Sphinx Documentation with Numpydoc
I’m finally back from my proposal and orals! Now that I’m done with that mess, here’s a fun little tutorial that I’ve already found helpful for myself. Hopef...
Posts by Tag
- Old Blogger 29
- Grad School 13
- Life 13
- Code 11
- Excision 5
- CodeStories 4
- Programming 3
- Genomics 2
- Recipe 2
- Data Science 2
- Data Analysis 2
- Marketing 2
- Excisions 1
- Math 1
- Hier 1
- Writing 1
- Python 1
- Django 1
- Invitae 1
- Engineering 1
- Education 1
- Tutorial 1
- Statistics 1
- Work 1
- Travel 1
- Food 1
- Poetry 1
Old Blogger
Using R in a Jupyter/Ipython Notebook with Ubuntu
I may have mentioned it before, but I love the Jupyter Notebook. It’s the only way I come close to keeping my code and analyses organized. I’m not a huge fan...
End of the Year Review (Part III)
This post contains the last three question. The final two concern the phrase “your scientific approach”, which I found a bit vague. I asked my PI for clarifi...
End of Year Review (Part II)
It's rarely fun to admit your failures, but here's a list of things I didn't mange to pull off in 2015. What are the goals and milestones you missed in 2...
End of Year Review (Part I)
My PI has requested that we answer a few questions as a reflection of the past year and as a mental preparation for the coming year. I figured it would be wo...
Teach Your Fourth Grader Python (Make a Game)
Welcome to the second post on introducing your child to Python! You should have Anaconda (or another version of Python) installed on your computer before con...
Teach Your Fourth Grader Python (Installing Anaconda)
It’s really never too early to start teaching your child to code. You may think, “What’s the point of teaching my kid to code so long before they have any id...
Calculating a Pearson Correlation Matrix
One of the great things about graduate school is you get to constantly realize how ignorant you are about how things work. If the domain name weren’t al...
Bot Battle
For those of you who don’t program, it may be hard to understand just how slow a process it usually is. Movies and other media don’t help this misunderstandi...
The Perceptron
Today in lab meeting, during our bi-weekly “Idea Potluck”, I dropped the ball while explaining how perceptrons work. We were running short on time, so I rush...
Bioinformatics Software
This isn't a long post, but I read something interesting the other day and wanted to repost it. First, here's the link to the blog: http://www.bioinf...
Excision Walkthrough
I take things too seriously sometimes. As far as I’m aware, I’ve always been like that. When I was a kid, I knew, deep down, that walkthroughs were bad. Mayb...
Excision Winner Announcement
Congratulations to Ankur Sundara for being the first person to complete Excision! For his dedication and problem-solving abilities, he’s won the first place ...
Base Camp
Welcome to Excision. Before we set off on our adventure, I think it’s only fair to give you some provisions for your journey. They come mostly in the form o...
The Protein Folding Answer
I need to issue a disclaimer before anything else. The script below is most definitely NOT the answer to protein folding. In fact, I make no claims at all ab...
Encryptions
Do you know the answer? Do you know the question?
The Protein Folding Problem
First, if you’ve never had the opportunity to visit xkcd, I highly suggest you do it. It’s a wonderful website. My personal favorite is the What If? feature....
Simple Sequence Similarity
I’ve mostly refrained from posting any of the code that I’ve been writing in the past months because the code seems scraped together in a “just get it done” ...
Syntax Highlighting
I had to follow a few different explanations on how to employ syntax highlighting on Blogger before I found a set of instructions that worked. In case anyone...
Be Right Back
I’m usually not a huge fan of television, but recently it has been convenient to watch an episode of something or other with my wife after dinner. I reason t...
Some Ethical Issues of Genomic Data
Yesterday I spent several hours attending an ethics class as well as a ethics/policy seminary. Both were great, and while I haven’t had a large amount of tim...
My First Rotation
I’m giving my first poster talk of my graduate school career tomorrow, along with approximately half of my cohort (the other half had their posters toda...
What is Genomics?
I just began my second of three rotations this week, so it’s been a busy transition time. But I thought I would share this short genomics video. It’s really ...
The Desktop
With my Birthday, Black Friday, and Christmas all right around the corner, I haven’t been able to keep myself from thinking about the possibility of purchasi...
What Did You Accomplish This Week?
A few weeks ago I was jokingly asked by a friend (who has never set foot in a lab) if I had made any great discoveries that week. I had just finished confirm...
Topic Results
For anyone who’s curious how the survey is going, below is the current average with error bars showing one standard deviation. I didn’t bother with any t...
A Prelude (Part II)
This second “housekeeping” post is the last I have planned for establishing the essence of this blog, I promise. In the coming weeks I’ll get into some deepe...
Logistic Map
</link> </link> Been playing around with some of the math functions in Python. I think it’s really cool how such a simple formula can...
A Prelude (Part I)
<!–Clue! Clue! Clue!
Grad School
PhD Reflections III (The End)
A hodgepodge of things I haven’t mentioned yet and thinking about what’s next
PhD Reflections II (The Middle)
The large center chunk where things start to feel routine
PhD Reflections I (The Start)
Starting a PhD in Bioinformatics at UNC-Chapel Hill
End of the Year Review (Part III)
This post contains the last three question. The final two concern the phrase “your scientific approach”, which I found a bit vague. I asked my PI for clarifi...
End of Year Review (Part II)
It's rarely fun to admit your failures, but here's a list of things I didn't mange to pull off in 2015. What are the goals and milestones you missed in 2...
End of Year Review (Part I)
My PI has requested that we answer a few questions as a reflection of the past year and as a mental preparation for the coming year. I figured it would be wo...
The Perceptron
Today in lab meeting, during our bi-weekly “Idea Potluck”, I dropped the ball while explaining how perceptrons work. We were running short on time, so I rush...
My First Rotation
I’m giving my first poster talk of my graduate school career tomorrow, along with approximately half of my cohort (the other half had their posters toda...
What is Genomics?
I just began my second of three rotations this week, so it’s been a busy transition time. But I thought I would share this short genomics video. It’s really ...
The Desktop
With my Birthday, Black Friday, and Christmas all right around the corner, I haven’t been able to keep myself from thinking about the possibility of purchasi...
What Did You Accomplish This Week?
A few weeks ago I was jokingly asked by a friend (who has never set foot in a lab) if I had made any great discoveries that week. I had just finished confirm...
Topic Results
For anyone who’s curious how the survey is going, below is the current average with error bars showing one standard deviation. I didn’t bother with any t...
Logistic Map
</link> </link> Been playing around with some of the math functions in Python. I think it’s really cool how such a simple formula can...
Life
2023 New Year’s Resolution Success!
It’s been a long time since I’ve made a New Year’s Resolution. I’m decent at sticking to a goal or plan once it’s made, so I usually don’t tie myself to New ...
Forgetting How to Care
It’s the wrong season for this sort of melancholy post, and yet, it’s also the most fitting. Going home for the holidays is supposed to be joyful: full of wa...
Children of the Corn
When I first learned to drive, my friend Seth and I took a short roadtrip to visit my cousin Becca at Ball State University in Southern Indiana. She introduc...
Arriving in Canada
I just happened across this piece of writing from June of 2018, when I interned at Google in Waterloo Canada. It’s a fun piece, so I figured it was worth col...
Hobbies I’m Trying Right Now
Sometimes, though certainly not always, I worry that I’ve over indexed my identity on my career. Lately, this feeling, combined with my tendency to allow my ...
My Erdős Number
My Erdős number is 4.
20 things I learned in my 20s
I turned 30 recently and have always enjoyed Sam Altman’s The days are long but the decades are short post. I decided to write something similar. A few notes...
Softdroid Interview
I got interviewed by a Russian tech news site recently, which isn’t something I ever expected to say. Kinda cool:
PhD Reflections III (The End)
A hodgepodge of things I haven’t mentioned yet and thinking about what’s next
PhD Reflections II (The Middle)
The large center chunk where things start to feel routine
PhD Reflections I (The Start)
Starting a PhD in Bioinformatics at UNC-Chapel Hill
PhD Reflections IV (The Takeaway)
The Most Important Thing I Learned in Graduate School
Be Right Back
I’m usually not a huge fan of television, but recently it has been convenient to watch an episode of something or other with my wife after dinner. I reason t...
Code
Get your First Git Contribution
I had a friend transition from her PhD to industry recently, and she messaged me expressing some annoyance at learning git.
Easily Accept Payments with Django and Stripe
Taking payments is simple, once you know where to look.
Tackling Webdev as a Bioinformatician: why is it so hard?
The web is amazing and amazingly complex
Sphinx Documentation with Numpydoc
I’m finally back from my proposal and orals! Now that I’m done with that mess, here’s a fun little tutorial that I’ve already found helpful for myself. Hopef...
Using R in a Jupyter/Ipython Notebook with Ubuntu
I may have mentioned it before, but I love the Jupyter Notebook. It’s the only way I come close to keeping my code and analyses organized. I’m not a huge fan...
Teach Your Fourth Grader Python (Make a Game)
Welcome to the second post on introducing your child to Python! You should have Anaconda (or another version of Python) installed on your computer before con...
Teach Your Fourth Grader Python (Installing Anaconda)
It’s really never too early to start teaching your child to code. You may think, “What’s the point of teaching my kid to code so long before they have any id...
Bot Battle
For those of you who don’t program, it may be hard to understand just how slow a process it usually is. Movies and other media don’t help this misunderstandi...
Simple Sequence Similarity
I’ve mostly refrained from posting any of the code that I’ve been writing in the past months because the code seems scraped together in a “just get it done” ...
Syntax Highlighting
I had to follow a few different explanations on how to employ syntax highlighting on Blogger before I found a set of instructions that worked. In case anyone...
Excision
Excision Walkthrough
I take things too seriously sometimes. As far as I’m aware, I’ve always been like that. When I was a kid, I knew, deep down, that walkthroughs were bad. Mayb...
Excision Winner Announcement
Congratulations to Ankur Sundara for being the first person to complete Excision! For his dedication and problem-solving abilities, he’s won the first place ...
The Protein Folding Answer
I need to issue a disclaimer before anything else. The script below is most definitely NOT the answer to protein folding. In fact, I make no claims at all ab...
Encryptions
Do you know the answer? Do you know the question?
A Prelude (Part I)
<!–Clue! Clue! Clue!
CodeStories
A Retrospective of InPyBio-20
I recently finished teaching my first virtual CodeStories class, Intermediate Python for Bioinformatics 2020 (InPyBio-20). The course was eight weeks long an...
Easily Accept Payments with Django and Stripe
Taking payments is simple, once you know where to look.
Tackling Webdev as a Bioinformatician: why is it so hard?
The web is amazing and amazingly complex
Programming
ChuckSort
The internet is pretty cool; right now I’m watching some Harvard lectures on advanced algorithms. This one’s about sorting.
Using Covid-19 to Explain Community Detection (Part II)
A simple explanation of the Louvain algorithm
Using COVID-19 to Explain Community Detection (Part I)
Illustrating a use case for the Louvain algorithm
Genomics
The Protein Folding Problem
First, if you’ve never had the opportunity to visit xkcd, I highly suggest you do it. It’s a wonderful website. My personal favorite is the What If? feature....
Some Ethical Issues of Genomic Data
Yesterday I spent several hours attending an ethics class as well as a ethics/policy seminary. Both were great, and while I haven’t had a large amount of tim...
Recipe
Zesty Beef Gnocchi
I’ve been enjoying spending a lot of time in the kitchen recently, and have been playing around with some recipes I’ve made. Incidentally, I’ve also been lis...
Chocolate Protein Muffins
A tasty way to supplement a classic baked good with some extra protein.
Data Science
Using Covid-19 to Explain Community Detection (Part II)
A simple explanation of the Louvain algorithm
Using COVID-19 to Explain Community Detection (Part I)
Illustrating a use case for the Louvain algorithm
Data Analysis
Post to HN on Sundays for the most points.
A quick analysis of when HN stories are posted.
Marketing
Post to HN on Sundays for the most points.
A quick analysis of when HN stories are posted.
Excisions
Base Camp
Welcome to Excision. Before we set off on our adventure, I think it’s only fair to give you some provisions for your journey. They come mostly in the form o...
Math
Calculating a Pearson Correlation Matrix
One of the great things about graduate school is you get to constantly realize how ignorant you are about how things work. If the domain name weren’t al...
Hier
Building a Web App Using Only Python
What is Anvil?
Writing
A Method for Writing Cohesively
Before Junior year of high school, I was a terrible writer. Terrible. For a given assignment, I’d have some insightful thought in my head, clear as day, and ...
Python
10 Rules for Falling in Love with Jupyter Notebooks
Conventions I established while using a Notebook everyday during my PhD
Django
Easily Accept Payments with Django and Stripe
Taking payments is simple, once you know where to look.
Invitae
What’s a Bioinformatics Systems Engineer?
Spoiler: everyone means something different. What do we mean?
Engineering
What’s a Bioinformatics Systems Engineer?
Spoiler: everyone means something different. What do we mean?
Education
ChuckSort
The internet is pretty cool; right now I’m watching some Harvard lectures on advanced algorithms. This one’s about sorting.
Tutorial
Get your First Git Contribution
I had a friend transition from her PhD to industry recently, and she messaged me expressing some annoyance at learning git.
Statistics
Class night: T-tests and Linear Regression
We had our first class night, which was a lot of fun. I’ve been meaning to reread this blog post Common statistical tests are linear models (or: how to teach...
Work
Four Years of Invitae
This was my last week at Invitae after four years there. It was my first industry role, and fully qualified as a “journey”. Because I’m continuing to experim...
Travel
Tunisia
I just got back from Tunisia for the first time since I was 5-6, and wanted to capture some of my thoughts in a standard travel blog post. Here’s a highlight...
Food
One New Food Per Grocery Run
Without particularly trying, I’ve fallen into the habit this year of making sure one food that I don’t normally buy ends up in my shopping cart when I go to ...
Poetry
Sanctum
Humble is as Humble does. Subtle can be Muscle flush. Stumble now, and trouble thus: Jumble, Mumble, come Fuss. Puzzle is the Shuffle of; K...