Andreas Prlic | 30 Jul 18:51 2015
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BioJava 4 in Debian

Hi,

Thanks to Olivier Sallou's help, BioJava 4 has been accepted and is now also available as a Debian package.

Andreas
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Jan Stourac | 16 Jul 07:52 2015
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Wiki login using Google Account

Dear BioJava team,

today I wanted to fix some broken links on your wiki, but my attempt to login using my Google Account ends up in this error message:

================================

OpenID 2.0 for Google Accounts has gone away

If you've been redirected to this page, it means that you're using a website that doesn't support the latest sign-in standards from Google. We no longer provide this legacy sign-in service for Google accounts, and recommend using an alternative method to sign in on that website. If you previously used your Google account to sign in, you may be able to recover your account using a “forgot password” feature, or by contacting that websites’ support team.

Some websites use OpenID 2.0 for authentication when you're signing in, and to access data that you've given them permission to access. OpenID 2.0 was replaced by OpenID Connect, and since April 20, 2015, no longer works for Google Accounts. OpenID 2.0 support was shut down in order to focus on the newer open standard OpenID Connect, which provides greater security for your account.

================================

Are you please planning to add support for this "latest sign-in standards" or should I create OpenID itself?

Thank you in advance,
Jan Stourac.

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Spencer Bliven | 14 Jul 19:11 2015

Re: Accessing Genbank entries via biojava

Markus,

Good to hear from you! Are you still developing scabio for your class?

There has been a lot of GenBank work recently, so make sure you're using 4.1.0. There are definitely reader and writer classes. They should take an InputStream if you open an http stream. There's also a GenbankProxySequenceReader which can fetch from NCBI.

You can also post questions like this to biojava-l <at> lists.open-bio.org.

Cheers,
Spencer

On Fri, Jul 10, 2015 at 5:22 PM, Markus Gumbel <m.gumbel <at> hs-mannheim.de> wrote:

Dear Spencer,

 

I hope you remember me: We once met in Berlin and you contributed to the scabio repository. Now I have question: Is it possible with biojava4 (or 3) to access Genbank sequences directly over the web? I haven’t found any suitable classes in the javadocs and even Google isn’t very informative. Thanks for you answer!

 

Best,

 

Markus

 

 

Dr. Markus Gumbel, Professor Medical Informatics / Foreign Student Advisor at the Department of Computer Science

Mannheim University of Applied Sciences, Department of Computer Science/Institute f. Medical Informatics

Paul-Wittsack-Straße 10, D-68163 Mannheim, Germany

Phone: +49 621 292-6246, http://mi.informatik.hs-mannheim.de/gumbel/en

 

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Rose, Peter | 2 Jul 07:51 2015

[Job] Postdoctoral Fellow Computational Biology

San Diego Supercomputer Center
Postdoctoral Fellow

 
Summary: We are looking for two highly motivated post-docs as part of our
new project ³Compressive Structural Bioinformatics² funded by the US
National Institutes of Health (NIH) Big Data to Knowledge (BD2K)
initiative. 

The Challenge: To enable efficient research on the rapidly growing number
of 3D molecular structures of ever increasing size and complexity. Develop
highly scalable 3D structural search, analysis, workflow, data-exchange,
and visualization tools.

 
Qualifications: Ph.D. in structural bioinformatics, structural biology,
bioinformatics, computational biology or chemistry, computer science, or
related discipline. Experience with scientific software development as
demonstrated by publications or participation in open source software
projects. Experience with several programming languages, including Java,
JavaScript, C++, or Python, and software development tools. Strong skills
in applied mathematics and algorithm design are required. Experience with
distributed parallel computing or 3D visualization applications are a
plus. Excellent interpersonal, written, and oral presentation skills are
essential.

Note, this position is reviewed annually on the basis of performance and
can be renewed for a maximum of three years.

Our Environment:

The Structural Bioinformatics Group (http://bioinformatics.sdsc.edu
<http://bioinformatics.sdsc.edu/>) at the San Diego Supercomputer Center
(SDSC) (http://www.sdsc.edu <http://www.sdsc.edu/>) is involved in
research and development activities centered around 3D structures of
proteins and nucleic acids, the integration of structural data with other
domains such as Medicine, Genomics, Biology, Drug Discovery, and the
development of scalable solution to Big Data problems in Structural
Bioinformatics. Our group leads the RCSB Protein Data Bank (PDB)
west-coast operations. The RCSB PDB (http://www.rcsb.org
<http://www.rcsb.org/>) represents the preeminent source of experimentally
determined macromolecular structure information for research and teaching
in biology, biological chemistry, and medicine. With over 300,000 unique
users from over 160 countries around the world, the RCSB PDB is one of the
leading worldwide Biological Databases.

As an Organized Research Unit of UC San Diego, SDSC is a world leader in
data-intensive computing and cyber infrastructure, providing resources,
services, and expertise to the national research community, including
industry and academia.

 
To apply, please send cover letter and resume to Dr. Peter Rose
(pwrose <at> ucsd.edu).

 
--
Peter Rose, Ph.D.
Site Head, RCSB Protein Data Bank West (http://www.rcsb.org
<http://www.rcsb.org/>)
Principal Investigator, Structural Bioinformatics Laboratory
(http://bioinformatics.sdsc.edu <http://bioinformatics.sdsc.edu/>)
San Diego Supercomputer Center (http://www.sdsc.edu <http://www.sdsc.edu/>)
University of California, San Diego
+1-858-822-5497 <file://localhost/tel/%252B1-858-822-5497>

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Rose, Peter | 2 Jul 07:35 2015

[Job] Computational Biologist/Structural Bioinformatics/Big Data Analytics

Computational and Data Science Research Specialist

				The Structural Bioinformatics Group at the San Diego
Supercomputer Center (SDSC) is seeking an exceptional scientific
software developer to work on our new project ³Compressive Structural
Bioinformatics² funded by the US National Institutes of Health (NIH) Big
Data to Knowledge (BD2K) initiative
<https://datascience.nih.gov/bd2k/funded-programs/software>.
 The Challenge is to enable efficient research on the rapidly growing
number of 3D molecular structures of ever increasing size and
complexity, and develop highly scalable 3D structural search, analysis,
workflow, data-exchange, and visualization tools.

				Our team values open discussion and contribution. Starting from
your first day, you will shape software and services used by thousands
of people around the world. Have a great idea? Let's hear it. Want to
try a new technology? Let's learn it. Want to write code at scale? Let's
 do it. Everyone at our organization is passionate about what we do, and
 that is why we are leaders in our field. We want to hear from skilled
scientists and software developers, people passionate about their craft
and what they can bring to the field.

				The Structural Bioinformatics Group is involved in research and
development activities centered around 3D structures of proteins and
nucleic acids, the integration of structural data with other domains
such as Medicine, Genomics, Biology, Drug Discovery, and the development
 of scalable solution to Big Data problems in Structural Bioinformatics.
 Our group leads the RCSB Protein Data Bank (PDB) (http://www.rcsb.org)
west-coast operations, which represents the preeminent source of
experimentally determined macromolecular structure information for
research and teaching in biology, biological chemistry, and medicine.
With over 300,000 unique users from over 160 countries around the world,
 the RCSB PDB is one of the leading worldwide Biological Databases.

				This position researches, designs, develops, and deploys
innovative, highly scalable solutions for 3D structure visualization,
structural queries, and large-scale analyses of 3D macromolecular
complexes. Develops protocols for the efficient network data transfer
using custom compression and streaming techniques to facilitate 3D
visualization of large complexes on any device from phone, tablet, to
laptop and desktop. Designs distributed parallel workflows for
structural queries and analysis of the PDB archive.

				Qualifications:
				
					
* Bachelor's degree in Structural Bioinformatics, Bioinformatics,
 Computational Biology, Computer Science or comparable combination of
education and experience with considerable focus in scientific software
development demonstrated by publications, participation in open source
or other types of software projects. Strong skills in applied
Mathematics and algorithm design. MS or Ph.D. degree preferred.

	
				    
* Experience in the representation and data structures of
ligands, proteins, nucleic acids, and associated sequence information.
Experience with 3D structure and sequence analysis algorithms.

	
					
* Advanced experience in one or more of the following object
oriented programming languages:Java, JavaScript, C++, or Python.
Experience with software development tools including IDEs, Maven, Git,
and continuous integration tools.	

					
					
* Experience in one or more of the following: development of 3D
visualization applications and knowledge of OpenGL/WebGL, development of
 distributed parallel programming models using "Big Data" frameworks
such as Apache Hadoop or Spark, setup of these frameworks on compute
clusters, or development of workflow applications.

					
* Demonstrated effective communication and interpersonal skills.
Demonstrated ability to communicate technical information to technical
and non-technical personnel at various levels in the organization and to
 external research and education audiences.
				

				For more requirements or to apply, please view the UCSD job page
(http://jobs.ucsd.edu/bulletin/job.aspx?cat=information&sortby=post&jobnum_
in=77059).
				
				
				

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Rose, Peter | 2 Jul 07:26 2015

[Job] Java Web Developer Positions at RCSB Protein Data Bank, UC San Diego

The Research Collaboratory for Structural Bioinformatics (RCSB) Protein
Data Bank (www.rcsb.org)
 is seeking exceptional developers, and we know we're not alone in our
search. So why choose to work with us? Our team values open discussion
and contribution. Starting from your first day, you will shape software
and services used by thousands of people around the world. RCSB PDB can
trace its lineage back to the 1970's, but we still operate like a
start-up. Have a great idea? Let's hear it. Want to try a new
technology? Let's learn it. Want to write code at scale? Let's do it.
Everyone at our organization is passionate about what we do, and that is
 why we are leaders in our field. We want to hear from skilled
Developers, people passionate about their craft and what they can bring
to the field. We are currently looking for experienced developers to
join our team of agile software Developers at the University of
California, San Diego.

The RCSB Protein Data Bank (www.rcsb.org)
 is one of the world's leading biological databases with more than
300,000 unique users per month from over 160 countries. It enables
access to the singular global archive of the three-dimensional
structures of proteins and nucleic acids and is a key resource for the
design of new medicines, biofuels, nanomaterials, and enables
fundamental discoveries in biology and medicine.
Experienced web developer will be part of our agile team of
scientists and software developers who expand the capabilities of our
databases, search engines, websites, web services, and visualization and
 analysis tools. The candidate will implement cutting edge technology on
 our in-house cloud using industry standards and best web development
Practices.

QUALIFICATIONS

* BS Degree in Computer Science; or comparable combination of
education and experience with considerable focus in web and software
development.

* Experience developing the presentation layer of a
dynamic, database-driven web application using HTML, CSS, JSON,
JavaScript, JavaScript libraries, and Java/JSP. Experience in adoptive
layouts for mobile devices and browser compatibility.

* Experience with RDBMS such as MySQL, including data
modeling and experience with object-relational mapping tools such as
Hibernate. Experience with object storage, such as NoSQL databases is a
plus.

* Advanced experience in the Java programming language and Java EE
technology.

* Experience in agile software development and test-driven
design. Experience with build tools such as Maven and continuous
integration systems such as Bamboo, Jenkins, or Travis.

For more requirements or to apply, please view the UCSD job page
(https://jobs.ucsd.edu/bulletin/job.aspx?cat=new&sortby=post&jobnum_in=7589
6).

--
Peter Rose, Ph.D.
Site Head, RCSB Protein Data Bank West (http://www.rcsb.org)
San Diego Supercomputer Center (http://bioinformatics.sdsc.edu)
University of California, San Diego
+1-858-822-5497

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Rose, Peter | 27 Jun 19:30 2015

[Job] Postdoctoral positions in Big Data/Structural Bioinformatics at University of California, San Diego

Summary: We are looking for two highly motivated post-docs as part of our
new project ³Compressive Structural Bioinformatics² funded by the US
National Institutes of Health (NIH) Big Data to Knowledge (BD2K)
initiative. 

The Challenge: To enable efficient research on the rapidly growing number
of 3D molecular structures of ever increasing size and complexity. Develop
highly scalable 3D structural search, analysis, workflow, data-exchange,
and visualization tools.

Qualifications: Ph.D. in structural bioinformatics, structural biology,
bioinformatics, computational biology or chemistry, computer science, or
related discipline. Experience with scientific software development as
demonstrated by publications or participation in open source software
projects. Experience with several programming languages, including Java,
JavaScript, C++, or Python, and software development tools. Strong skills
in applied mathematics and algorithm design are required. Experience with
distributed parallel computing or 3D visualization applications are a
plus. Excellent interpersonal, written, and oral presentation skills are
essential.

Note, this position is reviewed annually on the basis of performance and
can be renewed for a maximum of three years.

Our Environment:

The Structural Bioinformatics Group (http://bioinformatics.sdsc.edu) at
the San Diego Supercomputer Center (SDSC) (http://www.sdsc.edu) is
involved in research and development activities centered around 3D
structures of proteins and nucleic acids, the integration of structural
data with other domains such as Medicine, Genomics, Biology, Drug
Discovery, and the development of scalable solution to Big Data problems
in Structural Bioinformatics. Our group leads the RCSB Protein Data Bank
(PDB) west-coast operations. The RCSB PDB (http://www.rcsb.org) represents
the preeminent source of experimentally determined macromolecular
structure information for research and teaching in biology, biological
chemistry, and medicine. With over 300,000 unique users from over 160
countries around the world, the RCSB PDB is one of the leading worldwide
Biological Databases. Our group is involved in the National Institutes of
Health (NIH) Big Data to Knowledge (BD2K) initiative.

As an Organized Research Unit of UC San Diego, SDSC is a world leader in
data-intensive computing and cyber infrastructure, providing resources,
services, and expertise to the national research community, including
industry and academia.

To apply, please send cover letter and resume to Dr. Peter Rose
(pwrose <at> ucsd.edu).

--
Peter Rose, Ph.D.
Site Head, RCSB Protein Data Bank West (http://www.rcsb.org)
Principal Investigator, Structural Bioinformatics Laboratory
(http://bioinformatics.sdsc.edu)
San Diego Supercomputer Center (http://www.sdsc.edu)
University of California, San Diego
+1-858-822-5497

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Biojava-l mailing list  -  Biojava-l <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biojava-l

Rose, Peter | 27 Jun 19:26 2015

[Job] Java Web Developers at RCSB PDB, University of California, San Diego

The RCSB PDB is seeking exceptional Developers, and we know we're not alone in our search. So why choose to work with us? Our team values open discussion and contribution. Starting from your first day, you will shape software and services used by thousands of people around the world. Our organization can trace its lineage back to the 1970's, but we still operate like a start up. Have a great idea, let's hear it. Want to try a new technology, let's learn it. Want to write code at scale, let's do it. Everyone at our organization is passionate about what we do, and that is why we are leaders in our field. We want to hear from skilled Developers, people passionate about their craft and what they can bring to the field.

We are looking for two experienced Developers to join our team of agile software Developers at the University of California, San Diego. By joining our team, a successful applicant would be able to contribute to a variety of projects ranging from:

  • Front end development using HTML, CSS, Javascript, JSP, and NodeJS

    • Our core business is our website and web services

  • Middleware development that leverages Memcached, Hibernate and RabbitMQ

    • How we scale to meet tens of thousands of unique users every day

  • Back end development using Java, MySQL/MariaDB, and NoSQL solutions

    • How we incorporate and add value to the scientific community

  • Special projects

    • Search using Apache Solr

    • Scalable solutions built on top of OpenStack, Hadoop, and Spark


The RCSB Protein Data Bank (www.rcsb.org) is one of the world’s leading biological databases with more than 300,000 unique users per month from over 160 countries. It enables access to the singular global archive of the three-dimensional structures of proteins and nucleic acids and is a key resource for the design of new medicines, biofuels, nanomaterials, and enables fundamental discoveries in biology and medicine.

Requirements:

  • BS degree in Computer Science or related field

  • A minimum of 2 years of experience developing dynamic, highly scalable, database-driven web applications using HTML, CSS, JavaScript and Java/JSP

  • Demonstrable experience with database design and systems

    • Experience with NoSQL database systems, object-relational mapping using Hibernate and distributed parallel computing is a plus

  • Citable experience using agile software development and test-driven design


For more requirements or to apply, please view the UCSD job page.

--

Peter Rose, Ph.D.

Site Head, RCSB Protein Data Bank West (http://www.rcsb.org)

Principal Investigator, Structural Bioinformatics Laboratory (http://bioinformatics.sdsc.edu)

San Diego Supercomputer Center (http://www.sdsc.edu)

University of California, San Diego

+1-858-822-5497

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Andreas Prlic | 27 Jun 00:37 2015
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BioJava 4.1.0 released

BioJava 4.1.0 has been released and is available using Maven from Maven Central as well as through manual download.

This release contains over 240 commits from 8 authors.
https://github.com/biojava/biojava/compare/5131f3aaff5a5bbbf221f5f52cfe3b849a002d87...biojava-4.1.0

BioJava 4.1.0 offers a few new features, as well several bug-fixes.

New Features:

* New algorithm for multiple structure alignments
* Improved visualization of structural alignments in Jmol
* Support for the ECOD protein classification
* Better mmCIF support: limited write support, better parsing

About BioJava:

BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats, and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language.

Happy BioJava-ing,

Andreas
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Guoying Qi | 25 Jun 15:38 2015
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Partial ORGANISM_SCIENTIFIC name returned from PDB 4xcw

For PDB 4xcw, only partial organism scientific name returned by the following method:

getOrganismScientific()
org.biojava.nbio.structure.Compound 

HELICOBACTER PYLORI (STRAIN J99 / ATCC 7

I traced back to PDBFileParser,  it seems this PDB file being treated in legacy format and the line length being trimmed into 72.

Can this problem be fixed somehow?

Thanks.

Guoying Qi
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Toorn, H.W.P. van den (Henk | 15 Jun 10:58 2015
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Fasta parsing question

Dear List,

I've just started using BioJava 4.0.0 in my projects, and wanted to ask 
a question about parsing large Fasta files. There is the option to read 
parts of the fasta file.

FastaReader.process(number)

The problem I have is that it's not documented what happens if the file 
is read in its entirety. I was expecting a null or an empty map, or even 
some exception, but none happened and the parser kept on producing 
(empty) sequences.

Could anyone enlighten me? I'm probably missing the point here. Maybe 
there is a better way to do this (there used to be the SequenceIterator 
if I remember correctly, but I can't find that in version 4.0).

Regards, Henk

My setup: windows 7 64-bit, java 1.8.0_45 64 bit, BioJava 4.0.0 via Maven.
--

-- 

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Gmane