ZFIN Jobs

Created by Christian Pich
Last updated: May 28, 2021 by Yvonne Bradford

ZFIN is currently hiring for 2 positions

Full Stack Developer

Scientific Curator



Full Stack Developer

The Zebrafish Information Network (ZFIN, zfin.org), located at the University of Oregon (UO) in Eugene, is seeking an experienced and motivated full-stack software developer to work with a small team of developers and biologists to design and develop cutting-edge front and back end genomic-focused applications.

Model organisms such as the zebrafish are studied extensively by scientists around the world to reveal critical insights into human biology, health, and disease.  The web-based curation and database applications you will help develop are fundamental resources used by the international biological community to drive their zebrafish research. ZFIN has recently joined forces with 5 other model organism databases to form a large consortium of scientists and developers spread across more than ten institutions in Europe and North America. The Alliance of Genome Resources (www.alliancegenome.org), is a major new initiative and platform of database infrastructure, tools, APIs, and displays designed to facilitate the use of model organisms in research.

Working on both ZFIN and Alliance applications with a variety of different stakeholders, from bench biologists to DevOps engineers, you will have an outstanding opportunity to contribute to dynamic and high-impact international projects, using cutting-edge technologies in an Agile software development environment.

Your role

You will work on the next exciting phase of development of software and infrastructure for the ZFIN and Alliance platforms. The evolving technology stacks are primarily cloud-native (UO, AWS), and deploy a number of back-end and front-end technologies, including Java, Python, JavaScript (React, JQuery), relational and graph databases (PostgreSQL, Neo4J), document databases (Solr, Elasticsearch), and DevOps tools (GoCD, Jenkins, Github, Jira). The development methodology is based on the Agile software development philosophy (Scrum). Since the project and stack is continually growing and evolving, there is a real opportunity for you to propose, create, and implement new solutions in a highly collaborative environment unhindered by technical debt or legacy code.

Your experience

You are an experienced developer who is well-versed in creating robust, well-designed, and well-documented code and processes. You should be comfortable switching between different programming languages and database technologies, and be willing and eager to learn and adapt to new technologies as the project matures. You should also be able to meet deadlines and take responsibility for delivering timely software and data releases. Specifically, you should have:

  • Bachelor’s Degree or higher in Computer Science / Engineering, Computer Information Systems, Bioinformatics, Information Retrieval or related field, from an accredited university

  • Experience developing software in one or more of the following areas:

    • Front-end applications, for example JavaScript / jQuery / React, HTML5, CSS

    • Back-end applications, for example Java, Hibernate, Spring MVC, Python, Groovy, or Perl

    • Relational databases / SQL programming languages, for example PostgreSQL, Oracle, or MySQL

    • Graph databases, for example Neo4j, and/or document databases, for example Solr or Elasticsearch

  • A keen interest in working with biologists and software developers to create technological solutions for biomedical applications

  • Strong analytical, problem solving, and trouble-shooting skills

  • Ability to handle multiple tasks with minimal oversight

  • Ability to be flexible with quickly changing business needs and new technologies

You might also have

  • At least two years experience working as a full-time software developer

  • Experience working with biological data and databases (especially genomics)

  • Experience with any of:

    • Linux command line and shell scripting

    • version control systems such as Git/GitHub, Subversion, or CVS

    • build systems such as Gradle, Ant, make, or Jenkins

    • application testing, user interface design, usability testing

    • mobile app development

    • bioinformatics tools such as BLAST, GBrowse, or JBrowse

    • developing and deploying software for the cloud – AWS experience considered a plus

    • Agile software development environment – Scrum experience considered a plus

Why join us

At ZFIN, we encourage personal and professional development and are committed to ensuring our employees feel valued, supported, and empowered to reach their potential at work. In addition, our employees have access to a wide range of outstanding benefits including:

  • 22 days annual leave per year plus 8 Federal holidays

  • Medical, Dental, and Vision insurance for yourself and your eligible dependents (most employees pay only 5% of the total premiums)

  • Choice of Oregon Public Service Retirement or Voluntary Contribution Retirement plans

  • Flexible Spending accounts

  • Tuition Benefits

  • Annual salary review

  • Flexible work arrangements

  • Casual dress code

  • Access to University Library

  • Access to the University Fitness Center

  • Discounts for athletic event tickets, the University Bookstore, and Museums

  • Free use of Eugene city transportation

  • Relocation to Eugene, Oregon is encouraged but not required



Please apply for this position on the University of Oregon Careers site.   Applications must be either in PDF or a MS Word readable format; other formats will be ignored.    

The University of Oregon is an AA/EO/ADA institution committed to cultural diversity. We invite applications from candidates who share our commitment to diversity.



Scientific Curator

Job Title: Scientific Curator 

Employer: University of Oregon, Institute of Neuroscience 

Location: Eugene, OR 97403-1254 

Job Type: Full Time 

 

Job Description 

ZFIN, the Zebrafish Information Network, seeks a scientific curator to join our dynamic, interactive team of biologists and computer scientists at the University of Oregon in Eugene, OR. 

 Scientific curation is the process of translating scientific knowledge from research articles into databases where disparate pieces of scientific data are integrated to generate scientific knowledgebases that help propel research forward and is an attractive career path for creative scientists looking to take their career in a digital direction. 

 As a ZFIN scientific curator you will: 

  • Read the latest zebrafish literature and add published data, including mutants, gene expression, phenotype, human disease model, and gene ontology data to the ZFIN database.  

  • Work with research laboratories to incorporate direct data submissions into ZFIN. 

  • Integrate data from external resources, such as the whole genome sequence, with curated data available in ZFIN. 

  • Collaborate with computer scientists to facilitate cross-species comparisons and strengthen the link between zebrafish research data and the understanding of human disease. 

  • Work with computer scientists developing ZFIN web pages to increase access to scientific data. 

  • Actively contribute to integration of zebrafish research data at the Alliance of Genome Resources, http://alliancegenome.org . 

  • Attend and present posters and talks at scientific meetings. 

  • Contribute to production of ZFIN publications and grants. 

 

Required: 

Ph.D. degree in life sciences or M.Sc. degree with 3 years of independent research experience  

Significant research experience in developmental genetics 

Ability to work at a computer the majority of the time 

Strong written and verbal communication skills 

Strong attention to detail 

Proven ability to handle multiple complex tasks simultaneously 

Proven ability to work effectively independently as well as on cross-functional teams 

 

Preferred: 

Ph.D. in life sciences 

Experience with major biological databases (NCBI, model organism databases, Ensembl, UniProt, etc.) 

Experience with bioinformatics tools (eg. BLAST) 

Familiarity with ontologies such as anatomy ontologies, gene ontology, etc. 

Basic skills in a scripting language such as Perl or Python 

 

Relocation to Eugene is preferred, but not required 

For more information about ZFIN and this position, please visit:  http://zfin.org  

 To apply: 

Send a single PDF including a cover letter, curriculum vitae and contact information for three references to   jobs@zfin.org 

 To ensure consideration, please submit application materials by 07/15/2021.  The position will remain open until filled. 

 

 You will be notified before references are contacted. 

 

 The University of Oregon is committed to creating a more inclusive and diverse institution and seeks candidates with demonstrated potential to contribute positively to its diverse community.  An equal-opportunity, affirmative-action institution committed to cultural diversity and compliance with the Americans with Disabilities Act