Seeking CS Undergrad for Employment with Maine-eDNA

April 29, 2021 Maine-eDNA, News

We are seeking an undergraduate student employee to join the Maine-eDNA team, a large NSF EPSCoR funded project (https://umaine.edu/edna/). One goal of the project is to build an integrated data repository of environmental DNA (eDNA), which is DNA obtained from fresh and marine water samples and subjected to high throughput sequencing.

As part of the Maine-eDNA team, undergraduate employees will gain hands-on research experience and other professional skills to advance their careers. The student will work with UMaine Coordinated Operating Research Entities (CORE) environmental DNA (eDNA) Laboratory and the eDNA Data Management Team to facilitate parsing sequencing metadata files for subsequent upload to the Maine-eDNA deployment of MyTardis (GitHub, doi).

MyTardis is a multi-user data management web application built on the Django web framework for scientific instruments. The student will contribute to an Extract, Transform, and Load (ETL) pipeline of DNA sequencing results to ingest into MyTardis.

The student will contribute to the existing data parser (GitHub) to extract and post outputs from an Illumina MiSeq Sequencer to MyTardis via an Application Programming Interface (RESTful API). Additional parsing tasks may also be adapted from the MyTardis NGS Ingestor (GitHub). The student will work closely with the eDNA Data Management team to assess needs and create a Graphic User Interface (e.g., tkinter) for the parser.

The applicant should have a desire to learn and work through problems. Coding will be required and there will be an end of project technical report and presentation open to eDNA colleagues.

The position is full-time (40 hours per week at $12.30 per hour) during May through August, with the option to continue working part-time during the academic year.

Required

  • Programming experience (Python)

Desired

  • Familiarity with GitHub and collaborative coding practices (branch, pull, push, etc)
  • Familiarity with Databases with respect to web application design
  • Familiarity with Linux environments (CentOS, Ubuntu)