Jose Duarte | 4 May 02:08 2016

BioJava 4.2.1 released

BioJava 4.2.1 has been released and is available using Maven from Maven Central as well as manual download. This is purely a bug fix release correcting issues found since the 4.2.0 release.

Please see the full release notes at:




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!

Jose
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Rose, Peter | 2 May 23:46 2016

Postdoc position: Structural Bioinformatics/Big Data at UC San Diego

Summary: We are looking for a highly motivated postdoc as part of our new project “Compressive Structural Bioinformatics” 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. Current algorithms used in Structural Bioinformatics do not scale well with the rapid growth in structural data. In this project, we will employ the latest advances in computer science to develop highly scalable, distributed parallel algorithms to overcome these limitations.

 

Qualifications: Ph.D. in one or more of the following research areas

·      Computer Science with a focus on large scale scientific computing

·      Structural Bioinformatics with a focus on new methods development

·      Computational Structural Biology with a focus on improved structure solution methods

 

Experience with the development and performance optimization of scientific software. Demonstrated proficiency in a high-level programming language, such as Java or Python and experience with state of the art software development tools. Strong skills in applied mathematics and algorithm design are required. High productivity demonstrated by publications and contributions to open source software projects. Experience in the development and application of modern distributed parallel computing environments, such as Apache Big Data projects including Apache Spark is 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 two 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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Andreas Prlic | 9 Apr 21:08 2016
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biojava wiki update

Hi,

The BioJava wiki page at biojava.org went down a few days ago due to a server hack that is still being investigated. In the meanwhile we have switched the homepage 


to the developmental new homepage that is built on top of jekyll and github pages at


I just did another conversion of the mediawiki database to markdown and pushed it there. There is still a lot of cleanup required but I feel that we should move forward and work on making this the new and permanent biojava.org site.

There are still some unsolved problems: e.g. how do we host javadocs and the downloads that we used to provide. Much of the download nowadays happens via maven central, but we still have a few custom files.

Andreas

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Spencer Bliven | 15 Mar 15:58 2016
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BioJava Wiki

I have finished upgrading the BioJava wiki. In an effort to curb spam, users are now required to log in using a Google account. This is more secure for you, since your password is seen only by Google and not by this wiki, and also greatly reduces spam accounts.

If you previously used the email address associated with your google account on this wiki, your account should be automatically connected. If not, a new user will automatically be created based on your email address. If you previously used non-google email with your account and would like to keep the same username, DO NOT log in. Instead, email spencer.bliven <at> gmail.com with your username and google-associated email for manual conversion.

Sorry for the hassle, and please let me know if anything appears broken.


-Spencer

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Jose Duarte | 11 Mar 20:53 2016

BioJava 4.2.0 released

BioJava 4.2.0 has been released and is available using Maven from Maven Central as well as through manual download.

This release contains over 750 commits from 10 contributors.


BioJava 4.2.0 offers a few new features, as well as many bug-fixes. It is the fist release that requires Java 1.7 as a minimum. 

New Features:

* Secondary structure assignment full implementation (DSSP compatible)
* New SearchIO framework to interface blast (or blast-like) searches
* Unified StructureIdentifier framework
* More complete mmCIF and chemical components parsing: bonds, sites, charges
* Many improvements in symmetry detection code


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!

Jose

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Rose, Peter | 1 Mar 07:41 2016

[Job] Postdoctoral position: Big Data/Computational Biology at UC San Diego

Summary: We are looking for a highly motivated postdoc as part of our new project “Compressive Structural Bioinformatics” 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. Current algorithms used in Structural Bioinformatics do not scale well with the rapid growth in structural data. In this project, we will employ the latest advances in computer science to develop highly scalable, distributed parallel algorithms to overcome these limitations.

 

Qualifications: Ph.D. in one or more of the following research areas

·       Computer Science with a focus on large scale scientific computing

·       Structural Bioinformatics with a focus on new methods development

·       Computational Structural Biology with a focus on improved structure solution methods

 

Experience with the development and performance optimization of scientific software. Demonstrated proficiency in a high-level programming language, such as Java or Python and experience with state of the art software development tools. Strong skills in applied mathematics and algorithm design are required. High productivity demonstrated by publications and contributions to open source software projects. Experience in the development and application of modern distributed parallel computing environments, such as Apache Big Data projects including Apache Spark is 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 two 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    
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Spencer Bliven | 29 Feb 18:15 2016
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Row order from multiple sequence alignment

I'm creating a multiple sequence alignment using Alignments.getMultipleSequenceAlignment, as described in the cookbook. The problem is that the returned profile has rows in a different order than the input array of sequenced. How can I map from an index in the inputs to the rows of the profile?

Thanks,
Spencer

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Andreas Prlic | 12 Jan 19:06 2016
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Re: [Biojava-dev] Increasing Java version requirement for BioJava

Based on some RCSB PDB analytics data, I'd estimate that about 2/3 of all users are already on 1.8. However there is still a significant number of users on 1.7 (somewhere around 1/4). 

As such my vote is to upgrade to 1.7 for now and move to 1.8 at some point in the future, when 1.7 usage has declined further.

Andreas






On Tue, Jan 12, 2016 at 8:56 AM, Terry Casstevens <tmc46 <at> cornell.edu> wrote:
Dear Spencer,

I'm the lead developer for the Tassel software, and we use the Biojava
libraries.  We've required Java 8 for Tassel since August 2014.  If
you change, some users will need to upgrade Java regardless.  I
recommend going to Java 8.

maizegenetics.net/tassel

Best,

Terry


On Tue, Jan 12, 2016 at 7:16 AM, Spencer Bliven
<spencer.bliven <at> gmail.com> wrote:
> There has been some informal discussion of increasing the Java version
> requirement for BioJava from the current Java 6 to either 7 or 8. It would
> be great to hear from the larger BioJava community about whether this would
> be a welcome change or not.
>
> I will start the discussion by listing what I see as the pros and cons of
> setting each version as the minimum requirement for BioJava.
>
> Java 6:
> ---------
> + Greatest backwards compatibility
> - No updates since Feb 2013*
> - Some dependencies are not compatible, requiring the use of older versions
> (currently only log4j, but could be others in the future)
>
> Java 7:
> ---------
> + Most popular version currently
> + Some minor language features added
> - No updates since Apr 2015*
>
> Java 8:
> ---------
> + Tons of awesome new programming features, e.g. lambda functions
> + Only version supported by Oracle
> - Not available for many systems
>
> * Note that all versions are backwards compatible, so you can always use a
> more up-to-date JDK for downstream projects. Running outdated software is
> generally a bad idea, so users are encouraged to use the Java 8 JRE,
> regardless of the minimum BioJava requirement.
>
>
> One thing I would like to get a sense of is how many BioJava users are still
> using 6 and 7. <at> emckee2006 mentioned on github that they still have some
> servers on 6. I know that getting Java 8 installed on CentOS is rather
> painful, so probably some users haven't yet updated to 8.
>
> Let me know if I missed anything!
>
>
> Cheers,
>
> Spencer
>
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev <at> mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biojava-dev
_______________________________________________
biojava-dev mailing list
biojava-dev <at> mailman.open-bio.org
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--
-----------------------------------------------------------------------
Dr. Andreas Prlic
RCSB PDB Protein Data Bank
Technical & Scientific Team Lead
University of California, San Diego

Editor Software Section 
PLOS Computational Biology

BioJava Project Lead
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Steve Darnell | 12 Jan 18:58 2016

Re: [Biojava-dev] Increasing Java version requirement for BioJava

Hi Spencer,

TL;DR +1 Java 8

I am a senior scientist and team lead at DNASTAR. After nearly 2 years since general availability, we have
begun our migration to Java 8. The new language features in Java 8 make it more desirable for development
than Java 7 and it is the only version of Java with public updates (all others require paid support).  Java 8
is also widely deployable.

* Windows: Vista, 7, 8, Server 2008
* Mac OS X: 10.8+
* Linux: Oracle 5.5+, RHEL 5.5+, Suse 10 SP2+, Ubuntu 12.04+
* Solaris: 10 Update 9+

I feel we have been pretty conservative with our decision to upgrade. I also recommend BioJava skip to Java 8.

-Steve

-----Original Message-----
From: biojava-dev [mailto:biojava-dev-bounces+darnells=dnastar.com <at> mailman.open-bio.org] On
Behalf Of Terry Casstevens
Sent: Tuesday, January 12, 2016 10:56 AM
To: Spencer Bliven
Cc: biojava-dev; Biojava-l <at> lists.open-bio.org
Subject: Re: [Biojava-dev] Increasing Java version requirement for BioJava

Dear Spencer,

I'm the lead developer for the Tassel software, and we use the Biojava libraries.  We've required Java 8 for
Tassel since August 2014.  If you change, some users will need to upgrade Java regardless.  I recommend
going to Java 8.

maizegenetics.net/tassel

Best,

Terry

On Tue, Jan 12, 2016 at 7:16 AM, Spencer Bliven <spencer.bliven <at> gmail.com> wrote:
> There has been some informal discussion of increasing the Java version 
> requirement for BioJava from the current Java 6 to either 7 or 8. It 
> would be great to hear from the larger BioJava community about whether 
> this would be a welcome change or not.
>
> I will start the discussion by listing what I see as the pros and cons 
> of setting each version as the minimum requirement for BioJava.
>
> Java 6:
> ---------
> + Greatest backwards compatibility
> - No updates since Feb 2013*
> - Some dependencies are not compatible, requiring the use of older 
> versions (currently only log4j, but could be others in the future)
>
> Java 7:
> ---------
> + Most popular version currently
> + Some minor language features added
> - No updates since Apr 2015*
>
> Java 8:
> ---------
> + Tons of awesome new programming features, e.g. lambda functions Only 
> + version supported by Oracle
> - Not available for many systems
>
> * Note that all versions are backwards compatible, so you can always 
> use a more up-to-date JDK for downstream projects. Running outdated 
> software is generally a bad idea, so users are encouraged to use the 
> Java 8 JRE, regardless of the minimum BioJava requirement.
>
>
> One thing I would like to get a sense of is how many BioJava users are 
> still using 6 and 7.  <at> emckee2006 mentioned on github that they still 
> have some servers on 6. I know that getting Java 8 installed on CentOS 
> is rather painful, so probably some users haven't yet updated to 8.
>
> Let me know if I missed anything!
>
>
> Cheers,
>
> Spencer
>
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev <at> mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biojava-dev
_______________________________________________
biojava-dev mailing list
biojava-dev <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biojava-dev

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Spencer Bliven | 12 Jan 13:16 2016
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Increasing Java version requirement for BioJava

There has been some informal discussion of increasing the Java version requirement for BioJava from the current Java 6 to either 7 or 8. It would be great to hear from the larger BioJava community about whether this would be a welcome change or not.

I will start the discussion by listing what I see as the pros and cons of setting each version as the minimum requirement for BioJava.

Java 6:
---------
+ Greatest backwards compatibility
- No updates since Feb 2013*
- Some dependencies are not compatible, requiring the use of older versions (currently only log4j, but could be others in the future)

Java 7:
---------
+ Most popular version currently
+ Some minor language features added
- No updates since Apr 2015*

Java 8:
---------
+ Tons of awesome new programming features, e.g. lambda functions
+ Only version supported by Oracle
- Not available for many systems

* Note that all versions are backwards compatible, so you can always use a more up-to-date JDK for downstream projects. Running outdated software is generally a bad idea, so users are encouraged to use the Java 8 JRE, regardless of the minimum BioJava requirement.


One thing I would like to get a sense of is how many BioJava users are still using 6 and 7. <at> emckee2006 mentioned on github that they still have some servers on 6. I know that getting Java 8 installed on CentOS is rather painful, so probably some users haven't yet updated to 8.

Let me know if I missed anything!


Cheers,

Spencer


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Christopher Gillies | 16 Dec 16:45 2015
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org.biojava.nbio.genome.parsers.gff.Location union() and intersect() do not work as described in API

Hi biojava,

I am using version 4.1.0 and I am getting some unexpected behavior from the Location class.

Please see the unit test below. The union operator returns 51227381 as the bioEnd() but it should be 51227382.

Location l1 = Location.fromBio(51227320, 51227381, '+');
Location l2 = Location.fromBio(51227323, 51227382, '+');

Location union = l1.union(l2);
assertEquals(51227320,union.bioStart());
assertEquals(51227382,union.bioEnd());

The documentation for the intersection method says that it will return null when there is no overlap for two
locations, but the code appears to fail for boundary conditions. The following unit test fails.
Shouldn’t the intersection method return null for this test case?

Location l1 = Location.fromBio(100, 200, '+');
Location l2 = Location.fromBio(1, 99, '+');
Location intersection = l1.intersection(l2);
assertNull(intersection);

Thanks,

Chris
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Gmane