-like interface with multiple panes.
  Probably its best feature is that it has excellent mobile apps that sync
  with the desktop version.  Therefore I often use it for taking notes during talks.
  So if you saw me fiddling with my phone during your recent talk, either your talk
   was really boring and I was checking my email, or your talk was really interesting
   and I was taking notes.
</p><p>Another cool choice is
  <a href="http://flyingmeat.com/voodoopad/">VoodooPad</a>,
  which I used for several years.
VoodooPad is essentially a personal Wiki, i.e., you
can create new pages in your notebook to keep organised.  But, unlike
regular Wikis, it's easy to change formatting, copy and paste pdfs of
  graphs, etc.  It's Mac-only.

<p>You might also look at <a href="http://www.barebones.com/products/yojimbo/">Yojimbo</a>.  It has good reviews, but I haven't had a chance to try it.</p>
</div>
<div class="software">
  <p>
I am in love with <a href="http://www.alfredapp.com/">Alfred</a> (the computer program). It is an application
launcher, which is a program that allows you to start applications anywhere on your machine using only a
few keystrokes. You
start the launcher with a hotkey (say, Cmd-Space), it comes up instantly, and you type in PPT.
    A menu comes up with all of your applications and documents that whose name (NOT contents, like Spotlight) contains "PPT".
    You could scroll through this list, but you don't need to, because it has been cunningly ordered so that PowerPoint is at the top.
    You press Enter, and PowerPoint launches.  That's it.  It took you more time to read this paragraph than it would have to find and run any
    application on your machine.
</p><p>Alternatives: <a href="http://quicksilver.blacktree.com/">Quicksilver</a> was a popular launcher
that I used for many years, but these days it is slow and not really kept up to date. It was also never
really documented, so learning to use it means reading a lot of breathless <a href="http://lifehacker.com">Lifehacker</a>
posts about how if you just click a checkbox three levels down in the preferences, hit Cmd-Ctrl-Shift-Space, and click your heels three times,
QuickSilver will actually send a message to your IoT-enabled toaster
to start cooking bread for you.
Other launchers that I have heard of are as <a href="http://www.obdev.at/products/launchbar/index.html">LaunchBar</a> and <a href="http://www.petermaurer.de/nasi.php?section=butler&amp;layout=default">Butler</a>.</p>
</div>
<div class="software">
<p>
As for mail clients, the default client Mail.app is all right,
but the keyboard shortcuts are crap and I got fed up with it
for interacting poorly with the University IMAP server.
After a long search, I have settled on 
<a href="http://freron.com">MailMate</a>, a lightweight but
amazingly powerful and customizable client.
Not for the fainthearted, but very effective.
</p>
</div>
<div class="software">
<p>
  For editing code, my favourite port of Emacs to OS X is <a
href="http://aquamacs.org/">Aquamacs Emacs</a>.  I have used several
Aqua Emacs ports over the years, and this is hands-down the most
Mac-like. For a while I used <a href="http://macromates.com/">TextMate</a>, which is also very well-done; it has many powerful Emacs-like figures, but in a fully
Mac-like package.  Its interface for multi-file projects is
  significantly better than Emacs. But in the end I decided
that I wanted Emacs. (I'm not fussy about editors, I switch
back and forth between Emacs and vi every day.)
</p>
</div>
<div class="software">
<p>
I have recently discovered that Apple's Pages looks like an excellent tool
for making scientific posters.  I had been looking for a good tool for YEARS
that lacked the overkill factor of InDesign. I've only tried it for a simple A4 sign
so far, but I'll post an update once I try it for a poster.
</p>
</div>
<div class="software">
<p>
For editing TeX, I have just started using <a href="http://texpadapp.com/">TeXPad</a>,
which is impressive. Previously I have used <a
href="http://www.uoregon.edu/~koch/texshop/texshop.html">TeXShop,</a>
which is also good. I also know people who have liked
<a href="http://itexmac.sourceforge.net/">iTeXMac</a>.
</p>  
</div>
<div class="software">
<p>
I use <a href="http://bibdesk.sourceforge.net/">BibDesk</a> to
 manage my BibTeX file. It has
 excellent support for pulling entries off of the Web (e.g., from
 Google Scholar). Alternatively, if all I have is a text citation, it also has a
 nice interface to highlight which text goes to which fields.  The
 only thing it lacks is iPad support.
</p>  
</div>
<div class="software">
<p>
I am really liking <a href="https://slack.com">Slack</a>
for group-local chat. It's basically IRC with really nice apps
and really easy signup.
</p>
</div>
<div class="software">
<p>
Having written all of the code for my dissertation in Java, my main advice for Java development is: Don't.
It must be said, however, that the state of the art for Java development environments are better than perhaps
any other high-level programming language.
In this respect you can do no better than <a href="http://www.jetbrains.com/idea/">IntelliJ IDEA</a>.  
I have only
occasionally used <a href="http://www.eclipse.org/">Eclipse</a>,
but my impression is that Eclipse has most of the same features, but a
significantly worse interface&mdash;and this is a real problem,
because the whole point of an IDE is to
get things done quickly.
</p>
</div>
<div class="software">
<p>
  Of course, for statistical computing and graphs, there is <a href="http://cran.r-project.org/">R</a>.  The latest Mac versions are quite nice.
</p>
</div>
<div class="software">
<p>
You definitely want a package manager to allow you to download
and build open source Unix tools easily.
For example, this is a great way to get a TeX installation.
You should know about <a href="http://macports.org/">MacPorts</a>, a large repository of free Unix software that has been ported to OS X.
An older alternative to MacPorts that people also used to use
 <a href="http://fink.sourceforge.net/">fink</a>.  
These days, however, the cool kids are using 
<a href="http://brew.sh">homebrew</a>. I'm not cool,
so I just use MacPorts.
</p>
</div>
<div class="software">
<p>
<a href="http://www.omnigroup.com/applications/omnigraffle/">OmniGraffle</a> is great for drawing graphical models and such.
</p>
</div>
<div class="software">
<p>I have recently been converted to the <a href="http://www.youneedabudget.com/">YNAB</a>
budgeting system.  It's a well explained electronic version of the envelope
budgeting system. 
</p></div>
<div class="software">
<p>
A common problem is how to get LaTeX equations into PowerPoint or KeyNote.
Mostly I use
<a
  href="http://pierre.chachatelier.fr/latexit/latexit-home.php?lang=en">LaTeXIt</a>
  for this, which is pretty nice.
  For PowerPoint only, there is also <a
href="http://texpoint.necula.org/">TexPoint</a>, which integrates
  directly into PowerPoint rather than being a separate application.
</p>

<p> You should also become familiar with the presenter tools in
Keynote or Powerpoint that show your time and next slide on the laptop
display while your slide is sent to the projector.  These are to die
for.</p>
</div>

<h2>Web apps</h2>

<div class="software">
<p>
I keep all my bookmarks in <a href="http://pinboard.in">Pinboard</a>.
This is a social bookmarking site like 
<a href="http://www.delicious.com/">del.icio.us</a>, except that it is not social.
Basically, it stores all of your bookmarks on a web site that you can access from all of your devices.
I use web-based bookmarking rather than browser bookmarking because (a) a hierarchical foldering system is extremely cumbersome, (b) I can access my bookmarks from
any device.
Perhaps you are curious about
<a href="http://pinboard.in/u:casutton/">my bookmarks</a>?
</p>
</div>
<div class="software">
<p>
To keep organized, I use <a href="http://rememberthemilk.com">Remember the Milk</a>.
It has an excellent iPhone app that is easily worth the $25 a year that it costs.
I used to use 
<a href="http://www.omnigroup.com/applications/omnifocus/">OmniFocus</a>,
but RtM is simpler and faster.
</p>
</div>
<div class="software">
<p>
<a href="http://www.tripit.com/">TripIt</a> is a slick way to organize your travel arrangement.
It parses the confirmation emails that you received from just about every travel site you use
and integrates them into a single itinerary.  This way you can have all of my confirmation
numbers on the go, using the TripIt mobile app.
There is a very slick way to set up your account.  Simply forward a confirmation
email to <code>plans@tripit.com</code> and it will create an account
from your email address.
</div>

<h2 id="ipad">iPhone / iPad apps</h2>

<p>
A lot of the iPad apps that I like are companions to either a desktop or a Web app that I use.
This is probably because: (a) no one has done mobile Web apps well,
and (b) the iPad platform hasn't figured out how to handle storage,
(I don't mean that sarcastically; it's actually hard)
so apps like to use the cloud.
</p>

<ul>
  <li><a href="http://www.goodiware.com/goodreader.html">GoodReader</a> is a good PDF viewer.
    Current versions support annotation, including highlighting, text, and freehand drawing.
    It works very well with DropBox. Just put a symlink to your papers folder in your DropBox
    folder on your computer.  Then tell GoodReader where your DropBox papers folder is.
    Now GoodReader will sync (manually) as you add papers!  Neat.

  <li><a href="http://www.evernote.com/about/download/ipad.php">Evernote</a> is great for notetaking and
     syncs with the desktop app like a charm.

  <li>I really like using my iPhone to scan in handwritten notes
and whiteboards from meetings. Scanner apps will remove the background
and convert the image to black and white, vastly reducing
the amount of space it takes up. I've used several of these,
but my current favourite is the scanner app from Evernote
called <a href="https://evernote.com/products/scannable/">Scannable</a>,
which has a nice interace and (surprise) integrates very well
with Evernote.

  <li><a href="http://www.strongapp.me">Strong</a> is an amazingly simple and elegant workout tracker for iPhones, especially well suited for weight training.

  <li>The <a href="http://www.amazon.co.uk/gp/kindle/ipad">Kindle</a> app is a good reader
       and a lifesaver when I "must have" a particular book.

  <li><a href="http://blog.rememberthemilk.com/2011/05/introducing-remember-the-milk-for-ipad/">Remember the Milk</a> has a well done iPad app for your todo list.
  

  <li>Diversions: <a href="http://asherv.com/threes/">Threes</a>, <a href="http://papersplea.se">Papers Please</a>,
<a href="https://telltale.com/series/the-walking-dead/">The Walking Dead: The Game</a> (it's better than the TV series).

</ul>