April 17, 2013

Plain Text Notes and Evernote

As a follow-up to my Tools & Toys Guide to Research Implements, I will go into more detail about how I use plain text notes and Evernote.

Plain Text

I use nvALT and Simplenote for my plain text notes. nvALT runs on my desktop, stores my notes as plain text files in Dropbox, and syncs with Simplenote, my preferred iOS plain text solution. I have my nvALT hotkey set to ⌥ + Space, allowing quick access to my notes anywhere in OS X. On iOS, I keep Simplenote in the dock. While tagging is an option, search in both apps works well, so I don’t use any tags.

Anything that is suitable for plain text gets stored in nvALT/Simplenote rather than Evernote. For me, the speed and simplicity of plain text is important. I have notes with everything from lists, frequent flyer numbers, and keyboard shortcuts I commonly forget.


My main use for Evernote is my paperless file cabinet”. Storing PDF scans of any paper documents I need to keep in Evernote allows me to quickly search not only the name of the document, but the OCRed content as well, making it easy to find what I’m looking for.1 I also store magazine pages from my iPad, photos of handwritten notes2, MS Office/iWork documents I need for reference3, and archives of plain text notes I no longer need.

As for tags, I use them in Evernote for ease of finding documents. Since the default date for a note is the date of last modification, I want to be able to search through my paperless file cabinet by the date on the document. Rather than depending on OCR for that, I have a tag for each year and month. I use a few other tags to classify documents, but most of my organization comes from Notebooks and Stacks (groups of notebooks).

Note: If you have sensitive documents in Evernote that you don’t want stored and indexed in the cloud, you can create a local notebook. The downside to this is that you won’t have the ability to search within the document.4


Storing all my notes in the cloud gives me easy access to them from anywhere. If you are interested in learning more about Evernote and how to make it work the best way possible for you, I highly recommend reading Evernote Essentials. For nvALT, Macdrifter has some great tips.

  1. PDF OCR is only available if you have Evernote Premium.

  2. Evernote OCR only recognizes handwriting in images. Image OCR is available to everyone.

  3. Evernote recently added the ability to search within attached MS Office and iWork documents if you are a Premium subscriber.

  4. If you decide this is a route you want to go but still want to have the search capability, PDFPen does a great job with OCR. If you save OCR to your PDF before you import it into Evernote, you can search the text of a document while still keeping it off the cloud.

April 10, 2013

Running Unplugged

Last night I went for my second outdoor run of the year and I decided to leave my headphones at home. Being connected all day, it felt good to listen to my mind, body, and surroundings.

I could hear my feet hitting the pavement and my breating.

I could feel my heat beating.

My mind felt relaxed and I just let it wander.

I was able to take in the sounds of the city and of nature.

I am going to make running unplugged” a habit.

February 27, 2013

Arq Backup and Amazon Glacier

After some issues with TimeMachine, I recently switched up my backups from TimeMachine/Crashplan+ to to CarbonCopyCloner/Arq Backup.

My choice to move to Arq Backup was fueled by the fact that while Crashplan+ Family Unlimited costs $149.99/year, Amazon offers storage on S3 for $0.130 per GB/month and on Glacier for $0.01 per GB/month. With the ~100 GB (inclusive of incremental backups) that I want backed up in the cloud, it will only cost me about $19.20/year (~95% of my data on Glacier) to store my backups with Amazon. Adding in the few dollars it will cost me in data transfer, PUT, and GET request charges from S3/Glacier, my yearly cost certainly won’t exceed $25-30. I justify storing most of my data in Glacier because I make regular backups of my home directory to my NAS using Carbon Copy Cloner. Every few months, I also make a full clone to an external drive. The data I backup to S3 is whatever I keep in Dropbox — any critical files and files I am currently working on.

What’s the catch? Amazon Glacier charges you a retrieval fee of $0.01/GB if you need to retrieve more than 5% of your average monthly storage, Also, if you delete data within 90 days of upload, you are charged a prorated $0.03/GB early deletion fee.

Within Arq, a great feature is the ability to limit your storage on S3 by either a monthly dollar or GB amount. When you hit your max, Arq automatically prunes the oldest incremental backups (leaving at least one for each backup folder). While many people complain about the lack of this feature for Glacier, it makes sense that it is not included due to the early deletion fee. After a great conversation on ADN, I learned that many were having trouble manually deleting their Arq Glacier backups. Since it looked like the feature was there, I decided to contact the developer to get the question answered.

Stefan responded:

If you remove a folder from Arq that’s being backed up to Glacier, Arq puts the folder in its trash”. If you then open Arq’s trash, select that folder, and click Delete Permanently”, Arq will delete all the Glacier archives and attempt to delete the Glacier vault. The vault delete will fail because Amazon has to update its inventory”, which it does once/day. The next day, browse under Other Backup Sets” in Arq, find that vault, select it and click Delete” to delete it.

It seems that the confusion stems from the fact that Amazon only inventories Glacier vaults once a day. Once you delete the backup folder from Arq, it gets disconnected from your Arq set and once the inventory is updated (sometime within the next day), you can then delete the backup on Glacier.

January 18, 2013

Simplify for the Best

I recently read about the love metric” from Patrick Rhone:

This year: Only hold onto things you love. Next year: Only hold onto things you not only still love, but love even more.

It sounds like the perfect way to simplify the clutter in your life and make sure you’re getting the most enjoyment out of the things you own. Thinking about it brought me back to Dustin Curtis’ idea of only owning the best:

…the time it takes to find the best of something is completely worth it. It’s better to have a few fantastic things designed for you than to have many untrustworthy things poorly designed to please everyone.

I can see a huge parallel between these two statements. The things you continue to love more every year are the things that are the best. In the long run, it is a waste of time and money to settle for something less than the best. The result is a better life with less things and less clutter. Dustin sums it up with one great sentence:

The result–being able to blindly trust the things you own–is intensely liberating.

My wife and I are making it a goal in 2013 to simplify our lives, getting rid of the clutter and making do with less to have the best.

August 3, 2012

Second Crack and Webfaction

In the process of migrating scientifics to Second Crack over the past few days, I decided that it would be useful to publish a tutorial on how to get it running on Webfaction.

While the readme comes with fairly thorough instructions, there are some differences due to how Webfaction works. If you are on another web host and are having similar issues, some of these tips may help you get things running as well.

Installing Dropbox

Dropbox is not a necessary part of Second Crack, but it makes publishing to your blog much easier. In order to get Dropbox running, log into your server via SSH and follow the instructions from Dropbox.

As noted in the instructions, when you run the app for the first time you will be prompted to authorize your account. For security, I recommend setting up a secondary account on your server and then sharing your blog source folder (I will refer to this folder as Blog”) with that secondary account.

You will also want to upload the CLI python script to your home directory on your server (/home/username). Running the script with the command autostart” will set up your server to automatically start Dropbox so it is always running.

python dropbox.py autostart

Installing inotify-tools

Second Crack takes advantage of inotifywait (part of inotify-tools) to update your static files whenever Dropbox is updated. This is also optional, but without inotify-tools, your static files will only be updated whenever your cron runs the update script (more on cron later).

To install inotify-tools:

  1. Download the source from GitHub

  2. Extract and upload to your home directory (/home/username)

  3. Log in via SSH and change into the inotify-tools directory (using the cd command)

  4. Run the following commands to install (each step may take a few minutes):

     ./configure --prefix=$HOME
     make install

Install Second Crack Changes

After downloading Second Crack from GitHub there are a few changes that need to be made to the files.

  1. Rename config.php.example to config.php and open it in your favorite text editor.

  2. Input all your settings, making sure your paths are correct (replace username with your Webfaction username).

     Updater::$source_path   = '/home/*username*/Dropbox/Blog';
     Template::$template_dir = '/home/*username*/Dropbox/Blog/templates';
     Updater::$dest_path     = '/home/*username*/secondcrack/www';
     Updater::$cache_path    = '/home/*username*/secondcrack/cache';
  3. In order for Second Crack to run on Webfaction, you also need to make a change to engine/update.sh. Find all of the php commands, and change them to /usr/local/bin/php53. This allows Second Crack to run under PHP 5.3 rather than the Webfaction default of PHP 5.2.

  4. Move the files in the example-templates” folder to a folder called templates” inside your Blog” folder in Dropbox.

  5. Upload the whole secondcrack” folder to your home directory.

  6. Add the following to your cron on your server (crontab -e):

     * * * * * /home/*username*/secondcrack/engine/update.sh /home/*username*/Dropbox/Blog /home/*username*/secondcrack

Now that everything is set up, you can publish your first post.

Publishing in Second Crack

The template for a blog post looks like this:

My draft title
Tags: tag1, tag2
Type: post

Draft content.

A few notes on the formatting: the dividing line must be the same length as your title and tags are optional.

Create a drafts” folder in your Blog” folder and save the post as a .md file. If everything is set up, a _previews” folder will be created inside drafts” containing an HTML file with a preview of your post. If you are happy with how it looks, publishing is as easy as moving the .md file to the _publish-now” folder.

I by no means am an expert, so if you find problems with my walkthrough or don’t feel I’ve explained something enough, feel free to ping me on Twitter!

March 1, 2012

OmniFocus: My Refined To-do Strategy

Back in January I discussed my thoughts in re-evaluating my to-do and calendering strategies. While my basic principles have remained the same, I have switched my to-dos over to OmniFocus and adjusted my calendering strategy.


If you read my previous post, you know I switched from Remember the Milk (RTM) to Wunderlist. While Wunderlist is great if you just want simple lists, I missed some of the more advanced features from RTM. While RTM is free on the web, if you want to be able to sync to their mobile apps more than once every 24 hours, you must be a pro member ($24.99/year). While more expensive to start, OmniFocus is OS X ($79.99/$49.99 eduation) iOS ($19.99 iPhone/$39.99 iPad) software, so you aren’t stuck paying a yearly fee.


After reading Shawn Blanc’s article on why he loves OmniFocus so much, I decided that I had to give it a go. I’ve had an OmniFocus license for a long time (I got a really good deal because I was involved with the beta) so I was able to test it out without having to find room in my grad student budget.

On the surface, OmniFocus looks a little underwhelming. If you are familiar with software from the OmniGroup, you should know from experience that this is never the case. For those of you who aren’t, everything the OmniGroup makes is top notch and extremely powerful. While there is quite a big learning curve, the app has a great manual (gasp…read the manual?) and there are many great web resources.

After using the app for about two weeks, I feel like I have a good grasp on many of the advanced fetures. One of my favorites is the amazing control you have over the views in the apps. I am not only able to look at my projects and contexts, but I also have created custom views for work, home, and for when I’m on the go.

The iPhone app also has a really powerful and unique view — forecast. The forecast view pulls in the next five days of due to-dos and items from your calendars and lays them out along with options to view the past and future. With my calendar events and to-dos all in one place, it makes it easy to get an overview of my day.


Since I recently upgraded from the original Droid to an iPhone 4S, I decided to make the plunge from Google Calendar over to iCloud calendars. While my setup remains the same (Fantastical on my Mac and Agenda on my iPhone), I have adjusted my strategy a bit.

Since switching to OmniFocus, I have started putting only things that have to be done on a certain day on my calendar — the change here is that if a task can be completed before it’s due, it goes in OmniFocus rather than my calendar. The start date feature in OmniFocus is extremely useful for this because I can hide events from my views until they are able to be actively worked on. This keeps things from getting too cluttered, part of the reason I previously put more on my calendar.

This quote from Shawn Blanc is a great way to sum up my search:

Finding the right tool to keep track of your projects sometimes feels more like a journey than a destination. Many task-management apps have come and gone (some of us have tried them all). But in the past few years, as task-management software has increased its footprint on the Mac, the one app which has stayed in active development and which continues to grow and improve is OmniFocus.

I feel like I have settled in for good at this point, but you never know! I’d love to hear what tools you use!