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News/BBOP Job Openings

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We're casting a wide net to find the right people for these two positions. To formally apply please go to the links below. If you have questions, please send them to Suzanna Lewis (selewis at lbl dot gov) and copy Chris Mungall (cjm at berkeleybop dot org). Please forward if you know of anyone who might be interested in looking at these for a fit.

https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=79548

https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=79554

Here are the two position descriptions:

Project Lead- Software Developer (Berkeley Bioinformatics Open-Source Projects-79548)

Description

This is not your typical programming job. This job requires imagination, technical savvy, drive, and a vision of bringing the latest developments in the software industry to bear on the challenges of medical diagnosis, systems biology, and biodiversity. There are large untapped opportunities in the ongoing explosion of molecular data. This position calls for an individual who can see potential connections between the latest developments in software technology and the challenges of biology, and use these insights to produce robust, flexible software that empowers researchers in the biological sciences. This experience will position them uniquely in the emerging computational genomics job market.

The Berkeley Bioinformatics Open-Source Projects is a small group of energetic individuals who are dedicated to developing tools and applying computational technologies to address fundamental biological research needs. Since 2003 BBOP has been supported by NIH research grants to innovate and build advanced data management and analysis technologies. Currently senior team members are Principal Investigators for the Gene Ontology Consortium (gene function and evolution), the Monarch Initiative (genotype to phenotype analysis), and the Apollo project (collaborative genome annotation). Everyone on the team is motivated to advance research by pioneering effective new strategies that can meet the many challenges of biological data management, representation, visualization and analysis. The group is highly collaborative and travel frequently to work with a global network of diverse investigators.

BBOP is seeking an experienced software engineer with strong technical project leadership ability. They will contribute to building an infrastructure that providing an ability to navigate multi-scale spatial and temporal phenotypes across in vivo and in vitro model systems in the context of genetic and genomic data, using semantics and statistics.

Responsibilities

The primary role will be developing and extending web-based genomics and functional collaborative annotation environments. These include: Apollo, a web based genomic annotation editor designed to support geographically dispersed researchers providing real-time synchronization across multiple clients, PAINT, a phylogenetically-based protein family functional annotation tool, and Noctua, an OWL-based graphical editor for richly describing the interplay of integrated gene networks and functional annotation data.

As a full stack engineer, this individual will be responsible for designing and implementing all aspects of the technology stack, working both server-side and client-side. They will also be responsible for supporting the open-source developer community, answering questions regarding the software, and occasionally traveling for workshops and conferences both nationally and internationally. In addition they will be responsible for cross-project integration, providing functionality for the Gene Ontology Project and the Monarch Initiative, and other international collaborative software/data projects.

Qualifications

Essential

  • B.S. in Computer Engineering, Bioinformatics or a related field with a minimum of five years related experience, or an equivalent combination of education and experience. Advanced degree is preferred.
  • Experience in development with JavaScript in client contexts:
    • Experience in understanding and using a variety of libraries and resources in an application
    • Experience with client testing frameworks a plus
    • Experience with frameworks such as Bootstrap and jQuery (UI)
    • Experience with CSS and CSS 3 (e.g. responsive layout, media queries) a plus
  • Experience in development with JavaScript in server contexts:
    • NodeJS and npm experience
    • Experience with server unit testing frameworks
  • Familiarity with Java, including Java web application development and servlet container experience (Jetty/Tomcat).
  • Demonstrated experience in developing robust web-based user-facing software projects.
  • Familiarity with current issues in web development and design (e.g. HTML5, WebSockets).
  • Experience with a range of database technologies (e.g. relational, NoSQL, triplestores).
  • Excellent verbal and written communication skills.
  • Ability to perform research and make independent decisions about approaches and tools to reach specific goals.
  • Ability to apply analytical skills and creativity to solve complex software and data management problems.

Desirable

  • Familiarity with genomics data and ontologies (in particular, the GO)
  • Experience with semantically annotated data
  • Familiarity with OWL and associated reasoners
  • Experience with collaborative coding and build tools (github, maven, …)

Notes

This is a 1 year term appointment with the possibility of renewal and with the possibility of conversion to career based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs. Work will be performed at the Lawrence Berkeley National Laboratory. Job may require occasional travel, weekend, and after-hours work.

Software Developer (Berkeley Bioinformatics Open-Source Projects-79554)

Description

This position opens the door to tons of opportunities for growth for someone interested in computational genomics. The current explosion of molecular data means there is also a demand for people who can build the bridges between the latest technology developments that will meet the challenges of medical diagnosis, systems biology, and biodiversity. The successful applicant will be working in a positive environment that recognizes and values the contribution of every team member. People who are enthusiastic and energized by the idea of contributing to fundamental research insights into genes, pathways, gene expression, protein and genetic interactions, orthology, disease, phenotypes.

The Berkeley Bioinformatics Open-Source Projects is dedicated to developing tools and applying computational technologies that address biological research questions. Since 2003 BBOP has been supported by NIH research grants to develop and apply advanced data management and analysis technologies. Currently senior team members are Principal Investigators for the Gene Ontology Consortium (gene function and evolution), the Monarch Initiative (genotype to phenotype analysis), and the Apollo project (collaborative genome annotation).

BBOP is seeking an eager bioinformaticist who will contribute to all aspects of software development cycles and infrastructure, including initial R&D, developing test suites, deployment to production systems, and maintenance once software is released to the biological research community. The position requires the ability to: deliver bug fixes, changes, and features quickly; test and evaluate alternative technologies (e.g. Rhino vs. V8); develop effective test suites; handle user issues; and provide system reliability with minimal downtime.

Responsibilities

Initially the primary role will be supporting the GOC, in particular the AmiGO web-based tools for searching and browsing the terms and gene product annotations described by the Gene Ontology. AmiGO’s component parts are currently broken into three modules: the GOlr backend (a Solr document store), some legacy Perl in the frontend, and a JavaScript UI and API that communicates directly with the GOlr backend.

Requirements

Essential

  • B.S. in Computer Science, Bioinformatics or a related field with a minimum of two years related experience, or an equivalent combination of education and experience. MS degree is preferred.
  • Experience with collaborative coding and build tools (Jira, Confluence, SVN, Git, maven).
  • Demonstrable strong experience with Debian-based GNU/Linux systems (Ubuntu a plus).
  • Experience with “Cloud” and virtual machine management using KVM (libvirt tools a plus).
  • Experience with development for and deployment to cloud/PaaS:
    • AWS, Heroku, OpenShift, etc.
  • Client and server unit test experience (Selenium, HTMLUnit, …).
  • Experience with system monitoring (e.g. Nagios, Munin).
  • Familiarity with Java, including Java web application development and servlet container experience (Jetty/Tomcat).
  • Demonstrable fluency in Perl (server-side).
  • Experience with installing and tuning of common software servers and services (e.g. LAMP, Jetty + Solr, Apache, Nginx, Tomcat, Jenkins, OpenSSH, MySQL, Postgres…).
  • Experience with Drupal deployment, development, and management:
  • PHP, Drupal plugin, and theme development a plus.
  • Transferable skill sets with similar CMSs a plus.

Desirable

  • Familiarity with JavaScript (client-side).
  • Experience with big data wrangling, particularly genomic data.
  • Experience with team approaches to software construction.
  • Experience with RAID and LVM.
  • Prefer experience with bulk administration and setup tools:
    • apt-dater, Puppet, etc.
    • Debian packaging a plus.
  • Familiarity with networking and file systems (NFS and Fibre Channel, others a plus).
  • Experience with system/data backup and system/data recovery methods a plus.

Notes

This is a 1 year term appointment with the possibility of renewal and with the possibility of conversion to career based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs. Work will be performed at the Lawrence Berkeley National Lab in Berkeley, CA.


Posted to the GMOD News on 2014/06/27