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[go-friends] Two Open positions with the Berkeley Bioinformatics OpenSource Project

Monica Munoz-Torres mcmunozt at lbl.gov
Thu Jun 26 15:47:06 PDT 2014


Dear colleagues,

We are casting a wide net to find the right people for these two positions.
To formally apply please go to the links below. Should you have any
questions, please send them to Suzi Lewis <selewis at lbl.gov> and please copy
Chris Mungall <cjmungall at lbl.gov>.

Please feel free to pass around this message if you know of anyone who
might be interested in looking at these for a fit.

*- Project Lead / Software Developer:*
https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=79548

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


Below are the descriptions for these two positions:


*Project Lead / Software Developer*

*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*

*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.



-- 
 Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
Google Scholar Profile: http://goo.gl/sXYTE

Mailing Address:
Joint Genome Institute (400-0415)
for the US Department of Energy
2800 Mitchell Dr. Ste 100
Walnut Creek, CA 94598-1631
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