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

    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.

SPECIAL CONDITIONS

    A background check is required.


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



-- 
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 | 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.

 

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)

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

University of California, San Diego

+1-858-822-5497

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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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--
Best Regards

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

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ADITYA MANTHA | 14 Aug 20:13 2015
Picon

(no subject)

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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John Stalker | 7 Aug 15:29 2015

Constructing (wrapping) DNASequence from a SequenceView<NucleotideCompound>

Hi there,
  I’m working on some code multi-frame translation code and I think I’m missing a fundamental property here.

  I want to be using DNASequence, RNASequence, and ProteinSequence classes, but operations I’m using end up returning Sequence<C> or SequenceView<C>.  What is the conversion / wrapper path from the latter to the former?

  So for example, if I get a subSequence from DNASequence, I have a SequenceView<NucleotideCompound>.  How do I wrap that in a new DNASequence?  Similarly, when I have instances of Sequence<AminoAcidCompound> (the result of TranscriptionEngine.multipleFrameTranslation), how do I wrap that with ProteinSequence?
  Looking a the constructors for the main *Sequence classes, there’s nothing (save String) that stands out.  The implementations of SequenceReader (for DNASequence) and ProxySequenceReader (for RNASequence and ProteinSequence…why are these not all the same interface is another question) don’t stand out as being appropriate.

  I’m might just be dense here, but any help would be appreciated!  Thanks!
John
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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
Picon

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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