Hacker Within, University of California, Davis

Capturing software builds with Docker

2016-04-14T00:00:00+00:00

Attending

Anyone interested in learning about
1) using the container technology called Docker to capture software deployment for

building reproducible scientific software and / or
teaching and /or
apps on the cloud

2) how to update the HackerWithin Davis chapter website and use the fancy web framework Jekyll

Capturing software builds with `Docker` [Karen Ng]

As software gets more and more complicated nowadays, Docker provides safe encapsulated environments to capture the requirements, installation and deployment steps. Gone are the days when one has to spend hours to read through manuals and stack-overflow to build a piece of software, only to find the build broke other software on the machine. In this talk, I will explain how Docker works and why it is more lightweight than virtual machines. Then we will have some fun building and hacking the HackerWithin Davis chapter website using Docker. If we have time left during the hands-on session, we can also pull the Docker image of Hortonworks Data Platform to play with Hadoop or the Jupyter stack image to play with Spark notebooks.

Short bio

I am a Physics PhD final year student eager to learn about different data technologies. I have just completed two internships related to scalable data analytics. The first one was at the Lawrence Livermore National Lab., where I built an end-to-end data analytics pipeline with Spark and Hadoop. The second one was at the Lawrence Berkeley National Lab. (NERSC), where I worked on parallelizing the computation of an astrophysics project. I am looking for good data science career opportunities to utilize my analytics skills.

Prerequisites

Git,
Docker
Virtual Box (if you do not have Linux as your OS)

After installing Docker, you can test that it work by starting the Docker daemon.

For Linux users, executing: $ sudo docker -d & will start the Docker daemon in the background.

For Mac and Windows users, run the Docker daemon by looking for an application called Docker quickstart terminal and start it.

After the Docker daemon is up and running (in the quickstart terminal), execute:

$ docker pull karenyng/hackerwithin_dockerfile

To download the Docker file that we are going to use. (Linux users may need prepend sudo to the above command.)

Attendees should also be familiar with basic shell commands and a text editor on their laptops.

Materials

Docker file for the Hackerwithin Davis Chapter website
Slides

Lightning Talks

Please let us know if you’d like to give and informal 3-5 minute lightning talk. Post and issue or a pull request at:

https://github.com/thehackerwithin/davis

Data Science in the Intensive Care Unit [Greg Rehm]

Greg Rehm is a UC Davis Computer Science Masters Student. He will talk about gathering patient data in hospital ICUs and what we can do with that data to improve quality of care.

Meeting Materials

materials

Relational Databases with SQL

2016-03-10T00:00:00+00:00

Attending

Anyone interested in learning about structured databases for storing and organizing your data.

Relation Databases with SQL [Jim Vanderveen]

This will be a short “hands-on” introduction to the Structured Query Language (SQL) with SQLite, demonstrating basic CRUD (Create, Read, Update, Delete) operations and your new best friend, the Data Dictionary. If time permits, we’ll also cover additional topics such as NULL values, logically linking multiple tables using JOIN, and some aggregations, e.g. COUNT and SUM.

Short bio

I’ve been hacking computers since 1976 when I taught myself BASIC. I started working with SQL and relational databases circa 1995. Lately I’ve been doing database programming for the UC Davis Library, and playing with network- and database “Internet of Things” projects in my spare time.

Prerequisites

Attendees should have followed the Software Carpentry Standard Installation on their laptops. In particular, you will need to have SQLite installed.

The linked installation instructions will setup a basic environment on your operating system of choice (Windows, Mac, Linux) that will give you access to BASH, Python, Git, and R. In addition, you will need an up-to-date web browser.

Attendees should also be familiar with a text editor on their laptops.

Materials

https://github.com/jimvanderveen/sql-tutorial-01

Lightning Talks

Please let us know if you’d like to give and informal 3-5 minute lightning talk. Post and issue or a pull request at:

https://github.com/thehackerwithin/davis

Optimal Control with Direct Collocation [Jason Moore]

I’ll give a demo of some software that I’ve been developing that allows you to express optimal control problems as a high mathematical level and automatically solve trajectory optimization and parameter estimation problems.

ShareLaTeX Continuous Integration [Kenneth Lyons]

ShareLaTeX provides a continuous integration (CI) service which automatically rebuilds your LaTeX document hosted on GitHub each time you push a commit. I will briefly walk through setting up ShareLaTeX CI and demonstrate it in action.

Introduction to Stan, a probabilistic programming language for Bayesian inference. [Matt Espe]

Stan is an open source, simple programming language for creating probabilistic models and conducting inference via several methods (Hamiltonian Monte Carlo, variational inference, and optimization). Runs in C++, with interfaces to many popular analysis programs (R, Python, Julia, command-line, Stata, etc.).

http://mc-stan.org/

Meeting Materials

materials

Git Internals

2016-02-11T00:00:00+00:00

Attending

Anyone interested in learning a bit more about what makes the version control system, Git, tick.

Git Internals with Michael Hannon

As I noticed the haphazard computing practices at the company, I tried to bring to the company the gospel of Duncan, leading to my giving an introductory talk about git, which I had been using rather casually for a number of years. That exercise piqued my interest in git. Where do those monstrous ID numbers come from in the first place? Where do the files really go when you make a new commit or switch to a new branch? What is this HEAD thing that keeps popping up in discussions of git.

This talk is basically a core dump of my brief exploration of those kinds of questions.

Short bio

My educational background is in physics, with an emphasis on computational physics. Through a circuitous route, I wound up managing a small computer-support group in the UCD Physics department, which I did until I retired.

I got interested in computational statistics when I accompanied my wife (a research scientist with a group in the Stanford medical school, applying statistics to genetics) to one of Duncan Temple Lang’s classes. There I discovered that (a) the material was interesting, and (b) and lot of my background was relevant to the topics.

I currently have a cheesy, hourly job at Stanford, supporting my wife’s computing efforts. I’m also an unpaid consultant to a small, start-up company in Davis. (It pays to stay in school ;-)

Prerequisites

You should have basic familiarity with Git and/or other version control systems. Additionally, we will be using basic BASH commands and some Python scripts, so basics in programming will be helpful. Be sure to install the needed software shown below before coming to the tutorial.

Installation

Software Carpentry Standard Installation

Materials

https://github.com/DavisDaddy/hacker-talks/tree/master/internals

Lightning Talks

Please let us know if you’d like to give and informal 3-5 minute lightning talk. Post and issue or a pull request at:

https://github.com/thehackerwithin/davis

6:00 PM: Automated Image Recognition [Carl Stahmer]

6:05 PM: Introduction to Stan, a probabilistic programming language for Bayesian inference. [Matt Espe]

http://mc-stan.org/

Meeting Materials

materials

Web Scraping

2016-01-14T00:00:00+00:00

Attending

Anyone interested in scraping websites for data collection purposes.

Duncan Temple Lang

Duncan is a Professor of Statistics and the Director of the UC Davis Data Science Initiative. See his website for more information about him.

Web Scraping

Instructional materials will be added here before the meeting. Please check back.

Meeting

We will spend some time setting up the future talks and goals for the group.

Lightning Talks

Please let us know if you’d like to give and informal 3-5 minute lightning talk. Post and issue or a pull request at:

https://github.com/thehackerwithin/davis

Jason K. Moore : Symbolic Mathematics with Python

Jason is a lead developer with the SymPy project. SymPy is a computer aided algebra (CAS) system that allows you to use the computer instead of pencil and paper to work out mathematical relationships. It can do algebra, trigonometry, calculus, linear algebra, and much more. SymPy is used to power a number of apps on different platforms and is used to drive symbolic computation in other languages like Octave, Julia, and Sage in addition to Python. SymPy is an open source package developed by close to 500 developers from all around the world and provides similar functionality as proprietary programs such as Maple, Mathematica, MathCAD, etc. It is utilized for high level research in fields such as physics, mathematics, and engineering.

Meeting Materials

materials

Hacker Within, University of California, Davis

Capturing software builds with Docker

Attending

Capturing software builds with Docker [Karen Ng]

Short bio

Prerequisites

Materials

Lightning Talks

Data Science in the Intensive Care Unit [Greg Rehm]

Meeting Materials

Relational Databases with SQL

Attending

Relation Databases with SQL [Jim Vanderveen]

Short bio

Prerequisites

Materials

Lightning Talks

Optimal Control with Direct Collocation [Jason Moore]

ShareLaTeX Continuous Integration [Kenneth Lyons]

Introduction to Stan, a probabilistic programming language for Bayesian inference. [Matt Espe]

Meeting Materials

Git Internals

Attending

Git Internals with Michael Hannon

Short bio

Prerequisites

Installation

Materials

Lightning Talks

6:00 PM: Automated Image Recognition [Carl Stahmer]

6:05 PM: Introduction to Stan, a probabilistic programming language for Bayesian inference. [Matt Espe]

Meeting Materials

Web Scraping

Attending

Duncan Temple Lang

Web Scraping

Meeting

Lightning Talks

Jason K. Moore : Symbolic Mathematics with Python

Meeting Materials

Capturing software builds with `Docker` [Karen Ng]