Section outline

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  • Thursday, July 30, 2015; 8:30 AM - 9:20 AM

    Lecture: Tables and relationships, normalization, data types, and data dictionaries.

    Going from data collection forms to data tables in which rows correspond to records/entities and columns correspond to fields/attributes. The concept of a data dictionary or "meta-data". Multi-table relational database and data normalization. Primary and foreign keys. One-to-Many, Many-to-Many, and One-to-One relationships.

    IMPORTANT: The course labs require a MyResearch and REDCap account from UCSF Academic Research Systems (ARS).  We will submit the initial account request for all registered students in EPI 218. You should receive an email from ARS asking you to fill out an online attestation form in order to activate your MyResearch and REDCap account.  See the "Prospectus" memo below.

    Faculty:  Michael Kohn

    Location:      Mission Hall 1400

    • Prospectus:

    • Welcome to Database Management for Clinical Research File
    • Lecture 1 Powerpoint File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Required Reading:

      Chapter 16 -- "Data Management" in Designing Clinical Research (Hulley et al), 4th Edition

    • Assignment:

      Work through the Chapter 16 ("Data Management") Exercises starting on page 301 of Designing Clinical Research (Hulley et al), 4th Edition.

      These are not to turn in (especially since the answers are in the book).

       

    • Final Project Due Date:  Early Warning - EPI 218 Final Project is due by midnight on 9/16/2015.

       

    • Final Project File

  • Thursday, July 30, 2015; 9:30 AM - 10:30 AM

    Computer Lab: Access: creating tables, relationships, and data entry forms

    Creating a table in design or “data dictionary” view. Field names, types, and descriptions; validation rules, primary and foreign keys, lookup tables, and relationships between tables. Creating data entry forms/subforms.

    Faculty:  Michael Kohn, Josh Senyak, Maria Garcia, Emily Hurstak, Juno Obedin-Maliver, Danielle Usatin
     
    Location:      Mission Hall 1400

    • Optional Reading:

    • Assignment:

      Complete Lab 1 on creating tables, relationships, and data entry forms in Access.

    • Epi 218 Lab 1 Instructions File
    • Data Collection Forms for Lab 1 File

    • Assignment Due Date: Upload completed Access accdb file, LASTNAMElab1.accdb, below by 8/6/2015 at midnight.

    • Lab 1 Assignment

      Upload LastNameLab1.accdb by clicking on the "Lab 1" link above.  The link won't work unless you are logged into the CLE syllabus site.

  • Thursday, August 6, 2015; 8:30 AM - 9:20 AM

    Lecture: Queries and on-screen forms

    Views/Select Queries; Action Queries: Update, Append, Delete; On-screen forms.

    Faculty: Michael Kohn

    Location:  Mission Hall 1400

    • Session Slides:

    • Lecture 2: Queries and Forms File

    • Session Audio/Video Recording (Access restricted to registered students):

  • Thursday, August 6, 2015; 9:30 AM - 10:30 AM

    Computer Lab: Filtering by form, queries, reports, and importing data

    Filtering by form. Writing select queries and reports for monitoring study progress. Importing data and appending and updating records.

    Faculty:  Michael Kohn, Josh Senyak, Maria Garcia, Emily Hurstak, Juno Obedin-Maliver, Danielle Usatin

    Location:      Mission Hall 1400

    • Assignment: Optional narrative description

    • Lab 2 Instructions File

    • Assignment Due Date:  Make sure that you upload the completed "Scavenger Hunt" worksheet* and both of the rtf files, “LastnameCountsByRace1.rtf” made prior to importing the new 2007 records and “LastnameCountsByRace2.rtf” made after importing the new records by 8/14/2015 at midnight.

      *You can also complete the "Scavenger Hunt" online below, but please be patient, we are just learning to use this feature of the Collaborative Learning Environment.

    • Lab 2 Assignment

      Upload Lab 2 files by clicking on the "Lab 2" link above.  

      The link won't work unless you are logged in.

      The files should include should include the following:

      “LastnameCountsByRace1.rtf” made prior to importing the new 2012-13  records

      “LastnameCountsByRace2.rtf” made after importing and the new records

      Your completed "Scavenger Hunt" worksheet.  

      (You can also try to answer the "Scavenger Hunt" questions online below, but remember that this is a new option and may not work perfectly.)

    • Lab 2 "Scavenger Hunt" Quiz

      Lab 2 includes a set of “scavenger hunt” questions for you to answer as you work through the lab.

      Note: This online version of the "scavenger hunt" is being beta tested and may not work perfectly.

    • Datasets:

    • Infant Jandice DB for Lab 2 File
    • Baby2012-13.xlsx File

  • Thursday, August 13, 2015; 8:30 AM - 9:20 AM

    Lecture: Wrap-Up of Relational Database Concepts

    Q&A: Execution and Results of the JIFee Study

    Faculty: Josh Senyak and Tom Newman

    Location:  Mission Hall 1400

    • Session Slides: Relating tables by keys

    • Lecture 3: Linking tables using keys File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Required Reading:

    • Newman TB, et al. -- NEJM Infant Jaundice Study URL
      Not available unless: Your ID number contains 02

  • Thursday, August 13, 2015; 9:30 AM - 10:30 AM

    Computer Lab: Creating queries, calculating derived fields, and exporting to Stata

    Faculty:  Michael Kohn, Josh Senyak, Maria Garcia, Emily Hurstak, Juno Obedin-Maliver, Danielle Usatin

    Location:  Mission Hall 1400

    • Optional Reading:

    • Assignment: Optional narrative description

    • Lab 3 Instructions File

    • Assignment Due Date: 
      Upload Lab 3 Worksheet by 8/20/2015 at midnight. See assignment file for details.

    • Datasets:

    • Infant Jaundice Database (Complete) File
    • Lab 3 Assignment

      Upload Lab 3 on the "Lab 3" link above.

      You must be logged in to use the link.

    • We need your REDCap username! URL

      Please complete this 30-second online survey as soon as possible to let us have your REDCap username.

  • Thursday, August 20, 2015; 8:30 AM - 9:20 AM

    Lecture: Web-based data entry forms: REDCap

    Faculty: Jennifer Creasman

    Location:  Mission Hall 1400

    • REDCap Powerpoint Presentation File

    • Session Audio/Video Recording (Access restricted to registered students):

  • Thursday, August 20, 2015; 9:30 AM - 10:30 AM

    Computer Lab: REDCap: basic functions, advantages and limitations

    Faculty:  Michael Kohn, Josh Senyak, Maria Garcia, Emily Hurstak, Juno Obedin-Maliver, Danielle Usatin
     
    Location:      Mission Hall 1400

    • Assignment: Lab 4 on REDCap is due by 23:59 on 8/27/2015. You will need to add your section leader as a user to your REDCap project. See the lab instructions for details.

    • Lab 4 Instructions File
    • We need your REDCap username! URL

      Please complete this 30-second online survey as soon as possible to let us have your REDCap username.

    • Lab 4 Assignment

      Please share your Lab 4 REDCap project with your section leader.  You do not need to upload a file.

      The deadline for sharing your project is 8/27 at 23:59.

  • Thursday, August 27, 2015; 8:30 AM - 9:20 AM

    Lecture: Database Platform Choice

    REDCap, Access, QuesGen, Oncore, SalesForce, ODK (but not Excel)

    Faculty: Josh Senyak

    Location:  Mission Hall 1400

    • Session Slides:

    • PowerPoint - Platform Choice File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Resources:

    • redCapSharedLibraryFromWithinYourStudy File

  • Thursday, August 27, 2015; 9:30 AM - 10:30 AM

    Computer Lab: REDCap: monitoring, reporting and exporting to Stata

    Faculty:  Michael Kohn, Josh Senyak, Maria Garcia, Emily Hurstak, Juno Obedin-Maliver, Danielle Usatin
     
    Location:      Mission Hall 1400

    • Assignment Due Date:  Lab 5 on REDCap was originally due at 23:59 on 9/3/2015, but because of technical difficulties, we have extended the deadline to 9/10/2015.

      You will need to send a Word document containing an "NIH Report" and a treasure hunt worksheet to the course email address. See the lab instructions for details.

    • EPI 218 Lab 5 Instructions File

    • Datasets:

    • DataDictionaryForREDCapIJSLab5.csv File
    • DataForREDCapIJSLab.csv File
    • Lab 5 Assignment

      Note: The deadline for Lab 5 has been extended to 9/10/2015.

      Upload your Lab 5 worksheet file by clicking on the "Lab 5" link above.  

      The link won't work unless you are logged in.

      The file should include should include your completed "Scavenger Hunt" worksheet, including your two Stata tables, 1) all included subjects by race and sex and 2) included Latino subjects by race and sex.

  • Thursday, September 3, 2015; 8:30 AM - 9:20 AM

    Lecture: Excel and Research Data Management; Chart Reviews  / QuesGen as an example of a full-featured, browser-based platform

    Faculty: Michael Kohn / Michael Jarrett

    Location:  Mission Hall 1400

  • Thursday, September 3, 2015; 9:30 AM - 10:30 AM

    Computer Lab: QuesGen: capabilities of a full-featured, browser-based platform
    Lab 6 Cancelled
    (Because of technical difficulties with Lab 5, the deadline to turn in Lab 5 has been pushed back to 9/10, and Lab 6 was converted into a demonstration of QuesGen.)

    Faculty:  Michael Kohn, Josh Senyak, Maria Garcia, Emily Hurstak, Juno Obedin-Maliver, Danielle Usatin
     
    Location:      Mission Hall 1400

  • Thursday, September 10, 2015; 8:30 AM - 9:20 AM

    Lecture: Research Database Demonstrations

    Faculty: Emily Hurstak, Danielle Usatin, Juno Obedin-Maliver

    Location:  Mission Hall 1400

    • Session Slides:

    • Session Audio/Video Recording (Access restricted to registered students):

    • Required Reading:

  • Thursday, September 10, 2015; 9:30 AM - 10:30 AM

    Computer Lab: Final project consultation

    Faculty:  Michael Kohn, Josh Senyak, Maria Garcia, Emily Hurstak, Juno Obedin-Maliver, Danielle Usatin
     
    Location:      Mission Hall 1400

    • Final Project Due Date: EPI 218 final project is due by midnight on 9/16/2015

    • Final Project (Assignment) File

      The link for uploading your final project is near the top of this syllabus page.

      1. We prefer that your database be populated with real data (de-identified if appropriate), but at least make sure to test your data collection system by entering several realistic test records.

      2. Make sure your field types are appropriate (e.g. if you are collecting a date, you should be using a date field type).

      3. All databases must include at least one on-screen data collection form.

      4. Access databases should be normalized.  REDCap databases should use the "Longitudinal" feature if appropriate.

      5. Extra credit will be awarded if your database includes a report, such as the "NIH Report" created in Lab 2.

      6. Extra credit will also be awarded if you provide a budget with your data collection and management plan.

    • Access Database plus Long Version of Infant Jaundice Study Protocol File

      This long version of the Infant Jaundice Study Protocol  represents a modification of the original R01  proposal and is not an example of the  kind of one-page protocol that we are  asking from you as Part B  of your Final Project.   The  Access database is included in this zip file.

    • Example Final Project Part A -- CT Syndesmosis Study File
    • Example Final Project Part B -- CT Syndesmosis Study File
    • Example Final Project Part A -- Anal Cytology Database File
    • Example Final Project B -- Anal Cytology Database File
    • Example Final Project -- VA ICD Database File