We are seeking an undergraduate student employee to join the Maine-eDNA team, a large NSF EPSCoR funded project (/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 91���� 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 (, ).

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

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We are seeking an undergraduate student employee to join the Maine-eDNA team, a large NSF EPSCoR funded project (/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. eDNA samples need to be stored at very low (-80C) temperatures in special freezers. Given the growing repository of stored samples we are seeking a creative student with proficient coding skills to help with design and creation of a Freezer Mapping application that will support fast and accurate location, management and retrieval of samples.

Freezer Mapping Project (This project can be done remotely)

Junior~Senior CS/New Media

As part of the Maine-eDNA team, the student will gain hands-on research experience and other professional skills to advance their career. The student will work with the 91���� Coordinated Operating Research Entities (CORE) environmental DNA (eDNA) Laboratory and the eDNA Data Management Team to facilitate the development of a web application for the management and tracking of eDNA samples.

The 91���� eDNA laboratory offers Next-Generation Sequencing, Digital Droplet PCR, and quantitative PCR. As these samples need to be stored within -80°C lab freezers to the preserve the DNA, fast and efficient tracking of sample attributes such as each sample’s remaining eDNA volume and location in the freezer is vital. The student will work closely with the eDNA laboratory to assess needs and produce a database web application built in the .

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, JavaScript, HTML, CSS)
• Familiarity with GitHub and collaborative coding practices
• Familiarity with Databases with respect to web application design
• Familiarity with Linux environments (CentOS, Ubuntu)

Desired

• Familiarity with Django Framework

Applicants must be a Maine resident or, if not a Maine resident, attending a university or college in Maine.

To apply, please send the following application materials to Maine EPSCoR at maine.epscor@maine.edu: (1) Cover letter explaining interest and qualifications for this position, (2) current resume or CV, (3) a copy of unofficial academic transcript, and (4) a list of the names and contact information of three references of anyone familiar with your work performance including teachers. Applications are being accepted immediately until positions are filled.

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While COVID-19 and subsequent restrictions have created a variety of challenges for many research projects, program personnel have been able to utilize the situation to develop their strategies, scientific and safety protocols, as well as team building.

“We couldn’t do any of this if we didn’t work together,” Crofton-Macdonald said. “That’s the key, especially with COVID-19. The teamwork has been very important, especially with these two sampling sessions. There are some veteran researchers and some brand-new graduate students who have been working together and learning from each other.”

The processes, which now include important safety measures such as social distancing and mask-wearing, have been iterative. Program personnel have been providing feedback regarding what works well with sampling, filtering, and analysis, and what is proving to be more difficult in practice. From here, Crofton-Macdonald will work with project leads in order to continuously improve aspects of the siting, sampling, and laboratory procedures.

“This is a large, complex program, but we’re finding ways to collaborate in a way that covers all of our research areas and objectives,” Crofton-Macdonald explained. “These sampling sessions are covering a large range of Maine’s coastal regions, and the samples are being sent to locations across the state for analysis, including the Gulf of Maine Research Institute (GMRI), Bigelow Laboratory for Ocean Sciences, the University of Maine, and others. In order to make this work, sharing supplies, equipment, and even some personnel in a safe and efficient way across the state has been crucial.”

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