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[Medicago] Two Open positions with the Berkeley Bioinformatics Open-Source Project.

medicago from net.bio.net via medicago%40net.bio.net (by medicago from net.bio.net)
Mon Jul 21 14:25:20 EST 2014


Sending on Behalf of the BBOP group at the Lawrence Berkeley National Labor=
atory
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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 questi=
ons, please send them to Suzi Lewis <selewis from lbl.gov<mailto:selewis from lbl.gov=
>> and please copy Chris Mungall <cjmungall from lbl.gov<mailto:cjmungall from lbl.go=
v>>.

We kindly ask that you please do not reply to this list with your questions=
.

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

- Project Lead / Software Developer:
https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=3Den&job=3D79548

- Software Developer:
https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=3Den&job=3D79554


Below are the descriptions for these two positions:


Project Lead / Software Developer

Description

This is not your typical programming job. This job requires imagination, te=
chnical savvy, drive, and a vision of bringing the latest developments in t=
he software industry to bear on the challenges of medical diagnosis, system=
s 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 softwa=
re technology and the challenges of biology, and use these insights to prod=
uce robust, flexible software that empowers researchers in the biological s=
ciences. This experience will position them uniquely in the emerging comput=
ational genomics job market.

The Berkeley Bioinformatics Open-Source Projects is a small group of energe=
tic individuals who are dedicated to developing tools and applying computat=
ional technologies to address fundamental biological research needs. Since =
2003 BBOP has been supported by NIH research grants to innovate and build a=
dvanced data management and analysis technologies. Currently senior team me=
mbers are Principal Investigators for the Gene Ontology Consortium (gene fu=
nction and evolution), the Monarch Initiative (genotype to phenotype analys=
is), and the Apollo project (collaborative genome annotation). Everyone on =
the team is motivated to advance research by pioneering effective new strat=
egies that can meet the many challenges of biological data management, repr=
esentation, visualization and analysis. The group is highly collaborative a=
nd travel frequently to work with a global network of diverse investigators=
.

BBOP is seeking an experienced software engineer with strong technical proj=
ect leadership ability. They will contribute to building an infrastructure =
that providing an ability to navigate multi-scale spatial and temporal phen=
otypes 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 fu=
nctional collaborative annotation environments. These include: Apollo, a we=
b based genomic annotation editor designed to support geographically disper=
sed 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 inter=
play 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 ope=
n-source developer community, answering questions regarding the software, a=
nd occasionally traveling for workshops and conferences both nationally and=
 internationally. In addition they will be responsible for cross-project in=
tegration, providing functionality for the Gene Ontology Project and the Mo=
narch Initiative, and other international collaborative software/data proje=
cts.

Qualifications

Essential
B.S. in Computer Engineering, Bioinformatics or a related field with a mini=
mum of five years related experience, or an equivalent combination of educa=
tion 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 plu=
s
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 servl=
et 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, t=
riplestores).
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, =85)
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 perform=
ance, continuing availability of funds, and ongoing operational needs. Work=
 will be performed at the Lawrence Berkeley National Laboratory.  Job may r=
equire occasional travel, weekend, and after-hours work.


---------------------------------------------------------------------------=
---


Software Developer

Description

This position opens the door to tons of opportunities for growth for someon=
e interested in computational genomics. The current explosion of  molecular=
 data means there is also a demand for people who can build the bridges bet=
ween the latest technology developments that will meet the challenges of me=
dical diagnosis, systems biology, and biodiversity. The successful applican=
t will be working in a positive environment that recognizes and values the =
contribution of every team member. People who are enthusiastic and energize=
d by the idea of contributing to fundamental research insights into genes, =
pathways, gene expression, protein and genetic interactions, orthology, dis=
ease, phenotypes.

The Berkeley Bioinformatics Open-Source Projects is dedicated to developing=
 tools and applying computational technologies that address biological rese=
arch questions. Since 2003 BBOP has been supported by NIH research grants t=
o develop and apply advanced data management and analysis technologies. Cur=
rently senior team members are Principal Investigators for the Gene Ontolog=
y Consortium (gene function and evolution), the Monarch Initiative (genotyp=
e to phenotype analysis), and the Apollo project (collaborative genome anno=
tation).

BBOP is seeking an eager bioinformaticist who will contribute to all aspect=
s 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 positio=
n requires the ability to: deliver bug fixes, changes, and features quickly=
; test and evaluate alternative technologies (e.g. Rhino vs. V8); develop e=
ffective test suites; handle user issues; and provide system reliability wi=
th minimal downtime.

Responsibilities

Initially the primary role will be supporting the GOC, in particular the Am=
iGO web-based tools for searching and browsing the terms and gene product a=
nnotations described by the Gene Ontology. AmiGO=92s component parts are cu=
rrently broken into three modules: the GOlr backend (a Solr document store)=
, some legacy Perl in the frontend, and a JavaScript UI and API that commun=
icates 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 =93Cloud=94 and virtual machine management using KVM (libvi=
rt tools a plus).
Experience with development for and deployment to cloud/PaaS:
AWS, Heroku, OpenShift, etc.
Client and server unit test experience (Selenium, HTMLUnit, =85).
Experience with system monitoring (e.g. Nagios, Munin).
Familiarity with Java, including Java web application development and servl=
et container experience (Jetty/Tomcat).
Demonstrable fluency in Perl (server-side).
Experience with installing and tuning of common software servers and servic=
es (e.g. LAMP, Jetty + Solr, Apache, Nginx, Tomcat, Jenkins, OpenSSH, MySQL=
, Postgres=85).
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 perform=
ance, 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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