The study of genetics is critical to the advancement of medical understanding. Around 60% of people will suffer from a health condition that was caused by a genetic mutation. So far, wide scale data analysis on genomic variations has been limited by technology. Our sponsor, Toby Hocking, has developed a machine learning model that uses pre-existing data to predict when these variations will occur.

Unfortunately, this model requires extensive programming knowledge to access. It is the responsibility of Team BlueBox over the next 9 months to design and implement an effective web application for the interaction of the data provided by Toby Hocking’s peak prediction model.

Envisioned Solution:

We intend to create a fully functional web application for interaction with our client’s supervised machine learning concept for peak prediction. It would allow users to interact with the generated peak labels and create graphics of the data. User access to data sets will be restricted by enabling an authentication functionality on the site that allows users to form project groups and collaborate.

Technologies:

Languages:

• Python

  Python will be our primary language for managing and updating our API. We will use Python to extend our API to reach all of our clients’ requirements.

• TeX

  LaTeX is a common math-based markup language that is useful for developing documents or presentations with equations or graphics in them. With 32% of the initial GitHub being in LaTeX, it is bound to play a large role with our project.

• R

  The R programming language, and open source software developed by statisticians, is the best data visualization software up to date. Since our project is data driven, R will play a significant role in providing graphics and helping gene scientists communicate their findings with others.

IDEs and Text Editors:

• R Studio

  R Studio provides an interface to help us efficiently use the R programming language.

• Visual Studio Code

  The primary interface for editing in multiple languages, mainly Python and HTML.

Version Control:

• Git and GitHub

  Our arguably most important tools in our software development repertoire are Git and Github. These softwares increase the efficiency of collaborative efforts within our team. Since everyone on the team is familiar with GitHub, introducing it into our software development process is intuitive and helpful.

Collaboration Tools

• Google Drive

  Google Drive is the primary form of file management for progress within the capstone project. It is also used for communication between the team members and the mentor as it provides real time updates on the progression of various assignments.

• Zoom

  Used as our primary form of communication for sponsor, client, and mentor.

• Discord

  Our primary tool for communication within the team. Used for group meetings as well as posting announcements and reminders.

• Trello

  Used as our method of showing assignments, due-dates, and distributing work for effective collaboration on capstone assignments and developing our project.

Other

• JBrowse

  JBrowse is currently the primary software for gene science visualization. In its current iteration, it does not provide all our clients’ preferred requirements. We will use JBrowse as a foundation for operations relating to gene science.

• GIMP

  A tool for graphic-design used for logo creation and other graphical aspects of the user interface of our team webpage and our project.

• Kdenlive

  A tool used for editing video used for creating our video presentations.