Coder/Designer

Final Project Links
Overview	Deliverables	Guilds	Project Manager	Quality Assurance	Data Analysis	Coder/Designer
		Teams	FunGals	Sulfiknights	Skinny Genes

The Coder/Designer is responsible for creating the Microsoft Access database that will be used by the Data Analyst to prepare an input workbook for GRNmap for the microarray dataset they are analyzing. The Coder/Designer is also the resident expert on the technology being used—assorted software, file management, version control, and troubleshooting. He or she coordinates with Dr. Dahlquist and fellow Coders/Designers in developing the Access database and storing it on Box.

Guild Members

• Sulfiknights: DeLisa Madere
• FunGals: Mike Armas
• Skinny Genes: Mihir

Milestones

The milestones do not necessarily correspond to particular weeks; instead they are sets of tasks grouped together. However, Milestone 3 is a hard prerequisite for proceeding to Milestone 4, so ideally the Coder/Coder guild should finish these milestones (they require some coordination; see below) as soon as possible.

Milestone 1: Annotated Bibliography

• The Coder/Designer will work with their teams to develop an annotated bibliography of papers relating to their team's assigned paper.

Milestone 2: Journal Club Presentation

• The Coder/Designer will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.

Milestone 3: Working Environment Setup

Coder/Designer work will require the following software/accounts. The Seaver 120 lab computers are already set up for this; this list is provided for Coders/Designers who need to work on a different computer or outside of the lab.

• Microsoft Access
• Box account (provided by LMU)
  • Databases created by the teams will be kept in a "BIOL367_Fall2019 > Final Project Database" Box folder.
  • Coder/Designer guild members have rights as editor to this folder; all others in the class can only view/download.
  • This folder will serve as as the version control mechanism for the Coder/Designer guild.

Milestone 4: Design a Database to Store Time-course Microarray Data from four sources

• Designer/Coders will work with the QA's to create a MS Access Database to store the yeast time-course microarray data for the dataset being analyzed by the Data Analysts.
• The starting point will be the database already used for the Week 10 assignment, which can be found here on Box.
  • This database is already populated with tables for the Dahlquist Lab microarray data, degradation rates from Neymotin et al. (2014), and initial guesses for production rates.
    • You may need to change the table names of these existing tables so that they make sense with the overall database design.
  • You will need to add one or more expression tables for the expression data from your team's article.
    • Work with your team's QA and Data Analysts to determine appropriate column headings for the expression table.
  • You will also need to create one or more tables with metadata about the other tables because now the database will contain data from multiple sources, not just one.
    • A major part of the design work will be to figure out what information needs to be in the metadata table so that queries can be easily and uniquely performed on the data.
    • Think about what information would someone need to know to be able to understand how the dataset works. Consult with the QA and Data Analysts to figure out the sample-data relationships and how that should be encoded.
• The GEO accession number for the Dahlquist lab data is GSE83656.

Milestone 5: Build an individual database for your team

• Once the design work has been completed, you need to actually import the data into the database.
• Initially, each team will have their own database so that the QA and Data analysts can validate and use the database.

Milestone 6: Validation and Quality Assurance on Database

• The QA will perform quality assurance to make sure that the database is correct and accurate.
  • In particular, the QA needs to make sure that all of the rows of data were imported into the database for the expression table(s).
  • The QA will make sure that both the ID (SGD systematic name) and Standard Names are included in each expression table and are correct.
• QA's will communicate to the Coder/Designers any changes needed to the database.

Milestone 7: Merge completed databases into a single database for the class

• As a guild, the Coder/Designers will merge their separate databases into a final product.
• With the QA's finalize the database schema diagram

Final Project Links
Overview	Deliverables	Guilds	Project Manager	Quality Assurance	Data Analysis	Coder/Designer
		Teams	FunGals	Sulfiknights	Skinny Genes