<p dir="ltr">I m doing some work on the amino acid properties module</p>
<div class="gmail_quote">On Jul 2, 2015 8:13 PM, <<a href="mailto:biojava-dev-request@mailman.open-bio.org">biojava-dev-request@mailman.open-bio.org</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send biojava-dev mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. [Job] Java Web Developer Positions at RCSB Protein Data Bank,<br>
UC San Diego (Rose, Peter)<br>
2. [Job] Computational Biologist/Structural Bioinformatics/Big<br>
Data Analytics (Rose, Peter)<br>
3. [Job] Postdoctoral Fellow Computational Biology (Rose, Peter)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 2 Jul 2015 05:26:27 +0000<br>
From: "Rose, Peter" <<a href="mailto:pwrose@ucsd.edu">pwrose@ucsd.edu</a>><br>
To: "<a href="mailto:biojava-l@mailman.open-bio.org">biojava-l@mailman.open-bio.org</a>" <<a href="mailto:biojava-l@mailman.open-bio.org">biojava-l@mailman.open-bio.org</a>>,<br>
"<a href="mailto:biojava-dev@mailman.open-bio.org">biojava-dev@mailman.open-bio.org</a>" <<a href="mailto:biojava-dev@mailman.open-bio.org">biojava-dev@mailman.open-bio.org</a>><br>
Subject: [Biojava-dev] [Job] Java Web Developer Positions at RCSB<br>
Protein Data Bank, UC San Diego<br>
Message-ID: <<a href="mailto:D1BA1991.17FBA%25pwrose@ucsd.edu">D1BA1991.17FBA%pwrose@ucsd.edu</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
The Research Collaboratory for Structural Bioinformatics (RCSB) Protein<br>
Data Bank (<a href="http://www.rcsb.org" rel="noreferrer" target="_blank">www.rcsb.org</a>)<br>
is seeking exceptional developers, and we know we're not alone in our<br>
search. So why choose to work with us? Our team values open discussion<br>
and contribution. Starting from your first day, you will shape software<br>
and services used by thousands of people around the world. RCSB PDB can<br>
trace its lineage back to the 1970's, but we still operate like a<br>
start-up. Have a great idea? Let's hear it. Want to try a new<br>
technology? Let's learn it. Want to write code at scale? Let's do it.<br>
Everyone at our organization is passionate about what we do, and that is<br>
why we are leaders in our field. We want to hear from skilled<br>
Developers, people passionate about their craft and what they can bring<br>
to the field. We are currently looking for experienced developers to<br>
join our team of agile software Developers at the University of<br>
California, San Diego.<br>
<br>
The RCSB Protein Data Bank (<a href="http://www.rcsb.org" rel="noreferrer" target="_blank">www.rcsb.org</a>)<br>
is one of the world's leading biological databases with more than<br>
300,000 unique users per month from over 160 countries. It enables<br>
access to the singular global archive of the three-dimensional<br>
structures of proteins and nucleic acids and is a key resource for the<br>
design of new medicines, biofuels, nanomaterials, and enables<br>
fundamental discoveries in biology and medicine.<br>
Experienced web developer will be part of our agile team of<br>
scientists and software developers who expand the capabilities of our<br>
databases, search engines, websites, web services, and visualization and<br>
analysis tools. The candidate will implement cutting edge technology on<br>
our in-house cloud using industry standards and best web development<br>
Practices.<br>
<br>
QUALIFICATIONS<br>
<br>
* BS Degree in Computer Science; or comparable combination of<br>
education and experience with considerable focus in web and software<br>
development.<br>
<br>
* Experience developing the presentation layer of a<br>
dynamic, database-driven web application using HTML, CSS, JSON,<br>
JavaScript, JavaScript libraries, and Java/JSP. Experience in adoptive<br>
layouts for mobile devices and browser compatibility.<br>
<br>
* Experience with RDBMS such as MySQL, including data<br>
modeling and experience with object-relational mapping tools such as<br>
Hibernate. Experience with object storage, such as NoSQL databases is a<br>
plus.<br>
<br>
* Advanced experience in the Java programming language and Java EE<br>
technology.<br>
<br>
* Experience in agile software development and test-driven<br>
design. Experience with build tools such as Maven and continuous<br>
integration systems such as Bamboo, Jenkins, or Travis.<br>
<br>
For more requirements or to apply, please view the UCSD job page<br>
(<a href="https://jobs.ucsd.edu/bulletin/job.aspx?cat=new&sortby=post&jobnum_in=7589" rel="noreferrer" target="_blank">https://jobs.ucsd.edu/bulletin/job.aspx?cat=new&sortby=post&jobnum_in=7589</a><br>
6).<br>
<br>
<br>
--<br>
Peter Rose, Ph.D.<br>
Site Head, RCSB Protein Data Bank West (<a href="http://www.rcsb.org" rel="noreferrer" target="_blank">http://www.rcsb.org</a>)<br>
San Diego Supercomputer Center (<a href="http://bioinformatics.sdsc.edu" rel="noreferrer" target="_blank">http://bioinformatics.sdsc.edu</a>)<br>
University of California, San Diego<br>
+1-858-822-5497<br>
<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Thu, 2 Jul 2015 05:35:12 +0000<br>
From: "Rose, Peter" <<a href="mailto:pwrose@ucsd.edu">pwrose@ucsd.edu</a>><br>
To: "<a href="mailto:biojava-l@mailman.open-bio.org">biojava-l@mailman.open-bio.org</a>" <<a href="mailto:biojava-l@mailman.open-bio.org">biojava-l@mailman.open-bio.org</a>>,<br>
"<a href="mailto:biojava-dev@mailman.open-bio.org">biojava-dev@mailman.open-bio.org</a>" <<a href="mailto:biojava-dev@mailman.open-bio.org">biojava-dev@mailman.open-bio.org</a>><br>
Subject: [Biojava-dev] [Job] Computational Biologist/Structural<br>
Bioinformatics/Big Data Analytics<br>
Message-ID: <<a href="mailto:D1BA1B9F.17FCB%25pwrose@ucsd.edu">D1BA1B9F.17FCB%pwrose@ucsd.edu</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Computational and Data Science Research Specialist<br>
<br>
The Structural Bioinformatics Group at the San Diego<br>
Supercomputer Center (SDSC) is seeking an exceptional scientific<br>
software developer to work on our new project ?Compressive Structural<br>
Bioinformatics? funded by the US National Institutes of Health (NIH) Big<br>
Data to Knowledge (BD2K) initiative<br>
<<a href="https://datascience.nih.gov/bd2k/funded-programs/software" rel="noreferrer" target="_blank">https://datascience.nih.gov/bd2k/funded-programs/software</a>>.<br>
The Challenge is to enable efficient research on the rapidly growing<br>
number of 3D molecular structures of ever increasing size and<br>
complexity, and develop highly scalable 3D structural search, analysis,<br>
workflow, data-exchange, and visualization tools.<br>
<br>
Our team values open discussion and contribution. Starting from<br>
your first day, you will shape software and services used by thousands<br>
of people around the world. Have a great idea? Let's hear it. Want to<br>
try a new technology? Let's learn it. Want to write code at scale? Let's<br>
do it. Everyone at our organization is passionate about what we do, and<br>
that is why we are leaders in our field. We want to hear from skilled<br>
scientists and software developers, people passionate about their craft<br>
and what they can bring to the field.<br>
<br>
The Structural Bioinformatics Group is involved in research and<br>
development activities centered around 3D structures of proteins and<br>
nucleic acids, the integration of structural data with other domains<br>
such as Medicine, Genomics, Biology, Drug Discovery, and the development<br>
of scalable solution to Big Data problems in Structural Bioinformatics.<br>
Our group leads the RCSB Protein Data Bank (PDB) (<a href="http://www.rcsb.org" rel="noreferrer" target="_blank">http://www.rcsb.org</a>)<br>
west-coast operations, which represents the preeminent source of<br>
experimentally determined macromolecular structure information for<br>
research and teaching in biology, biological chemistry, and medicine.<br>
With over 300,000 unique users from over 160 countries around the world,<br>
the RCSB PDB is one of the leading worldwide Biological Databases.<br>
<br>
This position researches, designs, develops, and deploys<br>
innovative, highly scalable solutions for 3D structure visualization,<br>
structural queries, and large-scale analyses of 3D macromolecular<br>
complexes. Develops protocols for the efficient network data transfer<br>
using custom compression and streaming techniques to facilitate 3D<br>
visualization of large complexes on any device from phone, tablet, to<br>
laptop and desktop. Designs distributed parallel workflows for<br>
structural queries and analysis of the PDB archive.<br>
<br>
Qualifications:<br>
<br>
<br>
* Bachelor's degree in Structural Bioinformatics, Bioinformatics,<br>
Computational Biology, Computer Science or comparable combination of<br>
education and experience with considerable focus in scientific software<br>
development demonstrated by publications, participation in open source<br>
or other types of software projects. Strong skills in applied<br>
Mathematics and algorithm design. MS or Ph.D. degree preferred.<br>
<br>
<br>
<br>
* Experience in the representation and data structures of<br>
ligands, proteins, nucleic acids, and associated sequence information.<br>
Experience with 3D structure and sequence analysis algorithms.<br>
<br>
<br>
<br>
* Advanced experience in one or more of the following object<br>
oriented programming languages:Java, JavaScript, C++, or Python.<br>
Experience with software development tools including IDEs, Maven, Git,<br>
and continuous integration tools.<br>
<br>
<br>
<br>
* Experience in one or more of the following: development of 3D<br>
visualization applications and knowledge of OpenGL/WebGL, development of<br>
distributed parallel programming models using "Big Data" frameworks<br>
such as Apache Hadoop or Spark, setup of these frameworks on compute<br>
clusters, or development of workflow applications.<br>
<br>
<br>
* Demonstrated effective communication and interpersonal skills.<br>
Demonstrated ability to communicate technical information to technical<br>
and non-technical personnel at various levels in the organization and to<br>
external research and education audiences.<br>
<br>
<br>
For more requirements or to apply, please view the UCSD job page<br>
(<a href="http://jobs.ucsd.edu/bulletin/job.aspx?cat=information&sortby=post&jobnum_
in=77059" rel="noreferrer" target="_blank">http://jobs.ucsd.edu/bulletin/job.aspx?cat=information&sortby=post&jobnum_<br>
in=77059</a>).<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 2 Jul 2015 05:51:02 +0000<br>
From: "Rose, Peter" <<a href="mailto:pwrose@ucsd.edu">pwrose@ucsd.edu</a>><br>
To: "<a href="mailto:biojava-l@mailman.open-bio.org">biojava-l@mailman.open-bio.org</a>" <<a href="mailto:biojava-l@mailman.open-bio.org">biojava-l@mailman.open-bio.org</a>>,<br>
"<a href="mailto:biojava-dev@mailman.open-bio.org">biojava-dev@mailman.open-bio.org</a>" <<a href="mailto:biojava-dev@mailman.open-bio.org">biojava-dev@mailman.open-bio.org</a>><br>
Subject: [Biojava-dev] [Job] Postdoctoral Fellow Computational Biology<br>
Message-ID: <<a href="mailto:D1BA1F55.17FEB%25pwrose@ucsd.edu">D1BA1F55.17FEB%pwrose@ucsd.edu</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
San Diego Supercomputer Center<br>
Postdoctoral Fellow<br>
<br>
<br>
Summary: We are looking for two highly motivated post-docs as part of our<br>
new project ?Compressive Structural Bioinformatics? funded by the US<br>
National Institutes of Health (NIH) Big Data to Knowledge (BD2K)<br>
initiative.<br>
<br>
The Challenge: To enable efficient research on the rapidly growing number<br>
of 3D molecular structures of ever increasing size and complexity. Develop<br>
highly scalable 3D structural search, analysis, workflow, data-exchange,<br>
and visualization tools.<br>
<br>
<br>
Qualifications: Ph.D. in structural bioinformatics, structural biology,<br>
bioinformatics, computational biology or chemistry, computer science, or<br>
related discipline. Experience with scientific software development as<br>
demonstrated by publications or participation in open source software<br>
projects. Experience with several programming languages, including Java,<br>
JavaScript, C++, or Python, and software development tools. Strong skills<br>
in applied mathematics and algorithm design are required. Experience with<br>
distributed parallel computing or 3D visualization applications are a<br>
plus. Excellent interpersonal, written, and oral presentation skills are<br>
essential.<br>
<br>
Note, this position is reviewed annually on the basis of performance and<br>
can be renewed for a maximum of three years.<br>
<br>
<br>
Our Environment:<br>
<br>
The Structural Bioinformatics Group (<a href="http://bioinformatics.sdsc.edu" rel="noreferrer" target="_blank">http://bioinformatics.sdsc.edu</a><br>
<<a href="http://bioinformatics.sdsc.edu/" rel="noreferrer" target="_blank">http://bioinformatics.sdsc.edu/</a>>) at the San Diego Supercomputer Center<br>
(SDSC) (<a href="http://www.sdsc.edu" rel="noreferrer" target="_blank">http://www.sdsc.edu</a> <<a href="http://www.sdsc.edu/" rel="noreferrer" target="_blank">http://www.sdsc.edu/</a>>) is involved in<br>
research and development activities centered around 3D structures of<br>
proteins and nucleic acids, the integration of structural data with other<br>
domains such as Medicine, Genomics, Biology, Drug Discovery, and the<br>
development of scalable solution to Big Data problems in Structural<br>
Bioinformatics. Our group leads the RCSB Protein Data Bank (PDB)<br>
west-coast operations. The RCSB PDB (<a href="http://www.rcsb.org" rel="noreferrer" target="_blank">http://www.rcsb.org</a><br>
<<a href="http://www.rcsb.org/" rel="noreferrer" target="_blank">http://www.rcsb.org/</a>>) represents the preeminent source of experimentally<br>
determined macromolecular structure information for research and teaching<br>
in biology, biological chemistry, and medicine. With over 300,000 unique<br>
users from over 160 countries around the world, the RCSB PDB is one of the<br>
leading worldwide Biological Databases.<br>
<br>
As an Organized Research Unit of UC San Diego, SDSC is a world leader in<br>
data-intensive computing and cyber infrastructure, providing resources,<br>
services, and expertise to the national research community, including<br>
industry and academia.<br>
<br>
<br>
To apply, please send cover letter and resume to Dr. Peter Rose<br>
(<a href="mailto:pwrose@ucsd.edu">pwrose@ucsd.edu</a>).<br>
<br>
<br>
--<br>
Peter Rose, Ph.D.<br>
Site Head, RCSB Protein Data Bank West (<a href="http://www.rcsb.org" rel="noreferrer" target="_blank">http://www.rcsb.org</a><br>
<<a href="http://www.rcsb.org/" rel="noreferrer" target="_blank">http://www.rcsb.org/</a>>)<br>
Principal Investigator, Structural Bioinformatics Laboratory<br>
(<a href="http://bioinformatics.sdsc.edu" rel="noreferrer" target="_blank">http://bioinformatics.sdsc.edu</a> <<a href="http://bioinformatics.sdsc.edu/" rel="noreferrer" target="_blank">http://bioinformatics.sdsc.edu/</a>>)<br>
San Diego Supercomputer Center (<a href="http://www.sdsc.edu" rel="noreferrer" target="_blank">http://www.sdsc.edu</a> <<a href="http://www.sdsc.edu/" rel="noreferrer" target="_blank">http://www.sdsc.edu/</a>>)<br>
University of California, San Diego<br>
+1-858-822-5497 <file://localhost/tel/%252B1-858-822-5497><br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
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End of biojava-dev Digest, Vol 147, Issue 1<br>
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</blockquote></div>