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[{"authors":null,"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"2525497d367e79493fd32b198b28f040","permalink":"/author/dr.-aya-mitani/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/author/dr.-aya-mitani/","section":"authors","summary":"","tags":null,"title":"Dr. Aya Mitani","type":"authors"},{"authors":null,"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"fd8aa9910b7fb8999990e013be368434","permalink":"/author/dr.-kuan-liu/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/author/dr.-kuan-liu/","section":"authors","summary":"","tags":null,"title":"Dr. Kuan Liu","type":"authors"},{"authors":null,"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"0279a91e17562452d5aa77011cc10e5f","permalink":"/author/dr.-matthew-castelo/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/author/dr.-matthew-castelo/","section":"authors","summary":"","tags":null,"title":"Dr. Matthew Castelo","type":"authors"},{"authors":null,"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"2bc71901ec0dda6a27b15bd6afcd6441","permalink":"/author/dr.-osvaldo-espin-garcia/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/author/dr.-osvaldo-espin-garcia/","section":"authors","summary":"","tags":null,"title":"Dr. Osvaldo Espin-Garcia","type":"authors"},{"authors":null,"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"ff6a91cfff6ac3be2092e597cbe5b072","permalink":"/author/juan-pablo-diaz-martinez/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/author/juan-pablo-diaz-martinez/","section":"authors","summary":"","tags":null,"title":"Juan Pablo Díaz-Martinez","type":"authors"},{"authors":null,"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"b4408db53699ee248821e22610efd568","permalink":"/author/larry-dong/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/author/larry-dong/","section":"authors","summary":"","tags":null,"title":"Larry Dong","type":"authors"},{"authors":null,"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"ddbc76c30b204ad4741b986d9f87b5f3","permalink":"/author/rebecca-christensen/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/author/rebecca-christensen/","section":"authors","summary":"","tags":null,"title":"Rebecca Christensen","type":"authors"},{"authors":null,"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"f76017eca0ef58bca076d16d0763faf2","permalink":"/author/rose-garrett/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/author/rose-garrett/","section":"authors","summary":"","tags":null,"title":"Rose Garrett","type":"authors"},{"authors":null,"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"382090d89a495b4edc4759ab969df1cc","permalink":"/author/rose-schmidt/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/author/rose-schmidt/","section":"authors","summary":"","tags":null,"title":"Rose Schmidt","type":"authors"},{"authors":[],"categories":null,"content":"Register now!    ","date":1664197200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1664197200,"objectID":"44418a6d29c7010ce83dd8b58e9132fd","permalink":"/event/github-2/","publishdate":"2017-01-01T00:00:00Z","relpermalink":"/event/github-2/","section":"event","summary":"A comprehensive workshop for Git and GitHub","tags":[],"title":"GitHub Workshop","type":"event"},{"authors":[],"categories":null,"content":"","date":1650456000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1650456000,"objectID":"680fe83613a73f25936969d9baab11e5","permalink":"/event/bayesian-meta-analysis/","publishdate":"2017-01-01T00:00:00Z","relpermalink":"/event/bayesian-meta-analysis/","section":"event","summary":"Meta-analysis, the pooling of evidence from independent sources, especially randomised controlled trials is now common in the medical research literature. Software advances have contributed to the widespread use of meta-analytic techniques.  In this workshop, we will show how meta-analysis models can be seen as generalized linear models. We will also see how to fit these models under a Bayesian perspective.","tags":[],"title":"An Introduction to Bayesian Meta-Analysis","type":"event"},{"authors":[],"categories":null,"content":"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 \u0026ldquo;Ten quick tips for machine learning in computational biology\u0026rdquo; (BioData Mining, 2017), which became well-known in the bioinformatics community.\n","date":1648472400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1648472400,"objectID":"e30481de207f8e3810afca1690a88919","permalink":"/event/machine-learning/","publishdate":"2017-01-01T00:00:00Z","relpermalink":"/event/machine-learning/","section":"event","summary":"Please join our upcoming workshop on introducing machine learning and its best practices by Dr. Davide Chicco a scientific research associate at the Institute of Health Policy, Management and Evaluation at the University of Toronto.","tags":[],"title":"Introduction to Machine Learning in Health Informatics","type":"event"},{"authors":[],"categories":null,"content":"","date":1646053200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1646053200,"objectID":"1997fdd4a5b4c8ab83f636aabfebb6ee","permalink":"/event/ggplot2/","publishdate":"2017-01-01T00:00:00Z","relpermalink":"/event/ggplot2/","section":"event","summary":"Words have power, but a picture is worth a thousand words. Multiply your power thousandfold by learning about ggplot2 in our upcoming workshop on Monday, February 28 at 1pm!","tags":[],"title":"Taking ggplot2 beyond single plots - Maximizing information transfer","type":"event"},{"authors":[],"categories":null,"content":"","date":1643029200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1643029200,"objectID":"b2f1ebdde1b35d7875ed62145332f661","permalink":"/event/high-performance-computing/","publishdate":"2017-01-01T00:00:00Z","relpermalink":"/event/high-performance-computing/","section":"event","summary":"In the era of self-driving cars and Snapchat filters, how can we use our latest computers to benefit highly computational analyses in research?","tags":[],"title":"High Performance Computing 101","type":"event"},{"authors":[],"categories":null,"content":"","date":1638190800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1638190800,"objectID":"661ce82f441641ba8a98bf9d02d4ef82","permalink":"/event/reproducibility/","publishdate":"2017-01-01T00:00:00Z","relpermalink":"/event/reproducibility/","section":"event","summary":"Given that results in many studies are difficult or impossible to reproduce, what research pipeline should we implement to facilitate research replicability for others?","tags":[],"title":"Reproducibility in Research","type":"event"},{"authors":[],"categories":null,"content":"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\u0026rsquo;s pull requests can be more fun while working side by side.\n","date":1635166800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1635166800,"objectID":"b4a733b88974635977be7dceca0e8c20","permalink":"/event/github-intro/","publishdate":"2017-01-01T00:00:00Z","relpermalink":"/event/github-intro/","section":"event","summary":"A beginner-friendly tutorial for introducing GitHub","tags":[],"title":"Introduction to GitHub","type":"event"},{"authors":[],"categories":null,"content":"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!\n","date":1632747600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1632747600,"objectID":"96c36ad0c3e8cb462a32f8598a33584b","permalink":"/event/tidyverse/","publishdate":"2017-01-01T00:00:00Z","relpermalink":"/event/tidyverse/","section":"event","summary":"A beginner-friendly tutorial for Tidyverse, an R toolbox to store, manipulate and transform data","tags":[],"title":"Introduction to Tidyverse","type":"event"},{"authors":null,"categories":null,"content":"Here is an Anaconda cheatsheet that contains some personal preferences that we have retained. If you do follow this, please let us know if something is not working correctly!\nWhat is Anaconda? 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.\nInstalling Anaconda  Go to the Anaconda website here. Click on the appropriate distribution (Mac or Linux) and download the Anaconda installer for Python 3.7. Open Terminal and execute the following commands:  cd ~/Downloads chmod +x Anaconda3-2020.02-MacOSX-x86_64.sh ./Anaconda3-2020.02-MacOSX-x86_64.sh  If you\u0026rsquo;re on a Linux distribution, the downloaded file has a different name, so execute the commands above with the downloaded file name.\n❗ You should reset your Terminal window by simply restarting it.\nSetting up your virtual environment 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.\n1 - Creating the virtual environment conda create -n YOUR_ENV_NAME python=3.7  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.\n2 - Creating a Terminal Shortcut My preference is to create a Terminal shortcut to activate the environment.\necho \u0026quot;alias SHORTCUT_COMMAND='conda activate YOUR_ENV_NAME'\u0026quot; | cat - ~/.bash_profile \u0026gt; ~/.bash_profile source ~/.bash_profile  If you are on a Linux distribution, replace ~/.bash_profile by ~/.bashrc due to the difference in file names.\n3 - Activating your environment With the shortcut created using the commands above, you can now activate the environment by simply typing its name in Terminal!\nYOUR_ENV_NAME  4 - Installing packages Say you want to install some Python packages called package1, package2 and package3. You can use the code below to do so.\nconda install -n YOUR_ENV_NAME package1 package2 package3  5 - Adding the environment to Jupyter 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\u0026rsquo;s definitely my favorite!). To add your newly created environment to Jupyter, run the following commands in Terminal.\nconda install -n YOUR_ENV_NAME ipykernel -c conda-forge python -m ipykernel install --user --name YOUR_ENV_NAME  Running into command not found: jupyter One of the packages that you may have to install is jupyter itself!\nconda install -n YOUR_ENV_NAME -c conda-forge jupyterlab  Ready to code! Your environment should be ready to use in your Jupyter notebooks!\n Other (hopefully) useful things Locating your virtual environment 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:\nsource activate YOUR_ENV_NAME # to activate your environment which python  You should get an output under the following format: SOME_DIRECTORY/YOUR_ENV_NAME/bin/python. The directory in which your environment is located is simply SOME_DIRECTORY.\nExample When which python is ran after activating my environment called ml, we obtain something like /Users/larry/anaconda3/envs/ml/bin/python. It follows that the directory where my conda environments are located is Users/larry/anaconda3/envs/.\nDeleting your environment Once you have located your environment (see above) and found the directory in which your environments are located and that we will call SOME_DIRECTORY. To delete your environment, run the following commands:\ncd SOME_DIRECTORY rm -rf YOUR_ENV_NAME  Removing your environment from Jupyter 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\u0026rsquo;t work. To remove the environment as an option in the Jupyter notebook, run the following.\njupyter kernelspec uninstall YOUR_ENV_NAME  ","date":1606867200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1606867200,"objectID":"11dbaed84d05f882c585587dd8dad7bc","permalink":"/resources/anaconda/","publishdate":"2020-12-02T00:00:00Z","relpermalink":"/resources/anaconda/","section":"resources","summary":"Here is an Anaconda cheatsheet that contains some personal preferences that we have retained. If you do follow this, please let us know if something is not working correctly!\nWhat is Anaconda?","tags":null,"title":"Conda environments and Jupyter notebooks","type":"resources"},{"authors":null,"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":-62135596800,"objectID":"f26b5133c34eec1aa0a09390a36c2ade","permalink":"/admin/config.yml","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/admin/config.yml","section":"","summary":"","tags":null,"title":"","type":"wowchemycms"},{"authors":null,"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":-62135596800,"objectID":"c1d17ff2b20dca0ad6653a3161942b64","permalink":"/people/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/people/","section":"","summary":"","tags":null,"title":"","type":"widget_page"}]