taking a look at spell checking...

.github/workflows/main.yml

@@ -0,0 +1,17 @@
+name: vsoch-check-spelling
+
+on:
+  push:
+    branches: [master]
+  pull_request: []
+
+jobs:
+  formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Check for typos
+        uses: crate-ci/typos@592b36d23c62cb378f6097a292bc902ee73f93ef # version 1.0.4
+        with: 
+          files: ./_posts

_posts/2008/2008-1-25-a-poem-from-last-year.md

@@ -12,7 +12,7 @@ English? Spanish? There are even some made up words in there… let’t be safe
 **Aeropuerto**
 
 En el muchedumbre del aeropuerto  
- leaking con conversacion y cafe  
+ leaking con conversation y cafe  
  me siento abajo del muro  
  siempre pidiendo, porque?
 

_posts/2008/2008-6-05-simplify-life-by-not-thinking-about-things-the-value-of-social-ignorance.md

@@ -24,7 +24,7 @@ There are many ways you might be attracted to a person, and when I say attractio
 
 Because you largely can’t answer that question, and more importantly, you don’t need to. The beautiful thing about this idea is the realization that it’s OK to not have yet found the other person, or other people, either friend or lover or confidant or running buddy, that might complement, complete, or fulfill you. Don’t jump to concussions, it doesn’t mean anything about you. But complete is a dangerous word, because with people, two incomplete people do not constitute a whole person. And this is exactly why it is best to focus on seeking personal fulfillment, whatever that means for you. And in pursuing what makes you happy, you will most certainly experience many types of relationships, learn from them, and hopefully find some rare sapphires.
 
-So I started this thought by saying "just stop thinking," but I think it’s important to still be aware- be aware of yourself, be aware of people that are directing energy toward you that you don’t know much about at all, aware of keeping in checks with dynamics that you do value, and be aware of the bases that found your relationships. This is another beautiful metaphor – the idea that friendships can be looked at like structures. Built on the wrong base, perhaps just for social purposes and lacking compassion and a connection with one another, is like trying to build a tower in a sand pit. Adding floors to that tower will be very challenging, as well as finding structural stability. This is an interesting conversation I had with another friend, actually about the dynamics of conversation. Look at trends in conversation over time, and ask if one person is simply filling in gaps with an occasional "cool, yeah, lol" when it is appropriate, and essentially adding nothing to the other person’s monologue, or does that person feel fed by what the other person has to say, and want to add something, respond, or challenge? It’s easier to evaluate yourself as a responder, listener, and contributer, than the other person, I think. So it’s interesting to think about what differentiates a rich conversation from one person telling things to another, and thinking that person is paying attention because he/she is responding at the appropriate time.
+So I started this thought by saying "just stop thinking," but I think it’s important to still be aware- be aware of yourself, be aware of people that are directing energy toward you that you don’t know much about at all, aware of keeping in checks with dynamics that you do value, and be aware of the bases that found your relationships. This is another beautiful metaphor – the idea that friendships can be looked at like structures. Built on the wrong base, perhaps just for social purposes and lacking compassion and a connection with one another, is like trying to build a tower in a sand pit. Adding floors to that tower will be very challenging, as well as finding structural stability. This is an interesting conversation I had with another friend, actually about the dynamics of conversation. Look at trends in conversation over time, and ask if one person is simply filling in gaps with an occasional "cool, yeah, lol" when it is appropriate, and essentially adding nothing to the other person’s monologue, or does that person feel fed by what the other person has to say, and want to add something, respond, or challenge? It’s easier to evaluate yourself as a responder, listener, and contributor, than the other person, I think. So it’s interesting to think about what differentiates a rich conversation from one person telling things to another, and thinking that person is paying attention because he/she is responding at the appropriate time.
 
 So it seems like there is a huge component of personal awareness, learning to abolish expectations, and as a result, find patience through your passions.
 

_posts/2009/2009-8-03-when-complacency-is-worth-it.md

@@ -15,7 +15,7 @@ The woman that helped me was pretty nice, and her slowness didn’t bother me so
 
 I think the difference is that I looked at her as another human being and not someone that was there to give me what I wanted. I felt grateful for her giving me the opportunity to slow down for a few moments, and observe something that I hadn’t given attention before. I was grateful for her kindness. I could have easily looked at the entire situation from another viewpoint – a negative one – how slow she was! And she forgot my discount! The couple wound up storming out to go to another storage place, arguing with each other, and I said “I hope your day looks up, it’s pretty nice outside, bye!” and returned to my car. I wonder how the rest of the couple’s day went? Did they find a storage spot, and if so, was it worth it? Money wise? Mood wise? Time wise? Did they potentially just close the door for returning to that place? Is playing the role of the angry customer even worth it?
 
-The question I really want to ask has to do with manipulation and using leverage and other manipulative strategies, maybe some passive agressive-ness, to get what you want. In a nutshell, it’s using people. I know a handful of people that get by with this strategy, and I find that when they ask me for something, the normal rewarding feeling that I get when helping someone that I care about just isn’t there. In a few of the cases, I can tell a relationship isn’t balanced, and my kindness is being taken advantage of, just by that feeling.
+The question I really want to ask has to do with manipulation and using leverage and other manipulative strategies, maybe some passive aggressive-ness, to get what you want. In a nutshell, it’s using people. I know a handful of people that get by with this strategy, and I find that when they ask me for something, the normal rewarding feeling that I get when helping someone that I care about just isn’t there. In a few of the cases, I can tell a relationship isn’t balanced, and my kindness is being taken advantage of, just by that feeling.
 
 Is this idea of networking any different? No matter what you call it, I can’t stand it. At the end of the day, the item may be obtained, the money may be saved, you may get what you desire at the use or abuse or guilt of someone else, but it’s such a dirty game, and I can’t imagine the manipulator will have many friends in the long run.
 

_posts/2010/2010-6-14-introducing-pumkinnappers.md

@@ -1,5 +1,5 @@
 ---
-title: "Introducing, PumkinNappers!"
+title: "Introducing, PumpkinNappers!"
 date: 2010-6-14 15:34:57
 tags:
   adventure
@@ -19,7 +19,7 @@ Attempt number two was somewhere around the Camel statue near the old Biology Bu
 
 We were originally worried that the title “Nash ‘Er Teeth” would imply that this geocache would be a hard find, but it wasn’t at all! It must have been in the 90s, so we started our excursion by heading into the wonderfully chilly Nasher museum. Anyone that stops by here to look for this cache should definitely bring an ID to gain access to the galleries at the Nasher, or minimally stop at the cafe inside for a cool drink.
 
-Once we were ready, we headed out the back door, past a triangular slab of stone, and down the path. We found a small cluster of woods within 100 feet of the museum, and then saw the aforementioned poison ivy, and then BOOM there it was! We had a few unsuccessful searches earlier in the day, and this was our first successful find as Team PumkinNappers, and what a great one it was!
+Once we were ready, we headed out the back door, past a triangular slab of stone, and down the path. We found a small cluster of woods within 100 feet of the museum, and then saw the aforementioned poison ivy, and then BOOM there it was! We had a few unsuccessful searches earlier in the day, and this was our first successful find as Team PumpkinNappers, and what a great one it was!
 
 [![](http://www.vsoch.com/blog/wp-content/uploads/2010/06/matt-00003-300x225.jpg "Matt finds the cache!")](http://www.vsoch.com/blog/wp-content/uploads/2010/06/matt-00003.jpg)
 
@@ -33,7 +33,7 @@ What a great first find! We then proceeded to head down Campus Drive and investi
 
 It sort of reminds me of the factory from Charlie and The Chocolate Factory!
 
-So this Geocaching thing is excellent! You feel like an adventurer, with the goal of finding the treasure, and exchanging something to leave your mark. Since we wound up taking a sheet of pumpkin and candy corn stickers, we have decided to call ourselves the PumkinNappers. It just makes sense :O)
+So this Geocaching thing is excellent! You feel like an adventurer, with the goal of finding the treasure, and exchanging something to leave your mark. Since we wound up taking a sheet of pumpkin and candy corn stickers, we have decided to call ourselves the PumpkinNappers. It just makes sense :O)
 
 [The official log can be found here.](http://www.geocaching.com/seek/log.aspx?LUID=e2016f4d-b492-45dc-817b-22d2643310ad)
 

_posts/2011/2011-1-02-peanut-butter-chip-cookies.md

@@ -64,7 +64,7 @@ This was a recipe that I found based on the ingredients that I happened to buy a
 
 [![](http://www.vsoch.com/blog/wp-content/uploads/2011/01/9.-Form-Balls-300x225.jpg "9. Form Balls")](http://www.vsoch.com/blog/wp-content/uploads/2011/01/9.-Form-Balls.jpg)
 
-**10.** Press fork slighty into the cookies to make the signature crosshatched top. Squiisshhhh…
+**10.** Press fork slightly into the cookies to make the signature crosshatched top. Squiisshhhh…
 
 [![](http://www.vsoch.com/blog/wp-content/uploads/2011/01/10.-Squish-300x225.jpg "10. Squish")](http://www.vsoch.com/blog/wp-content/uploads/2011/01/10.-Squish.jpg)
 

_posts/2011/2011-5-05-spring-reflections.md

@@ -16,7 +16,7 @@ It is usually the case that before a big life change, I find myself in some sort
 
 **Discovery and Balance**
 
-Two years ago I graduated from Duke and chose to enter a domain of work that spanned my two interests: neuroscience and computer science. I was not certain if academia was the right fit for me, and I most surely did not want to enter graduate school without being certain of my passion for a field of study. Fast forward two years, and I know that I’ve found my niche in terms of lifestyle and topic. I feel excited, (a little nervous!), and empowered to transition into being a full time research scientist. I feel very strongly that hard work and a committment to proactively pursue my goals, even if there are bumps and challenges along the way, will lead to good things. I know that I have much to learn, and I don’t have all the answers, but I feel confident in my ability to do what is right to be the best researcher that I can be.
+Two years ago I graduated from Duke and chose to enter a domain of work that spanned my two interests: neuroscience and computer science. I was not certain if academia was the right fit for me, and I most surely did not want to enter graduate school without being certain of my passion for a field of study. Fast forward two years, and I know that I’ve found my niche in terms of lifestyle and topic. I feel excited, (a little nervous!), and empowered to transition into being a full time research scientist. I feel very strongly that hard work and a commitment to proactively pursue my goals, even if there are bumps and challenges along the way, will lead to good things. I know that I have much to learn, and I don’t have all the answers, but I feel confident in my ability to do what is right to be the best researcher that I can be.
 
 More equal distribution between work and social stuffs is still something that many have articulated is an important component of a “balanced life,” and if this is true, I still am lacking the life experience or incentives to drastically shift my priorities. I still am more excited to relaxedly work over a weekend than take an impromptu beach trip that would eat up the entirety of the time. And I’m not sure that the idea of going out and drinking at some sort of happy hour is ever going to be my idea of fun. At this time in my life I still feel social fulfillment from interactions in with classmates or colleagues, and I balance out time sitting in front of a computer by going for an adventure run or bike ride. I think that there isn’t a “right” way to be as long as you are productive and happy with how you are. I cannot say if I will be as work focused in fifteen or twenty years as I am now, but given that I am about to start on what I hope to be a long and fulfilling career in academia, I think my mental state and priorities are just right.
 

_posts/2011/2011-7-04-the-holiday-weekend-an-epic-journey-of-independence.md

@@ -14,7 +14,7 @@ This is the story of an unfortunate adventure, for which one day of bad luck slo
 
 On Friday, July 2nd, I biked into the heart of Palo Alto to pay a visit to a sweet older woman that I had almost rented a room from. She told me her stories of traveling to Iraq, Europe, and South Africa, encouraged me to use the basement of the town hall as a resource for bike maps, and gave me hazelnut coffee brewed by her daughter somewhere in the hills of California. It was a different, and enjoyable experience, even though by the end my mind was drifting back to work. Mid afternoon I head out, and since I was already far from home, this somehow made it logical to go even farther to hit up the Safeway and obtain the rare, precious, jalapeno corn bread derivative that is the closest thing I can find to what used to be my life-staple back in North Carolina.
 
-So I bike, I shop, and I leave the store. I am just starting on my way home, crossing a massive intersection, and all of a sudden I feel like I am biking on a deflated beach ball. I am forced to stop right in the line of fire of the row of hungry-to-zoom-zoom cars, get off my bike, feel the tire, and to my horror, it’s completely flat. Crap. First I had to get out of the intersection, especially since I still had the oncoming traffic side to cross, and the little orange hand was already waving at me. I then realized that I was between 4 and 5 miles from home in high 80 degree weather with a poozied-out bike, a heavy bag of groceries, and a fully loaded backpack. So I walked it most of the way, and once I hit the far side of the Medical Campus was able to ride the Margaritte shuttle for the small distance home. It somehow made me very happy to see my little bike perched on the front of that massive bus – like an injured soldier loaded into the helicopter on his way to safety. I was also very grateful to the bus driver that helped me load and unload the bike from the bus. The entire trip on bike and foot calculated out to 18 miles, with 4 miles of walking with the bike. It was, simply put, a tiring day.
+So I bike, I shop, and I leave the store. I am just starting on my way home, crossing a massive intersection, and all of a sudden I feel like I am biking on a deflated beach ball. I am forced to stop right in the line of fire of the row of hungry-to-zoom-zoom cars, get off my bike, feel the tire, and to my horror, it’s completely flat. Crap. First I had to get out of the intersection, especially since I still had the oncoming traffic side to cross, and the little orange hand was already waving at me. I then realized that I was between 4 and 5 miles from home in high 80 degree weather with a poozied-out bike, a heavy bag of groceries, and a fully loaded backpack. So I walked it most of the way, and once I hit the far side of the Medical Campus was able to ride the Margaret shuttle for the small distance home. It somehow made me very happy to see my little bike perched on the front of that massive bus – like an injured soldier loaded into the helicopter on his way to safety. I was also very grateful to the bus driver that helped me load and unload the bike from the bus. The entire trip on bike and foot calculated out to 18 miles, with 4 miles of walking with the bike. It was, simply put, a tiring day.
 
 [![](http://www.vsoch.com/blog/wp-content/uploads/2011/07/mapofstupidity-300x193.png "Map of Stupidity")](http://www.vsoch.com/blog/wp-content/uploads/2011/07/mapofstupidity.png)
 

_posts/2013/2013-10-26-cluster-validation.md

@@ -23,7 +23,7 @@ Internal validation is the introverted validation method.  We figure out how go
 
 - **Stability validation**:  is like a game of Jenga.  We remove features one at a time from our clustering, and see how it holds up.  For each time that we remove a feature, we look at the average distance between means, the average proportion of non overlap, the Figure of Merit, and the average distance.  For all four of these metrics, we iteratively remove features, and dock points when there is huge change.  A value of 0 would be ideal, meaning that our clustering was stable.  For details, see the link to the clValid documentation above.
 
-- **Connectivity:** A good cluster should be close to its other cluster members.  That makes sense, right? If there is someone closed to me placed in another cluster, that's probably not a good clustering.  If there is someone very far from me placed in the same cluster, that doesn't sound great either.  So, intutively think of connectivity as a number between 0 and infinity that "gets at" how well connected a cluster is.  Specifically, if we have N mysterious lemurs, and are assessing L neighbors, the connectivity is:
+- **Connectivity:** A good cluster should be close to its other cluster members.  That makes sense, right? If there is someone closed to me placed in another cluster, that's probably not a good clustering.  If there is someone very far from me placed in the same cluster, that doesn't sound great either.  So, intuitively think of connectivity as a number between 0 and infinity that "gets at" how well connected a cluster is.  Specifically, if we have N mysterious lemurs, and are assessing L neighbors, the connectivity is:
 
 [![conn](http://www.vbmis.com/learn/wp-content/uploads/2013/10/conn.png)](http://www.vbmis.com/learn/wp-content/uploads/2013/10/conn.png)
 

_posts/2013/2013-12-29-introduction-to-the-genome-analysis-toolkit-gatk-i.md

@@ -328,7 +328,7 @@ INPUT=addrg_reads.bam
 
 So now we have another bam index file, with the same name but appended with "bai." Now, you would try the RealignerTargerCreator command from above once more, but with the addrg_reads.bam file.
 
-I'll admit to you that I've gone through this sequence of steps muliple times, and finally when I didn't get an error message on this step I wanted to dance! And guess what? It's tracking your every move too... sent to Amazon S3!
+I'll admit to you that I've gone through this sequence of steps multiple times, and finally when I didn't get an error message on this step I wanted to dance! And guess what? It's tracking your every move too... sent to Amazon S3!
 
 
 ```