VEuPathDB · ebapidb · Feb 15, 2022 · Feb 15, 2022 · Feb 15, 2022 · Feb 15, 2022
diff --git a/.DS_Store b/.DS_Store
diff --git a/.gitignore b/.gitignore
@@ -34,3 +34,4 @@ _posts/news/.DS_Store
 .DS_Store
 _posts/.DS_Store
 .DS_Store
+_posts/.DS_Store
diff --git a/_data/clinepi_faq.yml b/_data/clinepi_faq.yml
@@ -2,58 +2,43 @@
 - type: general
   question: "Introductory tour"
   answer: |
-           The video below provides a short overview of the major features of ClinEpiDB. You can
-           also find tutorials, workshop exercises, and additional resources on our
-           [Resources](/a/app/static-content/ClinEpiDB/resources.html){:target='_blank'} page.
-           <iframe style="margin-left:3em;margin-top:1em;" width="560" height="315" src="https://www.youtube.com/embed/535PcFrBH8M"></iframe>
+           The video below provides a short overview of the major features of ClinEpiDB. You can also visit our [Tutorials](/a/app/static-content/ClinEpiDB/tutorials.html){:target='_blank'}, [Workshops](/a/app/static-content/ClinEpiDB/workshops.html){:target='_blank'}, and [Resources](/a/app/static-content/ClinEpiDB/resources.html){:target='_blank'} pages for additional resources.
+           <iframe style="margin-left:3em;margin-top:1em;" width="560" height="315" src="https://www.youtube.com/embed/z6iMvkLo_q8"></iframe>
   uid: g1
   projects: "ClinEpiDB,AllClinEpiDB"
 - type: general
   question: "How do I cite ClinEpiDB?"
   answer: |
            If you want to cite ClinEpiDB directly, please use:
 
-           > Ruhamyankaka E, Brunk BP, Dorsey G *et al.* ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies. [version 1; peer review: 2 approved]. *Gates Open Res* 2019, 3:1661 (<https://doi.org/10.12688/gatesopenres.13087.2>{:target='_blank'})
+           > Ruhamyankaka E, Brunk BP, Dorsey G *et al.* ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies. [version 2; peer review: 2 approved]. *Gates Open Res* 2019, 3:1661 (<https://gatesopenresearch.org/articles/3-1661/v2>{:target='_blank'})
 
-           When citing a dataset that you accessed via ClinEpiDB, please include the dataset authors,
-           study name, date of release and release number on ClinEpiDB, study page URL, and the fact that
-           the data came from ClinEpiDB. For example, the citation for the PRISM Cohort study would be:
+           When citing a dataset that you accessed via ClinEpiDB, please include the dataset authors, study name, date of release and release number on ClinEpiDB, study page URL, and the fact that the data came from ClinEpiDB. For example, the citation for the PRISM Cohort study would be:
 
-           > Dorsey G, Kamya M, Greenhouse B, *et al.* Study: PRISM Cohort. *ClinEpiDB*. 2018, 5 (<https://clinepidb.org/ce/app/record/dataset/DS_0ad509829e>{:target='_blank'})
+           > Dorsey G, Kamya M, Greenhouse B, *et al.* Study: PRISM Cohort. *ClinEpiDB*. 2018, 5 (<https://clinepidb.org/ce/app/workspace/analyses/DS_0ad509829e/new/details>{:target='_blank'})
 
-           You can find the information on the study page by clicking the study name on the homepage
-           or on the dropdown 'Search a study' menu. The study name, release number, and release date
-           are at the top of the page, while authors are listed in the 'Principal Investigator and
-           Collaborators' table at the bottom of the page. You can also find links to original study
-           publications, which you may want to cite.
+           You can find the information on the study page by clicking the study name on the homepage or on the dropdown 'Search a study' menu. The study name, release number, and release date are at the top of the page, while authors are listed in the 'Principal Investigator and Collaborators' table at the bottom of the page. You can also find links to original study publications, which you may want to cite.
   uid: g2
   projects: "ClinEpiDB,AllClinEpiDB"
 - type: general
   question: "Can I use ClinEpiDB to analyze my own data?"
   answer: |
-           ClinEpiDB does not allow you to upload and analyze your own data. However, you can
-           [Contact Us](/a/app/contact-us){:target='_blank'} to inquire about having your own
+           At this time, ClinEpiDB does not allow you to upload and analyze your own data. However, you can [Contact Us](/a/app/contact-us){:target='_blank'} to inquire about having your own
            data loaded into the site.
   uid: g3
   projects: "ClinEpiDB,AllClinEpiDB"
 - type: general
   question: "How do I submit data?"
   answer: |
-           To start, you should [Contact Us](/a/app/contact-us){:target='_blank'} to inquire about
-           having your data loaded into ClinEpiDB. Tell us about the study objectives and design,
-           the size of the dataset, types of variables, and your funding source. Then, check out our
-           [Data Submission Guidelines](/documents/ClinEpiDBDatasetGuidelinesforDataProviders.pdf){:target='_blank'}
-           to learn more about how to prepare your data for us and what additional files we need.
-           If we are able to integrate your data, we'll give you access to a secure Box folder where
-           you can upload your data and accompanying files.
+           To start, you should [Contact Us](/a/app/contact-us){:target='_blank'} to inquire about  having your data loaded into ClinEpiDB. Tell us about the study objectives and design, the size of the dataset (including number of observations and variables), types of variables, and your funding source. Then, check out our [Data Submission Guidelines](/documents/ClinEpiDBDatasetGuidelinesforDataProviders.pdf){:target='_blank'} to learn more about how to prepare your data for us and what additional files we need. If we are able to integrate your data, we'll give you access to a secure Box folder where you can upload your data and accompanying files.
   uid: g4
   projects: "ClinEpiDB,AllClinEpiDB"
 - type: general
   question: "How does ClinEpiDB protect human subject data?"
   answer: |
-           1. We ask all users to agree to our [Data Access and Use Policy](/documents/DataAccessUsePolicyClinEpiDB.latest.pdf){:target='_blank'}
-           2. Direct identifiers such as names and GPS coordinates are removed for all studies. Dates are obfuscated, locations are generalized, and additional indirect identifiers are removed or obfuscated as needed on a case-by-case basis. For some studies, subject IDs are re-assigned to break the link to the institution's copy of the data
-           3. Data access restrictions are implemented as needed (see [Data Access and Use Policy](/documents/DataAccessUsePolicyClinEpiDB.latest.pdf){:target='_blank'})
+           1. We ask all users to agree to our [Data Access and Use Policy](/documents/DataAccessUsePolicyClinEpiDB.latest.pdf){:target='_blank'}.
+           2. Direct identifiers such as names are removed for all studies. Dates are obfuscated, locations are generalized, and additional indirect identifiers are removed or obfuscated as needed on a case-by-case basis. For some studies, subject IDs are re-assigned to break the link to the institution's copy of the data.
+           3. Data access restrictions are implemented as needed (see [Data Access and Use Policy](/documents/DataAccessUsePolicyClinEpiDB.latest.pdf){:target='_blank'}).
   uid: g5
   projects: "ClinEpiDB,AllClinEpiDB"
 - type: general
@@ -68,7 +53,7 @@
   question: "Can I access the code used for ClinEpiDB?"
   answer: |
            Yes! Our code is maintained using [Git](https://github.com/VEuPathDB?utf8=%E2%9C%93&q=ClinEpi&type=&language=){:target='_blank'},
-           and we welcome input from the community. For instance, check out our [Shiny app scripts](https://github.com/VEuPathDB/ClinEpiWebsite/tree/master/View/lib/R/shiny/apps){:target='_blank'}.
+           and we welcome input from the community.
   uid: g7
   projects: "ClinEpiDB,AllClinEpiDB"
 - type: general
@@ -101,42 +86,38 @@
 - type: using_site
   question: "Create an account"
   answer: |
-           1. Hover over the icon labeled 'Guest' in the top right-hand corner, then click 'Register'
-           2. Fill out the registration form then click the 'Register' button
-           3. A green text box should appear, indicating successful registration
-           4. Check your email to retrieve your temporary password
+           1. Hover over the icon labeled 'Guest' in the top right-hand corner, then click 'Register.'
+           2. Fill out the registration form then click the 'Register' button.
+           3. A green text box should appear, indicating successful registration.
+           4. Check your email to retrieve your temporary password.
 
-           Note: You only need one account for all VEuPathDB websites. This means that if you have
-           an account for other VEuPathDB resources such as PlasmoDB or MicrobiomeDB, you can log
-           into ClinEpiDB with those credentials and vice versa.
+           Note: You only need one account for all VEuPathDB websites. This means that if you have an account for other VEuPathDB resources such as PlasmoDB or MicrobiomeDB, you can log into ClinEpiDB with those credentials and vice versa.
   uid: u1
   projects: "ClinEpiDB,AllClinEpiDB"
 - type: using_site
   question: "Change your password"
   answer: |
-           1. Log in to your account
-           2. To access your account page, hover over the icon with your name beneath it in the top right-hand corner, then click your name in the window that appears
-           3. At the bottom of the 'My Account' page, click the blue 'Change your password' link
-           4. Complete the form and click 'Submit'
-           5. If you have successfully changed your password, green text will appear confirming the password change
+           1. Log in to your account.
+           2. To access your account page, hover over the icon with your name beneath it in the top right-hand corner, then click your name in the window that appears.
+           3. At the bottom of the 'My Account' page, click the blue 'Change your password' link.
+           4. Complete the form and click 'Submit.'
+           5. If you have successfully changed your password, green text will appear confirming the password change.
   uid: u2
   projects: "ClinEpiDB,AllClinEpiDB"
 - type: using_site
   question: "Find a variable within a study"
   answer: |
-           1. Start a search for your study of interest
-           2. Type into the search box at the top of the page. A drop down will apear listing
-           all variables that include your keyword in the label, description, or values
-           3. Click a variable to jump directly to its data
-           <iframe style="margin-left:3em;margin-top:3em;" width="560" height="315" src="https://www.youtube.com/embed/nU0cWYyf62E"></iframe>
+           1. Start an analysis for your study of interest.
+           2. Type into the search box on the left side of the page. This will restrict variables to those that include your keyword in the label, description, or values.
+           3. Click a variable to jump directly to its data.
   uid: u3
   projects: "ClinEpiDB,AllClinEpiDB"
 - type: using_site
   question: "Find a study of interest"
   answer: |
-           1. Go to 'All Studies' under the 'Search a Study' drop-down menu
-           2. Type keywords such as country, disease, or sample type into the search box at the top of the page
-           3. Use the 'Add/Remove Columns' button to add columns to see more information, or click the link under 'Study' to see the Study page and learn more
+           1. Go to 'All Studies' under the 'Search a Study' drop-down menu.
+           2. Type keywords such as country, disease, or sample type into the search box at the top of the page.
+           3. Use the 'Add/Remove Columns' button to add columns to see more information, or click the link under 'Study' to see the Study page and learn more.
            <iframe style="margin-left:3em;margin-top:3em;" width="560" height="315" src="https://www.youtube.com/embed/UzT139ih5L0"></iframe>
   uid: u4
   projects: "ClinEpiDB,AllClinEpiDB"
diff --git a/_data/clinepi_tutorials.yml b/_data/clinepi_tutorials.yml
@@ -1,116 +1,95 @@
 --- # clinepi tutorials page
 - type: tutorial
-  title: "Accessing ClinEpiDB data and exploring via the filters"
-  description: "This tutorial explains what types of data searches you can do and how to use the search filters and visualization tools built into the website."
+  title: "Find studies on ClinEpiDB"
+  description: "How to access datasets on the ClinEpiDB platform"
   uid: t1
   projects: "ClinEpiDB,AllClinEpiDB"
-  fileName: ClinEpiDBTutorial1.pdf
-  date: "Mar 18, 2018"
+  fileName: clinEpi_exercises/Tutorial1_NavigatingAccessDatasets.pdf
+  date: "Feb 18, 2022"
 - type: tutorial
-  title: "Understanding the results table"
-  description: "Learn about the tools available to view your search results and how to download the data."
+  title: "Learn the basics of a study analysis"
+  description: "Learn to navigate an analysis that you create"
   uid: t2
   projects: "ClinEpiDB,AllClinEpiDB"
-  fileName: ClinEpiDBTutorial2ResultstableanddownloadsFINAL.pdf
-  date: "Apr 11, 2018"
+  fileName: clinEpi_exercises/Tutorial2_NavigatingAnalysisLayout.pdf
+  date: "Feb 18, 2022"
 - type: tutorial
-  title: "Getting help and submitting feedback"
-  description: "Getting help and submitting feedback"
-  uid: t3
+  title: "Understand the size and shape of study data"
+  description: "Learn how to read the dataset diagram"
+  uid: t4
   projects: "ClinEpiDB,AllClinEpiDB"
-  fileName: General_2_get_help_or_submit_comment.pdf
-  date: "Apr 26, 2019"
+  fileName: clinEpi_exercises/Tutorial3_NavigatingDatasetDiagram.pdf
+  date: "Feb 18, 2022"
 - type: tutorial
-  title: "Downloading data"
-  description: "Learn the 2 ways to download data and extra resources available"
-  uid: t4
+  title: "Find information on study methodology"
+  description: "Use the View Study Details tab to learn how a study was conducted"
+  uid: t5
+  projects: "ClinEpiDB,AllClinEpiDB"
+  fileName: clinEpi_exercises/Tutorial4_NavigatingStudyDetails.pdf
+  date: "Feb 18, 2022"
+- type: tutorial
+  title: "Explore and subset data"
+  description: "Use the Browse and Subset tab to look for variables and filter"
+  uid: t6
+  projects: "ClinEpiDB,AllClinEpiDB"
+  fileName: clinEpi_exercises/Tutorial5_NavigatingBrowseSubset.pdf
+  date: "Feb 18, 2022"
+- type: tutorial
+  title: "Create graphs and other data visualizations"
+  description: "Use the Visualize tab to create data visualizations"
+  uid: t7
   projects: "ClinEpiDB,AllClinEpiDB"
-  fileName: download_file_README_tutorial.pdf
-  date: "Oct 14, 2020"
+  fileName: clinEpi_exercises/Tutorial6_NavigatingVisualize.pdf
+  date: "Feb 18, 2022"
+- type: tutorial
+  title: "Add notes to an analysis"
+  description: "Keep track of your work and thoughts in the Notes tab"
+  uid: t8
+  projects: "ClinEpiDB,AllClinEpiDB"
+  fileName: clinEpi_exercises/Tutorial7_NavigatingNotes.pdf
+  date: "Feb 18, 2022"
+- type: tutorial
+  title: "Get help and submit feedback"
+  description: "Request demos, help with a specific task, etc."
+  uid: t3
+  projects: "ClinEpiDB,AllClinEpiDB"
+  fileName: clinEpi_exercises/Tutorial_GettingHelp.pdf
+  date: "Feb 18, 2022"
 - type: video
-  title: "ClinEpiDB introductory tour"
+  title: "ClinEpiDB quick start guide"
   description: "Covers different tools the site offers to explore and visualize data"
   uid: v1
   projects: "ClinEpiDB,AllClinEpiDB"
   fileName: https://youtu.be/z6iMvkLo_q8
-  date: "Oct 20, 2021"
-- type: video
-  title: "Get the most out of the homepage"
-  description: "Covers the different features accessible from the ClinEpiDB homepage"
-  uid: v2
-  projects: "ClinEpiDB,AllClinEpiDB"
-  fileName: https://www.youtube.com/watch?v=emupZ983zPg&list=PLWzQB3i5sYAIp4urzLGB8jxvVZr6jvkZh&index=2
-  date: "Feb 12, 2018"
-- type: video
-  title: "Find a variable within a study"
-  description: "How to search for specific variables within a study"
-  uid: v3
-  projects: "ClinEpiDB,AllClinEpiDB"
-  fileName: https://www.youtube.com/watch?v=nU0cWYyf62E&list=PLWzQB3i5sYAIp4urzLGB8jxvVZr6jvkZh&index=8
-  date: "Nov 5, 2019"
+  date: "Feb 18, 2022"
 - type: exercise
-  title: "GEMS exercise: Age distributions of females vs. males with diarrheal illness longer than 3 days"
-  description: "GEMS exercise: Age distributions of females vs. males with diarrheal illness longer than 3 days"
+  title: "Navigating the ClinEpiDB platform"
+  description: "Use the PRISM2 ICEMR Cohort study to explore features of ClinEpiDB"
   uid: e1
   projects: "ClinEpiDB,AllClinEpiDB"
-  fileName: GEMS_DiarrheaDuration.pdf
-  date: "Apr 26, 2019"
+  fileName: clinEpi_exercises/Exercise_Navigating_PRISM2.pdf
+  date: "Feb 18, 2022"
 - type: exercise
-  title: "GEMS exercise: Prevalence of wasting and stunting and relationship to various pathogens"
-  description: "GEMS exercise: Prevalence of wasting and stunting and relationship to various pathogens"
+  title: "GEMS1 Case Control: Are rotavirus, Cryptosporidium, and Giardia infection associated with moderate-to-severe diarrhea?"
+  description: "Exercise that includes creating a subset and multiple visualizations"
   uid: e2
   projects: "ClinEpiDB,AllClinEpiDB"
-  fileName: GEMS_Anthropometry.pdf
-  date: "Apr 26, 2019"
+  fileName: clinEpi_exercises/Exercise_GEMS1_EDA.pdf
+  date: "Feb 18, 2022"
 - type: exercise
-  title: "GEMS exercise: Relationship between Giardia or Cryptosporidium and moderate-to-severe diarrhea"
-  description: "GEMS exercise: Relationship between Giardia or Cryptosporidium and moderate-to-severe diarrhea"
+  title: "WASH-B Kenya exercise: Do children in intervention arms have lower incidence of diarrhea compared to children in control arms?"
+  description: "Exercise that includes createing a subset and vizualizations"
   uid: e3
   projects: "ClinEpiDB,AllClinEpiDB"
-  fileName: GEMS_GiardiaMatched.pdf
-  date: "Apr 26, 2019"
+  fileName: clinEpi_exercises/Exercise_WASHBK_EDA.pdf
+  date: "Feb 18, 2022"
 - type: exercise
-  title: "India ICEMR cohort exercise: Poverty and the use of bednets"
-  description: "India ICEMR  cohort exercise: Poverty and the use of bednets"
+  title: "PRISM2 ICEMR Cohort exercise"
+  description: "Use the PRISM2 ICEMR Cohort study to explore features of ClinEpiDB"
   uid: e4
   projects: "ClinEpiDB,AllClinEpiDB"
-  fileName: India_longitudinal_bednet.pdf
-  date: "Apr 26, 2019"
-- type: exercise
-  title: "MAL-ED exercise: Using the Study Page to understand study methodologies"
-  description: "MAL-ED: the key to understanding the study methodologies"
-  uid: e5
-  projects: "ClinEpiDB,AllClinEpiDB"
-  fileName: MALED_1_data_set_page.pdf
-  date: "Apr 26, 2019"
-- type: exercise
-  title: "MAL-ED exercise: Accessing and exploring data via the filters"
-  description: "MAL-ED exercise: Accessing and exploring data via the filters"
-  uid: e6
-  projects: "ClinEpiDB,,AllClinEpiDB"
-  fileName: MALED_2_explore_data.pdf
-  date: "Apr 26, 2019"
-- type: exercise
-  title: "MAL-ED exercise: Building a search with Related Observations and revising the search strategy"
-  description: "MAL-ED exercise: Building a search with Related Observations and revising the search strategy"
-  uid: e7
-  projects: "ClinEpiDB,AllClinEpiDB"
-  fileName: MALED_3_related_observations.pdf
-  date: "Apr 26, 2019"
-- type: exercise
-  title: "PRISM exercise: House design and malaria incidence in children"
-  description: "PRISM exercise: House design and malaria incidence in children"
-  uid: e8
-  projects: "ClinEpiDB,AllClinEpiDB"
-  fileName: PRISM_dwelling.pdf
-  date: "Apr 26, 2019"
-- type: exercise
-  title: "PRISM exercise: Average age of first asymptomatic parasitemia"
-  description: "PRISM exercise: Average age of first asymptomatic parasitemia"
-  uid: e9
-  projects: "ClinEpiDB,AllClinEpiDB"
-  fileName: PRISM_asymptomaticAge.pdf
-  date: "Apr 26, 2019"
+  fileName: clinEpi_exercises/20220321_Exercise_Navigating_PRISM2.pdf
+  date: "Feb 18, 2022"
 - type: resource
   subtype: education
   title: "Data science specialization on Coursera"