Clinical Informatics Fellowship Training

Welcome to the public repository for some of the training materials associated with the Children's Hospital of Philadelphia Clinical Informatics Fellowship. These materials are publicly available for anyone to use, but are built with this particular use case in mind.

This repository is public and cannot contain trade secrets, PHI, PII, or commercializable intellectual property belonging to CHOP. Not all training materials can be hosted here because of these limitations. Links to other training materials in secure locations will be provided to program participants.

Links to Repository Contents

Reproducibility, Generalizability, and Reuse: How Technology Can Help	Training Course	Markdown
Introduction to SQL	Training Course	Markdown
Introduction to R and RStudio
R Markdown for Scientific Communication
Introduction to Arcus for the Clinician Researcher

About These Materials

The training materials here are built in markdown, and you can use the Liascript markdown renderer to make them into attractive, configurable training modules. To use Liascript, go to https://liascript.io and enter the url of the (raw) markdown.

For example, to use the training included in reproducibility.md, navigate to https://liascript.io add the url for the "raw" version of reproducibility.md, which is https://raw.githubusercontent.com/arcus/education_fellows/main/reproducibility.md. Together, that gives you this combined url: https://liascript.io/course/?https://raw.githubusercontent.com/arcus/education_fellows/main/reproducibility.md

A Few Notes and Caveats

If you use .css or .js scripts, it's important to know that you can't supply these scripts directly from GitHub. GitHub does not provide the appropriate metadata to indicate that the content of the files is of the correct type, which means that browsers won't include them.

One solution is to use a CDN that re-packages GitHub contents for use in a web page. For example, Liascript itself suggests using a CDN to provide a CSS script from GitHub.

Since CDNs generally have a refresh rate that doesn't meet the "let's try this really quickly" pace of development in GitHub, another option is to host your script in another publicly accessible location. In our case, we've made use of the AWS S3 service to host a custom css file. This means updating the S3 version of the file as well as the version hosted here, in this GitHub, but the extra headache is worth it.

CSS

Custom css is what allows us extra bells and whistles such as the CHOP Research Institute logo, custom "question" and "hint" boxes and enhanced block quote sections. We use a .css script hosted in AWS (but the source of which is stored here, in css/custom.css).

We could, however, use inline or block css within the markdown file itself. Liascript provides some examples of how to do this.

You can see examples of inline css embedded in

tags in reproducibility.md, around where the "horse" cartoon appears. Liascript seems to make some assumptions about image size and location that didn't work well for us, which is why we baked in some styling in that section just to make things explicit for Liascript.