In preparation forleaving Google, Iwanted a new computer in time to make sure I could get all thenon-Google stuff (pictures, blogging software, music) moved off myGooglemac. I got a maxed-out MacBook Pro 15' (16G RAM, 1T SSD) thus dumpingan estimated $1,000 profit into Apple’s cash hoard. What did I get for it andhow did I set it up?
- RNA-Seq is a technique that allows transcriptome studies (see also Transcriptomics technologies) based on next-generation sequencing technologies. This technique is largely dependent on bioinformatics tools developed to support the different steps of the process.
- Re: Running namd on Mac OS (Tue Jul 20 2010 - 13:06:51 CDT) Eric Perim. (Wed Mar 17 2010 - 07:45:19 CDT) Erica Smith. Parameter file for DMPC lipid and protein system but with CHARMM36 lipids (Mon Jan 03 2011 - 21:53:59 CST) Erik Nordgren. Re: Temperature during membrane equilibration (Fri Sep 09 2011 - 11:17:53 CDT).
- Ready Lisp is a binding together of several popular Common Lisp packages especially for Mac OS X, including: Aquamacs, SBCL and SLIME. Once downloaded, you’ll have a single application bundle which you can double-click – and find yourself in a fully configured Common Lisp REPL.
Choose 'Bacteria 16S rRNA' or 'Archaea 16S rRNA' as the gene for aligner depending on your previous Classifier results, fill in the rest of the form and select your sequence fasta file.Click on the 'Upload' button. On the Upload Sequences Confirmation page, click 'Continue'.
I’ve been using OS X for eleven years now, have learned a few things, andthere’s a chance that some of the tricks here could be useful to others.
State of the 2014 Art · I got a Pro rather than an Air because I want the big screen, big memory,and fast CPU, mostly for photo-editing with Lightroom.It’s a pretty wonderful computer, but that’s no more nor less than expected these days. Fast, quiet, and the Retina display as good asolution to a #firstworldproblem as I’ve seen in years.Except for, my Googlemac had a wonderful matte screen, and I didn’t see thatoption when I ordered this one.
I’ve had to tune the font sizes and line spacing in a bunch of apps;usually not to make them larger but smaller; something in the system isovercompensating for the Retina density and picking too-big sizes.
It’s sort of amusing: I’m looking at a shell command output or an Emacsbuffer and thinking “Wow, that looks great”. But bear in mind that I waslooking at more or less the same stuff two decades ago in an ASCII terminaland the fact that it was maybe one-tenth the resolution didn’t seem to botherme then.
But really, what can I say? The memory and disk are massive, the CPU isfast, the battery’s pretty good, nothing I’ve done yet has turned the fan on;everything works great.
OS X and its Apps · Eleven years in, and I am downto exactly one Apple app in daily use: Preview. I had been using Keynote alot, but the cloud competitors (for example from Google) are getting betterand better, so I’m easing off and may end up leaving it behind.
I still can’t go to a Chromebook or other cloud-centric device, because ofEmacs and Lightroom and Eclipse and so on. I could go to Windows but feel notemptation whatsoever; I’m too old now to not use Unix.
The Checklist · Here are the things that a seasoned OS X-ista who works on pictures andcode a lot needs to do to get a machine all tuned up and humming. This is thepart that might be helpful for other people.
Keyboard · First thing is, you need to speed up the key-repeat speed to the max,otherwise you’ll feel like either the computer is too slow or you’re gettingold.
Second, if you want your writing to appear a little more literate, downloadand installthis alternatekeyboard, described inBetter QuotesRedux, and then you’ll have “, ”, and ’ on option-L,option-;, and option-'.You need to drop that file into ~/Library/Keyboard Layouts andreboot; then it’ll show up as an international keyboard option.
Trackpad · I turn on “Tap to click”, “Secondary click”, and turn off everything else. There was a bad interaction where Lightroom wouldn’t let me resize with thecrop tool until I’d turned off everything. Most of that other stuff isreally only useful inside one Apple app or another.
Then you go into System Preferences, Accessibility/Trackpad Options, and“Enable dragging”. That lets you tap twice on anything and then drag itaround. Which used to be in the main Keypad prefs until Apple decided to hideit.
Fonts · For your monospace needs I recommend Raph Levien’s exquisiteInconsolata.
Emacs · You can build your own of course but I just got the latest binary fromEmacs For Mac OS X; it Just Works,and I work mine pretty hard.
Tooling · You’ll need to install XCode and its command-line toolsfirst.
Then you need Homebrew; none of the OSX package managers areperfect, but I find Homebrew the least bad. I used it to installImageMagick (the only OS X tool Iknow of where you can resize pictures on the command line) andaspell so far, and I’m sure there’ll bemore.
MySQL I got from Larry Ellison in a DMG and it seemed to Just Work, with alittle Prefs-screen thingie to control it too.
The built-in Perl and Ruby and are working fine, and I managed to get CPANto install DBD::mysql with only a little bit of library relocation. Go camein a DMG, no fuss no muss.
... all of which got me to the point where I can write and publish thewords you are now reading. Which feels like magic to me the first time itworks, because there aremany moving parts that have to worktogether.
The Dock · Put it on either the right or the left; on any modern Mac laptop, verticalspace is precious and horizontal space abundant. I don’t leave anything inthere permanently unless it’s something I always have running, so my Dock isalmost always identical to what’s-live-now.
Moving data · I’ve kind of gone off Migration Assistant because I find OS Xinstallations, like any other tool heavily used by a professional, build uplayers of crud and benefit from periodic sanitizing.
So I plugged in a terabyte USB disk and pushed all my non-Google stuff toit with Rsync, because I’ve foundthattar is sometimes upset by the super-long filenames in iTunes. Then I Rsync’ed it back onto thenew computer. Boy, is it ever faster sucking data off a USB disk onto an SSDthan the other way around.
Apache · Apple irritatingly discarded the System Prefs screen for controllingApache. So, to get things going, I did a sudo apachectl start toget it going on a one-time basis and somehow that’s sticky, I’ve rebooted acouple of times and it comes back up. OK then.
Thanks! · I picked the new box up less than 24 hours ago and here I am doingproductive work.Thanks are due to the OS X Morlocks at Apple, and to all the people out therein the OSS world who pull the tools and tricks together, for fun and becauseit’s The Right Thing To Do.
And I think to myself... what a wonderfulworld!
Comment feed for ongoing:
From: dave (Mar 08 2014, at 12:46)
Thanks for the heads up on Inconsolata. I'm a longtime ProFont user for monospace text, but I'll give this a shot for awhile.
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From: Eric (Mar 08 2014, at 13:06)
There is a hidden gem in osx called sips: lets you resize, strip/modify color profiles etc right from the command line. It's been around for years and since it's core image based will happily use your (considerable) gpu power to do its work.
Mac Os Versions
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From: Alex (Mar 08 2014, at 13:14)
Awesome writeup.
I wrote something similar on setting up a new mac for development here:
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From: dave (Mar 08 2014, at 13:43)
Ugh. Nope, Inconsolata is just too compressed horizontally. Compared with ProFont, the anti-aliasing makes it harder to read on my 27' U2711 and really tiny on the Retina display [comparing the fonts so they take up the same space vertically].
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From: d.w. (Mar 08 2014, at 14:12)
I usually end up stringing things together with NetPBM rather than ImageMagick, but I acknowledge that’s pretty much just habit, rather than one tool being better than the other.
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From: Federico Saravia (Mar 08 2014, at 14:24)
Nice piece of writing, thanks for the font advice on Inconsolata. I would like to share some other personal config that makes my life easier:
* Add some color for Terminal.app: https://gist.github.com/fsaravia/9439756
Mac Os Download
* Homebrew is working perfectly great for me (Mysql, redis, android-sdk, git, imagemagick and some more), just do not use sudo (as I've read you did on twitter), the plus side of having mysql installed through homebrew is that upgrading it is completely painless (brew update - brew upgrade)
* If you find yourself in the need of working with multiple rubiews, rvm or rbenv may be better choices than the system built in version
* Continuing with ruby, check out pow http://pow.cx/ for running multiple rack based apps without having to start-stop them every time
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From: Gordon Haff (Mar 08 2014, at 15:38)
I have mixed feelings on the glossy-everything trend that seems to be the norm these days. I suspect glossy is indeed better when the environment is right--but it often isn't. I went through the same thing buying a new TV for my sunroom which, as you might imagine from the name, has a lot of light during the day. I don't use the TV in that room much during the day and the glossy plasma is indeed wonderful at night, but matte screen have their advantages in sunlight and, I suspect, are the overall optimal choice for a lot of uses even though they've fallen out of favor.
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From: Evan (Mar 08 2014, at 15:43)
Don't forget to change this setting:
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From: Niket (Mar 08 2014, at 15:51)
I'm glad to hear your setup was quite minimal. Though I think there's a place for all day setups as people seem to like that experience, I'd rather just be building stuff.
I would recommend two additions on SW side:
1. QuickSilver which is lovely.
2. ZSH just because it's better for navigating around.
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From: Shrutarshi Basu (Mar 08 2014, at 15:52)
Personally I keep the dock on the bottom, but have it hidden and set to come open when I mouseover. I generally just have Firefox, iTerm2 and Emacs open all the time, use Cmd+Tab to switch and Alfred to open anything else, which is a long way of saying: I rarely actually use the dock.
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From: a (Mar 08 2014, at 15:55)
'I’m too old now to not use Unix'
So am I, and I'm not yet 30...
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From: Stephan Ango (Mar 08 2014, at 16:05)
Funny, I find Preview to be the first app I have to replace on any new Mac. I recommend Xee: http://xee.c3.cx/
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From: Jan (Mar 08 2014, at 16:48)
Regarding your 'Apache' issue: I've found http://clickontyler.com/web-sharing/ long time ago (actually, it must be at time of 10.8 landing) which provides an easy access to apache start and stop. However, you are probably faster typing the command.
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From: Trieu (Mar 08 2014, at 17:28)
Re: Font sizes being too big.
If you were using a 15' MBP w/ a matte display at Google, it was likely the 'high res' display (1680x1050). The retina MBP, while obviously much higher resolution, operates at a 'point' resolution of 1440x900. Going from the x1050 point resolution to x900 would explain why your application fonts seem bigger (because they are, just at a higher resolution).
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From: Mpherg (Mar 08 2014, at 17:34)
Dude, use Boxen http://boxen.github.com.
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From: Mike Packard (Mar 08 2014, at 18:02)
I remap caps lock to ctrl, even before speeding up the key repeat rate.
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From: Another Tim (Mar 08 2014, at 18:33)
> I picked the new box up less than 24 hours ago and here I am doing productive work.
Wow, not even 24 little hours?
Not to be a smug Linux weenie or anything, but I (and everyone I know) have a script that gets everything I might ever need downloaded, compiled, installed, and configured in less than an hour with a single command line invocation on any Debian flavor - call it an hour and a half maybe if we include the time to partition/format the hard drive and install the OS itself. What on earth could possibly make 'less than 24 hours' seem like a success? If this took you 'less than 24 hours' and that's a feat worthy of celebrating in a blog post, are most people spending literally days on end getting their Mac set up before they can use it? Serious questions from an Apple/Microsoft-phobe.
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From: Evan (Mar 08 2014, at 21:27)
Obviously a victim of a decade of brainwashing by the forces of google. Dude get a grip.
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From: Chully (Mar 09 2014, at 06:20)
Did you set the MBPr at the default Retina resolution (1440x900) or at one of the scaled resolutions? If it's at a scaled resolution, do you notice fuzzy text?
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From: Josh Lee (Mar 09 2014, at 06:34)
Re “Enable dragging” on the trackpad
A side effect of this option is it adds a delay to single taps: Without dragging, taps are registered instantaneously. It's a weird tradeoff once you notice; I have trackpad dragging disabled.
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From: Chris Adams (Mar 09 2014, at 07:15)
OS X has standard shortcuts for typographic quotes: Option+[ and Option+] for double and single quotes respectively, shift for the close.
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From: Jeff Schiller (Mar 09 2014, at 10:04)
Oh my, what an opportunity for people to tell you how you're doing it wrong! :)
In that vein, I'm with Shrutarshi Basu - keep the dock on the bottom and auto-hide. I use Spotlight (Cmd+Space) to launch everything anyway and just use the doc to hop to an active app if I've got a lot open (quickly mousing to the bottom feels quicker than mousing to the side).
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From: Steve (Mar 09 2014, at 10:45)
+1 for doing this with Boxen or similar. I'm in an organization that uses Chef quite a bit. We're starting to configure people's Mac dev workstations with kitchenplan (http://kitchenplan.github.io/kitchenplan), which is basically Boxen but using Chef cookbooks to do the configuration on the host.
Had a brand new MBPr fully configured in about an hour. (It was downloading a lot of software :) )
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From: Matěj Cepl (Mar 09 2014, at 11:31)
> Eleven years in, and I am down to exactly one Apple app in daily use: Preview.
OK, I see also the Lightroom, but otherwise. I know you know that somebody would write it: why in the world are you shelling money to the Mr. Jobs heirs and not buy a decent computer and install a decent distro of Linux on it? Emacs runs pretty well out here ;). And I am sure, we would find a Lightroom replacement as well (and Evince instead of Preview).
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From: Wub-Fur Internet Raadio (Mar 09 2014, at 12:33)
> just use the doc to hop to an active app
Unless your hand's already on the mouse Command-Tab's way faster/easier for switching between open applications
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From: Simon Griffee (Mar 09 2014, at 12:51)
Currently I use a Mac for the following reasons:
1. Best hardware
2. Unix elegance, usability and security with a nice graphical user interface
3. PDF is the operating system’s native display format
4. Lightroom
5. Textmate
I second the suggestion to use f.lux and also recommend [spectacle](https://github.com/eczarny/spectacle)
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From: Andrew Herron (Mar 09 2014, at 15:36)
As of 10.9 you no longer need the bloated 4.7gb Xcode just to get command line tools :)
In terminal:
xcode-select --install
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From: John (Mar 10 2014, at 11:47)
Do you use any of the new Thunderbolt-compatible laptop docks for using multiple monitors and other peripherals in your office?
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