GSoC documentation issue #111

GSoC-program.md

@@ -0,0 +1,25 @@
+@def title = "JuliaHealth - Google Summer of Code"
+@def hasmath = true
+
+
+#### GSoC 2023
+--------------------------------------
+## JuliaHealth's Tools for Patient-Level Predictions: Strengthening Capacity and Innovation
+
+
+[proposal] (https://docs.google.com/document/d/18-p6VG6MwvzFdyA45MvXyqxOLVEByFP6D_gff9-E1XE/edit#heading=h.zgq6k5hzq0t)
+
+__Student: Farida Abdelazeez__ 
+##### Email : [email protected]
+**Mentor: Jacob Zelko**
+##### Email : [email protected]
+
+
+### Project Summary
+
+Working with the OMOP CDM (Observational Medical Outcomes Partnership Common Data Model) involves handling large datasets that require a set of tools for extracting the necessary data efficiently. The first part of the project focuses on improving JuliaHealth's infrastructure by increasing the range of tools available to users. This involves enabling connections to various databases, and working with observational health data. Our second goal is to leverage the capacity built in the previous phase to develop a comprehensive framework for patient-level prediction. This framework will predict patient cohort outcomes with given treatments and will be tested on the mimic iii data, and potentially on real aggregated and anonymized patient data. 
+
+This Jupyter notebook shows the flow of creating a prediction model from OMOP CDM using developed packages through the program. You can find it on juliahealth website - the tutorial section.
+
+
+Poster in [JuliaCon](/assets/JuliaCon-gsoc.pdf) 2023 

_layout/head.html

@@ -20,6 +20,7 @@
         <li><a href="https://github.com/JuliaHealth">GitHub</a></li>
         <li><a href="/related-organizations">Related Organizations</a></li>
         <li><a href="/meeting-notes">Meeting Notes</a></li>
+        <li><a href="/GSoC-program">GSoC Program</a></li>
       </ul>
       <img src="/assets/hamburger.svg" id="menu-icon">
     </nav>

_rss/head.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+This is based on Yandex's https://yandex.com/support/zen/website/rss-modify.html
+
+The scope of this segment is the GLOBAL scope (variables defined in config.md).
+For instance 'website_url' or 'website_description'.
+
+Notes:
+* namespaces (xmlns): https://validator.w3.org/feed/docs/howto/declare_namespaces.html
+* best practices: https://www.rssboard.org/rss-profile
+* fd2rss convers markdown to html and fixes or removes relative links
+* fd_rss_feed_url is built out of {website_url}/{rss_file}.xml, you can change the
+rss_file variable in your config file if you want to use something different than 'feed'
+-->
+<rss version="2.0"
+  xmlns:content="http://purl.org/rss/1.0/modules/content/"
+  xmlns:dc="http://purl.org/dc/elements/1.1/"
+  xmlns:media="http://search.yahoo.com/mrss/"
+  xmlns:atom="http://www.w3.org/2005/Atom"
+  xmlns:georss="http://www.georss.org/georss">
+
+  <channel>
+    <title>
+      <![CDATA[  {{fd2rss website_title}}  ]]>
+    </title>
+    <link> {{website_url}} </link>
+    <description>
+      <![CDATA[  {{fd2rss website_description}}  ]]>
+    </description>
+    <atom:link
+      href="{{fd_rss_feed_url}}"
+      rel="self"
+      type="application/rss+xml" />
+<!--
+* items will be added here in chronological order
+* the channel will then be closed
+-->

_rss/item.xml

@@ -0,0 +1,60 @@
+<!--
+This is based on Yandex's https://yandex.com/support/zen/website/rss-modify.html
+
+The scope of this segment is the LOCAL scope (page variables). For instance 'rss_title'.
+
+Notes:
+* the local var rss_description (or rss) *must* be given otherwise the item
+is not generated.
+* rss_title if not given is inferred from page title
+* rss_pubdate if not given is inferred from the date of last modification
+* the full content is not added by default but can be if the variable rss_full_content
+is set to true (either globally or locally).
+* RFC822 or RFC1123 is a date format required by RSS.
+* there is debate about supporting one or several enclosures
+(see https://www.rssboard.org/rss-profile#element-channel-item-enclosure).
+We use the conservative 'only one' approach by default but you could tweak this by
+defining your own `rss_enclosures` variable with a list of string and use that.
+-->
+<item>
+  <title>
+    <![CDATA[  {{fd2rss rss_title}}  ]]>
+  </title>
+  <link> {{fd_full_url}} </link>
+  <guid> {{fd_full_url}} </guid>
+  <description>
+    <![CDATA[  {{fd2rss rss_description}}  ]]>
+  </description>
+
+  <!-- note that fd_page_html is already HTML, so we don't use fd2rss here -->
+  {{if rss_full_content}}
+  <content:encoded>
+    <![CDATA[  {{fix_relative_links fd_page_html}} ]]>
+  </content:encoded>
+  {{end}}
+
+  <!-- RFC1123 enforces a RSS-compliant date formatting -->
+  <pubDate>{{RFC822 rss_pubdate}}</pubDate>
+
+  <!-- if given this must be an email, see specs -->
+  {{isnotempty rss_author}}
+  <author> {{rss_author}} </author>
+  {{end}}
+  {{isnotempty author}}
+  <atom:author>
+    <atom:name>{{author}}</atom:name>
+  </atom:author>
+  {{end}}
+
+  {{isnotempty rss_category}}
+  <category> {{rss_category}} </category>
+  {{end}}
+
+  {{isnotempty rss_comments}}
+  <comments> {{rss_comments}} </comments>
+  {{end}}
+
+  {{isnotempty rss_enclosure}}
+  <enclosure> {{rss_enclosure}} </enclosure>
+  {{end}}
+</item>