Creating a tag cloud directory for the Post Kinds Plugin on WordPress

Yesterday after discovering it on Xavier Roy’s site I was reminded that the Post Kinds Plugin is built on a custom taxonomy and, as a result, has the ability to output its taxonomy in typical WordPress Tag Cloud widget. I had previously been maintaining/displaying a separate category structure for Kinds, which I always thought was a bit much in my category area. While it’s personally nice to have the metadata, I didn’t like how it made the categories so overwhelming and somehow disjointed.

For others who haven’t realized the functionality is hiding in the Post Kinds Plugin, here are some quick instructions for enabling the tag cloud widget:

  1. In the administrative UI, go to Appearance » Widgets in the menu structure.
  2. Drag the “Tag Cloud” widget to one of your available sidebars, footers, headers or available widget areas.
  3. Give the widget a title. I chose “Post Kinds”.
  4. Under the “Taxonomy” heading choose Kinds.
  5. If you want to show tag counts for your kinds, then select the checkbox.
  6. If necessary, select visibility if you want to create conditions for which pages, posts, etc. where the widget will appear.
  7. Finally click save.

You’ll end up with something in your widget area that looks something like this (depending on which Kinds you have enabled and which options you chose):

The tag cloud for the Post Kinds plugin data

If you’re interested in changing or modifying the output or display of your tag cloud, you can do so with the documentation for the Function Reference wp tag cloud in the WordPress Codex.

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👓 Sending your First Webmention from Scratch | Aaron Parecki

Read Sending your First Webmention from Scratch by Aaron PareckiAaron Parecki (Aaron Parecki)
Webmention is one of the fundamental indieweb building blocks. It enables rich interactions between websites, like posting a comment or favorite on one site from another site. This post will walk you through the simplest way to get started sending webmentions to other sites so that you can use your ...

A stupendous article, I just wish I’d had it all those many years ago. Thanks Aaron!

One useful thing for beginners that I don’t think got mentioned (pun intended!) in the article is that for receiving websites which don’t have a built in webmention form you can use a service like which will allow you to manually put in the sending site and the receiving site and it will act as a bridge to send the webmention for you.

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📺 Git Tutorial 5: Branches (Create, Merge, Delete a branch) | YouTube

Watched Git Tutorial 5: Branches (Create, Merge, Delete a branch) by codebasics from YouTube
In this tutorial, I'll cover a very powerful feature of git called branch. I will show you how you can manage alternate versions of your code by creating separate branches, how to merge branches and delete them.

📺 Git Tutorial 4: Undoing/Reverting/Resetting code changes | YouTube

Watched Git Tutorial 4: Undoing/Reverting/Resetting code changes by codebasics from YouTube
In this tutorial, we will cover how to undo or revert a code change. Also I will show you how to reset your git branch to any previous commit id.

📺 Git Tutorial 3: Basic Commands: add, commit, push | YouTube

Watched Git Tutorial 3: Basic Commands: add, commit, push by codebasics from YouTube
In this git tutorial we will learn how to commit a code change locally using git commit and how to upload it to remote using git push.

📺 Github Tutorial For Beginners – Github Basics for Mac or Windows & Source Control Basics | YouTube

Watched Github Tutorial For Beginners - Github Basics for Mac or Windows & Source Control Basics by from YouTube
If you've been wanting to learn Github, now's the perfect time! Github is seen as a big requirement by most employers these days and is very critical to business workflow. This Github tutorial will cover the basics of how to use Github and the command line.

Setting up WordPress for IndieWeb use

I spent some time this morning doing a dry run through setting up a suite of IndieWeb plugins on a fresh WordPress installation. Going off of a scant outline I talked for almost two hours describing IndieWeb functionality as I set it all up. Hopefully it will provide a useful guide to newcomers to the space until I can write up a more solid outline and take a more polished approach. Apologies in advance for the roughness of the audio, lack of quality, and even live mistakes. Hopefully folks won’t mind suffering through until we can come up with some better tutorials.

As prerequisites, I assume you’ve already got your own domain and have installed WordPress on a server or other host. I actually finish setting up the WordPress install as I start the video and then sign in for the first time as we begin.

While many of the core plugins are straightforward, there is a huge amount of leeway in how folks can choose (or not) to syndicate to sites like Twitter, Facebook, and others. Here I make the choice to use the Bridgy Publish plugin and only demonstrate it with Twitter. With one example shown, hopefully other silos can be set up with as well. The IndieWeb wiki details other options for those who want other methods.

At the end I walk through creating and syndicating a post to Twitter. Then I demonstrate commenting on that post using another CMS (WithKnown) from a separate domain.

I do my best to provide verbal descriptions and visual examples, but these can certainly be supplemented with further detail on the IndieWeb wiki. I hope to come back and add some diagrams at a later date, but this will have to suffice for now.​​​​​​​​​

For those who would like an audio only version of this talk, you can listen here (.mp3):

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👓 Site Building with WordPress and Elementor | Throw Out The Manual

Read Site Building with WordPress and Elementor by Tim Owens (Throw Out The Manual)
One of the biggest challenges for folks new to building a website with WordPress is that it feels very much like writing/blogging software out of the box. Yes, you can create pages, but as soon as you want to structure information in columns or do anything more complex than images and text you will quickly find you need to find a theme or a handful of plugins to get the job done (and if you don't know what you don't know, that's a huge hurdle). "Site Builder" plugins are becoming more and more popular and you even see more themes integrating them into their frameworks these days. Some are pretty good, some suck really badly. One I really like and wanted to demonstrate as a way to quickly get up and running with a WordPress site is Elementor which is both free (there's a Pro version that has more features I'll discuss in a bit) and incredibly user-friendly with a lot of great options.

While I know more than the average WordPress bear, I’ve never really seen the value of any of these site builders myself.

I am curious how some of these site builders will do with the upcoming release of Gutenberg, however.

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NIMBioS Tutorial: Uncertainty Quantification for Biological Models

Bookmarked NIMBioS Tutorial: Uncertainty Quantification for Biological Models (
NIMBioS will host an Tutorial on Uncertainty Quantification for Biological Models

Uncertainty Quantification for Biological Models

Meeting dates: June 26-28, 2017
Location: NIMBioS at the University of Tennessee, Knoxville

Marisa Eisenberg, School of Public Health, Univ. of Michigan
Ben Fitzpatrick, Mathematics, Loyola Marymount Univ.
James Hyman, Mathematics, Tulane Univ.
Ralph Smith, Mathematics, North Carolina State Univ.
Clayton Webster, Computational and Applied Mathematics (CAM), Oak Ridge National Laboratory; Mathematics, Univ. of Tennessee

Mathematical modeling and computer simulations are widely used to predict the behavior of complex biological phenomena. However, increased computational resources have allowed scientists to ask a deeper question, namely, “how do the uncertainties ubiquitous in all modeling efforts affect the output of such predictive simulations?” Examples include both epistemic (lack of knowledge) and aleatoric (intrinsic variability) uncertainties and encompass uncertainty coming from inaccurate physical measurements, bias in mathematical descriptions, as well as errors coming from numerical approximations of computational simulations. Because it is essential for dealing with realistic experimental data and assessing the reliability of predictions based on numerical simulations, research in uncertainty quantification (UQ) ultimately aims to address these challenges.

Uncertainty quantification (UQ) uses quantitative methods to characterize and reduce uncertainties in mathematical models, and techniques from sampling, numerical approximations, and sensitivity analysis can help to apportion the uncertainty from models to different variables. Critical to achieving validated predictive computations, both forward and inverse UQ analysis have become critical modeling components for a wide range of scientific applications. Techniques from these fields are rapidly evolving to keep pace with the increasing emphasis on models that require quantified uncertainties for large-scale applications. This tutorial will focus on the application of these methods and techniques to mathematical models in the life sciences and will provide researchers with the basic concepts, theory, and algorithms necessary to quantify input and response uncertainties and perform sensitivity analysis for simulation models. Concepts to be covered may include: probability and statistics, parameter selection techniques, frequentist and Bayesian model calibration, propagation of uncertainties, quantification of model discrepancy, adaptive surrogate model construction, high-dimensional approximation, random sampling and sparse grids, as well as local and global sensitivity analysis.

This tutorial is intended for graduate students, postdocs and researchers in mathematics, statistics, computer science and biology. A basic knowledge of probability, linear algebra, and differential equations is assumed.

Descriptive Flyer

Application deadline: March 1, 2017
To apply, you must complete an application on our online registration system:

  1. Click here to access the system
  2. Login or register
  3. Complete your user profile (if you haven’t already)
  4. Find this tutorial event under Current Events Open for Application and click on Apply

Participation in NIMBioS tutorials is by application only. Individuals with a strong interest in the topic are encouraged to apply, and successful applicants will be notified within two weeks after the application deadline. If needed, financial support for travel, meals, and lodging is available for tutorial attendees.

Summary Report. TBA

Live Stream. The Tutorial will be streamed live. Note that NIMBioS Tutorials involve open discussion and not necessarily a succession of talks. In addition, the schedule as posted may change during the Workshop. To view the live stream, visit A live chat of the event will take place via Twitter using the hashtag #uncertaintyTT. The Twitter feed will be displayed to the right of the live stream. We encourage you to post questions/comments and engage in discussion with respect to our Social Media Guidelines.

Source: NIMBioS Tutorial: Uncertainty Quantification for Biological Models

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NIMBioS Tutorial: Evolutionary Quantitative Genetics 2016

Bookmarked NIMBioS Tutorial: Evolutionary Quantitative Genetics 2016 by NIMBioS (
This tutorial will review the basics of theory in the field of evolutionary quantitative genetics and its connections to evolution observed at various time scales. Quantitative genetics deals with the inheritance of measurements of traits that are affected by many genes. Quantitative genetic theory for natural populations was developed considerably in the period from 1970 to 1990 and up to the present, and it has been applied to a wide range of phenomena including the evolution of differences between the sexes, sexual preferences, life history traits, plasticity of traits, as well as the evolution of body size and other morphological measurements. Textbooks have not kept pace with these developments, and currently few universities offer courses in this subject aimed at evolutionary biologists. There is a need for evolutionary biologists to understand this field because of the ability to collect large amounts of data by computer, the development of statistical methods for changes of traits on evolutionary trees and for changes in a single species through time, and the realization that quantitative characters will not soon be fully explained by genomics. This tutorial aims to fill this need by reviewing basic aspects of theory and illustrating how that theory can be tested with data, both from single species and with multiple-species phylogenies. Participants will learn to use R, an open-source statistical programming language, to build and test evolutionary models. The intended participants for this tutorial are graduate students, postdocs, and junior faculty members in evolutionary biology.

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