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 Running outdated software is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
_______________________________________________
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Editor Software Section 
PLOS Computational Biology

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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
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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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Daniel Katzel | 16 Sep 05:28 2015
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converting fastq format

Sorry if this has been asked many times, but I couldn't find it when searching the mailing list or popular forums. When I follow the BioJava cookbook to convert a Sanger fastq file into an illumina fastq I get validation errors.

The cookbook

http://biojava.org/wiki/BioJava:CookBook3:FASTQ#Convert_between_FASTQ_variants_using_streaming_API

says this will work:

FastqReader fastqReader = new IlluminaFastqReader(); final FastqWriter fastqWriter = new SangerFastqWriter(); final FileWriter fileWriter = new FileWriter(new File("sanger.fastq")))); InputStream in = ...
fastqReader.stream(in, new StreamListener() { <at> Override public void fastq(final Fastq fastq) { fastqWriter.append(fileWriter, fastq); } });


But instead it throws this error:

Caused by: java.io.IOException: sequence SRR062634.1 HWI-EAS110_103327062:6:1:1092:8469/1 not fastq-illumina format, was fastq-sanger
        at org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriter.validate(IlluminaFastqWriter.java:43)
        at org.biojava.nbio.sequencing.io.fastq.AbstractFastqWriter.append(AbstractFastqWriter.java:62)
        at org.biojava.nbio.sequencing.io.fastq.AbstractFastqWriter.append(AbstractFastqWriter.java:46)

My workaround was to create a new Fastq instance inside the StreamListener#fastq() method to manually convert the quality chars


 char[] oldQual = fastq.getQuality().toCharArray();
                    char[] newQual = new char[oldQual.length];
                    for(int i=0; i< oldQual.length; i++){
                        newQual[i] = FastqVariant.FASTQ_ILLUMINA.quality(FastqVariant.FASTQ_SANGER.qualityScore(oldQual[i]));
                    }
                  
                    Fastq newFastq = new FastqBuilder().withDescription(fastq.getDescription())
                                    .withSequence(fastq.getSequence())
                                    .withQuality(new String(newQual))
                                    .withVariant(FastqVariant.FASTQ_ILLUMINA)
                                    .build();
                    try {
                        fastqWriter.append(writer, newFastq);
                    } catch (IOException e) {
                       throw new UncheckedIOException(e);
                    }


Is that the correct way to do it? Is there a better way?

Thanks
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Khalil EL MAZOUARI | 30 Aug 15:16 2015

Re: Biojava-l Digest, Vol 150, Issue 8

Hi Jose,

I was using slf4j + logback.xml. Apparently I had a conflict with logback.xml and log4j2.xml from biojava!

Replacing logback.xml by log4j2.xml fixed the problem.

Thanks for your reply.

Khalil



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  1. Re: logging level (Jose Manuel Duarte)


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Message: 1
Date: Sun, 30 Aug 2015 13:57:44 +0200
From: Jose Manuel Duarte <jose.duarte <at> psi.ch>
To: <biojava-l <at> mailman.open-bio.org>
Subject: Re: [Biojava-l] logging level
Message-ID: <55E2EFB8.3010402 <at> psi.ch>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"

Hi Khalil

How exactly are you developing/deploying your application? Do you use
maven? Have you included any log4j2 configuration file at all?

You can surely always add a log4j2.xml config file to your project, in
there you can modify any logging configuration either for biojava or any
other part of your code that uses log4j2.

[biojava uses slf4j (a meta-logging framework which can use many
underlying implementations) and then log4j2 as the default implementation ]

Jose


On 28.08.2015 17:33, Khalil EL MAZOUARI wrote:
Hi,

when I add biojava-alignment-4.1.0 and biojava-phylo-4.1.0 to my app,
my logging level changes and is set by default to WARN.

Any idea how ?override? the logging level from biojava-4?

Thanks



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Khalil EL MAZOUARI | 28 Aug 17:33 2015

logging level

Hi,

when I add biojava-alignment-4.1.0 and biojava-phylo-4.1.0 to my app, my logging level changes and is set by default to WARN.

Any idea how ‘override’ the logging level from biojava-4?

Thanks



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Rose, Peter | 24 Aug 20:20 2015

[Job] Web Developer position at RCSB PDB at UCSD

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.

    For more information about SDSC, please visit: www.sdsc.edu


QUALIFICATIONS

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SPECIAL CONDITIONS

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The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, gender identity or sexual orientation. For the complete University of California nondiscrimination and affirmative action policy see: http://www-hr.ucsd.edu/saa/nondiscr.html



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University of California, San Diego
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Rose, Peter | 24 Aug 20:10 2015

[Job] Postdoctoral Position in Structural Bioinformatics at UCSD

Summary: We are looking for a highly motivated post-doc as part of our new project “Compressive Structural Bioinformatics” 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: 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.

 

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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).

 



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Jose Manuel Duarte | 15 Aug 10:18 2015
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Re: (no subject)

Hi Aditya

First of all some mail list etiquette: please always send your replies to the list so that everyone can benefit from the answers, second try to always have a subject so that people can easily find out if they are interested in the thread.

Regarding your question, in the biojava wiki we have a guide to set it up in Netbeans (simplest is option 3):

http://biojava.org/wiki/How_to_integrate_BioJava_in_NetBeans_IDE

I don't have so much experience with Netbeans, only with eclipse. For how to set up with eclipse, see:

http://biojava.org/wiki/BioJava3_eclipse

(especially option 3, which is the simplest and should work well with eclipse 4.4 or later)

Biojava uses maven as a build system and to take care of the external dependencies (like slf4j). Although not required for your project, it is recommendable to use maven in your project since it will make things easier. This is a quick guide to setting up a new maven project:

https://spring.io/guides/gs/maven/

Hope this helps

Jose


On 15.08.2015 06:21, ADITYA MANTHA wrote:
Thank you very much . But I am getting a "org/slf4j/LoggerFactory"  error . Even if i add the .jar file of slf4j , i am still having a problem . So can you tell me what all .jar files i have to install to use biojava in netbeans environment .

On Sat, Aug 15, 2015 at 2:06 AM, Jose Manuel Duarte <jose.duarte <at> psi.ch> wrote:
How to get and parse data from the PDB:

https://github.com/biojava/biojava-tutorial/blob/master/structure/firststeps.md

How to get the data once parsed the file into a Structure object:

https://github.com/biojava/biojava-tutorial/blob/master/structure/structure-data-model.md

Jose



On 14.08.2015 22:30, ADITYA MANTHA wrote:
well , i tried to. But i could not find a proper solution . Can you tell the specific example with some sample codes . As i am new to BioInformatics .

On Sat, Aug 15, 2015 at 1:48 AM, Jose Manuel Duarte <jose.duarte <at> psi.ch> wrote:
Did you check the biojava tutorial? It explains how to do the file parsing and how to retrieve the data:

https://github.com/biojava/biojava-tutorial

Jose




On 14.08.2015 20:13, ADITYA MANTHA wrote:
Currently, I am trying to implement Chou Fasman Algorithm in Java . For this i need to retrieve information regarding Name , Primary Sequence and Secondary Structure information  . Can someone help me out how to parse this data from a PDB file .

--
Best Regards

ADITYA MANTHA
Sophomore
Instrumentation Engineering
Department of Electrical Engineering
IIT KHARAGPUR
9800192364


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--
Best Regards

ADITYA MANTHA
Sophomore
Instrumentation Engineering
Department of Electrical Engineering
IIT KHARAGPUR
9800192364




--
Best Regards

ADITYA MANTHA
Sophomore
Instrumentation Engineering
Department of Electrical Engineering
IIT KHARAGPUR
9800192364

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Jose Manuel Duarte | 14 Aug 22:36 2015
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Re: (no subject)

How to get and parse data from the PDB:

https://github.com/biojava/biojava-tutorial/blob/master/structure/firststeps.md

How to get the data once parsed the file into a Structure object:

https://github.com/biojava/biojava-tutorial/blob/master/structure/structure-data-model.md

Jose


On 14.08.2015 22:30, ADITYA MANTHA wrote:
well , i tried to. But i could not find a proper solution . Can you tell the specific example with some sample codes . As i am new to BioInformatics .

On Sat, Aug 15, 2015 at 1:48 AM, Jose Manuel Duarte <jose.duarte <at> psi.ch> wrote:
Did you check the biojava tutorial? It explains how to do the file parsing and how to retrieve the data:

https://github.com/biojava/biojava-tutorial

Jose




On 14.08.2015 20:13, ADITYA MANTHA wrote:
Currently, I am trying to implement Chou Fasman Algorithm in Java . For this i need to retrieve information regarding Name , Primary Sequence and Secondary Structure information  . Can someone help me out how to parse this data from a PDB file .

--
Best Regards

ADITYA MANTHA
Sophomore
Instrumentation Engineering
Department of Electrical Engineering
IIT KHARAGPUR
9800192364


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--
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ADITYA MANTHA
Sophomore
Instrumentation Engineering
Department of Electrical Engineering
IIT KHARAGPUR
9800192364

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Gmane