From hlapp at drycafe.net  Sat Feb  5 18:45:47 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 5 Feb 2011 18:45:47 -0500
Subject: [Biojava-l] NESCent Seeks Hackathon Whitepapers
In-Reply-To: <0D7D89E4-C0D4-4347-A94C-21800E927746@ad.unc.edu>
References: <BF0025BB-27BC-440C-83A4-77172421C9C8@ad.unc.edu>
	<E3EBA44A-EFE4-4279-BD4D-38FC9D190413@nescent.org>
	<0D7D89E4-C0D4-4347-A94C-21800E927746@ad.unc.edu>
Message-ID: <066A2391-6041-408C-B26E-9B867DE785C7@drycafe.net>

The National Evolutionary Synthesis Center (NESCent), in keeping with  
its objective to promote collaborative development of open-source,  
reusable, and standards-supporting informatics resources, sponsors  
highly collaborative, face-to-face software development events, called  
"hackathons" (see [1]). To ensure that this program continues to be  
responsive to user needs and to tap into the expertise and creativity  
of the evolutionary biology community, NESCent is soliciting short  
whitepapers (2-6 pages) [2] on potential target areas for future  
hackathons.

To further encourage submissions, we have now distilled specific  
guidelines for proposing hackathon events, based on the experiences  
gained from events we have sponsored in the past:
http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines

The Center's Call for Informatics Whitepapers [3] includes not only  
hackathons, but also a large spectrum of other initiatives to be  
undertaken by the Center, including training, software development,  
collaborative ontology development, and coordination of data  
standards. Whitepapers are accepted at any time and reviewed on an on- 
going basis.

URLs:
[1] Collaborative cyberinfrastructure events and programs organized by  
NESCent:
http://informatics.nescent.org/wiki/Main_Page

[2] NESCent Call for Informatics Whitepapers
http://www.nescent.org/informatics/whitepapers.php

[3] Hackathon Whitepaper Guidelines:
http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines

[4] Past NESCent-sponsored hackathons:
http://informatics.nescent.org/wiki/Main_Page#Hackathons

From jayunit100 at gmail.com  Mon Feb  7 13:44:05 2011
From: jayunit100 at gmail.com (Jay Vyas)
Date: Mon, 7 Feb 2011 13:44:05 -0500
Subject: [Biojava-l] average or minimal energy structure for nmr
	structures...
Message-ID: <AANLkTikomYdY00izx-MMjUcORDmCBE=yZ7SsjDLJjEZr@mail.gmail.com>

Hi guys : Does anybody know a simple biojava way to calculate an average
structure, or alternatively, find the lowest energy structure from an nmr
structure with multiple models  ?
Im doing it using a set of nested for loops... I thought maybe there might
be support in the api.


  for(Group g1 : c.getAtomGroups())

for(Atom a1 : g1.getAtoms())

{

                       float xAvg,yAvg,zAvg;

for(int i = 0 ; i < s.nrModels(); i++)

{

                             ///etc....

}



}

-- 
Jay Vyas
MMSB/UCHC

From andreas at sdsc.edu  Tue Feb  8 01:38:14 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 7 Feb 2011 22:38:14 -0800
Subject: [Biojava-l] average or minimal energy structure for nmr
	structures...
In-Reply-To: <AANLkTikomYdY00izx-MMjUcORDmCBE=yZ7SsjDLJjEZr@mail.gmail.com>
References: <AANLkTikomYdY00izx-MMjUcORDmCBE=yZ7SsjDLJjEZr@mail.gmail.com>
Message-ID: <AANLkTik5cW47w2gT+XPkKwOGE8fTg4qzQh6ztuN4K0rS@mail.gmail.com>

Hi Jay,

You could calculate average coordinates and RMSD with BioJava. However
in terms of energy calculations BioJava can't do much so far...

Andreas

On Mon, Feb 7, 2011 at 10:44 AM, Jay Vyas <jayunit100 at gmail.com> wrote:
> Hi guys : Does anybody know a simple biojava way to calculate an average
> structure, or alternatively, find the lowest energy structure from an nmr
> structure with multiple models ??
> Im doing it using a set of nested for loops... I thought maybe there might
> be support in the api.
>
>
> ?for(Group g1 : c.getAtomGroups())
>
> for(Atom a1 : g1.getAtoms())
>
> {
>
> ? ? ? ? ? ? ? ? ? ? ? float xAvg,yAvg,zAvg;
>
> for(int i = 0 ; i < s.nrModels(); i++)
>
> {
>
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ///etc....
>
> }
>
>
>
> }
>
> --
> Jay Vyas
> MMSB/UCHC
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From uchathuranga at gmail.com  Wed Feb  9 00:19:00 2011
From: uchathuranga at gmail.com (udana chathuranga)
Date: Wed, 9 Feb 2011 10:49:00 +0530
Subject: [Biojava-l] Project Ideas GSOC 2011
Message-ID: <AANLkTi=YSJFNPWT9Mj6zS+nH7vKoRiraTYES5NvG6mtd@mail.gmail.com>

hi,

I am a student a University of Moratuwa , Sri lanka. I am planning to
participate gsoc 2011 and I would like to work on a project regarding
bioinfomatics. So I would like to know whether you are planning to be a
mentor organization this year also. If so i would like to know what kinds of
projects that you are planning to propose.

Thanks
Regard
udana

From andreas at sdsc.edu  Wed Feb  9 00:49:23 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 8 Feb 2011 21:49:23 -0800
Subject: [Biojava-l] Project Ideas GSOC 2011
In-Reply-To: <AANLkTi=YSJFNPWT9Mj6zS+nH7vKoRiraTYES5NvG6mtd@mail.gmail.com>
References: <AANLkTi=YSJFNPWT9Mj6zS+nH7vKoRiraTYES5NvG6mtd@mail.gmail.com>
Message-ID: <AANLkTikvuhaxu2wgkbQseiLGWoL6nPDDpq0sF1KHrWnB@mail.gmail.com>

Hi Udana,

It is a bit early, but given the success form last year I think it is
for sure that BioJava (as part of the the Open Bioinformatics
Foundation) will apply again to become a mentoring organisation.
Google will announce the list of accepted mentoring organizations on
March 18th, afterwards the time to discuss proposals will start.

http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs#timeline

Last year we had several Mentor proposed projects. Google is also very
interested in seeing student proposed projects and they recommend
those due to their high success rate. If you want to prepare a
proposal you could already start thinking of what kind of project you
would like to work on. Similarly, everybody else who wants to propose
a project and perhaps become a mentor can also start to think about
that. Still we will have to wait until March 18th before we will know
if there is actually any funding this year.

Andreas


On Tue, Feb 8, 2011 at 9:19 PM, udana chathuranga
<uchathuranga at gmail.com> wrote:
> hi,
>
> I am a student a University of Moratuwa , Sri lanka. I am planning to
> participate gsoc 2011 and I would like to work on a project regarding
> bioinfomatics. So I would like to know whether you are planning to be a
> mentor organization this year also. If so i would like to know what kinds of
> projects that you are planning to propose.
>
> Thanks
> Regard
> udana
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From uchathuranga at gmail.com  Wed Feb  9 01:13:34 2011
From: uchathuranga at gmail.com (udana chathuranga)
Date: Wed, 9 Feb 2011 11:43:34 +0530
Subject: [Biojava-l] Project Ideas GSOC 2011
In-Reply-To: <AANLkTikvuhaxu2wgkbQseiLGWoL6nPDDpq0sF1KHrWnB@mail.gmail.com>
References: <AANLkTi=YSJFNPWT9Mj6zS+nH7vKoRiraTYES5NvG6mtd@mail.gmail.com>
	<AANLkTikvuhaxu2wgkbQseiLGWoL6nPDDpq0sF1KHrWnB@mail.gmail.com>
Message-ID: <AANLkTimBMbvyT=O8+cc2efJ5FwHtFtf_m+uZtX2WCuDc@mail.gmail.com>

Hi Andreas,

Thanks for the quick reply.I appreciate your help and I want know how I can
contribute to the project even if you are not participating for this year
gsoc project. I have studied bioinfomatics as one of my subject in the
university and I would like to apply those knowledge in to this project. I
would be thankful if you can guide me to start to participate in the
project.
I have solid background on java and bioinomatics related areas like
    Biological Sequence data analysis -

The Sequence assembly problem, The Gene Finding Problem, The Sequence
Alignment Problem, The Genome Rearrangement problem, The Protein Folding
Problem, The Motif Discovery Problem

    Phylogenetics

    Biological Network Motifs


Above mention areas are some of the subjects that I have learned in our
course and I would like to know how can I apply this knowledge to this
project?




Thanks

Regards

Udana

From andreas at sdsc.edu  Wed Feb  9 11:27:35 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 9 Feb 2011 08:27:35 -0800
Subject: [Biojava-l] Project Ideas GSOC 2011
In-Reply-To: <AANLkTimBMbvyT=O8+cc2efJ5FwHtFtf_m+uZtX2WCuDc@mail.gmail.com>
References: <AANLkTi=YSJFNPWT9Mj6zS+nH7vKoRiraTYES5NvG6mtd@mail.gmail.com>
	<AANLkTikvuhaxu2wgkbQseiLGWoL6nPDDpq0sF1KHrWnB@mail.gmail.com>
	<AANLkTimBMbvyT=O8+cc2efJ5FwHtFtf_m+uZtX2WCuDc@mail.gmail.com>
Message-ID: <AANLkTimEmbFJJ_CC14KuoY04agd2+WkyzQTVeKAn1pdv@mail.gmail.com>

Hi Udana,

There is some overlap between your background and many aspects of
BioJava. I recommend taking a look at the Cookbook for a start
learning more about BioJava. To give you an idea of what was going on
last year, the two biojava related projects that were funded were

A) Development of an all Java multiple sequence alignment module
B) Identification and classification of posttranslational protein modifications.

Here the project pages for more details:
http://biojava.org/wiki/Google_Summer_of_Code

Andreas

On Tue, Feb 8, 2011 at 10:13 PM, udana chathuranga
<uchathuranga at gmail.com> wrote:
> Hi Andreas,
>
> Thanks for the quick reply.I appreciate your help and I want know how I can
> contribute to the project even if you are not participating for this year
> gsoc project. I have studied bioinfomatics as one of my subject in the
> university and I would like to apply those knowledge in to this project. I
> would be thankful if you can guide me to start to participate in the
> project.
> I have solid background on java and bioinomatics related areas like
> ? ? Biological Sequence data analysis -
>
> The Sequence assembly problem, The Gene Finding Problem, The Sequence
> Alignment Problem, The Genome Rearrangement problem, The Protein Folding
> Problem, The Motif Discovery Problem
>
> ??? Phylogenetics
>
> ??? Biological Network Motifs
>
> Above mention areas are some of the subjects that I have learned in our
> course and I would like to know how can I apply this knowledge to this
> project?
>
>
> Thanks
>
> Regards
>
> Udana
>


From uchathuranga at gmail.com  Wed Feb  9 13:45:55 2011
From: uchathuranga at gmail.com (udana chathuranga)
Date: Thu, 10 Feb 2011 00:15:55 +0530
Subject: [Biojava-l] Project Ideas GSOC 2011
In-Reply-To: <AANLkTimEmbFJJ_CC14KuoY04agd2+WkyzQTVeKAn1pdv@mail.gmail.com>
References: <AANLkTi=YSJFNPWT9Mj6zS+nH7vKoRiraTYES5NvG6mtd@mail.gmail.com>
	<AANLkTikvuhaxu2wgkbQseiLGWoL6nPDDpq0sF1KHrWnB@mail.gmail.com>
	<AANLkTimBMbvyT=O8+cc2efJ5FwHtFtf_m+uZtX2WCuDc@mail.gmail.com>
	<AANLkTimEmbFJJ_CC14KuoY04agd2+WkyzQTVeKAn1pdv@mail.gmail.com>
Message-ID: <AANLkTim5559ixchSSXNxVJLwcDYXH_R0u0_rxJhyFBKd@mail.gmail.com>

Hi Andreas,

First of all thanks for the guide.i have started reading the CookBook in
http://biojava.org/wiki/BioJava:CookBook. I have also did some sample coding
using the biojava3-core and found this
http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite and looked in
details about the fasta file format.About fasta file format I studied about
in the link http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml.

As you pointed out I have also looked in the last years two gsoc
projects.After going through those project I had this question what kinds of
modules that I can work on. I would like hear some suggestions about modules
that you are looking forward to.

I also like to know what kinds of file formats that I should look into in
the future in order to develop a good module to the system.

Thanks
regards
Udana

From jayunit100 at gmail.com  Wed Feb  9 14:22:05 2011
From: jayunit100 at gmail.com (Jay Vyas)
Date: Wed, 9 Feb 2011 14:22:05 -0500
Subject: [Biojava-l] average structure
Message-ID: <AANLkTikjULh4EYxKBLW1qeooPDWPp+aG_ivZ8MHfZ91+@mail.gmail.com>

Hi Guys : I was also wondering if biojava supported creating an average or
mean structure from a bundle........

-- 
Jay Vyas
MMSB/UCHC

From andreas at sdsc.edu  Wed Feb  9 16:48:40 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 9 Feb 2011 13:48:40 -0800
Subject: [Biojava-l] average structure
In-Reply-To: <AANLkTikjULh4EYxKBLW1qeooPDWPp+aG_ivZ8MHfZ91+@mail.gmail.com>
References: <AANLkTikjULh4EYxKBLW1qeooPDWPp+aG_ivZ8MHfZ91+@mail.gmail.com>
Message-ID: <AANLkTi=2pQfxZWLBRY4d=azcGEoxxLVwU3QEZ3XJuKhv@mail.gmail.com>

A geometric average should be easy to calculate. All NMR models have
the same number of atoms, so you could just average over all
alternative positions for an atom and use that to build up a mean
structure... However I would take that with a grain of salt and make
sure there are no distance violations by visual inspection and some
quality control scripts. There are standard/ideal coordinates
available for all amino acids, that you could use to compare with the
distances between atoms in your average structure.

Andreas

On Wed, Feb 9, 2011 at 11:22 AM, Jay Vyas <jayunit100 at gmail.com> wrote:
> Hi Guys : I was also wondering if biojava supported creating an average or
> mean structure from a bundle........
>
> --
> Jay Vyas
> MMSB/UCHC
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From craig.adrian.berry at gmail.com  Fri Feb 11 05:54:35 2011
From: craig.adrian.berry at gmail.com (Craig Berry)
Date: Fri, 11 Feb 2011 10:54:35 +0000
Subject: [Biojava-l] GFF3 Reader
Message-ID: <AANLkTikxH=P7tvh_9GtOjkBqh5Y0g1aq5qUhpD6K83F2@mail.gmail.com>

Can I just have someone validate this logic in the GFF3Reader for me
to see if this is a bug or not.

If I have a GFF3 file with the following line:

chrI	SGD	repeat_region	1	62	.	-	.	ID=TEL01L-TR;Name=TEL01L-TR;Note=Terminal%20stretch%20of%20telomeric%20repeats%20on%20the%20left%20arm%20of%20Chromosome%20I;dbxref=SGD:S000028864

When parsing the file then, the class calls Location.fromBio using the
start 1, end 62 and strand ?ve.
Since the strand is ?ve it needs to convert the positions to negative
values and reverse the start and end. However, as the javadocs
explains:

?In biocoordinates, the start index of a range is represented in
origin 1 (ie the very first index is 1, not 0),  and end= start +
length - 1.?

So before the end is reassigned its value is reduced by 1 and then
negated: e = - ( start ? 1) With a start value of 1 as in this case,
the end then becomes 0, such that the range now runs -62 to 0.

This causes a problem when adding this Feature to the feature
collection since it considers a position of value 0 to be on the +ve
strand, such that when Location.plus() is called the check for a
negative location (i.e. both start and end being < 0) returns false
and so you end up trying to create a Location with a ?ne start
position but a +ve end, which throws an IllegalArgumentException.

So is there something fishy here or not? I?m assuming that the GFF
content is valid.

Thanks in advance

Craig


From willishf at ufl.edu  Fri Feb 11 09:14:08 2011
From: willishf at ufl.edu (Scooter Willis)
Date: Fri, 11 Feb 2011 09:14:08 -0500
Subject: [Biojava-l] GFF3 Reader
In-Reply-To: <AANLkTikxH=P7tvh_9GtOjkBqh5Y0g1aq5qUhpD6K83F2@mail.gmail.com>
References: <AANLkTikxH=P7tvh_9GtOjkBqh5Y0g1aq5qUhpD6K83F2@mail.gmail.com>
Message-ID: <AANLkTim+WbePP6GCYN8aVv-dp4s6ijW_ucfdPJigne=3@mail.gmail.com>

Craig

I think I fixed this problem but not sure if it is in the current
released jar files. The < logic was wrong where 0 wasn't be treated
properly. I will send you an update jar to see if the problem goes
away.

Scooter

On Fri, Feb 11, 2011 at 5:54 AM, Craig Berry
<craig.adrian.berry at gmail.com> wrote:
> Can I just have someone validate this logic in the GFF3Reader for me
> to see if this is a bug or not.
>
> If I have a GFF3 file with the following line:
>
> chrI ? ?SGD ? ? repeat_region ? 1 ? ? ? 62 ? ? ?. ? ? ? - ? ? ? . ? ? ? ID=TEL01L-TR;Name=TEL01L-TR;Note=Terminal%20stretch%20of%20telomeric%20repeats%20on%20the%20left%20arm%20of%20Chromosome%20I;dbxref=SGD:S000028864
>
> When parsing the file then, the class calls Location.fromBio using the
> start 1, end 62 and strand ?ve.
> Since the strand is ?ve it needs to convert the positions to negative
> values and reverse the start and end. However, as the javadocs
> explains:
>
> ?In biocoordinates, the start index of a range is represented in
> origin 1 (ie the very first index is 1, not 0), ?and end= start +
> length - 1.?
>
> So before the end is reassigned its value is reduced by 1 and then
> negated: e = - ( start ? 1) With a start value of 1 as in this case,
> the end then becomes 0, such that the range now runs -62 to 0.
>
> This causes a problem when adding this Feature to the feature
> collection since it considers a position of value 0 to be on the +ve
> strand, such that when Location.plus() is called the check for a
> negative location (i.e. both start and end being < 0) returns false
> and so you end up trying to create a Location with a ?ne start
> position but a +ve end, which throws an IllegalArgumentException.
>
> So is there something fishy here or not? I?m assuming that the GFF
> content is valid.
>
> Thanks in advance
>
> Craig
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From uchathuranga at gmail.com  Fri Feb 11 10:15:19 2011
From: uchathuranga at gmail.com (udana chathuranga)
Date: Fri, 11 Feb 2011 20:45:19 +0530
Subject: [Biojava-l] Problem with MultipleSequenceAlignment
Message-ID: <AANLkTi=sp=niSqo89LccimaHdesSDr5038fwxqHixu66@mail.gmail.com>

hi all,

When I was going through the biojava cookbook as I was interested in this
project. I tried the example in the page
http://biojava.org/wiki/BioJava:CookBook3:MSA and I got a classnotfound
exception for the line "Profile<ProteinSequence, AminoAcidCompound> profile
= Alignments.
getMultipleSequenceAlignment(lst);".

Error Message:

Exception in thread "main" java.lang.NoClassDefFoundError:
org/forester/phylogenyinference/DistanceMatrix
    at
org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)
    at CookbookMSA.multipleSequenceAlignment(CookbookMSA.java:29)
    at CookbookMSA.main(CookbookMSA.java:18)
Caused by: java.lang.ClassNotFoundException:
org.forester.phylogenyinference.DistanceMatrix
    at java.net.URLClassLoader$1.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClassInternal(Unknown Source)

Is this a know issue or Am I doing something wrong with the code?

Thanks
Regards
udana.

From willishf at ufl.edu  Fri Feb 11 11:28:32 2011
From: willishf at ufl.edu (Scooter Willis)
Date: Fri, 11 Feb 2011 11:28:32 -0500
Subject: [Biojava-l] Problem with MultipleSequenceAlignment
In-Reply-To: <AANLkTi=sp=niSqo89LccimaHdesSDr5038fwxqHixu66@mail.gmail.com>
References: <AANLkTi=sp=niSqo89LccimaHdesSDr5038fwxqHixu66@mail.gmail.com>
Message-ID: <AANLkTinERM9uRMhML+6c7GP=ZG3FnBxYUnMW23LceR5Y@mail.gmail.com>

You are probably missing a reference to the forester jar file located
in the biojava3-phylo module.

On Fri, Feb 11, 2011 at 10:15 AM, udana chathuranga
<uchathuranga at gmail.com> wrote:
> hi all,
>
> When I was going through the biojava cookbook as I was interested in this
> project. I tried the example in the page
> http://biojava.org/wiki/BioJava:CookBook3:MSA and I got a classnotfound
> exception for the line "Profile<ProteinSequence, AminoAcidCompound> profile
> = Alignments.
> getMultipleSequenceAlignment(lst);".
>
> Error Message:
>
> Exception in thread "main" java.lang.NoClassDefFoundError:
> org/forester/phylogenyinference/DistanceMatrix
> ? ?at
> org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)
> ? ?at CookbookMSA.multipleSequenceAlignment(CookbookMSA.java:29)
> ? ?at CookbookMSA.main(CookbookMSA.java:18)
> Caused by: java.lang.ClassNotFoundException:
> org.forester.phylogenyinference.DistanceMatrix
> ? ?at java.net.URLClassLoader$1.run(Unknown Source)
> ? ?at java.security.AccessController.doPrivileged(Native Method)
> ? ?at java.net.URLClassLoader.findClass(Unknown Source)
> ? ?at java.lang.ClassLoader.loadClass(Unknown Source)
> ? ?at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
> ? ?at java.lang.ClassLoader.loadClass(Unknown Source)
> ? ?at java.lang.ClassLoader.loadClassInternal(Unknown Source)
>
> Is this a know issue or Am I doing something wrong with the code?
>
> Thanks
> Regards
> udana.
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From uchathuranga at gmail.com  Fri Feb 11 11:58:48 2011
From: uchathuranga at gmail.com (udana chathuranga)
Date: Fri, 11 Feb 2011 22:28:48 +0530
Subject: [Biojava-l] Problem with MultipleSequenceAlignment
In-Reply-To: <AANLkTinERM9uRMhML+6c7GP=ZG3FnBxYUnMW23LceR5Y@mail.gmail.com>
References: <AANLkTi=sp=niSqo89LccimaHdesSDr5038fwxqHixu66@mail.gmail.com>
	<AANLkTinERM9uRMhML+6c7GP=ZG3FnBxYUnMW23LceR5Y@mail.gmail.com>
Message-ID: <AANLkTi=QLet0bMETWXn0_+-09PTmMmqTUSsOXEnOwO5X@mail.gmail.com>

>
> <http://lists.open-bio.org/mailman/listinfo/biojava-l>

Hi Scooter,

Thanks Scooter, that's works.


Regards
udana

From mandarijnopw8 at gmail.com  Sun Feb 13 09:32:14 2011
From: mandarijnopw8 at gmail.com (Shamanou van Leeuwen)
Date: Sun, 13 Feb 2011 15:32:14 +0100
Subject: [Biojava-l] programming error
Message-ID: <4D57EB6E.8010004@gmail.com>

hi guys,

i made am making a tool to translate dna to protein using biojava.
But  i am getting some errors that is do not fully understand.
Can somebody please tell me what i am doing wrong?


script:
http://pastebin.com/TJSjkgqK

errors:
http://pastebin.com/iFXYWEZB

From anantpossible at gmail.com  Sun Feb 13 12:47:28 2011
From: anantpossible at gmail.com (Anant Jain)
Date: Sun, 13 Feb 2011 23:17:28 +0530
Subject: [Biojava-l] programming error
In-Reply-To: <4D57EB6E.8010004@gmail.com>
References: <4D57EB6E.8010004@gmail.com>
Message-ID: <AANLkTi=2QshZekR=hcV77bMh51h3wAynWjmnX+G8Hdjm@mail.gmail.com>

Hi Shamanou,

I can see the error is around line no 192~193, I would suggest you to print
the codons list first, like below.


192 SOP (CODON LIST);
193 prot = SymbolListViews.translate(codons,RNATools.getGeneticCode(
"UNIVERSAL"));

Paste result in mail thread then we can start debugging .

Regards,
Anant

On Sun, Feb 13, 2011 at 8:02 PM, Shamanou van Leeuwen <
mandarijnopw8 at gmail.com> wrote:

> hi guys,
>
> i made am making a tool to translate dna to protein using biojava.
> But  i am getting some errors that is do not fully understand.
> Can somebody please tell me what i am doing wrong?
>
>
> script:
> http://pastebin.com/TJSjkgqK
>
> errors:
> http://pastebin.com/iFXYWEZB
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
Anant Jain
B.Tech Bioinformatics, RHCE
Software Engineer,
Persistent Systems Limited, Pune

From willishf at ufl.edu  Sun Feb 13 14:11:58 2011
From: willishf at ufl.edu (Scooter Willis)
Date: Sun, 13 Feb 2011 14:11:58 -0500
Subject: [Biojava-l] programming error
In-Reply-To: <4D57EB6E.8010004@gmail.com>
References: <4D57EB6E.8010004@gmail.com>
Message-ID: <AANLkTim-u3avgK5529SiheMsgVPYMGD=J_eLfGX_Sq4J@mail.gmail.com>

Depending on what you need you may want to try out biojava3.

On Sun, Feb 13, 2011 at 9:32 AM, Shamanou van Leeuwen
<mandarijnopw8 at gmail.com> wrote:
> hi guys,
>
> i made am making a tool to translate dna to protein using biojava.
> But ?i am getting some errors that is do not fully understand.
> Can somebody please tell me what i am doing wrong?
>
>
> script:
> http://pastebin.com/TJSjkgqK
>
> errors:
> http://pastebin.com/iFXYWEZB
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From mandarijnopw8 at gmail.com  Sun Feb 13 21:27:32 2011
From: mandarijnopw8 at gmail.com (Shamanou van Leeuwen)
Date: Mon, 14 Feb 2011 03:27:32 +0100
Subject: [Biojava-l] programming error
In-Reply-To: <AANLkTim-u3avgK5529SiheMsgVPYMGD=J_eLfGX_Sq4J@mail.gmail.com>
References: <4D57EB6E.8010004@gmail.com>
	<AANLkTim-u3avgK5529SiheMsgVPYMGD=J_eLfGX_Sq4J@mail.gmail.com>
Message-ID: <4D589314.5040705@gmail.com>

On 13-02-11 20:11, Scooter Willis wrote:
> Depending on what you need you may want to try out biojava3.
>
> On Sun, Feb 13, 2011 at 9:32 AM, Shamanou van Leeuwen
> <mandarijnopw8 at gmail.com>  wrote:
>> hi guys,
>>
>> i made am making a tool to translate dna to protein using biojava.
>> But  i am getting some errors that is do not fully understand.
>> Can somebody please tell me what i am doing wrong?
>>
>>
>> script:
>> http://pastebin.com/TJSjkgqK
>>
>> errors:
>> http://pastebin.com/iFXYWEZB
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
i a, trying biojava 3 now but i am still doing something wrong.

http://pastebin.com/uLz934gr

From andreas at sdsc.edu  Mon Feb 14 03:16:48 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 14 Feb 2011 00:16:48 -0800
Subject: [Biojava-l] BioJava 3.0.1 released
Message-ID: <AANLkTin=yhdA5z0QDwz1Tz3O-rjGk6f6yzkV2GGbYrNe@mail.gmail.com>

BioJava 3.0.1 has been released and is available from
http://www.biojava.org/wiki/BioJava:Download .


The 3.0.1 release is mainly a bug fix release for the recent 3.0 code base,
which provides a major rewrite of the biojava.

A couple of noteworthy improvements:

- core: fixed an issue with sequence index positions, new utility methods
for memory efficient parsing of large fasta files

- structure: Fixed issues with PDB header parsing and more stability with
non-standard PDB files. Added new algorithm to automatically infer protein
domain boundaries.

- web services: Fixed wrong dependency on old codebase and overall
improvements in functionality of remote blast web service calls.

- protein modifications: Minor bugfixes

In parallel the biojava-legacy code base has been updated to version 1.8.1
and it contains a bug fix related to circular locations.

Thanks to all contributors for making this release possible.

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

From ayates at ebi.ac.uk  Mon Feb 14 05:07:12 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 14 Feb 2011 10:07:12 +0000
Subject: [Biojava-l] programming error
In-Reply-To: <4D589314.5040705@gmail.com>
References: <4D57EB6E.8010004@gmail.com>
	<AANLkTim-u3avgK5529SiheMsgVPYMGD=J_eLfGX_Sq4J@mail.gmail.com>
	<4D589314.5040705@gmail.com>
Message-ID: <C9323C5F-5952-4104-A251-F7016323DF90@ebi.ac.uk>

If you want to do frame based translation then there is an easier way of accomplishing this. The TranscriptionEngine allows you to translate in multiple frames and retrieve that information in a Map such as:

TranscriptionEngine te = TranscriptionEngine.getDefault();
Frame[] frames = Frame.getForwardFrames();
Map<Frame, Sequence<AminoAcidCompound>> results = te.multipleFrameTranslation(dna, frames);

Change the static call on Frame to Frame.getAllFrames() then you will do a full 6 frame translation.

Also I would avoid calling the getSequenceAsString() method until you need to output it to screen. The Sequence interface provides an adequate set of methods for testing length of a sequence. However if you want is the longest translation then I would replace that with (assuming the above code):

List<Sequence<AminoAcidCompound>> translations = new ArrayList<Sequence<AminoAcidCompound>>(results.getValues());
Collections.sort(translations, new Comparator<Sequence<AminoAcidCompound>>() {
  public int compare(Sequence<AminoAcidCompound> o1, Sequence<AminoAcidCompound> o2) {
    Integer o1Length = o1.getLength();
    Integer o2Length = o2.getLength();
    return o1Length.compareTo(o2Length);
  }
});
Sequence<AminoAcidCompound> longest = translations.get(translations.size()-1);

However I would like to see what errors you are pulling up from BioJava3 in case there is a scenario we are not currently taking into account

Andy

On 14 Feb 2011, at 02:27, Shamanou van Leeuwen wrote:

> On 13-02-11 20:11, Scooter Willis wrote:
>> Depending on what you need you may want to try out biojava3.
>> 
>> On Sun, Feb 13, 2011 at 9:32 AM, Shamanou van Leeuwen
>> <mandarijnopw8 at gmail.com>  wrote:
>>> hi guys,
>>> 
>>> i made am making a tool to translate dna to protein using biojava.
>>> But  i am getting some errors that is do not fully understand.
>>> Can somebody please tell me what i am doing wrong?
>>> 
>>> 
>>> script:
>>> http://pastebin.com/TJSjkgqK
>>> 
>>> errors:
>>> http://pastebin.com/iFXYWEZB
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>> 
>>> 
> i a, trying biojava 3 now but i am still doing something wrong.
> 
> http://pastebin.com/uLz934gr
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/






From andreas at sdsc.edu  Mon Feb 14 10:42:57 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 14 Feb 2011 07:42:57 -0800
Subject: [Biojava-l] programming error
In-Reply-To: <C9323C5F-5952-4104-A251-F7016323DF90@ebi.ac.uk>
References: <4D57EB6E.8010004@gmail.com>
	<AANLkTim-u3avgK5529SiheMsgVPYMGD=J_eLfGX_Sq4J@mail.gmail.com>
	<4D589314.5040705@gmail.com>
	<C9323C5F-5952-4104-A251-F7016323DF90@ebi.ac.uk>
Message-ID: <AANLkTin11qUmm9iRJZfaMu57ZqNKSAwiHACqo5U4zWxL@mail.gmail.com>

Hi Andy,

Could we get a Cookbook page for this? sounds like it would be good to have
a bit more docu on this topic ...

Thanks!

Andreas

On Mon, Feb 14, 2011 at 2:07 AM, Andy Yates <ayates at ebi.ac.uk> wrote:

> If you want to do frame based translation then there is an easier way of
> accomplishing this. The TranscriptionEngine allows you to translate in
> multiple frames and retrieve that information in a Map such as:
>
> TranscriptionEngine te = TranscriptionEngine.getDefault();
> Frame[] frames = Frame.getForwardFrames();
> Map<Frame, Sequence<AminoAcidCompound>> results =
> te.multipleFrameTranslation(dna, frames);
>
> Change the static call on Frame to Frame.getAllFrames() then you will do a
> full 6 frame translation.
>
> Also I would avoid calling the getSequenceAsString() method until you need
> to output it to screen. The Sequence interface provides an adequate set of
> methods for testing length of a sequence. However if you want is the longest
> translation then I would replace that with (assuming the above code):
>
> List<Sequence<AminoAcidCompound>> translations = new
> ArrayList<Sequence<AminoAcidCompound>>(results.getValues());
> Collections.sort(translations, new
> Comparator<Sequence<AminoAcidCompound>>() {
>  public int compare(Sequence<AminoAcidCompound> o1,
> Sequence<AminoAcidCompound> o2) {
>    Integer o1Length = o1.getLength();
>    Integer o2Length = o2.getLength();
>    return o1Length.compareTo(o2Length);
>  }
> });
> Sequence<AminoAcidCompound> longest =
> translations.get(translations.size()-1);
>
> However I would like to see what errors you are pulling up from BioJava3 in
> case there is a scenario we are not currently taking into account
>
> Andy
>
> On 14 Feb 2011, at 02:27, Shamanou van Leeuwen wrote:
>
> > On 13-02-11 20:11, Scooter Willis wrote:
> >> Depending on what you need you may want to try out biojava3.
> >>
> >> On Sun, Feb 13, 2011 at 9:32 AM, Shamanou van Leeuwen
> >> <mandarijnopw8 at gmail.com>  wrote:
> >>> hi guys,
> >>>
> >>> i made am making a tool to translate dna to protein using biojava.
> >>> But  i am getting some errors that is do not fully understand.
> >>> Can somebody please tell me what i am doing wrong?
> >>>
> >>>
> >>> script:
> >>> http://pastebin.com/TJSjkgqK
> >>>
> >>> errors:
> >>> http://pastebin.com/iFXYWEZB
> >>> _______________________________________________
> >>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>
> >>>
> > i a, trying biojava 3 now but i am still doing something wrong.
> >
> > http://pastebin.com/uLz934gr
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------

From ayates at ebi.ac.uk  Mon Feb 14 11:13:35 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 14 Feb 2011 16:13:35 +0000
Subject: [Biojava-l] programming error
In-Reply-To: <AANLkTin11qUmm9iRJZfaMu57ZqNKSAwiHACqo5U4zWxL@mail.gmail.com>
References: <4D57EB6E.8010004@gmail.com>
	<AANLkTim-u3avgK5529SiheMsgVPYMGD=J_eLfGX_Sq4J@mail.gmail.com>
	<4D589314.5040705@gmail.com>
	<C9323C5F-5952-4104-A251-F7016323DF90@ebi.ac.uk>
	<AANLkTin11qUmm9iRJZfaMu57ZqNKSAwiHACqo5U4zWxL@mail.gmail.com>
Message-ID: <7CBE613F-7F05-47C6-B917-8A1A3EF82E4C@ebi.ac.uk>

I've added a bit to the original cookbook page we had. I can migrate these changes to the cookbook front page later on in the week

Andy

On 14 Feb 2011, at 15:42, Andreas Prlic wrote:

> Hi Andy,
> 
> Could we get a Cookbook page for this? sounds like it would be good to have a bit more docu on this topic ...
> 
> Thanks!
> 
> Andreas
> 
> On Mon, Feb 14, 2011 at 2:07 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> If you want to do frame based translation then there is an easier way of accomplishing this. The TranscriptionEngine allows you to translate in multiple frames and retrieve that information in a Map such as:
> 
> TranscriptionEngine te = TranscriptionEngine.getDefault();
> Frame[] frames = Frame.getForwardFrames();
> Map<Frame, Sequence<AminoAcidCompound>> results = te.multipleFrameTranslation(dna, frames);
> 
> Change the static call on Frame to Frame.getAllFrames() then you will do a full 6 frame translation.
> 
> Also I would avoid calling the getSequenceAsString() method until you need to output it to screen. The Sequence interface provides an adequate set of methods for testing length of a sequence. However if you want is the longest translation then I would replace that with (assuming the above code):
> 
> List<Sequence<AminoAcidCompound>> translations = new ArrayList<Sequence<AminoAcidCompound>>(results.getValues());
> Collections.sort(translations, new Comparator<Sequence<AminoAcidCompound>>() {
>  public int compare(Sequence<AminoAcidCompound> o1, Sequence<AminoAcidCompound> o2) {
>    Integer o1Length = o1.getLength();
>    Integer o2Length = o2.getLength();
>    return o1Length.compareTo(o2Length);
>  }
> });
> Sequence<AminoAcidCompound> longest = translations.get(translations.size()-1);
> 
> However I would like to see what errors you are pulling up from BioJava3 in case there is a scenario we are not currently taking into account
> 
> Andy
> 
> On 14 Feb 2011, at 02:27, Shamanou van Leeuwen wrote:
> 
> > On 13-02-11 20:11, Scooter Willis wrote:
> >> Depending on what you need you may want to try out biojava3.
> >>
> >> On Sun, Feb 13, 2011 at 9:32 AM, Shamanou van Leeuwen
> >> <mandarijnopw8 at gmail.com>  wrote:
> >>> hi guys,
> >>>
> >>> i made am making a tool to translate dna to protein using biojava.
> >>> But  i am getting some errors that is do not fully understand.
> >>> Can somebody please tell me what i am doing wrong?
> >>>
> >>>
> >>> script:
> >>> http://pastebin.com/TJSjkgqK
> >>>
> >>> errors:
> >>> http://pastebin.com/iFXYWEZB
> >>> _______________________________________________
> >>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>
> >>>
> > i a, trying biojava 3 now but i am still doing something wrong.
> >
> > http://pastebin.com/uLz934gr
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> --
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> 
> 
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 
> 
> -- 
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/






From andreas at sdsc.edu  Mon Feb 14 18:57:07 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 14 Feb 2011 15:57:07 -0800
Subject: [Biojava-l] programming error
In-Reply-To: <7CBE613F-7F05-47C6-B917-8A1A3EF82E4C@ebi.ac.uk>
References: <4D57EB6E.8010004@gmail.com>
	<AANLkTim-u3avgK5529SiheMsgVPYMGD=J_eLfGX_Sq4J@mail.gmail.com>
	<4D589314.5040705@gmail.com>
	<C9323C5F-5952-4104-A251-F7016323DF90@ebi.ac.uk>
	<AANLkTin11qUmm9iRJZfaMu57ZqNKSAwiHACqo5U4zWxL@mail.gmail.com>
	<7CBE613F-7F05-47C6-B917-8A1A3EF82E4C@ebi.ac.uk>
Message-ID: <AANLkTikzm-VZV8+DRUvsH=oveX329gN0ku8m0g2ZChDH@mail.gmail.com>

Thanks Andy,

yea, would be good to add links on the cookbook front page, otherwise the
sections are hard to find...

Andreas

On Mon, Feb 14, 2011 at 8:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:

> I've added a bit to the original cookbook page we had. I can migrate these
> changes to the cookbook front page later on in the week
>
> Andy
>
> On 14 Feb 2011, at 15:42, Andreas Prlic wrote:
>
> > Hi Andy,
> >
> > Could we get a Cookbook page for this? sounds like it would be good to
> have a bit more docu on this topic ...
> >
> > Thanks!
> >
> > Andreas
> >
> > On Mon, Feb 14, 2011 at 2:07 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> > If you want to do frame based translation then there is an easier way of
> accomplishing this. The TranscriptionEngine allows you to translate in
> multiple frames and retrieve that information in a Map such as:
> >
> > TranscriptionEngine te = TranscriptionEngine.getDefault();
> > Frame[] frames = Frame.getForwardFrames();
> > Map<Frame, Sequence<AminoAcidCompound>> results =
> te.multipleFrameTranslation(dna, frames);
> >
> > Change the static call on Frame to Frame.getAllFrames() then you will do
> a full 6 frame translation.
> >
> > Also I would avoid calling the getSequenceAsString() method until you
> need to output it to screen. The Sequence interface provides an adequate set
> of methods for testing length of a sequence. However if you want is the
> longest translation then I would replace that with (assuming the above
> code):
> >
> > List<Sequence<AminoAcidCompound>> translations = new
> ArrayList<Sequence<AminoAcidCompound>>(results.getValues());
> > Collections.sort(translations, new
> Comparator<Sequence<AminoAcidCompound>>() {
> >  public int compare(Sequence<AminoAcidCompound> o1,
> Sequence<AminoAcidCompound> o2) {
> >    Integer o1Length = o1.getLength();
> >    Integer o2Length = o2.getLength();
> >    return o1Length.compareTo(o2Length);
> >  }
> > });
> > Sequence<AminoAcidCompound> longest =
> translations.get(translations.size()-1);
> >
> > However I would like to see what errors you are pulling up from BioJava3
> in case there is a scenario we are not currently taking into account
> >
> > Andy
> >
> > On 14 Feb 2011, at 02:27, Shamanou van Leeuwen wrote:
> >
> > > On 13-02-11 20:11, Scooter Willis wrote:
> > >> Depending on what you need you may want to try out biojava3.
> > >>
> > >> On Sun, Feb 13, 2011 at 9:32 AM, Shamanou van Leeuwen
> > >> <mandarijnopw8 at gmail.com>  wrote:
> > >>> hi guys,
> > >>>
> > >>> i made am making a tool to translate dna to protein using biojava.
> > >>> But  i am getting some errors that is do not fully understand.
> > >>> Can somebody please tell me what i am doing wrong?
> > >>>
> > >>>
> > >>> script:
> > >>> http://pastebin.com/TJSjkgqK
> > >>>
> > >>> errors:
> > >>> http://pastebin.com/iFXYWEZB
> > >>> _______________________________________________
> > >>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > >>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> > >>>
> > >>>
> > > i a, trying biojava 3 now but i am still doing something wrong.
> > >
> > > http://pastebin.com/uLz934gr
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> > --
> > Andrew Yates                   Ensembl Genomes Engineer
> > EMBL-EBI                       Tel: +44-(0)1223-492538
> > Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> > Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> >
> >
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> >
> >
> > --
> > -----------------------------------------------------------------------
> > Dr. Andreas Prlic
> > Senior Scientist, RCSB PDB Protein Data Bank
> > University of California, San Diego
> > (+1) 858.246.0526
> > -----------------------------------------------------------------------
>
> --
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>
>
>
>
>

From andreas at sdsc.edu  Tue Feb 15 21:45:49 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 15 Feb 2011 18:45:49 -0800
Subject: [Biojava-l] GSoC status
Message-ID: <AANLkTikPBs2NwDw-ekrNqWX3CVxsjQsLnZKxtzn=72xS@mail.gmail.com>

Hi Udana,

I would like to motivate student proposed projects as much as possible this
year. This means if you want to distinguish yourself with your application,
it would be great if you would suggest a project by yourself that you find
exciting. If our application to become a sponsoring organisation gets
approved by Google, we will start discussing proposals around March 18th. We
will probably suggest possible projects at some point, but I really would
like to give preference to student proposed projects this year.

To get ideas about possible student proposed projects I recommend getting a
module that is related to your studies and try to do some work with it. This
might give you ideas about what is missing and what could be added in a
project.

Andreas



On Tue, Feb 15, 2011 at 11:35 AM, udana chathuranga
<uchathuranga at gmail.com>wrote:

> Hi Andreas,
>
> Any updates about project ideas to gsoc2011 ?
>
>
>
>
> Thanks
> Regards
> Udana
>

From jw12 at sanger.ac.uk  Thu Feb 17 09:30:08 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 17 Feb 2011 14:30:08 +0000
Subject: [Biojava-l] DAS Workshop Registration Closing Soon
Message-ID: <0BCCE860-9AEA-4377-A9D6-F28E264DE43A@sanger.ac.uk>

Registration closes for the DAS workshop at 5pm this Friday GMT.  
Limited places still available.
Please note that for the tutorials day (Day 1) it is advisable to know  
at least one of PERL, Java or Javascript.
Further information and registration from here: http://www.ebi.ac.uk/training/onsite/110302DAS.html

There are still a few places for short talks on the second day if you  
have anything to talk about of interest to the DAS community.

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314










-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From watson at ebi.ac.uk  Fri Feb 18 03:46:53 2011
From: watson at ebi.ac.uk (James Watson)
Date: Fri, 18 Feb 2011 08:46:53 +0000
Subject: [Biojava-l] Hands-on training at EBI - Programmatic access to
 biological databases (Java)
Message-ID: <4D5E31FD.6080905@ebi.ac.uk>

*Date:* 9-13 May 2011
*Venue:* EMBL-EBI, Hinxton, Nr Cambridge, CB10 1SD, UK
*Registration Deadline:* 9th April 2011

This Java-based course in programmatic access to biological databases is 
ideal for bioinformaticians and biological researchers looking to 
develop data analysis pipelines or access data in an automated manner 
for integration into their own applications.

What will it cover?
- Introduction to Web Services and resources available at the EBI
- REST & SOAP - their application to EBI services and databases
- BioMart and BioMart Web Services
- Linking services together to construct workflows (Taverna, Enfin, Encore)

For a more detailed programme and information on registration please go 
to http://www.ebi.ac.uk/training/handson/course_110509_progjava.html

Many thanks,

James Watson

-- 
James D Watson
Scientific Training Officer
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Tel: +44(0)1223 492541

http://www.ebi.ac.uk/training/

Upcoming hands on training courses
(http://www.ebi.ac.uk/training/handson/):

28 Mar -- 1 Apr 2011: PSIMEx Workshop: Interactions and Pathways
9-13 May 2011: Programmatic access to biological databases (Java)
23-27 May 2011: FEBS: In silico systems biology for complex diseases: network reconstruction, analysis and network based modelling


From bli0406 at gmail.com  Wed Feb 23 02:16:29 2011
From: bli0406 at gmail.com (Bo Li)
Date: Wed, 23 Feb 2011 02:16:29 -0500
Subject: [Biojava-l] question regarding MSA
Message-ID: <A4406D27-913C-40BD-9EEA-89EE6AB85F29@gmail.com>

Hi,

Sorry for the bothering.  I tried the MSA feature by following the link:

http://www.biojava.org/wiki/BioJava:CookBook3:MSA

However, I can't see the symbols like ".", ":", and "*" like I can see  
from the output ClustalW.

So is there a way for users to obtain such information in the output  
from MSA?

Thanks,
Bo Li

From andreas at sdsc.edu  Thu Feb 24 03:06:59 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 24 Feb 2011 00:06:59 -0800
Subject: [Biojava-l] question regarding MSA
In-Reply-To: <A4406D27-913C-40BD-9EEA-89EE6AB85F29@gmail.com>
References: <A4406D27-913C-40BD-9EEA-89EE6AB85F29@gmail.com>
Message-ID: <AANLkTikiNMn_MenmqT=zCvD5KjrJOjjehb_vCZOECpWr@mail.gmail.com>

Hi Bo Li,

The printing method currently does not add those characters to the
display of the aligned sequences. If you need it you would have to
patch the printing method...

Andreas

On Tue, Feb 22, 2011 at 11:16 PM, Bo Li <bli0406 at gmail.com> wrote:
> Hi,
>
> Sorry for the bothering. ?I tried the MSA feature by following the link:
>
> http://www.biojava.org/wiki/BioJava:CookBook3:MSA
>
> However, I can't see the symbols like ".", ":", and "*" like I can see from
> the output ClustalW.
>
> So is there a way for users to obtain such information in the output from
> MSA?
>
> Thanks,
> Bo Li
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From p.v.troshin at dundee.ac.uk  Thu Feb 24 10:33:41 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Thu, 24 Feb 2011 15:33:41 +0000
Subject: [Biojava-l] Isoelectric point and molecular weight calculations
	with BioJava
Message-ID: <4D667A55.5040404@dundee.ac.uk>

Hi,

I've noticed that BioJava up to about version 1.7 had an 
org.biojava.bio.proteomics package, which had methods for isoelectric 
point and molecular weight calculations for peptides. I could not find 
this package in the BioJava 3.0.1 API. I?d like to use these methods and 
wonder if there are any equivalent methods available in the latest 
version of BioJava?

Thank you for your help,

Kind regards,
Peter

Dr Peter Troshin
Bioinformatics Software Developer
Phone: +44 (0)1382 388589
Fax: +44 (0)1382 385764
The Barton Group
College of Life Sciences
Medical Sciences Institute
University of Dundee
Dundee
DD1 5EH
UK




From andreas at sdsc.edu  Thu Feb 24 11:54:14 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 24 Feb 2011 08:54:14 -0800
Subject: [Biojava-l] Isoelectric point and molecular weight calculations
 with BioJava
In-Reply-To: <4D667A55.5040404@dundee.ac.uk>
References: <4D667A55.5040404@dundee.ac.uk>
Message-ID: <AANLkTim=otw02=CnK6nK3ps3JsU5=S-nSg+VCeRCNF4E@mail.gmail.com>

Hi Peter,

if you get a copy of biojava 1.8, it is still there. However I would
like to port this to biojava 3 as well.. George do you want to help me
with that, since you are one of the authors of this package? The basic
support for chemistry in BioJava 3 is a bit better... (e.g. Element
class)

Andreas

On Thu, Feb 24, 2011 at 7:33 AM, Peter Troshin <p.v.troshin at dundee.ac.uk> wrote:
> Hi,
>
> I've noticed that BioJava up to about version 1.7 had an
> org.biojava.bio.proteomics package, which had methods for isoelectric point
> and molecular weight calculations for peptides. I could not find this
> package in the BioJava 3.0.1 API. I?d like to use these methods and wonder
> if there are any equivalent methods available in the latest version of
> BioJava?
>
> Thank you for your help,
>
> Kind regards,
> Peter
>
> Dr Peter Troshin
> Bioinformatics Software Developer
> Phone: +44 (0)1382 388589
> Fax: +44 (0)1382 385764
> The Barton Group
> College of Life Sciences
> Medical Sciences Institute
> University of Dundee
> Dundee
> DD1 5EH
> UK
>
>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From p.v.troshin at dundee.ac.uk  Thu Feb 24 12:44:07 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Thu, 24 Feb 2011 17:44:07 +0000
Subject: [Biojava-l] Isoelectric point and molecular weight calculations
 with BioJava
In-Reply-To: <AANLkTim=otw02=CnK6nK3ps3JsU5=S-nSg+VCeRCNF4E@mail.gmail.com>
References: <4D667A55.5040404@dundee.ac.uk>
	<AANLkTim=otw02=CnK6nK3ps3JsU5=S-nSg+VCeRCNF4E@mail.gmail.com>
Message-ID: <4D6698E7.3080202@dundee.ac.uk>

Hi Andreas,

In fact I'd be happy to help with the development of the tools for 
simple physico-chemical properties calculation for peptides. We could 
port George?s code (assuming he is happy with this) from BioJava 1.8 but 
we can also provide a few other methods. A couple of projects in the lab 
where I work would have benefited from having these calculations readily 
available.

I was thinking about participation in the Google Summer of Code (GoSC) 
this year as a mentor, and I think this would be an easy project for a 
student. What do you think about this?

Thank you for your prompt reply.

Regards,
Peter



On 24/02/2011 16:54, Andreas Prlic wrote:
> Hi Peter,
>
> if you get a copy of biojava 1.8, it is still there. However I would
> like to port this to biojava 3 as well.. George do you want to help me
> with that, since you are one of the authors of this package? The basic
> support for chemistry in BioJava 3 is a bit better... (e.g. Element
> class)
>
> Andreas
>
> On Thu, Feb 24, 2011 at 7:33 AM, Peter Troshin<p.v.troshin at dundee.ac.uk>  wrote:
>> Hi,
>>
>> I've noticed that BioJava up to about version 1.7 had an
>> org.biojava.bio.proteomics package, which had methods for isoelectric point
>> and molecular weight calculations for peptides. I could not find this
>> package in the BioJava 3.0.1 API. I?d like to use these methods and wonder
>> if there are any equivalent methods available in the latest version of
>> BioJava?
>>
>> Thank you for your help,
>>
>> Kind regards,
>> Peter
>>
>> Dr Peter Troshin
>> Bioinformatics Software Developer
>> Phone: +44 (0)1382 388589
>> Fax: +44 (0)1382 385764
>> The Barton Group
>> College of Life Sciences
>> Medical Sciences Institute
>> University of Dundee
>> Dundee
>> DD1 5EH
>> UK
>>
>>
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>


From gwaldon at geneinfinity.org  Thu Feb 24 14:15:06 2011
From: gwaldon at geneinfinity.org (George Waldon)
Date: Thu, 24 Feb 2011 13:15:06 -0600
Subject: [Biojava-l] Isoelectric point and molecular weight calculations
 with BioJava
In-Reply-To: <4D6698E7.3080202@dundee.ac.uk>
References: <4D667A55.5040404@dundee.ac.uk>
	<AANLkTim=otw02=CnK6nK3ps3JsU5=S-nSg+VCeRCNF4E@mail.gmail.com>
	<4D6698E7.3080202@dundee.ac.uk>
Message-ID: <20110224131506.17104xy7rpe7n30g@gator1273.hostgator.com>

Hello Peter & Andreas

I effectively did some work on these methods, mostly fixing and adding  
the ExPASy algorithm that was kindly provided to me. I think it makes  
a lot of sense to port all physico-chemical property calculations  
related to amino acids and polypeptides to bj3, as suggested by  
Andreas, and I definitively support the effort. We could smoothly  
deprecate the bj1 package when this is done. Let me know how I could  
help.

Thanks
George

Quoting Peter Troshin <p.v.troshin at dundee.ac.uk>:

> Hi Andreas,
>
> In fact I'd be happy to help with the development of the tools for  
> simple physico-chemical properties calculation for peptides. We  
> could port George?s code (assuming he is happy with this) from  
> BioJava 1.8 but we can also provide a few other methods. A couple of  
> projects in the lab where I work would have benefited from having  
> these calculations readily available.
>
> I was thinking about participation in the Google Summer of Code  
> (GoSC) this year as a mentor, and I think this would be an easy  
> project for a student. What do you think about this?
>
> Thank you for your prompt reply.
>
> Regards,
> Peter
>
>
>
> On 24/02/2011 16:54, Andreas Prlic wrote:
>> Hi Peter,
>>
>> if you get a copy of biojava 1.8, it is still there. However I would
>> like to port this to biojava 3 as well.. George do you want to help me
>> with that, since you are one of the authors of this package? The basic
>> support for chemistry in BioJava 3 is a bit better... (e.g. Element
>> class)
>>
>> Andreas
>>
>> On Thu, Feb 24, 2011 at 7:33 AM, Peter  
>> Troshin<p.v.troshin at dundee.ac.uk>  wrote:
>>> Hi,
>>>
>>> I've noticed that BioJava up to about version 1.7 had an
>>> org.biojava.bio.proteomics package, which had methods for isoelectric point
>>> and molecular weight calculations for peptides. I could not find this
>>> package in the BioJava 3.0.1 API. I?d like to use these methods and wonder
>>> if there are any equivalent methods available in the latest version of
>>> BioJava?
>>>
>>> Thank you for your help,
>>>
>>> Kind regards,
>>> Peter
>>>
>>> Dr Peter Troshin
>>> Bioinformatics Software Developer
>>> Phone: +44 (0)1382 388589
>>> Fax: +44 (0)1382 385764
>>> The Barton Group
>>> College of Life Sciences
>>> Medical Sciences Institute
>>> University of Dundee
>>> Dundee
>>> DD1 5EH
>>> UK
>>>
>>>
>>>
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>
>




From willishf at ufl.edu  Thu Feb 24 23:08:53 2011
From: willishf at ufl.edu (Scooter Willis)
Date: Thu, 24 Feb 2011 23:08:53 -0500
Subject: [Biojava-l] Isoelectric point and molecular weight calculations
 with BioJava
In-Reply-To: <20110224131506.17104xy7rpe7n30g@gator1273.hostgator.com>
References: <4D667A55.5040404@dundee.ac.uk>
	<AANLkTim=otw02=CnK6nK3ps3JsU5=S-nSg+VCeRCNF4E@mail.gmail.com>
	<4D6698E7.3080202@dundee.ac.uk>
	<20110224131506.17104xy7rpe7n30g@gator1273.hostgator.com>
Message-ID: <AANLkTinSAg-X3g79eO-w0sQmiR0PNr6fW6h6dHaAzxqw@mail.gmail.com>

We put in some basics regarding modeling amino acid properties in the
core module but really didn't have any pressing use cases to drive the
api beyond calculating the mass of a peptide. We currently have
getMolecularWeight() as a method in AbstractCompound but never added a
getSequenceMolecularWeight() to AbstractSequence. It would be great to
get the attributes/features of amino acids properly modeled in core
and extend when reasonable useful summary methods at higher levels.
You should be able to query mass of a peptide and have it valid for an
amino acid with a PTM which means the amino acid needs to support the
ability to be modified in a flexible manner. I spent the last year+
developing a software suite for peptide detection in MS data for
deuterium exchange where automated PTM detection was important. Would
be great to get some focused attention on the core to make sure we can
model nucleotides and amino acids with a chemistry friendly API.

Thanks

Scooter

On Thu, Feb 24, 2011 at 2:15 PM, George Waldon <gwaldon at geneinfinity.org> wrote:
> Hello Peter & Andreas
>
> I effectively did some work on these methods, mostly fixing and adding the
> ExPASy algorithm that was kindly provided to me. I think it makes a lot of
> sense to port all physico-chemical property calculations related to amino
> acids and polypeptides to bj3, as suggested by Andreas, and I definitively
> support the effort. We could smoothly deprecate the bj1 package when this is
> done. Let me know how I could help.
>
> Thanks
> George
>
> Quoting Peter Troshin <p.v.troshin at dundee.ac.uk>:
>
>> Hi Andreas,
>>
>> In fact I'd be happy to help with the development of the tools for simple
>> physico-chemical properties calculation for peptides. We could port George?s
>> code (assuming he is happy with this) from BioJava 1.8 but we can also
>> provide a few other methods. A couple of projects in the lab where I work
>> would have benefited from having these calculations readily available.
>>
>> I was thinking about participation in the Google Summer of Code (GoSC)
>> this year as a mentor, and I think this would be an easy project for a
>> student. What do you think about this?
>>
>> Thank you for your prompt reply.
>>
>> Regards,
>> Peter
>>
>>
>>
>> On 24/02/2011 16:54, Andreas Prlic wrote:
>>>
>>> Hi Peter,
>>>
>>> if you get a copy of biojava 1.8, it is still there. However I would
>>> like to port this to biojava 3 as well.. George do you want to help me
>>> with that, since you are one of the authors of this package? The basic
>>> support for chemistry in BioJava 3 is a bit better... (e.g. Element
>>> class)
>>>
>>> Andreas
>>>
>>> On Thu, Feb 24, 2011 at 7:33 AM, Peter Troshin<p.v.troshin at dundee.ac.uk>
>>> ?wrote:
>>>>
>>>> Hi,
>>>>
>>>> I've noticed that BioJava up to about version 1.7 had an
>>>> org.biojava.bio.proteomics package, which had methods for isoelectric
>>>> point
>>>> and molecular weight calculations for peptides. I could not find this
>>>> package in the BioJava 3.0.1 API. I?d like to use these methods and
>>>> wonder
>>>> if there are any equivalent methods available in the latest version of
>>>> BioJava?
>>>>
>>>> Thank you for your help,
>>>>
>>>> Kind regards,
>>>> Peter
>>>>
>>>> Dr Peter Troshin
>>>> Bioinformatics Software Developer
>>>> Phone: +44 (0)1382 388589
>>>> Fax: +44 (0)1382 385764
>>>> The Barton Group
>>>> College of Life Sciences
>>>> Medical Sciences Institute
>>>> University of Dundee
>>>> Dundee
>>>> DD1 5EH
>>>> UK
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>
>>
>>
>
>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From andreas at sdsc.edu  Fri Feb 25 00:12:17 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 24 Feb 2011 21:12:17 -0800
Subject: [Biojava-l] Isoelectric point and molecular weight calculations
 with BioJava
In-Reply-To: <AANLkTinSAg-X3g79eO-w0sQmiR0PNr6fW6h6dHaAzxqw@mail.gmail.com>
References: <4D667A55.5040404@dundee.ac.uk>
	<AANLkTim=otw02=CnK6nK3ps3JsU5=S-nSg+VCeRCNF4E@mail.gmail.com>
	<4D6698E7.3080202@dundee.ac.uk>
	<20110224131506.17104xy7rpe7n30g@gator1273.hostgator.com>
	<AANLkTinSAg-X3g79eO-w0sQmiR0PNr6fW6h6dHaAzxqw@mail.gmail.com>
Message-ID: <AANLkTimmZ+CnKNZJw2RWuQ9GMYT8h6QqMx+U4Ph2=JCL@mail.gmail.com>

Great, seems we have an agreement that we want to improve
functionality for this. How complex is this going to be? From quickly
checking the 1.8 source it looks like just a few classes that need to
be converted and not too painful.  What other functionality would you
like to see that is currently not there?

Andreas


On Thu, Feb 24, 2011 at 8:08 PM, Scooter Willis <willishf at ufl.edu> wrote:
> We put in some basics regarding modeling amino acid properties in the
> core module but really didn't have any pressing use cases to drive the
> api beyond calculating the mass of a peptide. We currently have
> getMolecularWeight() as a method in AbstractCompound but never added a
> getSequenceMolecularWeight() to AbstractSequence. It would be great to
> get the attributes/features of amino acids properly modeled in core
> and extend when reasonable useful summary methods at higher levels.
> You should be able to query mass of a peptide and have it valid for an
> amino acid with a PTM which means the amino acid needs to support the
> ability to be modified in a flexible manner. I spent the last year+
> developing a software suite for peptide detection in MS data for
> deuterium exchange where automated PTM detection was important. Would
> be great to get some focused attention on the core to make sure we can
> model nucleotides and amino acids with a chemistry friendly API.
>
> Thanks
>
> Scooter
>
> On Thu, Feb 24, 2011 at 2:15 PM, George Waldon <gwaldon at geneinfinity.org> wrote:
>> Hello Peter & Andreas
>>
>> I effectively did some work on these methods, mostly fixing and adding the
>> ExPASy algorithm that was kindly provided to me. I think it makes a lot of
>> sense to port all physico-chemical property calculations related to amino
>> acids and polypeptides to bj3, as suggested by Andreas, and I definitively
>> support the effort. We could smoothly deprecate the bj1 package when this is
>> done. Let me know how I could help.
>>
>> Thanks
>> George
>>
>> Quoting Peter Troshin <p.v.troshin at dundee.ac.uk>:
>>
>>> Hi Andreas,
>>>
>>> In fact I'd be happy to help with the development of the tools for simple
>>> physico-chemical properties calculation for peptides. We could port George?s
>>> code (assuming he is happy with this) from BioJava 1.8 but we can also
>>> provide a few other methods. A couple of projects in the lab where I work
>>> would have benefited from having these calculations readily available.
>>>
>>> I was thinking about participation in the Google Summer of Code (GoSC)
>>> this year as a mentor, and I think this would be an easy project for a
>>> student. What do you think about this?
>>>
>>> Thank you for your prompt reply.
>>>
>>> Regards,
>>> Peter
>>>
>>>
>>>
>>> On 24/02/2011 16:54, Andreas Prlic wrote:
>>>>
>>>> Hi Peter,
>>>>
>>>> if you get a copy of biojava 1.8, it is still there. However I would
>>>> like to port this to biojava 3 as well.. George do you want to help me
>>>> with that, since you are one of the authors of this package? The basic
>>>> support for chemistry in BioJava 3 is a bit better... (e.g. Element
>>>> class)
>>>>
>>>> Andreas
>>>>
>>>> On Thu, Feb 24, 2011 at 7:33 AM, Peter Troshin<p.v.troshin at dundee.ac.uk>
>>>> ?wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I've noticed that BioJava up to about version 1.7 had an
>>>>> org.biojava.bio.proteomics package, which had methods for isoelectric
>>>>> point
>>>>> and molecular weight calculations for peptides. I could not find this
>>>>> package in the BioJava 3.0.1 API. I?d like to use these methods and
>>>>> wonder
>>>>> if there are any equivalent methods available in the latest version of
>>>>> BioJava?
>>>>>
>>>>> Thank you for your help,
>>>>>
>>>>> Kind regards,
>>>>> Peter
>>>>>
>>>>> Dr Peter Troshin
>>>>> Bioinformatics Software Developer
>>>>> Phone: +44 (0)1382 388589
>>>>> Fax: +44 (0)1382 385764
>>>>> The Barton Group
>>>>> College of Life Sciences
>>>>> Medical Sciences Institute
>>>>> University of Dundee
>>>>> Dundee
>>>>> DD1 5EH
>>>>> UK
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>
>>>
>>>
>>
>>
>>
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------


From flf.mib at gmail.com  Fri Feb 25 17:21:19 2011
From: flf.mib at gmail.com (=?ISO-8859-1?Q?Fran=E7ois_Le_Fevre?=)
Date: Fri, 25 Feb 2011 23:21:19 +0100
Subject: [Biojava-l] biojava3 and symbol
Message-ID: <4D682B5F.60807@gmail.com>

Hello
I am a newbie in biojava3.
I have installed the maven version.

I have a question : is there a way to go from DNASequence to SymbolList?
I would like to study codons and their frequency in several organisms.
It was easy with biojava with

"SymbolList codons  = SymbolListViews.windowedSymbolList(seq, 3);"
and
"DistributionTrainerContext"

But now I am a little lost between maven biojava3 and biojava.
So if anyone could explain me how to get codons view from DNASequence, 
it could be great.

Thanks a lot!

Francois


-- 
----------------------
Francois LE FEVRE


From andreas at sdsc.edu  Mon Feb 28 01:04:46 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sun, 27 Feb 2011 22:04:46 -0800
Subject: [Biojava-l] biojava3 and symbol
In-Reply-To: <4D682B5F.60807@gmail.com>
References: <4D682B5F.60807@gmail.com>
Message-ID: <AANLkTimif0X8c6W=Yz-Ojy6xOuysABceCZSpqHa232kq@mail.gmail.com>

Hi Francois,

SymbolLists are part of BioJava 1.8 (the legacy version) and not 3.0.
You might want to get the previous version installed. It is available
from Maven as well...

Andreas

2011/2/25 Fran?ois Le Fevre <flf.mib at gmail.com>:
> Hello
> I am a newbie in biojava3.
> I have installed the maven version.
>
> I have a question : is there a way to go from DNASequence to SymbolList?
> I would like to study codons and their frequency in several organisms.
> It was easy with biojava with
>
> "SymbolList codons ?= SymbolListViews.windowedSymbolList(seq, 3);"
> and
> "DistributionTrainerContext"
>
> But now I am a little lost between maven biojava3 and biojava.
> So if anyone could explain me how to get codons view from DNASequence, it
> could be great.
>
> Thanks a lot!
>
> Francois
>
>
> --
> ----------------------
> Francois LE FEVRE
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From ayates at ebi.ac.uk  Mon Feb 28 05:06:16 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 28 Feb 2011 10:06:16 +0000
Subject: [Biojava-l] biojava3 and symbol
In-Reply-To: <4D682B5F.60807@gmail.com>
References: <4D682B5F.60807@gmail.com>
Message-ID: <245D3308-6EB9-44C0-A954-DEA0D9D28F94@ebi.ac.uk>

Hi Francois,

To get a windowed view over any sequence you should use the following:

DNASequence seq = new DNASequence("ATGCTG");
Iterable<SequenceView<NucleotideCompound>> w = new WindowedSequence<NucleotideCompound>(seq, 3);
for(SequenceView<NucelotideCompound> triplet: w) {
  System.out.println(triplet);
}

HTH

Andy

On 25 Feb 2011, at 22:21, Fran?ois Le Fevre wrote:

> Hello
> I am a newbie in biojava3.
> I have installed the maven version.
> 
> I have a question : is there a way to go from DNASequence to SymbolList?
> I would like to study codons and their frequency in several organisms.
> It was easy with biojava with
> 
> "SymbolList codons  = SymbolListViews.windowedSymbolList(seq, 3);"
> and
> "DistributionTrainerContext"
> 
> But now I am a little lost between maven biojava3 and biojava.
> So if anyone could explain me how to get codons view from DNASequence, it could be great.
> 
> Thanks a lot!
> 
> Francois
> 
> 
> -- 
> ----------------------
> Francois LE FEVRE
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/






From flf.mib at gmail.com  Mon Feb 28 06:12:51 2011
From: flf.mib at gmail.com (Francois Le Fevre)
Date: Mon, 28 Feb 2011 12:12:51 +0100
Subject: [Biojava-l] biojava3 and symbol
In-Reply-To: <245D3308-6EB9-44C0-A954-DEA0D9D28F94@ebi.ac.uk>
References: <4D682B5F.60807@gmail.com>
	<245D3308-6EB9-44C0-A954-DEA0D9D28F94@ebi.ac.uk>
Message-ID: <AANLkTin0ogxP=C0FDU0fb1y7oEWOQ4ZWEy6avYSH=LOR@mail.gmail.com>

perfect thank a lot.
Have a good day
Francois

2011/2/28 Andy Yates <ayates at ebi.ac.uk>

> Hi Francois,
>
> To get a windowed view over any sequence you should use the following:
>
> DNASequence seq = new DNASequence("ATGCTG");
> Iterable<SequenceView<NucleotideCompound>> w = new
> WindowedSequence<NucleotideCompound>(seq, 3);
> for(SequenceView<NucelotideCompound> triplet: w) {
>  System.out.println(triplet);
> }
>
> HTH
>
> Andy
>
> On 25 Feb 2011, at 22:21, Fran?ois Le Fevre wrote:
>
> > Hello
> > I am a newbie in biojava3.
> > I have installed the maven version.
> >
> > I have a question : is there a way to go from DNASequence to SymbolList?
> > I would like to study codons and their frequency in several organisms.
> > It was easy with biojava with
> >
> > "SymbolList codons  = SymbolListViews.windowedSymbolList(seq, 3);"
> > and
> > "DistributionTrainerContext"
> >
> > But now I am a little lost between maven biojava3 and biojava.
> > So if anyone could explain me how to get codons view from DNASequence, it
> could be great.
> >
> > Thanks a lot!
> >
> > Francois
> >
> >
> > --
> > ----------------------
> > Francois LE FEVRE
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>
>
>
>
>


-- 


Francois Le Fevre
Management Informatique Innovation Biotechnologies
Paris, France
-
Avant d'imprimer, pensez ? l'environnement


From p.v.troshin at dundee.ac.uk  Mon Feb 28 10:18:15 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Mon, 28 Feb 2011 15:18:15 +0000
Subject: [Biojava-l] Isoelectric point and molecular weight calculations
 with BioJava
In-Reply-To: <AANLkTimmZ+CnKNZJw2RWuQ9GMYT8h6QqMx+U4Ph2=JCL@mail.gmail.com>
References: <4D667A55.5040404@dundee.ac.uk>	<AANLkTim=otw02=CnK6nK3ps3JsU5=S-nSg+VCeRCNF4E@mail.gmail.com>	<4D6698E7.3080202@dundee.ac.uk>	<20110224131506.17104xy7rpe7n30g@gator1273.hostgator.com>	<AANLkTinSAg-X3g79eO-w0sQmiR0PNr6fW6h6dHaAzxqw@mail.gmail.com>
	<AANLkTimmZ+CnKNZJw2RWuQ9GMYT8h6QqMx+U4Ph2=JCL@mail.gmail.com>
Message-ID: <4D6BBCB7.3010203@dundee.ac.uk>

>>>What other functionality would you
>>>like to see that is currently not there?


I think that the methods below would be a good starting point, then the 
Google Summer of Code student can propose something else that he/she 
would fancy implementing.

   Molecular weight
   Extinction coefficient
   Instability index
   Aliphatic index
   Grand Average of Hydropathy
   Isoelectric point
   Number of amino acids in the protein (His, Met, Cys)

I know BioJava projects were managed under Open Bioinformatics 
Foundation (OBF) during last years GSoC. Is there a page for this year 
GSoC ideas somewhere?

Regards,
Peter


On 25/02/2011 05:12, Andreas Prlic wrote:
> Great, seems we have an agreement that we want to improve
> functionality for this. How complex is this going to be? From quickly
> checking the 1.8 source it looks like just a few classes that need to
> be converted and not too painful.  What other functionality would you
> like to see that is currently not there?
>
> Andreas
>
>
> On Thu, Feb 24, 2011 at 8:08 PM, Scooter Willis<willishf at ufl.edu>  wrote:
>> We put in some basics regarding modeling amino acid properties in the
>> core module but really didn't have any pressing use cases to drive the
>> api beyond calculating the mass of a peptide. We currently have
>> getMolecularWeight() as a method in AbstractCompound but never added a
>> getSequenceMolecularWeight() to AbstractSequence. It would be great to
>> get the attributes/features of amino acids properly modeled in core
>> and extend when reasonable useful summary methods at higher levels.
>> You should be able to query mass of a peptide and have it valid for an
>> amino acid with a PTM which means the amino acid needs to support the
>> ability to be modified in a flexible manner. I spent the last year+
>> developing a software suite for peptide detection in MS data for
>> deuterium exchange where automated PTM detection was important. Would
>> be great to get some focused attention on the core to make sure we can
>> model nucleotides and amino acids with a chemistry friendly API.
>>
>> Thanks
>>
>> Scooter
>>
>> On Thu, Feb 24, 2011 at 2:15 PM, George Waldon<gwaldon at geneinfinity.org>  wrote:
>>> Hello Peter&  Andreas
>>>
>>> I effectively did some work on these methods, mostly fixing and adding the
>>> ExPASy algorithm that was kindly provided to me. I think it makes a lot of
>>> sense to port all physico-chemical property calculations related to amino
>>> acids and polypeptides to bj3, as suggested by Andreas, and I definitively
>>> support the effort. We could smoothly deprecate the bj1 package when this is
>>> done. Let me know how I could help.
>>>
>>> Thanks
>>> George
>>>
>>> Quoting Peter Troshin<p.v.troshin at dundee.ac.uk>:
>>>
>>>> Hi Andreas,
>>>>
>>>> In fact I'd be happy to help with the development of the tools for simple
>>>> physico-chemical properties calculation for peptides. We could port George?s
>>>> code (assuming he is happy with this) from BioJava 1.8 but we can also
>>>> provide a few other methods. A couple of projects in the lab where I work
>>>> would have benefited from having these calculations readily available.
>>>>
>>>> I was thinking about participation in the Google Summer of Code (GoSC)
>>>> this year as a mentor, and I think this would be an easy project for a
>>>> student. What do you think about this?
>>>>
>>>> Thank you for your prompt reply.
>>>>
>>>> Regards,
>>>> Peter
>>>>
>>>>
>>>>
>>>> On 24/02/2011 16:54, Andreas Prlic wrote:
>>>>> Hi Peter,
>>>>>
>>>>> if you get a copy of biojava 1.8, it is still there. However I would
>>>>> like to port this to biojava 3 as well.. George do you want to help me
>>>>> with that, since you are one of the authors of this package? The basic
>>>>> support for chemistry in BioJava 3 is a bit better... (e.g. Element
>>>>> class)
>>>>>
>>>>> Andreas
>>>>>
>>>>> On Thu, Feb 24, 2011 at 7:33 AM, Peter Troshin<p.v.troshin at dundee.ac.uk>
>>>>>   wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I've noticed that BioJava up to about version 1.7 had an
>>>>>> org.biojava.bio.proteomics package, which had methods for isoelectric
>>>>>> point
>>>>>> and molecular weight calculations for peptides. I could not find this
>>>>>> package in the BioJava 3.0.1 API. I?d like to use these methods and
>>>>>> wonder
>>>>>> if there are any equivalent methods available in the latest version of
>>>>>> BioJava?
>>>>>>
>>>>>> Thank you for your help,
>>>>>>
>>>>>> Kind regards,
>>>>>> Peter
>>>>>>
>>>>>> Dr Peter Troshin
>>>>>> Bioinformatics Software Developer
>>>>>> Phone: +44 (0)1382 388589
>>>>>> Fax: +44 (0)1382 385764
>>>>>> The Barton Group
>>>>>> College of Life Sciences
>>>>>> Medical Sciences Institute
>>>>>> University of Dundee
>>>>>> Dundee
>>>>>> DD1 5EH
>>>>>> UK
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>
>


From uchathuranga at gmail.com  Thu Feb 10 12:01:57 2011
From: uchathuranga at gmail.com (udana chathuranga)
Date: Thu, 10 Feb 2011 17:01:57 -0000
Subject: [Biojava-l] Problem with Multiple Sequence Alignment in BioJava
Message-ID: <AANLkTimQm+oNnNhbcciBf7JjA3vVADnkxD109Pq56cWO@mail.gmail.com>

hi all,

When I was going through the biojava cookbook as I was interested in this
project. I tried the example in the page
http://biojava.org/wiki/BioJava:CookBook3:MSA and I got a classnotfound
exception for the line "Profile<ProteinSequence, AminoAcidCompound> profile
= Alignments.getMultipleSequenceAlignment(lst);".

Error Message:

Exception in thread "main" java.lang.NoClassDefFoundError:
org/forester/phylogenyinference/DistanceMatrix
    at
org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)
    at CookbookMSA.multipleSequenceAlignment(CookbookMSA.java:29)
    at CookbookMSA.main(CookbookMSA.java:18)
Caused by: java.lang.ClassNotFoundException:
org.forester.phylogenyinference.DistanceMatrix
    at java.net.URLClassLoader$1.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClassInternal(Unknown Source)

Is this a know issue or Am I doing something wrong with the code?
Help me on this I have attached the java source file that I have tried.

Thanks
Regards
udana.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: CookbookMSA.java
Type: application/octet-stream
Size: 1579 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biojava-l/attachments/20110210/eb50655d/attachment.obj>

From hlapp at drycafe.net  Sat Feb  5 23:45:47 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 5 Feb 2011 18:45:47 -0500
Subject: [Biojava-l] NESCent Seeks Hackathon Whitepapers
In-Reply-To: <0D7D89E4-C0D4-4347-A94C-21800E927746@ad.unc.edu>
References: <BF0025BB-27BC-440C-83A4-77172421C9C8@ad.unc.edu>
	<E3EBA44A-EFE4-4279-BD4D-38FC9D190413@nescent.org>
	<0D7D89E4-C0D4-4347-A94C-21800E927746@ad.unc.edu>
Message-ID: <066A2391-6041-408C-B26E-9B867DE785C7@drycafe.net>

The National Evolutionary Synthesis Center (NESCent), in keeping with  
its objective to promote collaborative development of open-source,  
reusable, and standards-supporting informatics resources, sponsors  
highly collaborative, face-to-face software development events, called  
"hackathons" (see [1]). To ensure that this program continues to be  
responsive to user needs and to tap into the expertise and creativity  
of the evolutionary biology community, NESCent is soliciting short  
whitepapers (2-6 pages) [2] on potential target areas for future  
hackathons.

To further encourage submissions, we have now distilled specific  
guidelines for proposing hackathon events, based on the experiences  
gained from events we have sponsored in the past:
http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines

The Center's Call for Informatics Whitepapers [3] includes not only  
hackathons, but also a large spectrum of other initiatives to be  
undertaken by the Center, including training, software development,  
collaborative ontology development, and coordination of data  
standards. Whitepapers are accepted at any time and reviewed on an on- 
going basis.

URLs:
[1] Collaborative cyberinfrastructure events and programs organized by  
NESCent:
http://informatics.nescent.org/wiki/Main_Page

[2] NESCent Call for Informatics Whitepapers
http://www.nescent.org/informatics/whitepapers.php

[3] Hackathon Whitepaper Guidelines:
http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines

[4] Past NESCent-sponsored hackathons:
http://informatics.nescent.org/wiki/Main_Page#Hackathons


From jayunit100 at gmail.com  Mon Feb  7 18:44:05 2011
From: jayunit100 at gmail.com (Jay Vyas)
Date: Mon, 7 Feb 2011 13:44:05 -0500
Subject: [Biojava-l] average or minimal energy structure for nmr
	structures...
Message-ID: <AANLkTikomYdY00izx-MMjUcORDmCBE=yZ7SsjDLJjEZr@mail.gmail.com>

Hi guys : Does anybody know a simple biojava way to calculate an average
structure, or alternatively, find the lowest energy structure from an nmr
structure with multiple models  ?
Im doing it using a set of nested for loops... I thought maybe there might
be support in the api.


  for(Group g1 : c.getAtomGroups())

for(Atom a1 : g1.getAtoms())

{

                       float xAvg,yAvg,zAvg;

for(int i = 0 ; i < s.nrModels(); i++)

{

                             ///etc....

}



}

-- 
Jay Vyas
MMSB/UCHC


From andreas at sdsc.edu  Tue Feb  8 06:38:14 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 7 Feb 2011 22:38:14 -0800
Subject: [Biojava-l] average or minimal energy structure for nmr
	structures...
In-Reply-To: <AANLkTikomYdY00izx-MMjUcORDmCBE=yZ7SsjDLJjEZr@mail.gmail.com>
References: <AANLkTikomYdY00izx-MMjUcORDmCBE=yZ7SsjDLJjEZr@mail.gmail.com>
Message-ID: <AANLkTik5cW47w2gT+XPkKwOGE8fTg4qzQh6ztuN4K0rS@mail.gmail.com>

Hi Jay,

You could calculate average coordinates and RMSD with BioJava. However
in terms of energy calculations BioJava can't do much so far...

Andreas

On Mon, Feb 7, 2011 at 10:44 AM, Jay Vyas <jayunit100 at gmail.com> wrote:
> Hi guys : Does anybody know a simple biojava way to calculate an average
> structure, or alternatively, find the lowest energy structure from an nmr
> structure with multiple models ??
> Im doing it using a set of nested for loops... I thought maybe there might
> be support in the api.
>
>
> ?for(Group g1 : c.getAtomGroups())
>
> for(Atom a1 : g1.getAtoms())
>
> {
>
> ? ? ? ? ? ? ? ? ? ? ? float xAvg,yAvg,zAvg;
>
> for(int i = 0 ; i < s.nrModels(); i++)
>
> {
>
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ///etc....
>
> }
>
>
>
> }
>
> --
> Jay Vyas
> MMSB/UCHC
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From uchathuranga at gmail.com  Wed Feb  9 05:19:00 2011
From: uchathuranga at gmail.com (udana chathuranga)
Date: Wed, 9 Feb 2011 10:49:00 +0530
Subject: [Biojava-l] Project Ideas GSOC 2011
Message-ID: <AANLkTi=YSJFNPWT9Mj6zS+nH7vKoRiraTYES5NvG6mtd@mail.gmail.com>

hi,

I am a student a University of Moratuwa , Sri lanka. I am planning to
participate gsoc 2011 and I would like to work on a project regarding
bioinfomatics. So I would like to know whether you are planning to be a
mentor organization this year also. If so i would like to know what kinds of
projects that you are planning to propose.

Thanks
Regard
udana


From andreas at sdsc.edu  Wed Feb  9 05:49:23 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 8 Feb 2011 21:49:23 -0800
Subject: [Biojava-l] Project Ideas GSOC 2011
In-Reply-To: <AANLkTi=YSJFNPWT9Mj6zS+nH7vKoRiraTYES5NvG6mtd@mail.gmail.com>
References: <AANLkTi=YSJFNPWT9Mj6zS+nH7vKoRiraTYES5NvG6mtd@mail.gmail.com>
Message-ID: <AANLkTikvuhaxu2wgkbQseiLGWoL6nPDDpq0sF1KHrWnB@mail.gmail.com>

Hi Udana,

It is a bit early, but given the success form last year I think it is
for sure that BioJava (as part of the the Open Bioinformatics
Foundation) will apply again to become a mentoring organisation.
Google will announce the list of accepted mentoring organizations on
March 18th, afterwards the time to discuss proposals will start.

http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs#timeline

Last year we had several Mentor proposed projects. Google is also very
interested in seeing student proposed projects and they recommend
those due to their high success rate. If you want to prepare a
proposal you could already start thinking of what kind of project you
would like to work on. Similarly, everybody else who wants to propose
a project and perhaps become a mentor can also start to think about
that. Still we will have to wait until March 18th before we will know
if there is actually any funding this year.

Andreas


On Tue, Feb 8, 2011 at 9:19 PM, udana chathuranga
<uchathuranga at gmail.com> wrote:
> hi,
>
> I am a student a University of Moratuwa , Sri lanka. I am planning to
> participate gsoc 2011 and I would like to work on a project regarding
> bioinfomatics. So I would like to know whether you are planning to be a
> mentor organization this year also. If so i would like to know what kinds of
> projects that you are planning to propose.
>
> Thanks
> Regard
> udana
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From uchathuranga at gmail.com  Wed Feb  9 06:13:34 2011
From: uchathuranga at gmail.com (udana chathuranga)
Date: Wed, 9 Feb 2011 11:43:34 +0530
Subject: [Biojava-l] Project Ideas GSOC 2011
In-Reply-To: <AANLkTikvuhaxu2wgkbQseiLGWoL6nPDDpq0sF1KHrWnB@mail.gmail.com>
References: <AANLkTi=YSJFNPWT9Mj6zS+nH7vKoRiraTYES5NvG6mtd@mail.gmail.com>
	<AANLkTikvuhaxu2wgkbQseiLGWoL6nPDDpq0sF1KHrWnB@mail.gmail.com>
Message-ID: <AANLkTimBMbvyT=O8+cc2efJ5FwHtFtf_m+uZtX2WCuDc@mail.gmail.com>

Hi Andreas,

Thanks for the quick reply.I appreciate your help and I want know how I can
contribute to the project even if you are not participating for this year
gsoc project. I have studied bioinfomatics as one of my subject in the
university and I would like to apply those knowledge in to this project. I
would be thankful if you can guide me to start to participate in the
project.
I have solid background on java and bioinomatics related areas like
    Biological Sequence data analysis -

The Sequence assembly problem, The Gene Finding Problem, The Sequence
Alignment Problem, The Genome Rearrangement problem, The Protein Folding
Problem, The Motif Discovery Problem

    Phylogenetics

    Biological Network Motifs


Above mention areas are some of the subjects that I have learned in our
course and I would like to know how can I apply this knowledge to this
project?




Thanks

Regards

Udana


From andreas at sdsc.edu  Wed Feb  9 16:27:35 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 9 Feb 2011 08:27:35 -0800
Subject: [Biojava-l] Project Ideas GSOC 2011
In-Reply-To: <AANLkTimBMbvyT=O8+cc2efJ5FwHtFtf_m+uZtX2WCuDc@mail.gmail.com>
References: <AANLkTi=YSJFNPWT9Mj6zS+nH7vKoRiraTYES5NvG6mtd@mail.gmail.com>
	<AANLkTikvuhaxu2wgkbQseiLGWoL6nPDDpq0sF1KHrWnB@mail.gmail.com>
	<AANLkTimBMbvyT=O8+cc2efJ5FwHtFtf_m+uZtX2WCuDc@mail.gmail.com>
Message-ID: <AANLkTimEmbFJJ_CC14KuoY04agd2+WkyzQTVeKAn1pdv@mail.gmail.com>

Hi Udana,

There is some overlap between your background and many aspects of
BioJava. I recommend taking a look at the Cookbook for a start
learning more about BioJava. To give you an idea of what was going on
last year, the two biojava related projects that were funded were

A) Development of an all Java multiple sequence alignment module
B) Identification and classification of posttranslational protein modifications.

Here the project pages for more details:
http://biojava.org/wiki/Google_Summer_of_Code

Andreas

On Tue, Feb 8, 2011 at 10:13 PM, udana chathuranga
<uchathuranga at gmail.com> wrote:
> Hi Andreas,
>
> Thanks for the quick reply.I appreciate your help and I want know how I can
> contribute to the project even if you are not participating for this year
> gsoc project. I have studied bioinfomatics as one of my subject in the
> university and I would like to apply those knowledge in to this project. I
> would be thankful if you can guide me to start to participate in the
> project.
> I have solid background on java and bioinomatics related areas like
> ? ? Biological Sequence data analysis -
>
> The Sequence assembly problem, The Gene Finding Problem, The Sequence
> Alignment Problem, The Genome Rearrangement problem, The Protein Folding
> Problem, The Motif Discovery Problem
>
> ??? Phylogenetics
>
> ??? Biological Network Motifs
>
> Above mention areas are some of the subjects that I have learned in our
> course and I would like to know how can I apply this knowledge to this
> project?
>
>
> Thanks
>
> Regards
>
> Udana
>



From uchathuranga at gmail.com  Wed Feb  9 18:45:55 2011
From: uchathuranga at gmail.com (udana chathuranga)
Date: Thu, 10 Feb 2011 00:15:55 +0530
Subject: [Biojava-l] Project Ideas GSOC 2011
In-Reply-To: <AANLkTimEmbFJJ_CC14KuoY04agd2+WkyzQTVeKAn1pdv@mail.gmail.com>
References: <AANLkTi=YSJFNPWT9Mj6zS+nH7vKoRiraTYES5NvG6mtd@mail.gmail.com>
	<AANLkTikvuhaxu2wgkbQseiLGWoL6nPDDpq0sF1KHrWnB@mail.gmail.com>
	<AANLkTimBMbvyT=O8+cc2efJ5FwHtFtf_m+uZtX2WCuDc@mail.gmail.com>
	<AANLkTimEmbFJJ_CC14KuoY04agd2+WkyzQTVeKAn1pdv@mail.gmail.com>
Message-ID: <AANLkTim5559ixchSSXNxVJLwcDYXH_R0u0_rxJhyFBKd@mail.gmail.com>

Hi Andreas,

First of all thanks for the guide.i have started reading the CookBook in
http://biojava.org/wiki/BioJava:CookBook. I have also did some sample coding
using the biojava3-core and found this
http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite and looked in
details about the fasta file format.About fasta file format I studied about
in the link http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml.

As you pointed out I have also looked in the last years two gsoc
projects.After going through those project I had this question what kinds of
modules that I can work on. I would like hear some suggestions about modules
that you are looking forward to.

I also like to know what kinds of file formats that I should look into in
the future in order to develop a good module to the system.

Thanks
regards
Udana


From jayunit100 at gmail.com  Wed Feb  9 19:22:05 2011
From: jayunit100 at gmail.com (Jay Vyas)
Date: Wed, 9 Feb 2011 14:22:05 -0500
Subject: [Biojava-l] average structure
Message-ID: <AANLkTikjULh4EYxKBLW1qeooPDWPp+aG_ivZ8MHfZ91+@mail.gmail.com>

Hi Guys : I was also wondering if biojava supported creating an average or
mean structure from a bundle........

-- 
Jay Vyas
MMSB/UCHC


From andreas at sdsc.edu  Wed Feb  9 21:48:40 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 9 Feb 2011 13:48:40 -0800
Subject: [Biojava-l] average structure
In-Reply-To: <AANLkTikjULh4EYxKBLW1qeooPDWPp+aG_ivZ8MHfZ91+@mail.gmail.com>
References: <AANLkTikjULh4EYxKBLW1qeooPDWPp+aG_ivZ8MHfZ91+@mail.gmail.com>
Message-ID: <AANLkTi=2pQfxZWLBRY4d=azcGEoxxLVwU3QEZ3XJuKhv@mail.gmail.com>

A geometric average should be easy to calculate. All NMR models have
the same number of atoms, so you could just average over all
alternative positions for an atom and use that to build up a mean
structure... However I would take that with a grain of salt and make
sure there are no distance violations by visual inspection and some
quality control scripts. There are standard/ideal coordinates
available for all amino acids, that you could use to compare with the
distances between atoms in your average structure.

Andreas

On Wed, Feb 9, 2011 at 11:22 AM, Jay Vyas <jayunit100 at gmail.com> wrote:
> Hi Guys : I was also wondering if biojava supported creating an average or
> mean structure from a bundle........
>
> --
> Jay Vyas
> MMSB/UCHC
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From craig.adrian.berry at gmail.com  Fri Feb 11 10:54:35 2011
From: craig.adrian.berry at gmail.com (Craig Berry)
Date: Fri, 11 Feb 2011 10:54:35 +0000
Subject: [Biojava-l] GFF3 Reader
Message-ID: <AANLkTikxH=P7tvh_9GtOjkBqh5Y0g1aq5qUhpD6K83F2@mail.gmail.com>

Can I just have someone validate this logic in the GFF3Reader for me
to see if this is a bug or not.

If I have a GFF3 file with the following line:

chrI	SGD	repeat_region	1	62	.	-	.	ID=TEL01L-TR;Name=TEL01L-TR;Note=Terminal%20stretch%20of%20telomeric%20repeats%20on%20the%20left%20arm%20of%20Chromosome%20I;dbxref=SGD:S000028864

When parsing the file then, the class calls Location.fromBio using the
start 1, end 62 and strand ?ve.
Since the strand is ?ve it needs to convert the positions to negative
values and reverse the start and end. However, as the javadocs
explains:

?In biocoordinates, the start index of a range is represented in
origin 1 (ie the very first index is 1, not 0),  and end= start +
length - 1.?

So before the end is reassigned its value is reduced by 1 and then
negated: e = - ( start ? 1) With a start value of 1 as in this case,
the end then becomes 0, such that the range now runs -62 to 0.

This causes a problem when adding this Feature to the feature
collection since it considers a position of value 0 to be on the +ve
strand, such that when Location.plus() is called the check for a
negative location (i.e. both start and end being < 0) returns false
and so you end up trying to create a Location with a ?ne start
position but a +ve end, which throws an IllegalArgumentException.

So is there something fishy here or not? I?m assuming that the GFF
content is valid.

Thanks in advance

Craig



From willishf at ufl.edu  Fri Feb 11 14:14:08 2011
From: willishf at ufl.edu (Scooter Willis)
Date: Fri, 11 Feb 2011 09:14:08 -0500
Subject: [Biojava-l] GFF3 Reader
In-Reply-To: <AANLkTikxH=P7tvh_9GtOjkBqh5Y0g1aq5qUhpD6K83F2@mail.gmail.com>
References: <AANLkTikxH=P7tvh_9GtOjkBqh5Y0g1aq5qUhpD6K83F2@mail.gmail.com>
Message-ID: <AANLkTim+WbePP6GCYN8aVv-dp4s6ijW_ucfdPJigne=3@mail.gmail.com>

Craig

I think I fixed this problem but not sure if it is in the current
released jar files. The < logic was wrong where 0 wasn't be treated
properly. I will send you an update jar to see if the problem goes
away.

Scooter

On Fri, Feb 11, 2011 at 5:54 AM, Craig Berry
<craig.adrian.berry at gmail.com> wrote:
> Can I just have someone validate this logic in the GFF3Reader for me
> to see if this is a bug or not.
>
> If I have a GFF3 file with the following line:
>
> chrI ? ?SGD ? ? repeat_region ? 1 ? ? ? 62 ? ? ?. ? ? ? - ? ? ? . ? ? ? ID=TEL01L-TR;Name=TEL01L-TR;Note=Terminal%20stretch%20of%20telomeric%20repeats%20on%20the%20left%20arm%20of%20Chromosome%20I;dbxref=SGD:S000028864
>
> When parsing the file then, the class calls Location.fromBio using the
> start 1, end 62 and strand ?ve.
> Since the strand is ?ve it needs to convert the positions to negative
> values and reverse the start and end. However, as the javadocs
> explains:
>
> ?In biocoordinates, the start index of a range is represented in
> origin 1 (ie the very first index is 1, not 0), ?and end= start +
> length - 1.?
>
> So before the end is reassigned its value is reduced by 1 and then
> negated: e = - ( start ? 1) With a start value of 1 as in this case,
> the end then becomes 0, such that the range now runs -62 to 0.
>
> This causes a problem when adding this Feature to the feature
> collection since it considers a position of value 0 to be on the +ve
> strand, such that when Location.plus() is called the check for a
> negative location (i.e. both start and end being < 0) returns false
> and so you end up trying to create a Location with a ?ne start
> position but a +ve end, which throws an IllegalArgumentException.
>
> So is there something fishy here or not? I?m assuming that the GFF
> content is valid.
>
> Thanks in advance
>
> Craig
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>



From uchathuranga at gmail.com  Fri Feb 11 15:15:19 2011
From: uchathuranga at gmail.com (udana chathuranga)
Date: Fri, 11 Feb 2011 20:45:19 +0530
Subject: [Biojava-l] Problem with MultipleSequenceAlignment
Message-ID: <AANLkTi=sp=niSqo89LccimaHdesSDr5038fwxqHixu66@mail.gmail.com>

hi all,

When I was going through the biojava cookbook as I was interested in this
project. I tried the example in the page
http://biojava.org/wiki/BioJava:CookBook3:MSA and I got a classnotfound
exception for the line "Profile<ProteinSequence, AminoAcidCompound> profile
= Alignments.
getMultipleSequenceAlignment(lst);".

Error Message:

Exception in thread "main" java.lang.NoClassDefFoundError:
org/forester/phylogenyinference/DistanceMatrix
    at
org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)
    at CookbookMSA.multipleSequenceAlignment(CookbookMSA.java:29)
    at CookbookMSA.main(CookbookMSA.java:18)
Caused by: java.lang.ClassNotFoundException:
org.forester.phylogenyinference.DistanceMatrix
    at java.net.URLClassLoader$1.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClassInternal(Unknown Source)

Is this a know issue or Am I doing something wrong with the code?

Thanks
Regards
udana.


From willishf at ufl.edu  Fri Feb 11 16:28:32 2011
From: willishf at ufl.edu (Scooter Willis)
Date: Fri, 11 Feb 2011 11:28:32 -0500
Subject: [Biojava-l] Problem with MultipleSequenceAlignment
In-Reply-To: <AANLkTi=sp=niSqo89LccimaHdesSDr5038fwxqHixu66@mail.gmail.com>
References: <AANLkTi=sp=niSqo89LccimaHdesSDr5038fwxqHixu66@mail.gmail.com>
Message-ID: <AANLkTinERM9uRMhML+6c7GP=ZG3FnBxYUnMW23LceR5Y@mail.gmail.com>

You are probably missing a reference to the forester jar file located
in the biojava3-phylo module.

On Fri, Feb 11, 2011 at 10:15 AM, udana chathuranga
<uchathuranga at gmail.com> wrote:
> hi all,
>
> When I was going through the biojava cookbook as I was interested in this
> project. I tried the example in the page
> http://biojava.org/wiki/BioJava:CookBook3:MSA and I got a classnotfound
> exception for the line "Profile<ProteinSequence, AminoAcidCompound> profile
> = Alignments.
> getMultipleSequenceAlignment(lst);".
>
> Error Message:
>
> Exception in thread "main" java.lang.NoClassDefFoundError:
> org/forester/phylogenyinference/DistanceMatrix
> ? ?at
> org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)
> ? ?at CookbookMSA.multipleSequenceAlignment(CookbookMSA.java:29)
> ? ?at CookbookMSA.main(CookbookMSA.java:18)
> Caused by: java.lang.ClassNotFoundException:
> org.forester.phylogenyinference.DistanceMatrix
> ? ?at java.net.URLClassLoader$1.run(Unknown Source)
> ? ?at java.security.AccessController.doPrivileged(Native Method)
> ? ?at java.net.URLClassLoader.findClass(Unknown Source)
> ? ?at java.lang.ClassLoader.loadClass(Unknown Source)
> ? ?at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
> ? ?at java.lang.ClassLoader.loadClass(Unknown Source)
> ? ?at java.lang.ClassLoader.loadClassInternal(Unknown Source)
>
> Is this a know issue or Am I doing something wrong with the code?
>
> Thanks
> Regards
> udana.
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>



From uchathuranga at gmail.com  Fri Feb 11 16:58:48 2011
From: uchathuranga at gmail.com (udana chathuranga)
Date: Fri, 11 Feb 2011 22:28:48 +0530
Subject: [Biojava-l] Problem with MultipleSequenceAlignment
In-Reply-To: <AANLkTinERM9uRMhML+6c7GP=ZG3FnBxYUnMW23LceR5Y@mail.gmail.com>
References: <AANLkTi=sp=niSqo89LccimaHdesSDr5038fwxqHixu66@mail.gmail.com>
	<AANLkTinERM9uRMhML+6c7GP=ZG3FnBxYUnMW23LceR5Y@mail.gmail.com>
Message-ID: <AANLkTi=QLet0bMETWXn0_+-09PTmMmqTUSsOXEnOwO5X@mail.gmail.com>

>
> <http://lists.open-bio.org/mailman/listinfo/biojava-l>

Hi Scooter,

Thanks Scooter, that's works.


Regards
udana


From mandarijnopw8 at gmail.com  Sun Feb 13 14:32:14 2011
From: mandarijnopw8 at gmail.com (Shamanou van Leeuwen)
Date: Sun, 13 Feb 2011 15:32:14 +0100
Subject: [Biojava-l] programming error
Message-ID: <4D57EB6E.8010004@gmail.com>

hi guys,

i made am making a tool to translate dna to protein using biojava.
But  i am getting some errors that is do not fully understand.
Can somebody please tell me what i am doing wrong?


script:
http://pastebin.com/TJSjkgqK

errors:
http://pastebin.com/iFXYWEZB


From anantpossible at gmail.com  Sun Feb 13 17:47:28 2011
From: anantpossible at gmail.com (Anant Jain)
Date: Sun, 13 Feb 2011 23:17:28 +0530
Subject: [Biojava-l] programming error
In-Reply-To: <4D57EB6E.8010004@gmail.com>
References: <4D57EB6E.8010004@gmail.com>
Message-ID: <AANLkTi=2QshZekR=hcV77bMh51h3wAynWjmnX+G8Hdjm@mail.gmail.com>

Hi Shamanou,

I can see the error is around line no 192~193, I would suggest you to print
the codons list first, like below.


192 SOP (CODON LIST);
193 prot = SymbolListViews.translate(codons,RNATools.getGeneticCode(
"UNIVERSAL"));

Paste result in mail thread then we can start debugging .

Regards,
Anant

On Sun, Feb 13, 2011 at 8:02 PM, Shamanou van Leeuwen <
mandarijnopw8 at gmail.com> wrote:

> hi guys,
>
> i made am making a tool to translate dna to protein using biojava.
> But  i am getting some errors that is do not fully understand.
> Can somebody please tell me what i am doing wrong?
>
>
> script:
> http://pastebin.com/TJSjkgqK
>
> errors:
> http://pastebin.com/iFXYWEZB
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
Anant Jain
B.Tech Bioinformatics, RHCE
Software Engineer,
Persistent Systems Limited, Pune


From willishf at ufl.edu  Sun Feb 13 19:11:58 2011
From: willishf at ufl.edu (Scooter Willis)
Date: Sun, 13 Feb 2011 14:11:58 -0500
Subject: [Biojava-l] programming error
In-Reply-To: <4D57EB6E.8010004@gmail.com>
References: <4D57EB6E.8010004@gmail.com>
Message-ID: <AANLkTim-u3avgK5529SiheMsgVPYMGD=J_eLfGX_Sq4J@mail.gmail.com>

Depending on what you need you may want to try out biojava3.

On Sun, Feb 13, 2011 at 9:32 AM, Shamanou van Leeuwen
<mandarijnopw8 at gmail.com> wrote:
> hi guys,
>
> i made am making a tool to translate dna to protein using biojava.
> But ?i am getting some errors that is do not fully understand.
> Can somebody please tell me what i am doing wrong?
>
>
> script:
> http://pastebin.com/TJSjkgqK
>
> errors:
> http://pastebin.com/iFXYWEZB
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>



From mandarijnopw8 at gmail.com  Mon Feb 14 02:27:32 2011
From: mandarijnopw8 at gmail.com (Shamanou van Leeuwen)
Date: Mon, 14 Feb 2011 03:27:32 +0100
Subject: [Biojava-l] programming error
In-Reply-To: <AANLkTim-u3avgK5529SiheMsgVPYMGD=J_eLfGX_Sq4J@mail.gmail.com>
References: <4D57EB6E.8010004@gmail.com>
	<AANLkTim-u3avgK5529SiheMsgVPYMGD=J_eLfGX_Sq4J@mail.gmail.com>
Message-ID: <4D589314.5040705@gmail.com>

On 13-02-11 20:11, Scooter Willis wrote:
> Depending on what you need you may want to try out biojava3.
>
> On Sun, Feb 13, 2011 at 9:32 AM, Shamanou van Leeuwen
> <mandarijnopw8 at gmail.com>  wrote:
>> hi guys,
>>
>> i made am making a tool to translate dna to protein using biojava.
>> But  i am getting some errors that is do not fully understand.
>> Can somebody please tell me what i am doing wrong?
>>
>>
>> script:
>> http://pastebin.com/TJSjkgqK
>>
>> errors:
>> http://pastebin.com/iFXYWEZB
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
i a, trying biojava 3 now but i am still doing something wrong.

http://pastebin.com/uLz934gr


From andreas at sdsc.edu  Mon Feb 14 08:16:48 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 14 Feb 2011 00:16:48 -0800
Subject: [Biojava-l] BioJava 3.0.1 released
Message-ID: <AANLkTin=yhdA5z0QDwz1Tz3O-rjGk6f6yzkV2GGbYrNe@mail.gmail.com>

BioJava 3.0.1 has been released and is available from
http://www.biojava.org/wiki/BioJava:Download .


The 3.0.1 release is mainly a bug fix release for the recent 3.0 code base,
which provides a major rewrite of the biojava.

A couple of noteworthy improvements:

- core: fixed an issue with sequence index positions, new utility methods
for memory efficient parsing of large fasta files

- structure: Fixed issues with PDB header parsing and more stability with
non-standard PDB files. Added new algorithm to automatically infer protein
domain boundaries.

- web services: Fixed wrong dependency on old codebase and overall
improvements in functionality of remote blast web service calls.

- protein modifications: Minor bugfixes

In parallel the biojava-legacy code base has been updated to version 1.8.1
and it contains a bug fix related to circular locations.

Thanks to all contributors for making this release possible.

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


From ayates at ebi.ac.uk  Mon Feb 14 10:07:12 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 14 Feb 2011 10:07:12 +0000
Subject: [Biojava-l] programming error
In-Reply-To: <4D589314.5040705@gmail.com>
References: <4D57EB6E.8010004@gmail.com>
	<AANLkTim-u3avgK5529SiheMsgVPYMGD=J_eLfGX_Sq4J@mail.gmail.com>
	<4D589314.5040705@gmail.com>
Message-ID: <C9323C5F-5952-4104-A251-F7016323DF90@ebi.ac.uk>

If you want to do frame based translation then there is an easier way of accomplishing this. The TranscriptionEngine allows you to translate in multiple frames and retrieve that information in a Map such as:

TranscriptionEngine te = TranscriptionEngine.getDefault();
Frame[] frames = Frame.getForwardFrames();
Map<Frame, Sequence<AminoAcidCompound>> results = te.multipleFrameTranslation(dna, frames);

Change the static call on Frame to Frame.getAllFrames() then you will do a full 6 frame translation.

Also I would avoid calling the getSequenceAsString() method until you need to output it to screen. The Sequence interface provides an adequate set of methods for testing length of a sequence. However if you want is the longest translation then I would replace that with (assuming the above code):

List<Sequence<AminoAcidCompound>> translations = new ArrayList<Sequence<AminoAcidCompound>>(results.getValues());
Collections.sort(translations, new Comparator<Sequence<AminoAcidCompound>>() {
  public int compare(Sequence<AminoAcidCompound> o1, Sequence<AminoAcidCompound> o2) {
    Integer o1Length = o1.getLength();
    Integer o2Length = o2.getLength();
    return o1Length.compareTo(o2Length);
  }
});
Sequence<AminoAcidCompound> longest = translations.get(translations.size()-1);

However I would like to see what errors you are pulling up from BioJava3 in case there is a scenario we are not currently taking into account

Andy

On 14 Feb 2011, at 02:27, Shamanou van Leeuwen wrote:

> On 13-02-11 20:11, Scooter Willis wrote:
>> Depending on what you need you may want to try out biojava3.
>> 
>> On Sun, Feb 13, 2011 at 9:32 AM, Shamanou van Leeuwen
>> <mandarijnopw8 at gmail.com>  wrote:
>>> hi guys,
>>> 
>>> i made am making a tool to translate dna to protein using biojava.
>>> But  i am getting some errors that is do not fully understand.
>>> Can somebody please tell me what i am doing wrong?
>>> 
>>> 
>>> script:
>>> http://pastebin.com/TJSjkgqK
>>> 
>>> errors:
>>> http://pastebin.com/iFXYWEZB
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>> 
>>> 
> i a, trying biojava 3 now but i am still doing something wrong.
> 
> http://pastebin.com/uLz934gr
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/







From andreas at sdsc.edu  Mon Feb 14 15:42:57 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 14 Feb 2011 07:42:57 -0800
Subject: [Biojava-l] programming error
In-Reply-To: <C9323C5F-5952-4104-A251-F7016323DF90@ebi.ac.uk>
References: <4D57EB6E.8010004@gmail.com>
	<AANLkTim-u3avgK5529SiheMsgVPYMGD=J_eLfGX_Sq4J@mail.gmail.com>
	<4D589314.5040705@gmail.com>
	<C9323C5F-5952-4104-A251-F7016323DF90@ebi.ac.uk>
Message-ID: <AANLkTin11qUmm9iRJZfaMu57ZqNKSAwiHACqo5U4zWxL@mail.gmail.com>

Hi Andy,

Could we get a Cookbook page for this? sounds like it would be good to have
a bit more docu on this topic ...

Thanks!

Andreas

On Mon, Feb 14, 2011 at 2:07 AM, Andy Yates <ayates at ebi.ac.uk> wrote:

> If you want to do frame based translation then there is an easier way of
> accomplishing this. The TranscriptionEngine allows you to translate in
> multiple frames and retrieve that information in a Map such as:
>
> TranscriptionEngine te = TranscriptionEngine.getDefault();
> Frame[] frames = Frame.getForwardFrames();
> Map<Frame, Sequence<AminoAcidCompound>> results =
> te.multipleFrameTranslation(dna, frames);
>
> Change the static call on Frame to Frame.getAllFrames() then you will do a
> full 6 frame translation.
>
> Also I would avoid calling the getSequenceAsString() method until you need
> to output it to screen. The Sequence interface provides an adequate set of
> methods for testing length of a sequence. However if you want is the longest
> translation then I would replace that with (assuming the above code):
>
> List<Sequence<AminoAcidCompound>> translations = new
> ArrayList<Sequence<AminoAcidCompound>>(results.getValues());
> Collections.sort(translations, new
> Comparator<Sequence<AminoAcidCompound>>() {
>  public int compare(Sequence<AminoAcidCompound> o1,
> Sequence<AminoAcidCompound> o2) {
>    Integer o1Length = o1.getLength();
>    Integer o2Length = o2.getLength();
>    return o1Length.compareTo(o2Length);
>  }
> });
> Sequence<AminoAcidCompound> longest =
> translations.get(translations.size()-1);
>
> However I would like to see what errors you are pulling up from BioJava3 in
> case there is a scenario we are not currently taking into account
>
> Andy
>
> On 14 Feb 2011, at 02:27, Shamanou van Leeuwen wrote:
>
> > On 13-02-11 20:11, Scooter Willis wrote:
> >> Depending on what you need you may want to try out biojava3.
> >>
> >> On Sun, Feb 13, 2011 at 9:32 AM, Shamanou van Leeuwen
> >> <mandarijnopw8 at gmail.com>  wrote:
> >>> hi guys,
> >>>
> >>> i made am making a tool to translate dna to protein using biojava.
> >>> But  i am getting some errors that is do not fully understand.
> >>> Can somebody please tell me what i am doing wrong?
> >>>
> >>>
> >>> script:
> >>> http://pastebin.com/TJSjkgqK
> >>>
> >>> errors:
> >>> http://pastebin.com/iFXYWEZB
> >>> _______________________________________________
> >>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>
> >>>
> > i a, trying biojava 3 now but i am still doing something wrong.
> >
> > http://pastebin.com/uLz934gr
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------


From ayates at ebi.ac.uk  Mon Feb 14 16:13:35 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 14 Feb 2011 16:13:35 +0000
Subject: [Biojava-l] programming error
In-Reply-To: <AANLkTin11qUmm9iRJZfaMu57ZqNKSAwiHACqo5U4zWxL@mail.gmail.com>
References: <4D57EB6E.8010004@gmail.com>
	<AANLkTim-u3avgK5529SiheMsgVPYMGD=J_eLfGX_Sq4J@mail.gmail.com>
	<4D589314.5040705@gmail.com>
	<C9323C5F-5952-4104-A251-F7016323DF90@ebi.ac.uk>
	<AANLkTin11qUmm9iRJZfaMu57ZqNKSAwiHACqo5U4zWxL@mail.gmail.com>
Message-ID: <7CBE613F-7F05-47C6-B917-8A1A3EF82E4C@ebi.ac.uk>

I've added a bit to the original cookbook page we had. I can migrate these changes to the cookbook front page later on in the week

Andy

On 14 Feb 2011, at 15:42, Andreas Prlic wrote:

> Hi Andy,
> 
> Could we get a Cookbook page for this? sounds like it would be good to have a bit more docu on this topic ...
> 
> Thanks!
> 
> Andreas
> 
> On Mon, Feb 14, 2011 at 2:07 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> If you want to do frame based translation then there is an easier way of accomplishing this. The TranscriptionEngine allows you to translate in multiple frames and retrieve that information in a Map such as:
> 
> TranscriptionEngine te = TranscriptionEngine.getDefault();
> Frame[] frames = Frame.getForwardFrames();
> Map<Frame, Sequence<AminoAcidCompound>> results = te.multipleFrameTranslation(dna, frames);
> 
> Change the static call on Frame to Frame.getAllFrames() then you will do a full 6 frame translation.
> 
> Also I would avoid calling the getSequenceAsString() method until you need to output it to screen. The Sequence interface provides an adequate set of methods for testing length of a sequence. However if you want is the longest translation then I would replace that with (assuming the above code):
> 
> List<Sequence<AminoAcidCompound>> translations = new ArrayList<Sequence<AminoAcidCompound>>(results.getValues());
> Collections.sort(translations, new Comparator<Sequence<AminoAcidCompound>>() {
>  public int compare(Sequence<AminoAcidCompound> o1, Sequence<AminoAcidCompound> o2) {
>    Integer o1Length = o1.getLength();
>    Integer o2Length = o2.getLength();
>    return o1Length.compareTo(o2Length);
>  }
> });
> Sequence<AminoAcidCompound> longest = translations.get(translations.size()-1);
> 
> However I would like to see what errors you are pulling up from BioJava3 in case there is a scenario we are not currently taking into account
> 
> Andy
> 
> On 14 Feb 2011, at 02:27, Shamanou van Leeuwen wrote:
> 
> > On 13-02-11 20:11, Scooter Willis wrote:
> >> Depending on what you need you may want to try out biojava3.
> >>
> >> On Sun, Feb 13, 2011 at 9:32 AM, Shamanou van Leeuwen
> >> <mandarijnopw8 at gmail.com>  wrote:
> >>> hi guys,
> >>>
> >>> i made am making a tool to translate dna to protein using biojava.
> >>> But  i am getting some errors that is do not fully understand.
> >>> Can somebody please tell me what i am doing wrong?
> >>>
> >>>
> >>> script:
> >>> http://pastebin.com/TJSjkgqK
> >>>
> >>> errors:
> >>> http://pastebin.com/iFXYWEZB
> >>> _______________________________________________
> >>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>
> >>>
> > i a, trying biojava 3 now but i am still doing something wrong.
> >
> > http://pastebin.com/uLz934gr
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> --
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> 
> 
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 
> 
> -- 
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/







From andreas at sdsc.edu  Mon Feb 14 23:57:07 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 14 Feb 2011 15:57:07 -0800
Subject: [Biojava-l] programming error
In-Reply-To: <7CBE613F-7F05-47C6-B917-8A1A3EF82E4C@ebi.ac.uk>
References: <4D57EB6E.8010004@gmail.com>
	<AANLkTim-u3avgK5529SiheMsgVPYMGD=J_eLfGX_Sq4J@mail.gmail.com>
	<4D589314.5040705@gmail.com>
	<C9323C5F-5952-4104-A251-F7016323DF90@ebi.ac.uk>
	<AANLkTin11qUmm9iRJZfaMu57ZqNKSAwiHACqo5U4zWxL@mail.gmail.com>
	<7CBE613F-7F05-47C6-B917-8A1A3EF82E4C@ebi.ac.uk>
Message-ID: <AANLkTikzm-VZV8+DRUvsH=oveX329gN0ku8m0g2ZChDH@mail.gmail.com>

Thanks Andy,

yea, would be good to add links on the cookbook front page, otherwise the
sections are hard to find...

Andreas

On Mon, Feb 14, 2011 at 8:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:

> I've added a bit to the original cookbook page we had. I can migrate these
> changes to the cookbook front page later on in the week
>
> Andy
>
> On 14 Feb 2011, at 15:42, Andreas Prlic wrote:
>
> > Hi Andy,
> >
> > Could we get a Cookbook page for this? sounds like it would be good to
> have a bit more docu on this topic ...
> >
> > Thanks!
> >
> > Andreas
> >
> > On Mon, Feb 14, 2011 at 2:07 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> > If you want to do frame based translation then there is an easier way of
> accomplishing this. The TranscriptionEngine allows you to translate in
> multiple frames and retrieve that information in a Map such as:
> >
> > TranscriptionEngine te = TranscriptionEngine.getDefault();
> > Frame[] frames = Frame.getForwardFrames();
> > Map<Frame, Sequence<AminoAcidCompound>> results =
> te.multipleFrameTranslation(dna, frames);
> >
> > Change the static call on Frame to Frame.getAllFrames() then you will do
> a full 6 frame translation.
> >
> > Also I would avoid calling the getSequenceAsString() method until you
> need to output it to screen. The Sequence interface provides an adequate set
> of methods for testing length of a sequence. However if you want is the
> longest translation then I would replace that with (assuming the above
> code):
> >
> > List<Sequence<AminoAcidCompound>> translations = new
> ArrayList<Sequence<AminoAcidCompound>>(results.getValues());
> > Collections.sort(translations, new
> Comparator<Sequence<AminoAcidCompound>>() {
> >  public int compare(Sequence<AminoAcidCompound> o1,
> Sequence<AminoAcidCompound> o2) {
> >    Integer o1Length = o1.getLength();
> >    Integer o2Length = o2.getLength();
> >    return o1Length.compareTo(o2Length);
> >  }
> > });
> > Sequence<AminoAcidCompound> longest =
> translations.get(translations.size()-1);
> >
> > However I would like to see what errors you are pulling up from BioJava3
> in case there is a scenario we are not currently taking into account
> >
> > Andy
> >
> > On 14 Feb 2011, at 02:27, Shamanou van Leeuwen wrote:
> >
> > > On 13-02-11 20:11, Scooter Willis wrote:
> > >> Depending on what you need you may want to try out biojava3.
> > >>
> > >> On Sun, Feb 13, 2011 at 9:32 AM, Shamanou van Leeuwen
> > >> <mandarijnopw8 at gmail.com>  wrote:
> > >>> hi guys,
> > >>>
> > >>> i made am making a tool to translate dna to protein using biojava.
> > >>> But  i am getting some errors that is do not fully understand.
> > >>> Can somebody please tell me what i am doing wrong?
> > >>>
> > >>>
> > >>> script:
> > >>> http://pastebin.com/TJSjkgqK
> > >>>
> > >>> errors:
> > >>> http://pastebin.com/iFXYWEZB
> > >>> _______________________________________________
> > >>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > >>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> > >>>
> > >>>
> > > i a, trying biojava 3 now but i am still doing something wrong.
> > >
> > > http://pastebin.com/uLz934gr
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> > --
> > Andrew Yates                   Ensembl Genomes Engineer
> > EMBL-EBI                       Tel: +44-(0)1223-492538
> > Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> > Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> >
> >
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> >
> >
> > --
> > -----------------------------------------------------------------------
> > Dr. Andreas Prlic
> > Senior Scientist, RCSB PDB Protein Data Bank
> > University of California, San Diego
> > (+1) 858.246.0526
> > -----------------------------------------------------------------------
>
> --
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>
>
>
>
>


From andreas at sdsc.edu  Wed Feb 16 02:45:49 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 15 Feb 2011 18:45:49 -0800
Subject: [Biojava-l] GSoC status
Message-ID: <AANLkTikPBs2NwDw-ekrNqWX3CVxsjQsLnZKxtzn=72xS@mail.gmail.com>

Hi Udana,

I would like to motivate student proposed projects as much as possible this
year. This means if you want to distinguish yourself with your application,
it would be great if you would suggest a project by yourself that you find
exciting. If our application to become a sponsoring organisation gets
approved by Google, we will start discussing proposals around March 18th. We
will probably suggest possible projects at some point, but I really would
like to give preference to student proposed projects this year.

To get ideas about possible student proposed projects I recommend getting a
module that is related to your studies and try to do some work with it. This
might give you ideas about what is missing and what could be added in a
project.

Andreas



On Tue, Feb 15, 2011 at 11:35 AM, udana chathuranga
<uchathuranga at gmail.com>wrote:

> Hi Andreas,
>
> Any updates about project ideas to gsoc2011 ?
>
>
>
>
> Thanks
> Regards
> Udana
>


From jw12 at sanger.ac.uk  Thu Feb 17 14:30:08 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 17 Feb 2011 14:30:08 +0000
Subject: [Biojava-l] DAS Workshop Registration Closing Soon
Message-ID: <0BCCE860-9AEA-4377-A9D6-F28E264DE43A@sanger.ac.uk>

Registration closes for the DAS workshop at 5pm this Friday GMT.  
Limited places still available.
Please note that for the tutorials day (Day 1) it is advisable to know  
at least one of PERL, Java or Javascript.
Further information and registration from here: http://www.ebi.ac.uk/training/onsite/110302DAS.html

There are still a few places for short talks on the second day if you  
have anything to talk about of interest to the DAS community.

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314










-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From watson at ebi.ac.uk  Fri Feb 18 08:46:53 2011
From: watson at ebi.ac.uk (James Watson)
Date: Fri, 18 Feb 2011 08:46:53 +0000
Subject: [Biojava-l] Hands-on training at EBI - Programmatic access to
 biological databases (Java)
Message-ID: <4D5E31FD.6080905@ebi.ac.uk>

*Date:* 9-13 May 2011
*Venue:* EMBL-EBI, Hinxton, Nr Cambridge, CB10 1SD, UK
*Registration Deadline:* 9th April 2011

This Java-based course in programmatic access to biological databases is 
ideal for bioinformaticians and biological researchers looking to 
develop data analysis pipelines or access data in an automated manner 
for integration into their own applications.

What will it cover?
- Introduction to Web Services and resources available at the EBI
- REST & SOAP - their application to EBI services and databases
- BioMart and BioMart Web Services
- Linking services together to construct workflows (Taverna, Enfin, Encore)

For a more detailed programme and information on registration please go 
to http://www.ebi.ac.uk/training/handson/course_110509_progjava.html

Many thanks,

James Watson

-- 
James D Watson
Scientific Training Officer
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Tel: +44(0)1223 492541

http://www.ebi.ac.uk/training/

Upcoming hands on training courses
(http://www.ebi.ac.uk/training/handson/):

28 Mar -- 1 Apr 2011: PSIMEx Workshop: Interactions and Pathways
9-13 May 2011: Programmatic access to biological databases (Java)
23-27 May 2011: FEBS: In silico systems biology for complex diseases: network reconstruction, analysis and network based modelling



From bli0406 at gmail.com  Wed Feb 23 07:16:29 2011
From: bli0406 at gmail.com (Bo Li)
Date: Wed, 23 Feb 2011 02:16:29 -0500
Subject: [Biojava-l] question regarding MSA
Message-ID: <A4406D27-913C-40BD-9EEA-89EE6AB85F29@gmail.com>

Hi,

Sorry for the bothering.  I tried the MSA feature by following the link:

http://www.biojava.org/wiki/BioJava:CookBook3:MSA

However, I can't see the symbols like ".", ":", and "*" like I can see  
from the output ClustalW.

So is there a way for users to obtain such information in the output  
from MSA?

Thanks,
Bo Li


From andreas at sdsc.edu  Thu Feb 24 08:06:59 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 24 Feb 2011 00:06:59 -0800
Subject: [Biojava-l] question regarding MSA
In-Reply-To: <A4406D27-913C-40BD-9EEA-89EE6AB85F29@gmail.com>
References: <A4406D27-913C-40BD-9EEA-89EE6AB85F29@gmail.com>
Message-ID: <AANLkTikiNMn_MenmqT=zCvD5KjrJOjjehb_vCZOECpWr@mail.gmail.com>

Hi Bo Li,

The printing method currently does not add those characters to the
display of the aligned sequences. If you need it you would have to
patch the printing method...

Andreas

On Tue, Feb 22, 2011 at 11:16 PM, Bo Li <bli0406 at gmail.com> wrote:
> Hi,
>
> Sorry for the bothering. ?I tried the MSA feature by following the link:
>
> http://www.biojava.org/wiki/BioJava:CookBook3:MSA
>
> However, I can't see the symbols like ".", ":", and "*" like I can see from
> the output ClustalW.
>
> So is there a way for users to obtain such information in the output from
> MSA?
>
> Thanks,
> Bo Li
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From p.v.troshin at dundee.ac.uk  Thu Feb 24 15:33:41 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Thu, 24 Feb 2011 15:33:41 +0000
Subject: [Biojava-l] Isoelectric point and molecular weight calculations
	with BioJava
Message-ID: <4D667A55.5040404@dundee.ac.uk>

Hi,

I've noticed that BioJava up to about version 1.7 had an 
org.biojava.bio.proteomics package, which had methods for isoelectric 
point and molecular weight calculations for peptides. I could not find 
this package in the BioJava 3.0.1 API. I?d like to use these methods and 
wonder if there are any equivalent methods available in the latest 
version of BioJava?

Thank you for your help,

Kind regards,
Peter

Dr Peter Troshin
Bioinformatics Software Developer
Phone: +44 (0)1382 388589
Fax: +44 (0)1382 385764
The Barton Group
College of Life Sciences
Medical Sciences Institute
University of Dundee
Dundee
DD1 5EH
UK





From andreas at sdsc.edu  Thu Feb 24 16:54:14 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 24 Feb 2011 08:54:14 -0800
Subject: [Biojava-l] Isoelectric point and molecular weight calculations
 with BioJava
In-Reply-To: <4D667A55.5040404@dundee.ac.uk>
References: <4D667A55.5040404@dundee.ac.uk>
Message-ID: <AANLkTim=otw02=CnK6nK3ps3JsU5=S-nSg+VCeRCNF4E@mail.gmail.com>

Hi Peter,

if you get a copy of biojava 1.8, it is still there. However I would
like to port this to biojava 3 as well.. George do you want to help me
with that, since you are one of the authors of this package? The basic
support for chemistry in BioJava 3 is a bit better... (e.g. Element
class)

Andreas

On Thu, Feb 24, 2011 at 7:33 AM, Peter Troshin <p.v.troshin at dundee.ac.uk> wrote:
> Hi,
>
> I've noticed that BioJava up to about version 1.7 had an
> org.biojava.bio.proteomics package, which had methods for isoelectric point
> and molecular weight calculations for peptides. I could not find this
> package in the BioJava 3.0.1 API. I?d like to use these methods and wonder
> if there are any equivalent methods available in the latest version of
> BioJava?
>
> Thank you for your help,
>
> Kind regards,
> Peter
>
> Dr Peter Troshin
> Bioinformatics Software Developer
> Phone: +44 (0)1382 388589
> Fax: +44 (0)1382 385764
> The Barton Group
> College of Life Sciences
> Medical Sciences Institute
> University of Dundee
> Dundee
> DD1 5EH
> UK
>
>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From p.v.troshin at dundee.ac.uk  Thu Feb 24 17:44:07 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Thu, 24 Feb 2011 17:44:07 +0000
Subject: [Biojava-l] Isoelectric point and molecular weight calculations
 with BioJava
In-Reply-To: <AANLkTim=otw02=CnK6nK3ps3JsU5=S-nSg+VCeRCNF4E@mail.gmail.com>
References: <4D667A55.5040404@dundee.ac.uk>
	<AANLkTim=otw02=CnK6nK3ps3JsU5=S-nSg+VCeRCNF4E@mail.gmail.com>
Message-ID: <4D6698E7.3080202@dundee.ac.uk>

Hi Andreas,

In fact I'd be happy to help with the development of the tools for 
simple physico-chemical properties calculation for peptides. We could 
port George?s code (assuming he is happy with this) from BioJava 1.8 but 
we can also provide a few other methods. A couple of projects in the lab 
where I work would have benefited from having these calculations readily 
available.

I was thinking about participation in the Google Summer of Code (GoSC) 
this year as a mentor, and I think this would be an easy project for a 
student. What do you think about this?

Thank you for your prompt reply.

Regards,
Peter



On 24/02/2011 16:54, Andreas Prlic wrote:
> Hi Peter,
>
> if you get a copy of biojava 1.8, it is still there. However I would
> like to port this to biojava 3 as well.. George do you want to help me
> with that, since you are one of the authors of this package? The basic
> support for chemistry in BioJava 3 is a bit better... (e.g. Element
> class)
>
> Andreas
>
> On Thu, Feb 24, 2011 at 7:33 AM, Peter Troshin<p.v.troshin at dundee.ac.uk>  wrote:
>> Hi,
>>
>> I've noticed that BioJava up to about version 1.7 had an
>> org.biojava.bio.proteomics package, which had methods for isoelectric point
>> and molecular weight calculations for peptides. I could not find this
>> package in the BioJava 3.0.1 API. I?d like to use these methods and wonder
>> if there are any equivalent methods available in the latest version of
>> BioJava?
>>
>> Thank you for your help,
>>
>> Kind regards,
>> Peter
>>
>> Dr Peter Troshin
>> Bioinformatics Software Developer
>> Phone: +44 (0)1382 388589
>> Fax: +44 (0)1382 385764
>> The Barton Group
>> College of Life Sciences
>> Medical Sciences Institute
>> University of Dundee
>> Dundee
>> DD1 5EH
>> UK
>>
>>
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>



From gwaldon at geneinfinity.org  Thu Feb 24 19:15:06 2011
From: gwaldon at geneinfinity.org (George Waldon)
Date: Thu, 24 Feb 2011 13:15:06 -0600
Subject: [Biojava-l] Isoelectric point and molecular weight calculations
 with BioJava
In-Reply-To: <4D6698E7.3080202@dundee.ac.uk>
References: <4D667A55.5040404@dundee.ac.uk>
	<AANLkTim=otw02=CnK6nK3ps3JsU5=S-nSg+VCeRCNF4E@mail.gmail.com>
	<4D6698E7.3080202@dundee.ac.uk>
Message-ID: <20110224131506.17104xy7rpe7n30g@gator1273.hostgator.com>

Hello Peter & Andreas

I effectively did some work on these methods, mostly fixing and adding  
the ExPASy algorithm that was kindly provided to me. I think it makes  
a lot of sense to port all physico-chemical property calculations  
related to amino acids and polypeptides to bj3, as suggested by  
Andreas, and I definitively support the effort. We could smoothly  
deprecate the bj1 package when this is done. Let me know how I could  
help.

Thanks
George

Quoting Peter Troshin <p.v.troshin at dundee.ac.uk>:

> Hi Andreas,
>
> In fact I'd be happy to help with the development of the tools for  
> simple physico-chemical properties calculation for peptides. We  
> could port George?s code (assuming he is happy with this) from  
> BioJava 1.8 but we can also provide a few other methods. A couple of  
> projects in the lab where I work would have benefited from having  
> these calculations readily available.
>
> I was thinking about participation in the Google Summer of Code  
> (GoSC) this year as a mentor, and I think this would be an easy  
> project for a student. What do you think about this?
>
> Thank you for your prompt reply.
>
> Regards,
> Peter
>
>
>
> On 24/02/2011 16:54, Andreas Prlic wrote:
>> Hi Peter,
>>
>> if you get a copy of biojava 1.8, it is still there. However I would
>> like to port this to biojava 3 as well.. George do you want to help me
>> with that, since you are one of the authors of this package? The basic
>> support for chemistry in BioJava 3 is a bit better... (e.g. Element
>> class)
>>
>> Andreas
>>
>> On Thu, Feb 24, 2011 at 7:33 AM, Peter  
>> Troshin<p.v.troshin at dundee.ac.uk>  wrote:
>>> Hi,
>>>
>>> I've noticed that BioJava up to about version 1.7 had an
>>> org.biojava.bio.proteomics package, which had methods for isoelectric point
>>> and molecular weight calculations for peptides. I could not find this
>>> package in the BioJava 3.0.1 API. I?d like to use these methods and wonder
>>> if there are any equivalent methods available in the latest version of
>>> BioJava?
>>>
>>> Thank you for your help,
>>>
>>> Kind regards,
>>> Peter
>>>
>>> Dr Peter Troshin
>>> Bioinformatics Software Developer
>>> Phone: +44 (0)1382 388589
>>> Fax: +44 (0)1382 385764
>>> The Barton Group
>>> College of Life Sciences
>>> Medical Sciences Institute
>>> University of Dundee
>>> Dundee
>>> DD1 5EH
>>> UK
>>>
>>>
>>>
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>
>





From willishf at ufl.edu  Fri Feb 25 04:08:53 2011
From: willishf at ufl.edu (Scooter Willis)
Date: Thu, 24 Feb 2011 23:08:53 -0500
Subject: [Biojava-l] Isoelectric point and molecular weight calculations
 with BioJava
In-Reply-To: <20110224131506.17104xy7rpe7n30g@gator1273.hostgator.com>
References: <4D667A55.5040404@dundee.ac.uk>
	<AANLkTim=otw02=CnK6nK3ps3JsU5=S-nSg+VCeRCNF4E@mail.gmail.com>
	<4D6698E7.3080202@dundee.ac.uk>
	<20110224131506.17104xy7rpe7n30g@gator1273.hostgator.com>
Message-ID: <AANLkTinSAg-X3g79eO-w0sQmiR0PNr6fW6h6dHaAzxqw@mail.gmail.com>

We put in some basics regarding modeling amino acid properties in the
core module but really didn't have any pressing use cases to drive the
api beyond calculating the mass of a peptide. We currently have
getMolecularWeight() as a method in AbstractCompound but never added a
getSequenceMolecularWeight() to AbstractSequence. It would be great to
get the attributes/features of amino acids properly modeled in core
and extend when reasonable useful summary methods at higher levels.
You should be able to query mass of a peptide and have it valid for an
amino acid with a PTM which means the amino acid needs to support the
ability to be modified in a flexible manner. I spent the last year+
developing a software suite for peptide detection in MS data for
deuterium exchange where automated PTM detection was important. Would
be great to get some focused attention on the core to make sure we can
model nucleotides and amino acids with a chemistry friendly API.

Thanks

Scooter

On Thu, Feb 24, 2011 at 2:15 PM, George Waldon <gwaldon at geneinfinity.org> wrote:
> Hello Peter & Andreas
>
> I effectively did some work on these methods, mostly fixing and adding the
> ExPASy algorithm that was kindly provided to me. I think it makes a lot of
> sense to port all physico-chemical property calculations related to amino
> acids and polypeptides to bj3, as suggested by Andreas, and I definitively
> support the effort. We could smoothly deprecate the bj1 package when this is
> done. Let me know how I could help.
>
> Thanks
> George
>
> Quoting Peter Troshin <p.v.troshin at dundee.ac.uk>:
>
>> Hi Andreas,
>>
>> In fact I'd be happy to help with the development of the tools for simple
>> physico-chemical properties calculation for peptides. We could port George?s
>> code (assuming he is happy with this) from BioJava 1.8 but we can also
>> provide a few other methods. A couple of projects in the lab where I work
>> would have benefited from having these calculations readily available.
>>
>> I was thinking about participation in the Google Summer of Code (GoSC)
>> this year as a mentor, and I think this would be an easy project for a
>> student. What do you think about this?
>>
>> Thank you for your prompt reply.
>>
>> Regards,
>> Peter
>>
>>
>>
>> On 24/02/2011 16:54, Andreas Prlic wrote:
>>>
>>> Hi Peter,
>>>
>>> if you get a copy of biojava 1.8, it is still there. However I would
>>> like to port this to biojava 3 as well.. George do you want to help me
>>> with that, since you are one of the authors of this package? The basic
>>> support for chemistry in BioJava 3 is a bit better... (e.g. Element
>>> class)
>>>
>>> Andreas
>>>
>>> On Thu, Feb 24, 2011 at 7:33 AM, Peter Troshin<p.v.troshin at dundee.ac.uk>
>>> ?wrote:
>>>>
>>>> Hi,
>>>>
>>>> I've noticed that BioJava up to about version 1.7 had an
>>>> org.biojava.bio.proteomics package, which had methods for isoelectric
>>>> point
>>>> and molecular weight calculations for peptides. I could not find this
>>>> package in the BioJava 3.0.1 API. I?d like to use these methods and
>>>> wonder
>>>> if there are any equivalent methods available in the latest version of
>>>> BioJava?
>>>>
>>>> Thank you for your help,
>>>>
>>>> Kind regards,
>>>> Peter
>>>>
>>>> Dr Peter Troshin
>>>> Bioinformatics Software Developer
>>>> Phone: +44 (0)1382 388589
>>>> Fax: +44 (0)1382 385764
>>>> The Barton Group
>>>> College of Life Sciences
>>>> Medical Sciences Institute
>>>> University of Dundee
>>>> Dundee
>>>> DD1 5EH
>>>> UK
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>
>>
>>
>
>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From andreas at sdsc.edu  Fri Feb 25 05:12:17 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 24 Feb 2011 21:12:17 -0800
Subject: [Biojava-l] Isoelectric point and molecular weight calculations
 with BioJava
In-Reply-To: <AANLkTinSAg-X3g79eO-w0sQmiR0PNr6fW6h6dHaAzxqw@mail.gmail.com>
References: <4D667A55.5040404@dundee.ac.uk>
	<AANLkTim=otw02=CnK6nK3ps3JsU5=S-nSg+VCeRCNF4E@mail.gmail.com>
	<4D6698E7.3080202@dundee.ac.uk>
	<20110224131506.17104xy7rpe7n30g@gator1273.hostgator.com>
	<AANLkTinSAg-X3g79eO-w0sQmiR0PNr6fW6h6dHaAzxqw@mail.gmail.com>
Message-ID: <AANLkTimmZ+CnKNZJw2RWuQ9GMYT8h6QqMx+U4Ph2=JCL@mail.gmail.com>

Great, seems we have an agreement that we want to improve
functionality for this. How complex is this going to be? From quickly
checking the 1.8 source it looks like just a few classes that need to
be converted and not too painful.  What other functionality would you
like to see that is currently not there?

Andreas


On Thu, Feb 24, 2011 at 8:08 PM, Scooter Willis <willishf at ufl.edu> wrote:
> We put in some basics regarding modeling amino acid properties in the
> core module but really didn't have any pressing use cases to drive the
> api beyond calculating the mass of a peptide. We currently have
> getMolecularWeight() as a method in AbstractCompound but never added a
> getSequenceMolecularWeight() to AbstractSequence. It would be great to
> get the attributes/features of amino acids properly modeled in core
> and extend when reasonable useful summary methods at higher levels.
> You should be able to query mass of a peptide and have it valid for an
> amino acid with a PTM which means the amino acid needs to support the
> ability to be modified in a flexible manner. I spent the last year+
> developing a software suite for peptide detection in MS data for
> deuterium exchange where automated PTM detection was important. Would
> be great to get some focused attention on the core to make sure we can
> model nucleotides and amino acids with a chemistry friendly API.
>
> Thanks
>
> Scooter
>
> On Thu, Feb 24, 2011 at 2:15 PM, George Waldon <gwaldon at geneinfinity.org> wrote:
>> Hello Peter & Andreas
>>
>> I effectively did some work on these methods, mostly fixing and adding the
>> ExPASy algorithm that was kindly provided to me. I think it makes a lot of
>> sense to port all physico-chemical property calculations related to amino
>> acids and polypeptides to bj3, as suggested by Andreas, and I definitively
>> support the effort. We could smoothly deprecate the bj1 package when this is
>> done. Let me know how I could help.
>>
>> Thanks
>> George
>>
>> Quoting Peter Troshin <p.v.troshin at dundee.ac.uk>:
>>
>>> Hi Andreas,
>>>
>>> In fact I'd be happy to help with the development of the tools for simple
>>> physico-chemical properties calculation for peptides. We could port George?s
>>> code (assuming he is happy with this) from BioJava 1.8 but we can also
>>> provide a few other methods. A couple of projects in the lab where I work
>>> would have benefited from having these calculations readily available.
>>>
>>> I was thinking about participation in the Google Summer of Code (GoSC)
>>> this year as a mentor, and I think this would be an easy project for a
>>> student. What do you think about this?
>>>
>>> Thank you for your prompt reply.
>>>
>>> Regards,
>>> Peter
>>>
>>>
>>>
>>> On 24/02/2011 16:54, Andreas Prlic wrote:
>>>>
>>>> Hi Peter,
>>>>
>>>> if you get a copy of biojava 1.8, it is still there. However I would
>>>> like to port this to biojava 3 as well.. George do you want to help me
>>>> with that, since you are one of the authors of this package? The basic
>>>> support for chemistry in BioJava 3 is a bit better... (e.g. Element
>>>> class)
>>>>
>>>> Andreas
>>>>
>>>> On Thu, Feb 24, 2011 at 7:33 AM, Peter Troshin<p.v.troshin at dundee.ac.uk>
>>>> ?wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I've noticed that BioJava up to about version 1.7 had an
>>>>> org.biojava.bio.proteomics package, which had methods for isoelectric
>>>>> point
>>>>> and molecular weight calculations for peptides. I could not find this
>>>>> package in the BioJava 3.0.1 API. I?d like to use these methods and
>>>>> wonder
>>>>> if there are any equivalent methods available in the latest version of
>>>>> BioJava?
>>>>>
>>>>> Thank you for your help,
>>>>>
>>>>> Kind regards,
>>>>> Peter
>>>>>
>>>>> Dr Peter Troshin
>>>>> Bioinformatics Software Developer
>>>>> Phone: +44 (0)1382 388589
>>>>> Fax: +44 (0)1382 385764
>>>>> The Barton Group
>>>>> College of Life Sciences
>>>>> Medical Sciences Institute
>>>>> University of Dundee
>>>>> Dundee
>>>>> DD1 5EH
>>>>> UK
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>
>>>
>>>
>>
>>
>>
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------



From flf.mib at gmail.com  Fri Feb 25 22:21:19 2011
From: flf.mib at gmail.com (=?ISO-8859-1?Q?Fran=E7ois_Le_Fevre?=)
Date: Fri, 25 Feb 2011 23:21:19 +0100
Subject: [Biojava-l] biojava3 and symbol
Message-ID: <4D682B5F.60807@gmail.com>

Hello
I am a newbie in biojava3.
I have installed the maven version.

I have a question : is there a way to go from DNASequence to SymbolList?
I would like to study codons and their frequency in several organisms.
It was easy with biojava with

"SymbolList codons  = SymbolListViews.windowedSymbolList(seq, 3);"
and
"DistributionTrainerContext"

But now I am a little lost between maven biojava3 and biojava.
So if anyone could explain me how to get codons view from DNASequence, 
it could be great.

Thanks a lot!

Francois


-- 
----------------------
Francois LE FEVRE



From andreas at sdsc.edu  Mon Feb 28 06:04:46 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sun, 27 Feb 2011 22:04:46 -0800
Subject: [Biojava-l] biojava3 and symbol
In-Reply-To: <4D682B5F.60807@gmail.com>
References: <4D682B5F.60807@gmail.com>
Message-ID: <AANLkTimif0X8c6W=Yz-Ojy6xOuysABceCZSpqHa232kq@mail.gmail.com>

Hi Francois,

SymbolLists are part of BioJava 1.8 (the legacy version) and not 3.0.
You might want to get the previous version installed. It is available
from Maven as well...

Andreas

2011/2/25 Fran?ois Le Fevre <flf.mib at gmail.com>:
> Hello
> I am a newbie in biojava3.
> I have installed the maven version.
>
> I have a question : is there a way to go from DNASequence to SymbolList?
> I would like to study codons and their frequency in several organisms.
> It was easy with biojava with
>
> "SymbolList codons ?= SymbolListViews.windowedSymbolList(seq, 3);"
> and
> "DistributionTrainerContext"
>
> But now I am a little lost between maven biojava3 and biojava.
> So if anyone could explain me how to get codons view from DNASequence, it
> could be great.
>
> Thanks a lot!
>
> Francois
>
>
> --
> ----------------------
> Francois LE FEVRE
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From ayates at ebi.ac.uk  Mon Feb 28 10:06:16 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 28 Feb 2011 10:06:16 +0000
Subject: [Biojava-l] biojava3 and symbol
In-Reply-To: <4D682B5F.60807@gmail.com>
References: <4D682B5F.60807@gmail.com>
Message-ID: <245D3308-6EB9-44C0-A954-DEA0D9D28F94@ebi.ac.uk>

Hi Francois,

To get a windowed view over any sequence you should use the following:

DNASequence seq = new DNASequence("ATGCTG");
Iterable<SequenceView<NucleotideCompound>> w = new WindowedSequence<NucleotideCompound>(seq, 3);
for(SequenceView<NucelotideCompound> triplet: w) {
  System.out.println(triplet);
}

HTH

Andy

On 25 Feb 2011, at 22:21, Fran?ois Le Fevre wrote:

> Hello
> I am a newbie in biojava3.
> I have installed the maven version.
> 
> I have a question : is there a way to go from DNASequence to SymbolList?
> I would like to study codons and their frequency in several organisms.
> It was easy with biojava with
> 
> "SymbolList codons  = SymbolListViews.windowedSymbolList(seq, 3);"
> and
> "DistributionTrainerContext"
> 
> But now I am a little lost between maven biojava3 and biojava.
> So if anyone could explain me how to get codons view from DNASequence, it could be great.
> 
> Thanks a lot!
> 
> Francois
> 
> 
> -- 
> ----------------------
> Francois LE FEVRE
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/







From flf.mib at gmail.com  Mon Feb 28 11:12:51 2011
From: flf.mib at gmail.com (Francois Le Fevre)
Date: Mon, 28 Feb 2011 12:12:51 +0100
Subject: [Biojava-l] biojava3 and symbol
In-Reply-To: <245D3308-6EB9-44C0-A954-DEA0D9D28F94@ebi.ac.uk>
References: <4D682B5F.60807@gmail.com>
	<245D3308-6EB9-44C0-A954-DEA0D9D28F94@ebi.ac.uk>
Message-ID: <AANLkTin0ogxP=C0FDU0fb1y7oEWOQ4ZWEy6avYSH=LOR@mail.gmail.com>

perfect thank a lot.
Have a good day
Francois

2011/2/28 Andy Yates <ayates at ebi.ac.uk>

> Hi Francois,
>
> To get a windowed view over any sequence you should use the following:
>
> DNASequence seq = new DNASequence("ATGCTG");
> Iterable<SequenceView<NucleotideCompound>> w = new
> WindowedSequence<NucleotideCompound>(seq, 3);
> for(SequenceView<NucelotideCompound> triplet: w) {
>  System.out.println(triplet);
> }
>
> HTH
>
> Andy
>
> On 25 Feb 2011, at 22:21, Fran?ois Le Fevre wrote:
>
> > Hello
> > I am a newbie in biojava3.
> > I have installed the maven version.
> >
> > I have a question : is there a way to go from DNASequence to SymbolList?
> > I would like to study codons and their frequency in several organisms.
> > It was easy with biojava with
> >
> > "SymbolList codons  = SymbolListViews.windowedSymbolList(seq, 3);"
> > and
> > "DistributionTrainerContext"
> >
> > But now I am a little lost between maven biojava3 and biojava.
> > So if anyone could explain me how to get codons view from DNASequence, it
> could be great.
> >
> > Thanks a lot!
> >
> > Francois
> >
> >
> > --
> > ----------------------
> > Francois LE FEVRE
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>
>
>
>
>


-- 


Francois Le Fevre
Management Informatique Innovation Biotechnologies
Paris, France
-
Avant d'imprimer, pensez ? l'environnement



From p.v.troshin at dundee.ac.uk  Mon Feb 28 15:18:15 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Mon, 28 Feb 2011 15:18:15 +0000
Subject: [Biojava-l] Isoelectric point and molecular weight calculations
 with BioJava
In-Reply-To: <AANLkTimmZ+CnKNZJw2RWuQ9GMYT8h6QqMx+U4Ph2=JCL@mail.gmail.com>
References: <4D667A55.5040404@dundee.ac.uk>	<AANLkTim=otw02=CnK6nK3ps3JsU5=S-nSg+VCeRCNF4E@mail.gmail.com>	<4D6698E7.3080202@dundee.ac.uk>	<20110224131506.17104xy7rpe7n30g@gator1273.hostgator.com>	<AANLkTinSAg-X3g79eO-w0sQmiR0PNr6fW6h6dHaAzxqw@mail.gmail.com>
	<AANLkTimmZ+CnKNZJw2RWuQ9GMYT8h6QqMx+U4Ph2=JCL@mail.gmail.com>
Message-ID: <4D6BBCB7.3010203@dundee.ac.uk>

>>>What other functionality would you
>>>like to see that is currently not there?


I think that the methods below would be a good starting point, then the 
Google Summer of Code student can propose something else that he/she 
would fancy implementing.

   Molecular weight
   Extinction coefficient
   Instability index
   Aliphatic index
   Grand Average of Hydropathy
   Isoelectric point
   Number of amino acids in the protein (His, Met, Cys)

I know BioJava projects were managed under Open Bioinformatics 
Foundation (OBF) during last years GSoC. Is there a page for this year 
GSoC ideas somewhere?

Regards,
Peter


On 25/02/2011 05:12, Andreas Prlic wrote:
> Great, seems we have an agreement that we want to improve
> functionality for this. How complex is this going to be? From quickly
> checking the 1.8 source it looks like just a few classes that need to
> be converted and not too painful.  What other functionality would you
> like to see that is currently not there?
>
> Andreas
>
>
> On Thu, Feb 24, 2011 at 8:08 PM, Scooter Willis<willishf at ufl.edu>  wrote:
>> We put in some basics regarding modeling amino acid properties in the
>> core module but really didn't have any pressing use cases to drive the
>> api beyond calculating the mass of a peptide. We currently have
>> getMolecularWeight() as a method in AbstractCompound but never added a
>> getSequenceMolecularWeight() to AbstractSequence. It would be great to
>> get the attributes/features of amino acids properly modeled in core
>> and extend when reasonable useful summary methods at higher levels.
>> You should be able to query mass of a peptide and have it valid for an
>> amino acid with a PTM which means the amino acid needs to support the
>> ability to be modified in a flexible manner. I spent the last year+
>> developing a software suite for peptide detection in MS data for
>> deuterium exchange where automated PTM detection was important. Would
>> be great to get some focused attention on the core to make sure we can
>> model nucleotides and amino acids with a chemistry friendly API.
>>
>> Thanks
>>
>> Scooter
>>
>> On Thu, Feb 24, 2011 at 2:15 PM, George Waldon<gwaldon at geneinfinity.org>  wrote:
>>> Hello Peter&  Andreas
>>>
>>> I effectively did some work on these methods, mostly fixing and adding the
>>> ExPASy algorithm that was kindly provided to me. I think it makes a lot of
>>> sense to port all physico-chemical property calculations related to amino
>>> acids and polypeptides to bj3, as suggested by Andreas, and I definitively
>>> support the effort. We could smoothly deprecate the bj1 package when this is
>>> done. Let me know how I could help.
>>>
>>> Thanks
>>> George
>>>
>>> Quoting Peter Troshin<p.v.troshin at dundee.ac.uk>:
>>>
>>>> Hi Andreas,
>>>>
>>>> In fact I'd be happy to help with the development of the tools for simple
>>>> physico-chemical properties calculation for peptides. We could port George?s
>>>> code (assuming he is happy with this) from BioJava 1.8 but we can also
>>>> provide a few other methods. A couple of projects in the lab where I work
>>>> would have benefited from having these calculations readily available.
>>>>
>>>> I was thinking about participation in the Google Summer of Code (GoSC)
>>>> this year as a mentor, and I think this would be an easy project for a
>>>> student. What do you think about this?
>>>>
>>>> Thank you for your prompt reply.
>>>>
>>>> Regards,
>>>> Peter
>>>>
>>>>
>>>>
>>>> On 24/02/2011 16:54, Andreas Prlic wrote:
>>>>> Hi Peter,
>>>>>
>>>>> if you get a copy of biojava 1.8, it is still there. However I would
>>>>> like to port this to biojava 3 as well.. George do you want to help me
>>>>> with that, since you are one of the authors of this package? The basic
>>>>> support for chemistry in BioJava 3 is a bit better... (e.g. Element
>>>>> class)
>>>>>
>>>>> Andreas
>>>>>
>>>>> On Thu, Feb 24, 2011 at 7:33 AM, Peter Troshin<p.v.troshin at dundee.ac.uk>
>>>>>   wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I've noticed that BioJava up to about version 1.7 had an
>>>>>> org.biojava.bio.proteomics package, which had methods for isoelectric
>>>>>> point
>>>>>> and molecular weight calculations for peptides. I could not find this
>>>>>> package in the BioJava 3.0.1 API. I?d like to use these methods and
>>>>>> wonder
>>>>>> if there are any equivalent methods available in the latest version of
>>>>>> BioJava?
>>>>>>
>>>>>> Thank you for your help,
>>>>>>
>>>>>> Kind regards,
>>>>>> Peter
>>>>>>
>>>>>> Dr Peter Troshin
>>>>>> Bioinformatics Software Developer
>>>>>> Phone: +44 (0)1382 388589
>>>>>> Fax: +44 (0)1382 385764
>>>>>> The Barton Group
>>>>>> College of Life Sciences
>>>>>> Medical Sciences Institute
>>>>>> University of Dundee
>>>>>> Dundee
>>>>>> DD1 5EH
>>>>>> UK
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>
>



From uchathuranga at gmail.com  Thu Feb 10 17:01:57 2011
From: uchathuranga at gmail.com (udana chathuranga)
Date: Thu, 10 Feb 2011 17:01:57 -0000
Subject: [Biojava-l] Problem with Multiple Sequence Alignment in BioJava
Message-ID: <AANLkTimQm+oNnNhbcciBf7JjA3vVADnkxD109Pq56cWO@mail.gmail.com>

hi all,

When I was going through the biojava cookbook as I was interested in this
project. I tried the example in the page
http://biojava.org/wiki/BioJava:CookBook3:MSA and I got a classnotfound
exception for the line "Profile<ProteinSequence, AminoAcidCompound> profile
= Alignments.getMultipleSequenceAlignment(lst);".

Error Message:

Exception in thread "main" java.lang.NoClassDefFoundError:
org/forester/phylogenyinference/DistanceMatrix
    at
org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)
    at CookbookMSA.multipleSequenceAlignment(CookbookMSA.java:29)
    at CookbookMSA.main(CookbookMSA.java:18)
Caused by: java.lang.ClassNotFoundException:
org.forester.phylogenyinference.DistanceMatrix
    at java.net.URLClassLoader$1.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClassInternal(Unknown Source)

Is this a know issue or Am I doing something wrong with the code?
Help me on this I have attached the java source file that I have tried.

Thanks
Regards
udana.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: CookbookMSA.java
Type: application/octet-stream
Size: 1579 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biojava-l/attachments/20110210/eb50655d/attachment-0002.obj>