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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
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Posts
Scraping Reddit, part 2
Published:
The last post dealt with using pushshift and handling requests to access posts and comments from Reddit. This post deals with using the Python Reddit API wrapper to accces posts and comments from Reddit and then using some NLP tools for some basic sentiment analysis.
Scraping Reddit, part 1
Published:
In light of recent internet trends about retail investors, I’m sure many of us have questions about the kinds of content that gets posted on reddit, and if there are home-grown, analytical ways of addressing these questions. I’ll be showing two ways of parsing submissions and comments to Reddit, this one focusing on using pushshift API endpoints using the requests library, some custom classes for processing these responses, and asyncio to handle asynchronous threading for multiple requests to pushshift.
Accessing FoldingAtHome data on AWS
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Some F@H data is freely accessible on AWS. This will be a relatively short post on accessing and navigating the data on AWS.
Poetry and Docker
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What is poetry and where does this fit in the python software/DS ecosystem? And some beginner forays into docker.
Exploring PyTorch + ANI + MD
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PyTorch + ANI + MD
Downloading and studying my message behavior
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Digital privacy is everywhere, and recent laws are pushing companies to disclose whatever personal information they may have on you. In the spirit of science, I’m going to make myself my own study subject and observe what Facebook has stored from my messenger history. Along the way, I’ll do some recursion, a little parallelization, some generators for data procesing, and basic visualization to observe my messenger behavior. Notebooks can be found here, but this one you can’t reproduce because I won’t be providing my messenger data (try this notebook on your own messenger data if you’re curious).
Lessons learned from accelerating foyer with dask
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Combining Foyer + Dask
Big data tools for MD simulation analysis
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Big data tools for MD simulation analysis
Digging through some Folding@Home data
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Learning cheminformatics from some Folding@Home data
Is being “clutch” a myth?
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Are some players more “clutch” than others?
NBA defensive schemes
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Team defensive schemes
Does a team’s defensive scheme influence opponents’ shot portfolios? I’m going to be using a different NBA API to query all the games for the 2018-2019 regular season. In each game, I’m going to log each “make” against a team’s defense. For example, Houston makes a 22-ft 3-point shot against Boston, I will log the distance at which Houston scored against Boston.
Molecular Modeling Software: OpenMM (part 2)
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Less-standard molecular modeling methods, combining rules, and OpenMM nonbonded forces
Molecular Modeling Software: OpenMM
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OpenMM
Molecular Modeling Software: OpenForceField
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Putting together open-source molecular modeling software
Molecular Modeling Software: Open Babel
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Open Babel
“Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.”
Molecular Modeling Software: Foyer
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Foyer
Foyer is an open-source Python package, part of the MoSDeF suite of tools for molecular modeling. In the description: “a package for atom-typing as well as applying and disseminating forcefields.”
Fantasy NBA 2
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Part 2 of evaluating fantasy NBA draft picks - modeling and sampling for expected fantasy output.
Fantasy NBA 1
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Part 1 of evaluating fantasy NBA draft picks - first gathering the relevant data.
Bayesian Methods 1
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First-attempt at using PyMC3 for Bayesian parameter estimation
Applying some principles from earlier mcmc posts/notebooks to estimate the parameters of a linear model
Molecular Modeling Software: ParmEd
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ParmEd
ParmEd is an open-source python package for molecular modeling applications. In the description: “Cross-program parameter and topology file editor and molecular mechanical simulator engine.”
Bayesian Methods and Molecular Modeling 1
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(Last updated: 2019-07-31). This is an ongoing post as I work through a tutorial I found.
Molecular Modeling 2
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Conducting a simulation
Running a simulation means taking a model and sampling sort of distribution with it. 
Technical Debt
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Technical debt is an ongoing, ever-pressing issue to any large, collaborative code base. If left unaddressed, technical debt can seriously cripple productivity.
Molecular Modeling Software: MDTraj
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Some anecdotes with analyzing simulations
Let’s say you’ve conducted a simulation. Everything up to that point (parametrization, initialization, actually running the simulation) will be assumed and probably discussed another day. What you have from a simulation is a trajectory (timeseries of coordinates), and now we have to derive some meaningful properties from this trajectory.
Molecular Modeling 1
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How do you model something?
Let’s talk about molecular modeling from both the chemistry and mathematic standpoints. When you want to model something, what do you need?
Introduction
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Hello world
This is my first post. I’m Alex. I’m from the Northern Virginia area. I like chemical engineering, chemistry, computer science, and scientific computing/data science.
portfolio
Portfolio item number 1
Short description of portfolio item number 1
Portfolio item number 2
Short description of portfolio item number 2
publications
Paper Title Number 1
Published in Journal 1, 2009
This paper is about the number 1. The number 2 is left for future work.
Recommended citation: Your Name, You. (2009). "Paper Title Number 1." Journal 1. 1(1). http://academicpages.github.io/files/paper1.pdf
Paper Title Number 2
Published in Journal 1, 2010
This paper is about the number 2. The number 3 is left for future work.
Recommended citation: Your Name, You. (2010). "Paper Title Number 2." Journal 1. 1(2). http://academicpages.github.io/files/paper2.pdf
Paper Title Number 3
Published in Journal 1, 2015
This paper is about the number 3. The number 4 is left for future work.
Recommended citation: Your Name, You. (2015). "Paper Title Number 3." Journal 1. 1(3). http://academicpages.github.io/files/paper3.pdf
talks
Talk 1 on Relevant Topic in Your Field
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This is a description of your talk, which is a markdown files that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
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This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.