Coder/Designer

Final Project Links
Overview	Deliverables	Guilds	Project Manager	Quality Assurance	Data Analysis	Coder/Designer
		Team	Yeast Beasts

The Coder/Designers are responsible for creating the Microsoft Access database that will be used by the Data Analysts to prepare an input workbook for GRNmap for the microarray dataset they are analyzing. The Coder/Designers are also the resident experts 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

• Dean
• Andrew

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.

• Coder/Designers can have a shared individual journal entry. Both students will be given the same grade and are expected to contribute equally to the electronic lab notebook.
• Detailed notes should be taken throughout consistent with reproducible research and contributing to the final deliverables.

Milestone 1: Journal Club Presentation

• The Coder/Designers will work with one of the QA's to create and deliver a Journal Club presentation about to their assigned paper.

Milestone 2: 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_Spring2024" 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 3: Design a database to store data needed to create a GRNmap input workbook

• Designer/Coders will work with the QA's to create a MS Access Database that will contain data needed to create a GRNmap input workbook. It will need to have the following tables:
  • A gene table that contains all of the gene IDs for the entire yeast genome, obtained from YeastMine.
  • An expression table to store the yeast time-course microarray data for the dataset being analyzed by the Data Analysts. You will consult with the Data Analysts and QA's to figure out the sample-data relationships and how that should be encoded as fields in the database.
  • A degradation_rates table that contains degradation rates from Neymotin et al. (2014). This table is provided at this link.
  • A production_rates table that contains initial guesses for the production rates for each gene. This table will be provided.
  • A network table that contains the gene regulatory network data from the Harbison et al. (2004) paper. Here is the link to the data.
  • A metadata table that encodes information about the database itself, i.e., other tables in the database.
    • 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.

Milestone 4: Build the database

• Once the design work has been completed, you need to actually import the data into the database.

Milestone 5: Validation, Quality Assurance, and Documentation of the Database

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

Milestone 6: Document the schema and design queries to create the GRNmap input workbook

• Assist the Data Analysts with the queries needed to creat a GRNmap input workbook

Final Project Links
Overview	Deliverables	Guilds	Project Manager	Quality Assurance	Data Analysis	Coder/Designer
		Team	Yeast Beasts