Bradford Condon PhD

Bioinformatics, Web & Mobile Development


Welcome to Tripal Country!

Tripal Logo

Tripal feature annotations might be a little unintuitive, especially for non-biologists. This guide is to solidify my own knowledge of what goes where and why: hopefully it will be helpful to some developers as well.

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Welcome to Tripal Country!

Tripal Logo

This is a short guide to demonstrate how to create new bundle types with Chado storage in Tripal 3. It was originally written as instructions for my Tripal Alchemist module. There is a similar guide on tripal.info which you can also review.

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Tripal Logo

The 2018 Tripal hackathon took place at the Plant & Animal Genomes conference in San Diego January 11th & 12th. I’d post the itinerary and workshop sessions were, but I didn’t take great notes. Instead, I’ll share about the sessions I took part in. Thursday we discussed Controlled Vocabularies in the morning, and Tripal Core issues (generally Tripal 3 issues) in the afternoon. Friday was a general round-table and a Tripal 3 bundles and fields live demo.

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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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As a Tripal developer, one of the fun things I get to do is contribute not only to the Tripal project, but also other parts of GMOD, the Generic Model Organism Database Project. I attended the January 10th 2018 GMOD hackathon at the Plant and Animal Genome XXVI conference hoping to make a few small changes to Chado, the SQL database schema that HardwoodGenomics uses with Tripal.

GMOD CHADO

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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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