index.xml

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    <title>Health Data Working Group</title>
    <link>/</link>
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    <description>Health Data Working Group</description>
    <generator>Wowchemy (https://wowchemy.com)</generator><language>en-us</language><lastBuildDate>Mon, 26 Sep 2022 13:00:00 +0000</lastBuildDate>
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      <title>Health Data Working Group</title>
      <link>/</link>
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    <item>
      <title>GitHub Workshop</title>
      <link>/event/github-2/</link>
      <pubDate>Mon, 26 Sep 2022 13:00:00 +0000</pubDate>
      <guid>/event/github-2/</guid>
      <description>&lt;div class=&#34;container&#34;&gt;
  &lt;div class=&#34;row&#34;&gt;
    &lt;div class=&#34;col text-center&#34;&gt;
      &lt;a href=&#34;https://survey.typeform.com/to/tRdyIk2X&#34; class=&#34;btn btn-outline-primary mt-3&#34; target=&#34;_blank&#34;&gt;Register now!&lt;/a&gt;
    &lt;/div&gt;
  &lt;/div&gt;
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&lt;!-- Slides can be added in a few ways:

- **Create** slides using Wowchemy&#39;s [*Slides*](https://wowchemy.com/docs/managing-content/#create-slides) feature and link using `slides` parameter in the front matter of the talk file
- **Upload** an existing slide deck to `static/` and link using `url_slides` parameter in the front matter of the talk file
- **Embed** your slides (e.g. Google Slides) or presentation video on this page using [shortcodes](https://wowchemy.com/docs/writing-markdown-latex/).

Further event details, including page elements such as image galleries, can be added to the body of this page. --&gt;
</description>
    </item>
    
    <item>
      <title>An Introduction to Bayesian Meta-Analysis</title>
      <link>/event/bayesian-meta-analysis/</link>
      <pubDate>Wed, 20 Apr 2022 12:00:00 +0000</pubDate>
      <guid>/event/bayesian-meta-analysis/</guid>
      <description>&lt;!-- Slides can be added in a few ways:

- **Create** slides using Wowchemy&#39;s [*Slides*](https://wowchemy.com/docs/managing-content/#create-slides) feature and link using `slides` parameter in the front matter of the talk file
- **Upload** an existing slide deck to `static/` and link using `url_slides` parameter in the front matter of the talk file
- **Embed** your slides (e.g. Google Slides) or presentation video on this page using [shortcodes](https://wowchemy.com/docs/writing-markdown-latex/).

Further event details, including page elements such as image galleries, can be added to the body of this page. --&gt;
</description>
    </item>
    
    <item>
      <title>Introduction to Machine Learning in Health Informatics</title>
      <link>/event/machine-learning/</link>
      <pubDate>Mon, 28 Mar 2022 13:00:00 +0000</pubDate>
      <guid>/event/machine-learning/</guid>
      <description>&lt;!-- Slides can be added in a few ways:

- **Create** slides using Wowchemy&#39;s [*Slides*](https://wowchemy.com/docs/managing-content/#create-slides) feature and link using `slides` parameter in the front matter of the talk file
- **Upload** an existing slide deck to `static/` and link using `url_slides` parameter in the front matter of the talk file
- **Embed** your slides (e.g. Google Slides) or presentation video on this page using [shortcodes](https://wowchemy.com/docs/writing-markdown-latex/).

Further event details, including page elements such as image galleries, can be added to the body of this page. --&gt;
&lt;p&gt;Dr. Davide Chicco is a scientific research associate at the Institute of Health Policy, Management and Evaluation at the University of Toronto where he works on machine learning and computational statistics applied to healthcare data. He received his PhD degree in computer engineering at Politecnico di Milano university (Milan, Italy) and then has worked as a postdoctoral researcher at the Princess Margaret Cancer Centre in Toronto. Dr. Chicco has worked on applications of machine learning to bioinformatics, epigenetics, and healthcare data and is the author of the article &lt;a href=&#34;https://biodatamining.biomedcentral.com/articles/10.1186/s13040-017-0155-3&#34;&gt;&amp;ldquo;Ten quick tips for machine learning in computational biology&amp;rdquo;&lt;/a&gt; (BioData Mining, 2017), which became well-known in the bioinformatics community.&lt;/p&gt;
</description>
    </item>
    
    <item>
      <title>Taking ggplot2 beyond single plots - Maximizing information transfer</title>
      <link>/event/ggplot2/</link>
      <pubDate>Mon, 28 Feb 2022 13:00:00 +0000</pubDate>
      <guid>/event/ggplot2/</guid>
      <description>&lt;!-- Slides can be added in a few ways:

- **Create** slides using Wowchemy&#39;s [*Slides*](https://wowchemy.com/docs/managing-content/#create-slides) feature and link using `slides` parameter in the front matter of the talk file
- **Upload** an existing slide deck to `static/` and link using `url_slides` parameter in the front matter of the talk file
- **Embed** your slides (e.g. Google Slides) or presentation video on this page using [shortcodes](https://wowchemy.com/docs/writing-markdown-latex/).

Further event details, including page elements such as image galleries, can be added to the body of this page. --&gt;
</description>
    </item>
    
    <item>
      <title>High Performance Computing 101</title>
      <link>/event/high-performance-computing/</link>
      <pubDate>Mon, 24 Jan 2022 13:00:00 +0000</pubDate>
      <guid>/event/high-performance-computing/</guid>
      <description>&lt;!-- Slides can be added in a few ways:

- **Create** slides using Wowchemy&#39;s [*Slides*](https://wowchemy.com/docs/managing-content/#create-slides) feature and link using `slides` parameter in the front matter of the talk file
- **Upload** an existing slide deck to `static/` and link using `url_slides` parameter in the front matter of the talk file
- **Embed** your slides (e.g. Google Slides) or presentation video on this page using [shortcodes](https://wowchemy.com/docs/writing-markdown-latex/).

Further event details, including page elements such as image galleries, can be added to the body of this page. --&gt;
</description>
    </item>
    
    <item>
      <title>Reproducibility in Research</title>
      <link>/event/reproducibility/</link>
      <pubDate>Mon, 29 Nov 2021 13:00:00 +0000</pubDate>
      <guid>/event/reproducibility/</guid>
      <description>&lt;!-- Slides can be added in a few ways:

- **Create** slides using Wowchemy&#39;s [*Slides*](https://wowchemy.com/docs/managing-content/#create-slides) feature and link using `slides` parameter in the front matter of the talk file
- **Upload** an existing slide deck to `static/` and link using `url_slides` parameter in the front matter of the talk file
- **Embed** your slides (e.g. Google Slides) or presentation video on this page using [shortcodes](https://wowchemy.com/docs/writing-markdown-latex/).

Further event details, including page elements such as image galleries, can be added to the body of this page. --&gt;
</description>
    </item>
    
    <item>
      <title>Introduction to GitHub</title>
      <link>/event/github-intro/</link>
      <pubDate>Mon, 25 Oct 2021 13:00:00 +0000</pubDate>
      <guid>/event/github-intro/</guid>
      <description>&lt;p&gt;In this workshop, we introduced the idea of git and basic commands for individual version control (git add, git commit, git push, git pull). There will be a follow-up workshop on how to collaborate with teammates using branching, issues and pull requests. As we intend to have this workshop in person, practice exercises such as merging each other&amp;rsquo;s pull requests can be more fun while working side by side.&lt;/p&gt;
&lt;!-- Slides can be added in a few ways:

- **Create** slides using Wowchemy&#39;s [*Slides*](https://wowchemy.com/docs/managing-content/#create-slides) feature and link using `slides` parameter in the front matter of the talk file
- **Upload** an existing slide deck to `static/` and link using `url_slides` parameter in the front matter of the talk file
- **Embed** your slides (e.g. Google Slides) or presentation video on this page using [shortcodes](https://wowchemy.com/docs/writing-markdown-latex/).

Further event details, including page elements such as image galleries, can be added to the body of this page. --&gt;
</description>
    </item>
    
    <item>
      <title>Introduction to Tidyverse</title>
      <link>/event/tidyverse/</link>
      <pubDate>Mon, 27 Sep 2021 13:00:00 +0000</pubDate>
      <guid>/event/tidyverse/</guid>
      <description>&lt;p&gt;We thank Nnenna for the workshop and all participants for attending! The links to the code, slides and recording are available on this webpage. See you in a month!&lt;/p&gt;
&lt;!-- Slides can be added in a few ways:

- **Create** slides using Wowchemy&#39;s [*Slides*](https://wowchemy.com/docs/managing-content/#create-slides) feature and link using `slides` parameter in the front matter of the talk file
- **Upload** an existing slide deck to `static/` and link using `url_slides` parameter in the front matter of the talk file
- **Embed** your slides (e.g. Google Slides) or presentation video on this page using [shortcodes](https://wowchemy.com/docs/writing-markdown-latex/).

Further event details, including page elements such as image galleries, can be added to the body of this page. --&gt;
</description>
    </item>
    
    <item>
      <title>Conda environments and Jupyter notebooks</title>
      <link>/resources/anaconda/</link>
      <pubDate>Wed, 02 Dec 2020 00:00:00 +0000</pubDate>
      <guid>/resources/anaconda/</guid>
      <description>&lt;p&gt;Here is an Anaconda cheatsheet that contains some personal preferences that we have retained. If you do follow this, &lt;em&gt;please&lt;/em&gt; let us know if something is not working correctly!&lt;/p&gt;
&lt;img src=&#34;anaconda.jpg&#34; width=65%&gt;
&lt;h1 id=&#34;what-is-anaconda&#34;&gt;What is Anaconda?&lt;/h1&gt;
&lt;p&gt;Simply put, Anaconda is an open-source package management system for Python. One of its most popular applications, Jupyter, is commonly used for data science related projects. In this article, we detail the steps from creating a virtual environment in Anaconda to using it in your Jupyter notebooks.&lt;/p&gt;
&lt;h3 id=&#34;installing-anaconda&#34;&gt;Installing Anaconda&lt;/h3&gt;
&lt;ol&gt;
&lt;li&gt;Go to the Anaconda website &lt;a href=&#34;https://www.anaconda.com/products/individual&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;here&lt;/a&gt;.&lt;/li&gt;
&lt;li&gt;Click on the appropriate distribution (Mac or Linux) and download the Anaconda installer for &lt;strong&gt;Python 3.7&lt;/strong&gt;.&lt;/li&gt;
&lt;li&gt;Open Terminal and execute the following commands:&lt;/li&gt;
&lt;/ol&gt;
&lt;pre&gt;&lt;code&gt;cd ~/Downloads
chmod +x Anaconda3-2020.02-MacOSX-x86_64.sh
./Anaconda3-2020.02-MacOSX-x86_64.sh
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;em&gt;&lt;strong&gt;If you&amp;rsquo;re on a Linux distribution, the downloaded file has a different name, so execute the commands above with the downloaded file name.&lt;/strong&gt;&lt;/em&gt;&lt;/p&gt;
&lt;p&gt;❗ You should reset your Terminal window by simply restarting it.&lt;/p&gt;
&lt;h1 id=&#34;setting-up-your-virtual-environment&#34;&gt;Setting up your virtual environment&lt;/h1&gt;
&lt;p&gt;Creating a virtual environment for your Python project has many benefits, including version control for you and your collaborators and managing sets of installed packages for separate projects. Here are 5 steps to creating your Anaconda virtual environment and using it in a Jupyter notebook.&lt;/p&gt;
&lt;h3 id=&#34;1---creating-the-virtual-environment&#34;&gt;1 - Creating the virtual environment&lt;/h3&gt;
&lt;pre&gt;&lt;code&gt;conda create -n YOUR_ENV_NAME python=3.7
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;The command above specifies Python version in the environment to be 3.7, since this is the most stable and updated version at the moment. However, you can use a different version if you prefer.&lt;/p&gt;
&lt;h3 id=&#34;2---creating-a-terminal-shortcut&#34;&gt;2 - Creating a Terminal Shortcut&lt;/h3&gt;
&lt;p&gt;My preference is to create a Terminal shortcut to activate the environment.&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;echo &amp;quot;alias SHORTCUT_COMMAND=&#39;conda activate YOUR_ENV_NAME&#39;&amp;quot; | cat - ~/.bash_profile &amp;gt; ~/.bash_profile
source ~/.bash_profile
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;em&gt;&lt;strong&gt;If you are on a Linux distribution, replace &lt;code&gt;~/.bash_profile&lt;/code&gt; by &lt;code&gt;~/.bashrc&lt;/code&gt; due to the difference in file names.&lt;/strong&gt;&lt;/em&gt;&lt;/p&gt;
&lt;h3 id=&#34;3---activating-your-environment&#34;&gt;3 - Activating your environment&lt;/h3&gt;
&lt;p&gt;With the shortcut created using the commands above, you can now activate the environment by simply typing its name in Terminal!&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;YOUR_ENV_NAME
&lt;/code&gt;&lt;/pre&gt;
&lt;h3 id=&#34;4---installing-packages&#34;&gt;4 - Installing packages&lt;/h3&gt;
&lt;p&gt;Say you want to install some Python packages called &lt;code&gt;package1&lt;/code&gt;, &lt;code&gt;package2&lt;/code&gt; and &lt;code&gt;package3&lt;/code&gt;. You can use the code below to do so.&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;conda install -n YOUR_ENV_NAME package1 package2 package3
&lt;/code&gt;&lt;/pre&gt;
&lt;h3 id=&#34;5---adding-the-environment-to-jupyter&#34;&gt;5 - Adding the environment to Jupyter&lt;/h3&gt;
&lt;p&gt;Often times, it would be desirable to be able to access the environment in a Jupyter notebook, which is often used for coding in Python (it&amp;rsquo;s definitely my favorite!). To add your newly created environment to Jupyter, run the following commands in Terminal.&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;conda install -n YOUR_ENV_NAME ipykernel -c conda-forge
python -m ipykernel install --user --name YOUR_ENV_NAME
&lt;/code&gt;&lt;/pre&gt;
&lt;h5 id=&#34;running-into-command-not-found-jupyter&#34;&gt;Running into &lt;code&gt;command not found: jupyter&lt;/code&gt;&lt;/h5&gt;
&lt;p&gt;One of the packages that you may have to install is jupyter itself!&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;conda install -n YOUR_ENV_NAME -c conda-forge jupyterlab
&lt;/code&gt;&lt;/pre&gt;
&lt;h1 id=&#34;ready-to-code&#34;&gt;Ready to code!&lt;/h1&gt;
&lt;p&gt;Your environment should be ready to use in your Jupyter notebooks!&lt;/p&gt;
&lt;/br&gt;
&lt;h1 id=&#34;other-hopefully-useful-things&#34;&gt;Other (hopefully) useful things&lt;/h1&gt;
&lt;h3 id=&#34;locating-your-virtual-environment&#34;&gt;Locating your virtual environment&lt;/h3&gt;
&lt;p&gt;My preference is to go the folder in which your environment is installed and simply removing it. To find the directory in which your virtual environment is located, you can do:&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;source activate YOUR_ENV_NAME # to activate your environment
which python
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;You should get an output under the following format: &lt;code&gt;SOME_DIRECTORY/YOUR_ENV_NAME/bin/python&lt;/code&gt;. The directory in which your environment is located is simply &lt;code&gt;SOME_DIRECTORY&lt;/code&gt;.&lt;/p&gt;
&lt;h5 id=&#34;example&#34;&gt;Example&lt;/h5&gt;
&lt;p&gt;When &lt;code&gt;which python&lt;/code&gt; is ran after activating my environment called &lt;code&gt;ml&lt;/code&gt;, we obtain something like &lt;code&gt;/Users/larry/anaconda3/envs/ml/bin/python&lt;/code&gt;. It follows that the directory where my conda environments are located is &lt;code&gt;Users/larry/anaconda3/envs/&lt;/code&gt;.&lt;/p&gt;
&lt;h3 id=&#34;deleting-your-environment&#34;&gt;Deleting your environment&lt;/h3&gt;
&lt;p&gt;Once you have located your environment (see above) and found the directory in which your environments are located and that we will call &lt;code&gt;SOME_DIRECTORY&lt;/code&gt;. To delete your environment, run the following commands:&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;cd SOME_DIRECTORY
rm -rf YOUR_ENV_NAME
&lt;/code&gt;&lt;/pre&gt;
&lt;h3 id=&#34;removing-your-environment-from-jupyter&#34;&gt;Removing your environment from Jupyter&lt;/h3&gt;
&lt;p&gt;Although you have deleted your environment and it no longer exists, for some reason the option to select it as a kernel is still available in your Jupyter notebook, although selecting it won&amp;rsquo;t work. To remove the environment as an option in the Jupyter notebook, run the following.&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;jupyter kernelspec uninstall YOUR_ENV_NAME
&lt;/code&gt;&lt;/pre&gt;
</description>
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      <title></title>
      <link>/admin/config.yml</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      <guid>/admin/config.yml</guid>
      <description></description>
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      <title></title>
      <link>/people/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      <guid>/people/</guid>
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