Difference between revisions of "GRNsight Gene Page Project"

Revision as of 16:01, 7 November 2017

Overal Deliverable

The GRNsight gene page project seeks to add significant functionality to GRNsight by allowing users to open a gene information page from a chosen gene in the currently displayed Saccharomyces cerevisiae gene regulation network. The gene information page shall open a new browser tab or window and display, in an informative and visually effective way, the information known about this gene based on five APIs: UniProt, Ensembl, SGD (YeastMine), NCBI, and JASPAR.

For this project, we shall restrict the current organism to just Saccharomyces cerevisiae. Because GRNsight can be used to display GRNs from any species—and in fact to display graphs that are not GRNs at all—the gene page functionality shall be robust enough to handle non-S. cerevisiae nodes in a graceful and informative manner.

To facilitate the development of the gene page, the class has been divided into four groups:

• Page Design
• Gene Database APIs
• JASPAR API
• Interaction and Integration

Each team is responsible for a specific portion of the overall gene page, detailed below. The members of each team will also have specific roles, also detailed below. Team members in a specific role are also expected to work with each other across teams as guilds, in order to keep each component of the project coordinated and consistent.

Common Deliverables

• You will give a final group PowerPoint presentation in class during the final exam period on Tuesday, December 12, 2:00pm.
• Final due date for all other deliverables is no later than Friday, December 15, 4:30pm (according to official final exam schedule for fall, 2017).
• The deliverables should be uploaded and organized onto one group wiki page, or alternately, delivered on digital media to either Dr. Dahlquist or Dr. Dionisio.
• Each member of the group will be assigned the same grade for the group project.
• Detailed specifications, particularly for the group report and individual assessment and reflection, are given on the GRNsight Gene Page Project Deliverables page.

Group Deliverables

Page Design Team

The Page Design team is responsible for the visual appearance and internal behavior of the gene page. The core deliverable of the team is the HTML/CSS/JavaScript code for this page, in a form that can be dynamically populated based on the gene chosen by the GRNsight user. The final page design shall also design messages and alerts for errors and warnings, such as when the user attempts to display a gene page for a node that does not correspond to a S. cerevisiae gene.

Gene Database APIs Team

The Gene Database APIs team is responsible for retrieving a gene’s data from the four APIs that have been seen in class and the assignments: UniProt, Ensembl, SGD (YeastMine), and NCBI. The core deliverable of the team is a single function, getGeneInformation(geneSymbol), which receives a single gene symbol as its parameter and returns a deferred object that asynchronously delivers the gene’s data back to the caller. The gene information function shall transparently call and integrate the data from the underlying APIs without further intervention by the caller.

As the project evolves, the signature of getGeneInformation may change in consultation with Drs. Dahlquist and Dionisio, but its primary function should not.

JASPAR API Team

The JASPAR API team is responsible for learning about and implementing a fifth API which has not yet been seen in class: JASPAR, an open-access API for transcription factor binding profiles. The learning curve for both the biology and technology of this API is factored into this team, which is why it is only responsible for this one API.

The coders in the JASPAR API team will work with the coders in the Gene Database APIs team to make sure that transcription factor information is properly integrated into the getGeneInformation function. The data analysis guild will work together to make sure that JASPAR information is effectively included in the gene page design.

Interaction and Integration Team

The Interaction and Integration team is responsible for bringing the gene page and API code together into a cohesive and seamless whole. The team’s coders will write the “glue code” across GRNsight, the gene page, and the getGeneInformation function so that the gene page is correctly triggered from a displayed GRN. This includes the code that initially opens the page from GRNsight as well as the code that populates this page based on the results delivered by the getGeneInformation function.

Individual Deliverable

The individual deliverable is an assessment and reflection on the process (either wiki or email, depending on your preference; see note in the linked section):

• Statement of work
• Assessment of the work done
• What was learned

Team Journal Entries

• Each team will write a combined journal entry for each week with contributions from all members.
• Week 11 Creation of page and combined annotated bibliography (12:01am 11/14)
• Week 12 (12:01am 11/21)
• Week 14 (12:01am 12/5)
• Week 15 (12:01am 12/12)

Groups

The project groups and roles are are:

1. Page Design
   • Project Manager/Quality Assurance:
   • Data Analysis:
   • Coder(s):
2. Gene Database APIs
   • Project Manager/Quality Assurance:
   • Data Analysis:
   • Coder(s):
3. JASPAR API
   • Project Manager/Quality Assurance:
   • Data Analysis:
   • Coder(s):
4. Interaction and Integration
   • Project Manager/Quality Assurance:
   • Data Analysis:
   • Coder(s):

Roles (Guilds)

As the project moves forward, we will use class time for team meetings. In addition, we will also have guild meetings where students sharing the same role can work together on common issues. Each student has been assigned a primary role in the project by the instructors (see above).

Project Manager (PM)

The project manager makes sure that individuals are fulfilling their roles and performing the tasks on time.

Quality Assurance (QA)

The Quality Assurance team member is the resident expert on species ID systems and formats. He or she should be proficient with Google Chrome Developer tools, code-savvy editors, curl, and the command line in general (as applicable) to check his or her team’s deliverable for accuracy, bugs, or any other quality-related issues.

In many cases, the same person holds the role of Project Manager and Quality Assurance, as these two roles go together as the ones who ensure that their team’s deliverable meets the overall project’s requirements.

Data Analysis (DA)

Coder (C)

The coder is the resident expert on the technology being used—assorted software, file management, version control, troubleshooting, programming. He or she coordinates with Drs. Dahlquist and Dionisio and fellow coders in developing the code base for the GRNsight gene page. GRNsight is written in JavaScript and is built on open source JavaScript libraries. Source code is hosted on GitHub and managed by Node.js.

Project Milestones

Specific project milestones are found on the individual guild pages.

Overall Flow

A successful project will have the following steps from end to end. Depending on the data and/or other issues that are encountered, one or more of these steps may go through iterations, repetitions, or refinements.

Guild Milestones

These are links to the respective milestone lists in the guild pages:

• Project Manager
• Quality Assurance
• Data Analysis
• Coder