Bradford Condon PhD

Bioinformatics, Web & Mobile Development


education

D3 logo

In the previous post, we learned about using scales to format our x and y axes, s well as our bar coloring.

In this post I want to address how to nest data with D3. We will use the nest method to automatically sort our samples by property, and we’ll use multiple x-scales to group them along the x-axis.

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D3 logo

In our previous lesson, we created this rudimentary plot.

D3 considers the upper left corner of the SVG to be 0,0. This means that the part of our code defining y values needs to be corrected.

To correct our inverted plot, let’s introduce D3 scales. As a quick reminder, we’re using the D3-3.x package: the latest version has slightly different scale function calls.

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D3 logo

D3js (Data-Driven Documents) is a Javascript library that manipulates the DOM and is often used to build SVG plots. I recently created an interactive plot for differential expression data as part of the Tripal Analysis Expression module. Because other Tripal modules use D3 v3.x, I was required to do the same (as opposed to v4, the latest version). While the API is available, I’m the sort of person who learns best from tutorials and examples, and I struggled to find enough v3 examples.

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introduction

I hosted my first Software Carpentry workshop on December 18th and 19th 2017 in Knoxville Tennessee with my co-instructors Meg Staton and Drew Steen.

I tried to follow the general recommendations and most things worked out great. Here are some lessons learned.

The Software Carpentry logo

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Software Carpentry

I am happy to announce I will be instructing a Software Carpentry Workshop at the University of Tennessee Knoxville. The workshop will be taught by myself, Meg Staton, and Drew Steen on December 18th and 19th, 2017 in 702 Strong Hall.

This workshop will cover the basics of:

  • Unix Shell
  • Git
  • R

Please visit the workshop website for more information and registration links.

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In a previous blog post, I announced my excitement for becoming a certified Software and Data Carpentry instructor. As I complete my checkout process, I also wanted to recap the most important points from the training. A lab meeting presentation of this recap cis available on google slides here.

Looking forward to teaching my first workshop in the next few months!

Data Carpentry Software Carpentry

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This week(September 25th & 26th 2017), I will be certified as a Software and Data Carpentry instructor. As of 2017-06-26, there were 968 instructors. Am I lucky number 1,000? Probably not. Still, exciting.

Data Carpentry Software Carpentry

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Expanding your horizons header NSF epscor

On April 29th 2017, the Expanding Your Horizons conference came to Kentucky for the first time. The conference was funded by an NSF EPSCoR (National Science Foundation Experimental Program to Stimulate Competitive Research for Education and Outreach) grant which I, along with Ellen Crocker and Susan Odom, was a PI on. I’m very grateful for all of the volunteers, corporate partners, parents, teachers, and students who made this conference a success.

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MOOCs (Massive Open Online Courses)  are an interesting development in higher education.  At their most impressive, they are a way for brilliant educators to reach thousands of students at a time, all across the world.  MOOCs have the potential to remove educational barriers like learning disabilities, economic constraints, geographic realities, or busy life schedules.  My alma mater, Cornell, launched their first wave of MOOCs last semester.  Cornell prides itself on catering to “any person, any study” and its not hard to see how MOOCs can drive this mission forward.

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