From harryzs1981 at gmail.com  Wed May  6 09:13:42 2009
From: harryzs1981 at gmail.com (sheng zhao)
Date: Wed, 6 May 2009 15:13:42 +0200
Subject: [Biojava-l] Biojava-doc in chm forma
Message-ID: <3d23b1eb0905060613m643adf87sdef55a05a083dd51@mail.gmail.com>

Hi

Where can I find Biojava-doc in chm format??

Thanks !

harry

From andreas at sdsc.edu  Thu May  7 08:59:32 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 7 May 2009 05:59:32 -0700
Subject: [Biojava-l] SVDSuperimposer
In-Reply-To: <4A02D2E7.9070705@wp.pl>
References: <4A02D2E7.9070705@wp.pl>
Message-ID: <59a41c430905070559v238e0df2p28478d5108dae4a@mail.gmail.com>

Hi Michal,

The SVD superimposer actually does the same Singular Value
Decomposition in both BioJava and BioPython. The difference is that
BioJava also contains a complete alignment algorithm that can
calculate a structure alignment, if the region of similarity between 2
proteins is not known a priori.

See also here:
http://biojava.org/wiki/BioJava:CookBook:PDB:align  and
http://biojava.org/wiki/BioJava:CookBook:PDB:aboutalign

Andreas

On Thu, May 7, 2009 at 5:24 AM, Michal Lorenc <m.t.lorenc at wp.pl> wrote:
> Hello Andreas,
> SVDSuperimposer from BioPython works only with proteins which have the same
> length, but in BioJava it does not matter.
>
> Do you published how SVDSuperimposer in BioJava works or do you know where
> could I found more information?
>
> Thank you in advance.
>
> Best regards,
>
> Michal
>

From raphael.andre.bauer at gmail.com  Fri May  8 09:13:44 2009
From: raphael.andre.bauer at gmail.com (=?UTF-8?Q?Raphael_Andr=C3=A9_Bauer?=)
Date: Fri, 8 May 2009 15:13:44 +0200
Subject: [Biojava-l] SVDSuperimposer
In-Reply-To: <59a41c430905070559v238e0df2p28478d5108dae4a@mail.gmail.com>
References: <4A02D2E7.9070705@wp.pl>
	<59a41c430905070559v238e0df2p28478d5108dae4a@mail.gmail.com>
Message-ID: <9b46aa30905080613o2ea91751sdd086c5d880cc435@mail.gmail.com>

On Thu, May 7, 2009 at 2:59 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Michal,
>
> The SVD superimposer actually does the same Singular Value
> Decomposition in both BioJava and BioPython. The difference is that
> BioJava also contains a complete alignment algorithm that can
> calculate a structure alignment, if the region of similarity between 2
> proteins is not known a priori.
>
> See also here:
> http://biojava.org/wiki/BioJava:CookBook:PDB:align ?and
> http://biojava.org/wiki/BioJava:CookBook:PDB:aboutalign

Maybe it is interesting for you to know that we developed a generic
algorithm for the structural alignment of RNA and proteins called
"LaJolla". The reference implementation is built using BioJava and
released as open source at http://lajolla.sourceforge.net. I think
LaJolla is straight forward to use and modify if you know how to use
Maven and the BioJava core classes.

Btw. The algorithm for the alignment of proteins used by BioJava
yielded sometimes strange results - but I did not do an exhaustive
evaluation. But maybe LaJolla is an alternative in those cases.

Additionally -- if the BioJava project is interested in integrating
LaJolla into BioJava this is really not a problem -- but I do not know
if it blurs the clean toolkit/library character of BioJava.

We are open for all suggestions regarding the algorithm and also
regarding a cooperation with BioJava...

Thanks,

Raphael
@Michal: LaJolla is also partly made in Poland -- so mabye you some
people by chance..

>
> Andreas
>
> On Thu, May 7, 2009 at 5:24 AM, Michal Lorenc <m.t.lorenc at wp.pl> wrote:
>> Hello Andreas,
>> SVDSuperimposer from BioPython works only with proteins which have the same
>> length, but in BioJava it does not matter.
>>
>> Do you published how SVDSuperimposer in BioJava works or do you know where
>> could I found more information?
>>
>> Thank you in advance.
>>
>> Best regards,
>>
>> Michal
>>
> _______________________________________________
> 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 May  8 13:37:41 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 8 May 2009 10:37:41 -0700
Subject: [Biojava-l] SVDSuperimposer
In-Reply-To: <9b46aa30905080613o2ea91751sdd086c5d880cc435@mail.gmail.com>
References: <4A02D2E7.9070705@wp.pl>
	<59a41c430905070559v238e0df2p28478d5108dae4a@mail.gmail.com>
	<9b46aa30905080613o2ea91751sdd086c5d880cc435@mail.gmail.com>
Message-ID: <59a41c430905081037n5b2ce541nc132dbfb2ea49b0a@mail.gmail.com>

Hi Raphael,

Thanks for posting the link to "LaJolla" (funny that you chose this
name, it is the part of the town where my university is located...).
This is very interesting and exactly the kind of applications we are
happy to see BioJava being used for.

Do you want to provide a link back to your project site at
http://biojava.org/wiki/BioJava:BioJavaInside and also add your paper
to the list of papers that are using BioJava?

About the  BioJava algorithm : If you have an example where the
BioJava structure comparison does not give the result you would
expect, could you send it to me so I can take a look ?

Thanks,
Andreas


On Fri, May 8, 2009 at 6:13 AM, Raphael Andr? Bauer
<raphael.andre.bauer at gmail.com> wrote:
> On Thu, May 7, 2009 at 2:59 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Hi Michal,
>>
>> The SVD superimposer actually does the same Singular Value
>> Decomposition in both BioJava and BioPython. The difference is that
>> BioJava also contains a complete alignment algorithm that can
>> calculate a structure alignment, if the region of similarity between 2
>> proteins is not known a priori.
>>
>> See also here:
>> http://biojava.org/wiki/BioJava:CookBook:PDB:align ?and
>> http://biojava.org/wiki/BioJava:CookBook:PDB:aboutalign
>
> Maybe it is interesting for you to know that we developed a generic
> algorithm for the structural alignment of RNA and proteins called
> "LaJolla". The reference implementation is built using BioJava and
> released as open source at http://lajolla.sourceforge.net. I think
> LaJolla is straight forward to use and modify if you know how to use
> Maven and the BioJava core classes.
>
> Btw. The algorithm for the alignment of proteins used by BioJava
> yielded sometimes strange results - but I did not do an exhaustive
> evaluation. But maybe LaJolla is an alternative in those cases.
>
> Additionally -- if the BioJava project is interested in integrating
> LaJolla into BioJava this is really not a problem -- but I do not know
> if it blurs the clean toolkit/library character of BioJava.
>
> We are open for all suggestions regarding the algorithm and also
> regarding a cooperation with BioJava...
>
> Thanks,
>
> Raphael
> @Michal: LaJolla is also partly made in Poland -- so mabye you some
> people by chance..
>
>>
>> Andreas
>>
>> On Thu, May 7, 2009 at 5:24 AM, Michal Lorenc <m.t.lorenc at wp.pl> wrote:
>>> Hello Andreas,
>>> SVDSuperimposer from BioPython works only with proteins which have the same
>>> length, but in BioJava it does not matter.
>>>
>>> Do you published how SVDSuperimposer in BioJava works or do you know where
>>> could I found more information?
>>>
>>> Thank you in advance.
>>>
>>> Best regards,
>>>
>>> Michal
>>>
>> _______________________________________________
>> 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  Mon May 11 00:30:30 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sun, 10 May 2009 21:30:30 -0700
Subject: [Biojava-l] Plans for next biojava release - modularization
Message-ID: <59a41c430905102130v6e878c6bgda582268e02824fe@mail.gmail.com>

Hi,

In case you are not subscribed to biojava-dev: we are having a
discussion about how to organize the code base for the next release of
biojava on the biojava-dev mailing list. If you want to follow this
discussion, but are not subscribed yet, you can do so here:
http://www.biojava.org/mailman/listinfo/biojava-dev

Andreas

From raphael.andre.bauer at gmail.com  Mon May 11 05:10:48 2009
From: raphael.andre.bauer at gmail.com (=?UTF-8?Q?Raphael_Andr=C3=A9_Bauer?=)
Date: Mon, 11 May 2009 11:10:48 +0200
Subject: [Biojava-l] SVDSuperimposer
In-Reply-To: <59a41c430905081037n5b2ce541nc132dbfb2ea49b0a@mail.gmail.com>
References: <4A02D2E7.9070705@wp.pl>
	<59a41c430905070559v238e0df2p28478d5108dae4a@mail.gmail.com> 
	<9b46aa30905080613o2ea91751sdd086c5d880cc435@mail.gmail.com> 
	<59a41c430905081037n5b2ce541nc132dbfb2ea49b0a@mail.gmail.com>
Message-ID: <9b46aa30905110210j5799359s6d72f50dccb3c74f@mail.gmail.com>

On Fri, May 8, 2009 at 7:37 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Raphael,
>
> Thanks for posting the link to "LaJolla" (funny that you chose this
> name, it is the part of the town where my university is located...).
> This is very interesting and exactly the kind of applications we are
> happy to see BioJava being used for.
Well. Phil Bourne and the PDB are there (and I think you are also
somehow connected to both)... I also heard that LaJolla might have
nice beaches, sunny weather and the surf?... So LaJolla definitely is
a good name for a boring structural RNA and protein alignment
algorithm...
>
> Do you want to provide a link back to your project site at
> http://biojava.org/wiki/BioJava:BioJavaInside and also add your paper
> to the list of papers that are using BioJava?
done
>
> About the ?BioJava algorithm : If you have an example where the
> BioJava structure comparison does not give the result you would
> expect, could you send it to me so I can take a look ?
I did not write down the examples (I thought, that the protein
alignment of BioJava is somehow alpha because of "personal
communication of..."). But the examples where simple. If I rediscover
them I will  let you know.

Maybe it is also of help to mention in the source code or on the
webpage of the cookbook: "If our protein alignment alg delivers
strange results please let us now..." or so.. So that users are aware
of submitting strange results...


Thanks,

Raphael

>
> Thanks,
> Andreas
>
>
> On Fri, May 8, 2009 at 6:13 AM, Raphael Andr? Bauer
> <raphael.andre.bauer at gmail.com> wrote:
>> On Thu, May 7, 2009 at 2:59 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> Hi Michal,
>>>
>>> The SVD superimposer actually does the same Singular Value
>>> Decomposition in both BioJava and BioPython. The difference is that
>>> BioJava also contains a complete alignment algorithm that can
>>> calculate a structure alignment, if the region of similarity between 2
>>> proteins is not known a priori.
>>>
>>> See also here:
>>> http://biojava.org/wiki/BioJava:CookBook:PDB:align ?and
>>> http://biojava.org/wiki/BioJava:CookBook:PDB:aboutalign
>>
>> Maybe it is interesting for you to know that we developed a generic
>> algorithm for the structural alignment of RNA and proteins called
>> "LaJolla". The reference implementation is built using BioJava and
>> released as open source at http://lajolla.sourceforge.net. I think
>> LaJolla is straight forward to use and modify if you know how to use
>> Maven and the BioJava core classes.
>>
>> Btw. The algorithm for the alignment of proteins used by BioJava
>> yielded sometimes strange results - but I did not do an exhaustive
>> evaluation. But maybe LaJolla is an alternative in those cases.
>>
>> Additionally -- if the BioJava project is interested in integrating
>> LaJolla into BioJava this is really not a problem -- but I do not know
>> if it blurs the clean toolkit/library character of BioJava.
>>
>> We are open for all suggestions regarding the algorithm and also
>> regarding a cooperation with BioJava...
>>
>> Thanks,
>>
>> Raphael
>> @Michal: LaJolla is also partly made in Poland -- so mabye you some
>> people by chance..
>>
>>>
>>> Andreas
>>>
>>> On Thu, May 7, 2009 at 5:24 AM, Michal Lorenc <m.t.lorenc at wp.pl> wrote:
>>>> Hello Andreas,
>>>> SVDSuperimposer from BioPython works only with proteins which have the same
>>>> length, but in BioJava it does not matter.
>>>>
>>>> Do you published how SVDSuperimposer in BioJava works or do you know where
>>>> could I found more information?
>>>>
>>>> Thank you in advance.
>>>>
>>>> Best regards,
>>>>
>>>> Michal
>>>>
>>> _______________________________________________
>>> 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 jp at javaclass.co.uk  Mon May 11 06:05:43 2009
From: jp at javaclass.co.uk (JP)
Date: Mon, 11 May 2009 11:05:43 +0100
Subject: [Biojava-l] FASTA header, loc attribute question
Message-ID: <4adc29060905110305l392a9792p2aa40590e97c9891@mail.gmail.com>

Hi there at Biojava,

I have two FASTA files - one containing amino acid sequences and the other
containing dna sequences.

In the AA FASTA file I have something like :

>FBpp0077713 type=protein;
loc=2L:join(384551..384894,385701..385746,386308..386576,386703..387270);
ID=FBpp0077713; name=al-PA; parent=FBgn0000061,FBtr0078053;
dbxref=FlyBase:FBpp0077713,GB_protein:AAF51505.1,GB_protein:AAF51505,FlyBase_Annotation_IDs:CG3935-PA,REFSEQ:NP_722629;
MD5=64a866db3e2913b97a2158c2de9d02f6; length=408; release=r5.9;
species=Dmel;
MGISEEIKLEELPQEAKLAHPDAVVLVDRAPGSSAASAGAALTVSMSVSG
GAPSGASGASGGTNSPVSDGNSDCEADEYAPKRKQRRYRTTFTSFQLEEL...
etc etc etc

I would like to parse this header line in particular the loc attribute and
extract it from the entry in the DNA FASTA file (so I get the genomic data
for the protein)

>FBgn0000061 type=gene; loc=2L:378116..387439; ID=FBgn0000061; name=al;
dbxref=FlyBase:FBgn0000061,FlyBase:FBan0003935,FlyBase_Annotation_IDs:CG3935,GB:AE003589,GB_protein:AAF51505,GB:AY121696,GB_protein:AAM52023,GB:BI485174,GB:CZ486795,GB:L08401,GB_protein:AAA28840,UniProt/Swiss-Prot:Q06453,INTERPRO:IPR000047,INTERPRO:IPR001356,INTERPRO:IPR003654,INTERPRO:IPR009057,INTERPRO:IPR012287,bdgpinsituexpr:al,dedb:5830,drsc:FBgn0000061,flight:FBgn0000061,flyatlas:FBgn0000061,flyexpress:FBgn0000061,flygrid:59464,flymine:FBgn0000061,geo:FBgn0000061,hdri:FBgn0000061,if:/gene/aristal.htm,orthologs:ensANOGA:ENSANGP00000011877,orthologs:ensBOSTA:ENSBTAP00000015907,orthologs:ensCANFA:ENSCAFP00000009888,orthologs:ensGALGA:ENSGALP00000005255,orthologs:ensHOMSA:ENSP00000298420,orthologs:ensMACMU:ENSMMUP00000007349,orthologs:ensMONDO:ENSMODP00000008388,orthologs:ensPANTR:ENSPTRP00000004281,orthologs:ensRATNO:ENSRNOP00000027186,orthologs:ensTETNI:GSTENP00015517001,orthologs:graORYSA:Q6YYB8,orthologs:graORYSA:Q8W0T5,orthologs:modCAEEL:WBGene00044330,orthologs:modDANRE:ZDB-GENE-990415-15,orthologs:modMUSMU:MGI:1097716,panther:FBgn0000061;
cyto_range=21C1-21C1; gbunit=AE014134; MD5=0f5568cf13aeb2c7076f11b1ce3d6b2f;
length=9324; release=r5.9; species=Dmel;
GTAGTTTGCTGCCGGCTCTGGAACAGCCCGGTCATCTCGTCGCGTTCGGT
TCCGATTCCGATTCGAATAGTCGAGCTGGGGATACATTGTTGTTTCCGGG
etc etc etc

I understand this is not exactly conventional, but does biojava support the
parsing of the loc attribute ? (join, complement etc.)

Many Thanks
JP


From holland at eaglegenomics.com  Mon May 11 06:27:23 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 11 May 2009 10:27:23 +0000
Subject: [Biojava-l] FASTA header, loc attribute question
In-Reply-To: <4adc29060905110305l392a9792p2aa40590e97c9891@mail.gmail.com>
References: <4adc29060905110305l392a9792p2aa40590e97c9891@mail.gmail.com>
Message-ID: <1242037643.15828.12.camel@buzzybee>

Short answer - no, not directly.

Longer answer - if you can write some code to snip out the Loc string
from the FASTA description line then there is existing code which can
convert the snipped Loc string into a RichLocation, which you can then
apply to the parsed FASTA sequence in order to extract the required
location. The Loc string parser is GenbankLocationParser, part of the
biojavax packages. This assumes that the Loc string conforms to Genbank
format location definitions.

cheers,
Richard

On Mon, 2009-05-11 at 11:05 +0100, JP wrote:
> Hi there at Biojava,
> 
> I have two FASTA files - one containing amino acid sequences and the other
> containing dna sequences.
> 
> In the AA FASTA file I have something like :
> 
> >FBpp0077713 type=protein;
> loc=2L:join(384551..384894,385701..385746,386308..386576,386703..387270);
> ID=FBpp0077713; name=al-PA; parent=FBgn0000061,FBtr0078053;
> dbxref=FlyBase:FBpp0077713,GB_protein:AAF51505.1,GB_protein:AAF51505,FlyBase_Annotation_IDs:CG3935-PA,REFSEQ:NP_722629;
> MD5=64a866db3e2913b97a2158c2de9d02f6; length=408; release=r5.9;
> species=Dmel;
> MGISEEIKLEELPQEAKLAHPDAVVLVDRAPGSSAASAGAALTVSMSVSG
> GAPSGASGASGGTNSPVSDGNSDCEADEYAPKRKQRRYRTTFTSFQLEEL...
> etc etc etc
> 
> I would like to parse this header line in particular the loc attribute and
> extract it from the entry in the DNA FASTA file (so I get the genomic data
> for the protein)
> 
> >FBgn0000061 type=gene; loc=2L:378116..387439; ID=FBgn0000061; name=al;
> dbxref=FlyBase:FBgn0000061,FlyBase:FBan0003935,FlyBase_Annotation_IDs:CG3935,GB:AE003589,GB_protein:AAF51505,GB:AY121696,GB_protein:AAM52023,GB:BI485174,GB:CZ486795,GB:L08401,GB_protein:AAA28840,UniProt/Swiss-Prot:Q06453,INTERPRO:IPR000047,INTERPRO:IPR001356,INTERPRO:IPR003654,INTERPRO:IPR009057,INTERPRO:IPR012287,bdgpinsituexpr:al,dedb:5830,drsc:FBgn0000061,flight:FBgn0000061,flyatlas:FBgn0000061,flyexpress:FBgn0000061,flygrid:59464,flymine:FBgn0000061,geo:FBgn0000061,hdri:FBgn0000061,if:/gene/aristal.htm,orthologs:ensANOGA:ENSANGP00000011877,orthologs:ensBOSTA:ENSBTAP00000015907,orthologs:ensCANFA:ENSCAFP00000009888,orthologs:ensGALGA:ENSGALP00000005255,orthologs:ensHOMSA:ENSP00000298420,orthologs:ensMACMU:ENSMMUP00000007349,orthologs:ensMONDO:ENSMODP00000008388,orthologs:ensPANTR:ENSPTRP00000004281,orthologs:ensRATNO:ENSRNOP00000027186,orthologs:ensTETNI:GSTENP00015517001,orthologs:graORYSA:Q6YYB8,orthologs:graORYSA:Q8W0T5,orthologs:modCAEEL:WBGene00044330,orthologs:modDA!
>  NRE:ZDB-GENE-990415-15,orthologs:modMUSMU:MGI:1097716,panther:FBgn0000061;
> cyto_range=21C1-21C1; gbunit=AE014134; MD5=0f5568cf13aeb2c7076f11b1ce3d6b2f;
> length=9324; release=r5.9; species=Dmel;
> GTAGTTTGCTGCCGGCTCTGGAACAGCCCGGTCATCTCGTCGCGTTCGGT
> TCCGATTCCGATTCGAATAGTCGAGCTGGGGATACATTGTTGTTTCCGGG
> etc etc etc
> 
> I understand this is not exactly conventional, but does biojava support the
> parsing of the loc attribute ? (join, complement etc.)
> 
> Many Thanks
> JP
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From thomas.covello at gmail.com  Mon May 11 16:33:43 2009
From: thomas.covello at gmail.com (Thomas Covello)
Date: Mon, 11 May 2009 14:33:43 -0600
Subject: [Biojava-l] NullPointerException when using Viterbi algorithm in
	HMM.
Message-ID: <2e367d7b0905111333o2d074f81if9a34545acb95b5b@mail.gmail.com>

Hello,
I am trying to use a Hidden Markov Model to classify a sequence, and I
am encountering a NullPointerException when I try to use the Viterbi
algorithm. My test case follows - if you want the code I am actually
using I can post it. The stack trace:

java.lang.NullPointerException
        at org.biojava.bio.dp.onehead.SingleDP.viterbi(SingleDP.java:648)
        at org.biojava.bio.dp.onehead.SingleDP.viterbi(SingleDP.java:512)
        at oxytricha_crap.Main.main(Main.java:69)

File: Main.java

package oxytricha_crap;

import org.biojava.bio.seq.*;
import org.biojava.bio.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.dp.*;
import org.biojava.bio.dist.*;
import java.util.*;
import org.biojava.bio.symbol.SymbolList;

public class Main {
    private static Alphabet DNA = DNATools.getDNA();
    private static State IES;
    private static State MDS;
    private static MarkovModel hmm = new SimpleMarkovModel(1, DNA, "MyHMM");

    static {
        try {
            Distribution IES_dist =
                DistributionFactory.DEFAULT.createDistribution(DNA);
            Distribution MDS_dist =
                DistributionFactory.DEFAULT.createDistribution(DNA);
            IES = new SimpleEmissionState("IES", Annotation.EMPTY_ANNOTATION,
                new int [] {1}, IES_dist);
            MDS = new SimpleEmissionState("MDS", Annotation.EMPTY_ANNOTATION,
                new int [] {1}, MDS_dist);
            hmm.addState(IES);
            hmm.addState(MDS);
            hmm.createTransition(MDS, hmm.magicalState());
            hmm.createTransition(hmm.magicalState(), MDS);
            hmm.createTransition(MDS, IES);
            hmm.createTransition(IES, MDS);
            hmm.createTransition(MDS, MDS);
            hmm.createTransition(IES, IES);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }

    public static void main(String[] args) {
        try {
            State currState;
            State lastState = hmm.magicalState();
            Iterator<State> states = Arrays.asList(new State [] {
                MDS, MDS, MDS, IES, IES, IES, MDS, MDS, IES, IES, MDS, MDS,
                MDS, MDS
            }).iterator();
            SymbolList sl = DNATools.createDNA("acgtgtctgagaga");

            HMMTrainer trainer = new SimpleHMMTrainer(hmm);
            trainer.startCycle();
            for (Symbol sym : (List<Symbol>)sl.toList()) {
                currState = states.next();
                if (currState != lastState && lastState != null)
                    trainer.recordTransition(lastState, currState, 1.0);
                trainer.recordEmittedSymbol(currState, sym, 1.0);
                lastState = currState;
            }
            trainer.recordTransition(MDS, hmm.magicalState(), 1.0);

            trainer.completeCycle();

            DP dp = DPFactory.DEFAULT.createDP(hmm);
            SymbolList unknown = DNATools.createDNA("acgtcgtacgtacgtacacaacga");
            StatePath spath = dp.viterbi(new SymbolList [] { unknown },
                ScoreType.PROBABILITY);
        } catch (Exception e) {
            e.printStackTrace();
        }

        System.exit(0);
    }
}

From mauleemacx at gmail.com  Wed May 13 07:21:57 2009
From: mauleemacx at gmail.com (mac LEE)
Date: Wed, 13 May 2009 19:21:57 +0800
Subject: [Biojava-l] biojava on Maven2 repository
Message-ID: <e71c81850905130421v391bf60dna5839f59e33c21db@mail.gmail.com>

Dear All,
Hello. Is it possible to place the biojava jar into the maven 2 repository?

regards,

jack Lee

-- 
Somewhere between heaven and hell
mauleemacx at gmail.com

From raphael.andre.bauer at gmail.com  Wed May 13 09:12:11 2009
From: raphael.andre.bauer at gmail.com (=?UTF-8?Q?Raphael_Andr=C3=A9_Bauer?=)
Date: Wed, 13 May 2009 15:12:11 +0200
Subject: [Biojava-l] biojava on Maven2 repository
In-Reply-To: <e71c81850905130421v391bf60dna5839f59e33c21db@mail.gmail.com>
References: <e71c81850905130421v391bf60dna5839f59e33c21db@mail.gmail.com>
Message-ID: <9b46aa30905130612g194a022eu4fdb30114773b70e@mail.gmail.com>

On Wed, May 13, 2009 at 1:21 PM, mac LEE <mauleemacx at gmail.com> wrote:
> Dear All,
> Hello. Is it possible to place the biojava jar into the maven 2 repository?

You have to install the biojava.jar manually into your local repository:
http://maven.apache.org/guides/mini/guide-3rd-party-jars-local.html

LaJolla is an application that uses that approach too... Maybe the
pom.xml of LaJolla is worth a look to see how it works...:
http://lajolla.svn.sourceforge.net/viewvc/lajolla/trunk/lajolla/pom.xml?revision=350&view=markup

Regards,

Raphael

>
> regards,
>
> jack Lee
>
> --
> Somewhere between heaven and hell
> mauleemacx at gmail.com
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From helpmedicine.savelife at gmail.com  Wed May 13 10:04:18 2009
From: helpmedicine.savelife at gmail.com (helpmedicine savelife)
Date: Wed, 13 May 2009 10:04:18 -0400
Subject: [Biojava-l] biojava on Maven2 repository
In-Reply-To: <9b46aa30905130612g194a022eu4fdb30114773b70e@mail.gmail.com>
References: <e71c81850905130421v391bf60dna5839f59e33c21db@mail.gmail.com>
	<9b46aa30905130612g194a022eu4fdb30114773b70e@mail.gmail.com>
Message-ID: <3d0f70fd0905130704h57eb09b6k33bf067b6f729768@mail.gmail.com>

I agree it is possible by setting up in local repository (I did the same for
my project I am currently working), but now that biojava is being used by
many, I guess it it is a good time to to make it accessible through maven2
by providing the project metadata information to Maven2.

Biojava Team - Is this possible?

Thanks,
Sandya

On Wed, May 13, 2009 at 9:12 AM, Raphael Andr? Bauer <
raphael.andre.bauer at gmail.com> wrote:

> On Wed, May 13, 2009 at 1:21 PM, mac LEE <mauleemacx at gmail.com> wrote:
> > Dear All,
> > Hello. Is it possible to place the biojava jar into the maven 2
> repository?
>
> You have to install the biojava.jar manually into your local repository:
> http://maven.apache.org/guides/mini/guide-3rd-party-jars-local.html
>
> LaJolla is an application that uses that approach too... Maybe the
> pom.xml of LaJolla is worth a look to see how it works...:
>
> http://lajolla.svn.sourceforge.net/viewvc/lajolla/trunk/lajolla/pom.xml?revision=350&view=markup
>
> Regards,
>
> Raphael
>
> >
> > regards,
> >
> > jack Lee
> >
> > --
> > Somewhere between heaven and hell
> > mauleemacx at gmail.com
> > _______________________________________________
> > 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 mauleemacx at gmail.com  Thu May 14 01:50:51 2009
From: mauleemacx at gmail.com (mac LEE)
Date: Thu, 14 May 2009 13:50:51 +0800
Subject: [Biojava-l] biojava on Maven2 repository
In-Reply-To: <3d0f70fd0905130704h57eb09b6k33bf067b6f729768@mail.gmail.com>
References: <e71c81850905130421v391bf60dna5839f59e33c21db@mail.gmail.com>
	<9b46aa30905130612g194a022eu4fdb30114773b70e@mail.gmail.com>
	<3d0f70fd0905130704h57eb09b6k33bf067b6f729768@mail.gmail.com>
Message-ID: <e71c81850905132250x4332497dh708336da0b67a8dd@mail.gmail.com>

Dear All,
I think putting Biojava on central Maven2 repository not only facilitate
current users. It also attracts new users as well, just think of how success
is the BioPerl project resided in CPAN is.  I strongly hope that there will
be central repository soon.
regards,
jack LEE

On Wed, May 13, 2009 at 10:04 PM, helpmedicine savelife <
helpmedicine.savelife at gmail.com> wrote:

> I agree it is possible by setting up in local repository (I did the same
> for
> my project I am currently working), but now that biojava is being used by
> many, I guess it it is a good time to to make it accessible through maven2
> by providing the project metadata information to Maven2.
>
> Biojava Team - Is this possible?
>
> Thanks,
> Sandya
>
> On Wed, May 13, 2009 at 9:12 AM, Raphael Andr? Bauer <
> raphael.andre.bauer at gmail.com> wrote:
>
> > On Wed, May 13, 2009 at 1:21 PM, mac LEE <mauleemacx at gmail.com> wrote:
> > > Dear All,
> > > Hello. Is it possible to place the biojava jar into the maven 2
> > repository?
> >
> > You have to install the biojava.jar manually into your local repository:
> > http://maven.apache.org/guides/mini/guide-3rd-party-jars-local.html
> >
> > LaJolla is an application that uses that approach too... Maybe the
> > pom.xml of LaJolla is worth a look to see how it works...:
> >
> >
> http://lajolla.svn.sourceforge.net/viewvc/lajolla/trunk/lajolla/pom.xml?revision=350&view=markup
> >
> > Regards,
> >
> > Raphael
> >
> > >
> > > regards,
> > >
> > > jack Lee
> > >
> > > --
> > > Somewhere between heaven and hell
> > > mauleemacx at gmail.com
> > > _______________________________________________
> > > 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
> >
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
Somewhere between heaven and hell
mauleemacx at gmail.com


From andreas at sdsc.edu  Thu May 14 09:38:08 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 14 May 2009 06:38:08 -0700
Subject: [Biojava-l] biojava on Maven2 repository
In-Reply-To: <3d0f70fd0905130704h57eb09b6k33bf067b6f729768@mail.gmail.com>
References: <e71c81850905130421v391bf60dna5839f59e33c21db@mail.gmail.com>
	<9b46aa30905130612g194a022eu4fdb30114773b70e@mail.gmail.com>
	<3d0f70fd0905130704h57eb09b6k33bf067b6f729768@mail.gmail.com>
Message-ID: <59a41c430905140638r74554c10wb9c97dddd8f05b6b@mail.gmail.com>

I will have a look at this, once we have mavenized the biojava build
process. In the meanwhile, perhaps somebody could post instructions
how to add biojava to a local maven repository on the wiki?

Andreas



On Wed, May 13, 2009 at 7:04 AM, helpmedicine savelife
<helpmedicine.savelife at gmail.com> wrote:
> I agree it is possible by setting up in local repository (I did the same for
> my project I am currently working), but now that biojava is being used by
> many, I guess it it is a good time to to make it accessible through maven2
> by providing the project metadata information to Maven2.
>
> Biojava Team - Is this possible?
>
> Thanks,
> Sandya
>
> On Wed, May 13, 2009 at 9:12 AM, Raphael Andr? Bauer <
> raphael.andre.bauer at gmail.com> wrote:
>
>> On Wed, May 13, 2009 at 1:21 PM, mac LEE <mauleemacx at gmail.com> wrote:
>> > Dear All,
>> > Hello. Is it possible to place the biojava jar into the maven 2
>> repository?
>>
>> You have to install the biojava.jar manually into your local repository:
>> http://maven.apache.org/guides/mini/guide-3rd-party-jars-local.html
>>
>> LaJolla is an application that uses that approach too... Maybe the
>> pom.xml of LaJolla is worth a look to see how it works...:
>>
>> http://lajolla.svn.sourceforge.net/viewvc/lajolla/trunk/lajolla/pom.xml?revision=350&view=markup
>>
>> Regards,
>>
>> Raphael
>>
>> >
>> > regards,
>> >
>> > jack Lee
>> >
>> > --
>> > Somewhere between heaven and hell
>> > mauleemacx at gmail.com
>> > _______________________________________________
>> > 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
>>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From niall at sgenomics.org  Thu May 14 09:55:31 2009
From: niall at sgenomics.org (Niall Haslam)
Date: Thu, 14 May 2009 15:55:31 +0200
Subject: [Biojava-l] Webservices clients in bio-java
Message-ID: <200905141555.31967.niall@sgenomics.org>

Hi all,

I was wondering if there was any interest in creating a set of maintained 
clients for popular webservices. Depending on how it goes and how feasible it 
is these could be included in biojava. I assume there are plenty of people 
writing and rewriting clients to these things. In the first instance we could 
just set up a repository for example code on using the servers.

I'm sure this would be a useful resource for java programmers. Unless someone 
wants to point me towards a pre-existing resource!

Niall.

From heuermh at acm.org  Thu May 14 12:34:53 2009
From: heuermh at acm.org (Michael Heuer)
Date: Thu, 14 May 2009 12:34:53 -0400 (EDT)
Subject: [Biojava-l] biojava on Maven2 repository
In-Reply-To: <59a41c430905140638r74554c10wb9c97dddd8f05b6b@mail.gmail.com>
Message-ID: <Pine.GSO.4.44.0905141219110.10420-100000@shell3.shore.net>

Hello Andreas,

The biojava jars can be manually uploaded to the central repository.  I
will do this for the 1.7 release.

Once the build migrates to maven, we can set up our own repository that
is mirrored to the central repository.   This is required if we have a
multi-module build, for example.  There may be a maven repo hosted at
open-bio.org already, I think the biomoby folks use one.

   michael


On Thu, 14 May 2009, Andreas Prlic wrote:

> I will have a look at this, once we have mavenized the biojava build
> process. In the meanwhile, perhaps somebody could post instructions
> how to add biojava to a local maven repository on the wiki?
>
> Andreas
>
>
>
> On Wed, May 13, 2009 at 7:04 AM, helpmedicine savelife
> <helpmedicine.savelife at gmail.com> wrote:
> > I agree it is possible by setting up in local repository (I did the same for
> > my project I am currently working), but now that biojava is being used by
> > many, I guess it it is a good time to to make it accessible through maven2
> > by providing the project metadata information to Maven2.
> >
> > Biojava Team - Is this possible?
> >
> > Thanks,
> > Sandya
> >
> > On Wed, May 13, 2009 at 9:12 AM, Raphael Andr? Bauer <
> > raphael.andre.bauer at gmail.com> wrote:
> >
> >> On Wed, May 13, 2009 at 1:21 PM, mac LEE <mauleemacx at gmail.com> wrote:
> >> > Dear All,
> >> > Hello. Is it possible to place the biojava jar into the maven 2
> >> repository?
> >>
> >> You have to install the biojava.jar manually into your local repository:
> >> http://maven.apache.org/guides/mini/guide-3rd-party-jars-local.html
> >>
> >> LaJolla is an application that uses that approach too... Maybe the
> >> pom.xml of LaJolla is worth a look to see how it works...:
> >>
> >> http://lajolla.svn.sourceforge.net/viewvc/lajolla/trunk/lajolla/pom.xml?revision=350&view=markup
> >>
> >> Regards,
> >>
> >> Raphael
> >>
> >> >
> >> > regards,
> >> >
> >> > jack Lee
> >> >
> >> > --
> >> > Somewhere between heaven and hell
> >> > mauleemacx at gmail.com
> >> > _______________________________________________
> >> > 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
> >>
> >
> > _______________________________________________
> > 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  Thu May 14 23:27:05 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 14 May 2009 20:27:05 -0700
Subject: [Biojava-l] biojava on Maven2 repository
In-Reply-To: <Pine.GSO.4.44.0905141219110.10420-100000@shell3.shore.net>
References: <59a41c430905140638r74554c10wb9c97dddd8f05b6b@mail.gmail.com>
	<Pine.GSO.4.44.0905141219110.10420-100000@shell3.shore.net>
Message-ID: <59a41c430905142027g2de44f57s6ef0c48f8c877c17@mail.gmail.com>

That would be helpful, thanks,
Andreas

On Thu, May 14, 2009 at 9:34 AM, Michael Heuer <heuermh at acm.org> wrote:
> Hello Andreas,
>
> The biojava jars can be manually uploaded to the central repository. ?I
> will do this for the 1.7 release.
>
> Once the build migrates to maven, we can set up our own repository that
> is mirrored to the central repository. ? This is required if we have a
> multi-module build, for example. ?There may be a maven repo hosted at
> open-bio.org already, I think the biomoby folks use one.
>
> ? michael
>
>
> On Thu, 14 May 2009, Andreas Prlic wrote:
>
>> I will have a look at this, once we have mavenized the biojava build
>> process. In the meanwhile, perhaps somebody could post instructions
>> how to add biojava to a local maven repository on the wiki?
>>
>> Andreas
>>
>>
>>
>> On Wed, May 13, 2009 at 7:04 AM, helpmedicine savelife
>> <helpmedicine.savelife at gmail.com> wrote:
>> > I agree it is possible by setting up in local repository (I did the same for
>> > my project I am currently working), but now that biojava is being used by
>> > many, I guess it it is a good time to to make it accessible through maven2
>> > by providing the project metadata information to Maven2.
>> >
>> > Biojava Team - Is this possible?
>> >
>> > Thanks,
>> > Sandya
>> >
>> > On Wed, May 13, 2009 at 9:12 AM, Raphael Andr? Bauer <
>> > raphael.andre.bauer at gmail.com> wrote:
>> >
>> >> On Wed, May 13, 2009 at 1:21 PM, mac LEE <mauleemacx at gmail.com> wrote:
>> >> > Dear All,
>> >> > Hello. Is it possible to place the biojava jar into the maven 2
>> >> repository?
>> >>
>> >> You have to install the biojava.jar manually into your local repository:
>> >> http://maven.apache.org/guides/mini/guide-3rd-party-jars-local.html
>> >>
>> >> LaJolla is an application that uses that approach too... Maybe the
>> >> pom.xml of LaJolla is worth a look to see how it works...:
>> >>
>> >> http://lajolla.svn.sourceforge.net/viewvc/lajolla/trunk/lajolla/pom.xml?revision=350&view=markup
>> >>
>> >> Regards,
>> >>
>> >> Raphael
>> >>
>> >> >
>> >> > regards,
>> >> >
>> >> > jack Lee
>> >> >
>> >> > --
>> >> > Somewhere between heaven and hell
>> >> > mauleemacx at gmail.com
>> >> > _______________________________________________
>> >> > 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
>> >>
>> >
>> > _______________________________________________
>> > 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  Sat May 16 15:10:56 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sat, 16 May 2009 12:10:56 -0700
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <200905141555.31967.niall@sgenomics.org>
References: <200905141555.31967.niall@sgenomics.org>
Message-ID: <59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>

Hi Niall.

Which webservices did you have in mind? Something that got recently
discussed on biojava-dev is support Blast webservices...

Andreas

On Thu, May 14, 2009 at 6:55 AM, Niall Haslam <niall at sgenomics.org> wrote:
> Hi all,
>
> I was wondering if there was any interest in creating a set of maintained
> clients for popular webservices. Depending on how it goes and how feasible it
> is these could be included in biojava. I assume there are plenty of people
> writing and rewriting clients to these things. In the first instance we could
> just set up a repository for example code on using the servers.
>
> I'm sure this would be a useful resource for java programmers. Unless someone
> wants to point me towards a pre-existing resource!
>
> Niall.
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From niall at sgenomics.org  Tue May 19 03:36:38 2009
From: niall at sgenomics.org (Niall Haslam)
Date: Tue, 19 May 2009 09:36:38 +0200
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>
References: <200905141555.31967.niall@sgenomics.org>
	<59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>
Message-ID: <200905190936.38541.niall@sgenomics.org>

On Saturday 16 May 2009 21:10, Andreas Prlic wrote:
> Which webservices did you have in mind? Something that got recently
> discussed on biojava-dev is support Blast webservices...

I think BLAST would obviously be one of the main ones to get started with. I 
have a client at the moment which goes as far as fetching the job-id and 
generating a link to the results, which is as much as I need. If I remember 
correctly, the BLAST parser at the moment doesn't deal with the responses 
from the EBI webservices (which I used).

Mark makes a valid point about the choice of technology. I would also 
recommend jax-ws and probably axis2 as the frameworks, but note that some 
clients will probably require axis1_4. Although its not clear which e-mail 
discussion you are referring to - is it one on the biojava-dev mailing list?

A lot of the client code is autogenerated, and I guess one question would be 
should we include this in any repository that we make? I have been using the 
wtp plugin in eclipse and this takes some of the pain out of generating 
clients. Though it does generate some rather large source files.

Niall.

From markjschreiber at gmail.com  Tue May 19 10:05:11 2009
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Tue, 19 May 2009 22:05:11 +0800
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <93b45ca50905190702l2169d7f4qf200ed04f33c17b5@mail.gmail.com>
References: <200905141555.31967.niall@sgenomics.org>
	<59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>
	<200905190936.38541.niall@sgenomics.org>
	<93b45ca50905190702l2169d7f4qf200ed04f33c17b5@mail.gmail.com>
Message-ID: <93b45ca50905190705qec04c48yb7a81c9b0715a50e@mail.gmail.com>

Hi Niall -

There was a recent discussion of generated code on the list. A good solution
for webservices may be to put the wsdl and high level api in the repository
and let jax-ws tools autogenerate the client biolerplate code.

Mark

On 19 May 2009, 3:39 PM, "Niall Haslam" <niall at sgenomics.org> wrote:

On Saturday 16 May 2009 21:10, Andreas Prlic wrote: > Which webservices did
you have in mind? Someth...
I think BLAST would obviously be one of the main ones to get started with. I
have a client at the moment which goes as far as fetching the job-id and
generating a link to the results, which is as much as I need. If I remember
correctly, the BLAST parser at the moment doesn't deal with the responses
from the EBI webservices (which I used).

Mark makes a valid point about the choice of technology. I would also
recommend jax-ws and probably axis2 as the frameworks, but note that some
clients will probably require axis1_4. Although its not clear which e-mail
discussion you are referring to - is it one on the biojava-dev mailing list?

A lot of the client code is autogenerated, and I guess one question would be
should we include this in any repository that we make? I have been using the
wtp plugin in eclipse and this takes some of the pain out of generating
clients. Though it does generate some rather large source files.

Niall. _______________________________________________ Biojava-l mailing
list - Biojava-l at lists.o...

From aaron_b_a at yahoo.com  Tue May 19 21:12:28 2009
From: aaron_b_a at yahoo.com (Aaron Brata Aditama)
Date: Tue, 19 May 2009 18:12:28 -0700 (PDT)
Subject: [Biojava-l] How to write pairwiseAlignment output in my own format?
Message-ID: <248630.13325.qm@web56107.mail.re3.yahoo.com>

There is a default output method in NeedlemanWunsch Class, and it writes output in its own format. How can I write output of paiwire alignment in my own format? For example, I want to get the aligned sequences and the score only.

Aaron Brata Aditama


      

From mike.thon at gmail.com  Thu May 21 14:06:56 2009
From: mike.thon at gmail.com (Michael Thon)
Date: Thu, 21 May 2009 20:06:56 +0200
Subject: [Biojava-l] CRC64Checksum example
Message-ID: <8EEAB8FC-4D9D-4417-90EC-DC9E4329648C@gmail.com>

Hi all - I need to compute a crc64 for some sequences and I thought  
that org.biojavax.utils.CRC64Checksum could do this for me.  Java  
throws a NullPointerException when I try to do:
   crc.update(seq);
where crc is a CRC64Checksum object and seq is a String containing a  
protein sequence.

Does anyone have some example code showing how to compute a crc using  
this class?
Many thanks
Mike Thon

From holland at eaglegenomics.com  Thu May 21 15:11:14 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Thu, 21 May 2009 20:11:14 +0100
Subject: [Biojava-l] CRC64Checksum example
In-Reply-To: <8EEAB8FC-4D9D-4417-90EC-DC9E4329648C@gmail.com>
References: <8EEAB8FC-4D9D-4417-90EC-DC9E4329648C@gmail.com>
Message-ID: <1242933074.29986.16.camel@buzzybee>

Could you provide the line you used to instantiate the CRC64Checksum
object, and the value that you're passing to update(seq), and the full
stacktrace you get when it fails? That'll all help us work out what's
wrong.

cheers,
Richard

On Thu, 2009-05-21 at 20:06 +0200, Michael Thon wrote:
> Hi all - I need to compute a crc64 for some sequences and I thought  
> that org.biojavax.utils.CRC64Checksum could do this for me.  Java  
> throws a NullPointerException when I try to do:
>    crc.update(seq);
> where crc is a CRC64Checksum object and seq is a String containing a  
> protein sequence.
> 
> Does anyone have some example code showing how to compute a crc using  
> this class?
> Many thanks
> Mike Thon
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From paolo.romano at istge.it  Wed May 27 12:15:09 2009
From: paolo.romano at istge.it (Paolo Romano)
Date: Wed, 27 May 2009 18:15:09 +0200
Subject: [Biojava-l] NETTAB 2009: Last Call for Participation
Message-ID: <200905271630.n4RGU87M030436@ibm43p.biotech.ist.unige.it>


Last Call for Participation

NETTAB 2009 Workshop on
"Technologies, Tools and Applications for 
Collaborative and Social Bioinformatics Research and Development"
with a Special Session on:
"Methods and Tools for RNA Structure and Functional Analysis"

June 10-13, 2009
Department of Computer Science, University of Catania, Italy

http://www.nettab.org/2009/


KEYNOTE TALKS

RNA WikiProject: Community annotation of RNA families
Alex Bateman, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

Who are you? Managing collaborative digital 
identities in bioinformatics with myExperiment
Duncan Hull, School of Chemistry, University of Manchester, Manchester, UK.

Semantically Integrated eCommunities in 
Biomedicine: Next-Generation Models of Biomedical Communication
Tim Clark, Director of Informatics, MassGeneral 
Institute for Neurodegenerative Disease Neurology 
Research Department, Massachusetts General Hospital, Boston, USA.

Bacterial Phylogeny and Taxonomy in the High-Throughput Sequencing World
Gabriel Valiente, Technical University of 
Catalonia, Department of Software, Barcelona, Spain.

Non coding RNAs (title to be confirmed)
Doron Betel, MSKCC - Computational Biology Center, New York, USA .


SELECTED ORAL COMMUNICATIONS

The DC-THERA Directory: A Knowledge Management 
System to Support Collaboration on Dendritic Cell and Immunology Research
Michaela Guendel, Ciro Scognamiglio, Marco Brandizi and Andrea Splendiani

Bioinformatics Experimentation in a New 
Agent-Based Infrastructure OpenKnowledge
Dietlind Gerloff, Xueping Quan, Adrian de 
Pinninck, Paolo Besana, Siu-wai Leung, Marco Schorlemmer and David Robertson

Abstraction based cooperation for the design of bioinformatics workflows
Fr?d?ric Cadier and Philippe Picouet

Biomedical applications in the EELA-2 Project
Leandro N Ciuffo and Rafael Mayo

Make Histri: collaborative curation of exchange 
histories of bacterial and archaeal type strains
Bert Verslyppe, Paul De Vos, Bernard De Baets and Peter Dawyndt

SBMM Assistant: Social Pathway Annotation
Ismael Navas-Delgado, Alejandro del 
Real-Chicharro, Francisca S?nchez-Jim?nez and Jose F Aldana Montes

GePh-CARD: an information exchange application 
for an Hub & Spoke Network for Skeletal Dysplasias
Marina Mordenti and Luca Sangiorgi

ProDaMa-C: a collaborative web application to 
generate specialized protein structure datasets
Giuliano Armano and Andrea Manconi

RNA tertiary structure prediction with ModeRNA
Magdalena Musielak, Kristian Rother, Tomasz Puton and Janusz M. Bujnicki

Improved heuristic for pairwise RNA secondary structure prediction
Olivier Perriquet and Pedro Barahona

Analysing the microRNA-17-92/Myc/E2F/RB Compound 
Toggle Switch by Theorem Proving
Giampaolo Bella and Pietro Li?

Mapping miRNA genes on human fragile sites and translocation breakpoints
Alfredo Ferro, rosalba giugno, Alessandro Lagan?, 
Alfredo Pulvirenti and Francesco Russo

MicroRNA.gr: A suite of web based tools for elucidating microRNA function
Giorgio L. Papadopoulos, Panagiotis Alexiou, 
Manolis Maragkakis, Martin Reczko and Artemis G. Hatzigeorgiou

miRScape: A Cytoscape Plugin to Annotate Biological Networks with microRNAs
Alfredo Ferro, rosalba giugno, Alessandro Lagan?, 
Misael Mongiov?, Giuseppe Pigola, Alfredo 
Pulvirenti, Gary Bader and Dennis Shasha


POSTERS

A web site supporting collaborative activities 
within the Italian Network for Oncology Bioinformatics
Silvia Giuliani, Elda Rossi, Stefania Parodi and Paolo Romano

Prediction of human targets for viral encoded microRNAs
Alessandro Lagan?, Stefano Forte, Rosalba Giugno, 
Alfredo Pulvirenti and Alfredo Ferro

Genome-wide microRNA target gene identification 
and annotation using multiple prediction algorithms
Dario Corrada, Luciano Milanesi and Daniele Catalucci

Design of highly specific synthetic miRNAs
Alessandro Lagan?, Stefano Forte, Angela Papa, 
Rosalba Giugno, Alfredo Pulvirenti, Dennis Shasha and Alfredo Ferro



NETTAB '09 - Ninth International Workshop on 
Network Tools and Applications in Biology
10-13 June 2009, Catania, Italy
http://www.nettab.org/2009/

Paolo Romano (paolo.romano at istge.it)
Bioinformatics
National Cancer Research Institute (IST)



From jimp at compbio.dundee.ac.uk  Thu May 28 08:29:19 2009
From: jimp at compbio.dundee.ac.uk (James Procter)
Date: Thu, 28 May 2009 13:29:19 +0100
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <93b45ca50905190705qec04c48yb7a81c9b0715a50e@mail.gmail.com>
References: <200905141555.31967.niall@sgenomics.org>	<59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>	<200905190936.38541.niall@sgenomics.org>	<93b45ca50905190702l2169d7f4qf200ed04f33c17b5@mail.gmail.com>
	<93b45ca50905190705qec04c48yb7a81c9b0715a50e@mail.gmail.com>
Message-ID: <4A1E839F.2050700@compbio.dundee.ac.uk>

Hi All.

Mark Schreiber wrote:
> There was a recent discussion of generated code on the list. A good solution
> for webservices may be to put the wsdl and high level api in the repository
> and let jax-ws tools autogenerate the client biolerplate code.

Just to clarify - by high-level API you mean the interface to the code
that takes biojava objects as arguments and translates them into
parameters for the service and vice versa for the results ?

With regard to the recent(ish) discussion about modularisation in BJ3,
I'd suggest that a module is created for each distinct WSDL containing
the glue code for connecting BJ objects with the boilerplate code. The
glue code implements factory methods to generate instances of
appropriate BJ service APIs, which are defined in a core BJ module. This
means that the WSDL + API implementation is decoupled from the BJ
service API.

Does that make sense (and/or am I simply stating the obvious here) ?

Jim.

-- 
-------------------------------------------------------------------
J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

From willishf at ufl.edu  Thu May 28 09:35:49 2009
From: willishf at ufl.edu (Scooter Willis)
Date: Thu, 28 May 2009 09:35:49 -0400
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <4A1E839F.2050700@compbio.dundee.ac.uk>
References: <200905141555.31967.niall@sgenomics.org>
	<59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>
	<200905190936.38541.niall@sgenomics.org>
	<93b45ca50905190702l2169d7f4qf200ed04f33c17b5@mail.gmail.com>
	<93b45ca50905190705qec04c48yb7a81c9b0715a50e@mail.gmail.com>
	<4A1E839F.2050700@compbio.dundee.ac.uk>
Message-ID: <7ceb4beb0905280635g7bbb028dw9c5d69a9290b5a16@mail.gmail.com>

Jim

I agree. I am planning on doing some testing of  a couple BLAST web services
interfaces(assuming more than one exists) and see what they truly have in
common and see how that would impact a BJ3 front end to multiple providers.
My assumption is that they will be the same. I noticed on the NCBI Blast
implementations the user was required to pass their email address as part of
the web service call. They are concerned with abuse from external processes
and they only allow one sequence per request.

>From wikipedia the following are listed as BLAST resources where more than
one may offer a web service interface. Should BioJava3 try and support more
than one?

Thanks

Scooter

Variations of BLAST

   - WU-BLAST <http://blast.wustl.edu/> ? the original gapping BLAST with
   statistics, developed and maintained by Warren Gish at Washington
   University in St.
Louis<http://en.wikipedia.org/wiki/Washington_University_in_St._Louis>
   - EBI's BLAST Services <http://www.ebi.ac.uk/Tools/blast> ?
EBI's<http://en.wikipedia.org/wiki/European_Bioinformatics_Institute>main
blast services page.
   - FSA-BLAST <http://www.fsa-blast.org/> ? a new, faster but still
   accurate version of NCBI BLAST based on recently published algorithmic
   improvements
   - NBIC mpiBLAST <http://services.nbic.nl:4080/bb/cgi-bin/bb_login.cgi> ?
   at the Netherlands Bioinformatics Centre
   - Parallel BLAST<http://www-users.cs.umn.edu/%7Erangwala/final_bglBLAST.pdf>?
a dual scheduling BLAST tested on the Blue Gene/L
   - mpiBLAST <http://www.mpiblast.org/> ? open-source parallel BLAST
   - A/G BLAST <http://developer.apple.com/darwin/projects/blast/> ?
   implementation for PowerPC G4/G5 processors and Mac OS X, from Apple
   Computer <http://en.wikipedia.org/wiki/Apple_Computer>'s Advanced
   Computation Group<http://en.wikipedia.org/wiki/Advanced_Computation_Group>and
   Genentech <http://en.wikipedia.org/wiki/Genentech>.
   - STRAP <http://3d-alignment.eu/> ? the protein workbench
STRAP<http://www.charite.de/bioinf/strap/>contains a comfortable BLAST
front-end with a cache for BLAST results

 [edit<http://en.wikipedia.org/w/index.php?title=BLAST&action=edit&section=13>
] Commercial versions

   - ThermoBLAST by DNA Software
Inc.<http://dnasoftware.com/ThermoBLAST/tabid/110/Default.aspx>? scans
entire genomes quickly and accurately combing the power of BLAST
   with the most advanced thermodynamics parameters
   - PatternHunter<http://www.bioinformaticssolutions.com/products/ph/index.php>?
an alternative software which provides similar functionality to BLAST
   while claiming increased speed and sensitivity
   - KoriBlast <http://www.korilog.com/products> ? a reliable graphical
   environment dedicated to sequence data mining. KoriBlast combines Blast
   searches with advanced data management capabilities and a state-of-the-art
   graphical user interface.
   - microbial identification BLAST <http://www.sepsitest-blast.de/> ? a
   quality controlled database for in-vitro diagnostics. SepsiTest combines
   broad-range-PCR using ultra-pure reagents with Blast searches in a quality
   controlled environment.




On Thu, May 28, 2009 at 8:29 AM, James Procter <jimp at compbio.dundee.ac.uk>wrote:

> Hi All.
>
> Mark Schreiber wrote:
> > There was a recent discussion of generated code on the list. A good
> solution
> > for webservices may be to put the wsdl and high level api in the
> repository
> > and let jax-ws tools autogenerate the client biolerplate code.
>
> Just to clarify - by high-level API you mean the interface to the code
> that takes biojava objects as arguments and translates them into
> parameters for the service and vice versa for the results ?
>
> With regard to the recent(ish) discussion about modularisation in BJ3,
> I'd suggest that a module is created for each distinct WSDL containing
> the glue code for connecting BJ objects with the boilerplate code. The
> glue code implements factory methods to generate instances of
> appropriate BJ service APIs, which are defined in a core BJ module. This
> means that the WSDL + API implementation is decoupled from the BJ
> service API.
>
> Does that make sense (and/or am I simply stating the obvious here) ?
>
> Jim.
>
> --
> -------------------------------------------------------------------
> J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No. SC015096.
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From markjschreiber at gmail.com  Thu May 28 10:11:36 2009
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Thu, 28 May 2009 22:11:36 +0800
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <93b45ca50905280709q6896f96fg598276de20222440@mail.gmail.com>
References: <200905141555.31967.niall@sgenomics.org>
	<59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>
	<200905190936.38541.niall@sgenomics.org>
	<93b45ca50905190702l2169d7f4qf200ed04f33c17b5@mail.gmail.com>
	<93b45ca50905190705qec04c48yb7a81c9b0715a50e@mail.gmail.com>
	<4A1E839F.2050700@compbio.dundee.ac.uk>
	<93b45ca50905280709q6896f96fg598276de20222440@mail.gmail.com>
Message-ID: <93b45ca50905280711q222a0c90ob93a3098ff1b97c7@mail.gmail.com>

By high level API I mean anything not machine generated. That could be
classes that use biojava objects or a more humanized or smarter interface to
the boilerplate code.

- Mark

On 28 May 2009, 2:53 PM, "James Procter" <jimp at compbio.dundee.ac.uk> wrote:

Hi All.

Mark Schreiber wrote: > There was a recent discussion of generated code on
the list. A good solutio...
Just to clarify - by high-level API you mean the interface to the code
that takes biojava objects as arguments and translates them into
parameters for the service and vice versa for the results ?

With regard to the recent(ish) discussion about modularisation in BJ3,
I'd suggest that a module is created for each distinct WSDL containing
the glue code for connecting BJ objects with the boilerplate code. The
glue code implements factory methods to generate instances of
appropriate BJ service APIs, which are defined in a core BJ module. This
means that the WSDL + API implementation is decoupled from the BJ
service API.

Does that make sense (and/or am I simply stating the obvious here) ?

Jim.

--
-------------------------------------------------------------------
J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

_______________________________________________ Biojava-l mailing list -
Biojava-l at lists.open-bio....

From andreas at sdsc.edu  Thu May 28 10:59:17 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 28 May 2009 07:59:17 -0700
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <4A1E839F.2050700@compbio.dundee.ac.uk>
References: <200905141555.31967.niall@sgenomics.org>
	<59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>
	<200905190936.38541.niall@sgenomics.org>
	<93b45ca50905190702l2169d7f4qf200ed04f33c17b5@mail.gmail.com>
	<93b45ca50905190705qec04c48yb7a81c9b0715a50e@mail.gmail.com>
	<4A1E839F.2050700@compbio.dundee.ac.uk>
Message-ID: <59a41c430905280759i503719eaxd2ac64436154be2d@mail.gmail.com>

makes sense and fits to the more detailed discussion we are having on
biojava-dev right now.

A


On Thu, May 28, 2009 at 5:29 AM, James Procter
<jimp at compbio.dundee.ac.uk> wrote:
> Hi All.
>
> Mark Schreiber wrote:
>> There was a recent discussion of generated code on the list. A good solution
>> for webservices may be to put the wsdl and high level api in the repository
>> and let jax-ws tools autogenerate the client biolerplate code.
>
> Just to clarify - by high-level API you mean the interface to the code
> that takes biojava objects as arguments and translates them into
> parameters for the service and vice versa for the results ?
>
> With regard to the recent(ish) discussion about modularisation in BJ3,
> I'd suggest that a module is created for each distinct WSDL containing
> the glue code for connecting BJ objects with the boilerplate code. The
> glue code implements factory methods to generate instances of
> appropriate BJ service APIs, which are defined in a core BJ module. This
> means that the WSDL + API implementation is decoupled from the BJ
> service API.
>
> Does that make sense (and/or am I simply stating the obvious here) ?
>
> Jim.
>
> --
> -------------------------------------------------------------------
> J. B. Procter ?(ENFIN/VAMSAS) ?Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764 ?http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No. SC015096.
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From jimp at compbio.dundee.ac.uk  Thu May 28 11:14:51 2009
From: jimp at compbio.dundee.ac.uk (James Procter)
Date: Thu, 28 May 2009 16:14:51 +0100
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <7ceb4beb0905280635g7bbb028dw9c5d69a9290b5a16@mail.gmail.com>
References: <200905141555.31967.niall@sgenomics.org>	
	<59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>	
	<200905190936.38541.niall@sgenomics.org>	
	<93b45ca50905190702l2169d7f4qf200ed04f33c17b5@mail.gmail.com>	
	<93b45ca50905190705qec04c48yb7a81c9b0715a50e@mail.gmail.com>	
	<4A1E839F.2050700@compbio.dundee.ac.uk>
	<7ceb4beb0905280635g7bbb028dw9c5d69a9290b5a16@mail.gmail.com>
Message-ID: <4A1EAA6B.7020202@compbio.dundee.ac.uk>

Hi Mark, and Scooter.

Mark Schreiber wrote:
> By high level API I mean anything not machine generated. That could be
> classes that use biojava objects or a more humanized or smarter
> interface to the boilerplate code.

ah. yes. that's what I thought. I'd really advocate keeping the Biojava
object adaptor glue for the autogenerated code separate from the core.
This is because (as I'm sure you know) there are no real object design
standards for bioinformatic services (apart from BioMOBY..) - so the
adaptor code is always going to be specific to the WSDL.

Scooter Willis wrote:
> I agree. I am planning on doing some testing of  a couple BLAST web
> services interfaces(assuming more than one exists) and see what they
> truly have in common and see how that would impact a BJ3 front end to
> multiple providers. My assumption is that they will be the same.
Of course, the actual functionality provided by all the servers will be
more or less the same (i.e. inputs and outputs), but servers will differ
in how they wrap the input and result data, how they support parameters,
and how they deal with polling and result retrieval (if they are at all
asynchronous).

 I
> noticed on the NCBI Blast implementations the user was required to pass
> their email address as part of the web service call. They are concerned
> with abuse from external processes and they only allow one sequence per
> request.
Yes. The NCBI has an automatic blacklisting system - too many requests
in a short space of time from a single IP will result in denial of
service for X (24?) hours. I'm not sure how something like Taverna
manages this kind of thing, but I expect this kind of user attribute
will have to be supported in the core web service model - that could
also provide authentication management support too (when users are using
secure or authenticated HTTP connections).


> From wikipedia the following are listed as BLAST resources where more
> than one may offer a web service interface. Should BioJava3 try and
> support more than one?
I would pick the two or three most popular/capable/geographically
widespread services to implement clients for, and then choose your
favourite one to start with (EBI,NCBI, and perhaps one in Japan - e.g.
http://xml.nig.ac.jp/wsdl/Blast.wsdl).

Implementing clients for two or three allows users a nice choice, and
should also capture most variation in the input/output and polling model
that is used. If any more need to be supported, then by then it should
be pretty clear how to go about implementing an API instance for a new WSDL.

You might also want to consider generalising the high-level interface to
non-Blast sequence search services, since they all take and return more
or less the same kind of data and results.

I suspect this discussion should move to the biojava-dev list!

Jim.



From jp at javaclass.co.uk  Thu May 28 14:54:42 2009
From: jp at javaclass.co.uk (JP)
Date: Thu, 28 May 2009 19:54:42 +0100
Subject: [Biojava-l] dN/dS ratio calculation biojava
Message-ID: <4adc29060905281154i6db465edt8c154bb30863296f@mail.gmail.com>

Hi there - is there a class or method which finds the dN/dS ratio
(nonsynonymous/synonymous rate ratio) for two sequences ?

Many Thanks
JP

From ayates at ebi.ac.uk  Fri May 29 04:23:34 2009
From: ayates at ebi.ac.uk (Andy Yates)
Date: Fri, 29 May 2009 09:23:34 +0100
Subject: [Biojava-l] dN/dS ratio calculation biojava
In-Reply-To: <4adc29060905281154i6db465edt8c154bb30863296f@mail.gmail.com>
References: <4adc29060905281154i6db465edt8c154bb30863296f@mail.gmail.com>
Message-ID: <4A1F9B86.6080309@ebi.ac.uk>

Hi JP,

No there isn't a class to calculate dN/dS. At a basic level dN/dS is a
very easy ratio to calculate if you take the very basic approach of
sequences of exact lengths. The basics of it are available from:

http://pubmlst.org/software/analysis/start/manual/dsdn.shtml

The best package I know of to calculate the rates though is codeml. It's
a very awkward program to run but it can be done & will produce the best
results. I can say for sure that the Ensembl Compara team use it to
calculate dN/dS rates for their homologous protein sets.

Hope that helps,

Andy

P.S. I say all of this from personal experience when I wrote a very
basic calculator using BioJava (and I don't know where the code got to).
The amount of work to produce that code vs. running a third party
application just makes it more cost effective to go for the 3rd party app

JP wrote:
> Hi there - is there a class or method which finds the dN/dS ratio
> (nonsynonymous/synonymous rate ratio) for two sequences ?
> 
> Many Thanks
> JP
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

From jogoodma at indiana.edu  Tue May 12 16:40:40 2009
From: jogoodma at indiana.edu (Josh Goodman)
Date: Tue, 12 May 2009 20:40:40 -0000
Subject: [Biojava-l] FASTA parsing bug ?
In-Reply-To: <49F822C6.1020809@eaglegenomics.com>
References: <4adc29060904280701q5d3dc760mb018f6b38a9e056f@mail.gmail.com>
	<49F71258.3060103@eaglegenomics.com>
	<4adc29060904280759q4b27a4eembd28974d46199532@mail.gmail.com>
	<49F71EF5.90702@eaglegenomics.com>
	<Pine.LNX.4.64.0904281552580.15441@conger.bio.indiana.edu>
	<49F822C6.1020809@eaglegenomics.com>
Message-ID: <4A09D8DC.1050307@indiana.edu>

Hi all,

I apologize for missing the "next day or so" window but here is my patch.  I'm attaching a patch
file for FastaFormat.java (1.7 tagged branch), the full source file, and a test class.  It seems to
work and performance is on par with the previous approach in my measurements.  One problem that I
couldn't quite figure out a way around is with the guessSymbolTokenization(BufferedInputStream
stream) method.  If the first sequence of the stream has a header length plus first line of sequence
length longer than 2000 characters it will fail to reset properly.

Cheers,
Josh

Richard Holland wrote:
> I'd love to see a proper solution to this that doesn't involve upping
> the read-ahead limit. I was aware that it might be the issue, but had no
> idea why it was not failing for other similar long sequences. I look
> forward to seeing your suggested fix!
> 
> thanks,
> Richard
> 
> Josh Goodman wrote:
>> Hi Richard and JP,
>>
>> I think I can be of some help as I'm the FlyBase developer responsible for 
>> generating these troublesome FASTA files :-).  The cause of this problem 
>> appears to be the description line length for the record FBpp0145470.
>>
>> The trouble lies in org.biojavax.bio.seq.io.FastaFormat in the while loop 
>> at line 196.  Biojava correctly reads in FBpp0145468 but throws an error 
>> when trying to parse FBpp0145469.  There is nothing wrong in FBpp0145469 
>> but when biojava reaches the end of the sequence it reads in the header 
>> for the next record (FBpp0145470).  It then tries to reset the 
>> BufferedReader to the start of FBpp0145470 but that is where the exception 
>> is thrown because line 197 sets the read ahead limit to 500 characters and 
>> the reader.readLine() command exceeds that limit.
>>
>> What isn't obvious to me is why other large definition lines that precede 
>> that line don't throw the same error (e.g. FBpp0157909).  I guess the 
>> javadoc on BufferedReader.mark() does say "may fail" but I assumed it 
>> would be more predictable than that.
>>
>> The file in question can be downloaded from 
>> ftp://ftp.flybase.net/genomes/Drosophila_grimshawi/dgri_r1.3_FB2008_07/fasta/dgri-all-translation-r1.3.fasta.gz.
>>
>> If there is interest in a solution that doesn't involve simply upping the 
>> read ahead limit I can put a patch file together in the next day or so.
>>
>> Cheers,
>> Josh
>>
>> On Tue, 28 Apr 2009, Richard Holland wrote:
>>
>>> You're right, doesn't look like newlines.
>>>
>>> The "Mark invalid" happens when the parser looks too far ahead in the
>>> file attempting to seek out the next valid sequence to parse. I'm not
>>> sure why this is happening.
>>>
>>> I don't have the time to test right now but if you could post the link
>>> to where someone could download the same FASTA as you're using, then it
>>> would make it possible for someone else to investigate in more detail.
>>>
>>> thanks,
>>> Richard
>>>
>>> JP wrote:
>>>> Thanks Richard for your prompt reply.
>>>>
>>>> I will not attach the fasta file I am parsing (12MB) its
>>>> dgri-all-translation-r1.3.fasta from the flybase project.
>>>>
>>>> If the file had any extra new lines I would see them when I loaded it in
>>>> a text editor - no ?
>>>>
>>>> I implemented the whole thing without using Biojava (for this part)
>>>>
>>>>     fr = new FileReader(fastaProteinFileName);
>>>>     br = new BufferedReader(fr);
>>>>     String fastaLine;
>>>>     String startAccession = '>' + accessionId.trim();
>>>>     String fastaEntry = "";
>>>>     boolean record = false;
>>>>     while ((fastaLine = br.readLine()) != null) {
>>>>         fastaLine = fastaLine.trim() + '\n';
>>>>         if (fastaLine.startsWith(startAccession)) {
>>>>             record = true;
>>>>         } else if (record && fastaLine.startsWith(">")) {
>>>>             record = false;
>>>>             break;
>>>>         }
>>>>         if (record) {
>>>>             fastaEntry += fastaLine;
>>>>         }
>>>>     }
>>>>
>>>>
>>>> Notice - I do not use regex - since I'd need to read the whole file and
>>>> then regex upon it (if the record is the first one - I just read that one).
>>>>
>>>> Cheers
>>>> JP
>>>>
>>>>
>>>> On Tue, Apr 28, 2009 at 3:27 PM, Richard Holland
>>>> <holland at eaglegenomics.com <mailto:holland at eaglegenomics.com>> wrote:
>>>>
>>>>     The "Mark invalid" exception is indicating that the parser has gone too
>>>>     far ahead in the file looking for a valid header. I'm not sure why but
>>>>     looking at your original query, there may be extra newlines embedded
>>>>     into your FASTA header line? That would definitely confuse it.
>>>>
>>>>     The parser is not able to currently pull out just one sequence - in
>>>>     effect this is a search facility, which it doesn't have. :(
>>>>
>>>>     thanks,
>>>>     Richard
>>>>
>>>>     JP wrote:
>>>>     > Hi all at BioJava,
>>>>     >
>>>>     > I am trying to parse several FASTA files using the following code:
>>>>     >
>>>>     > fr = new FileReader(fastaProteinFileName);
>>>>     >> br = new BufferedReader(fr);
>>>>     >>
>>>>     >> RichSequenceIterator protIter = IOTools.readFastaProtein(br, null);
>>>>     >> while (protIter.hasNext()) {
>>>>     >>      BioEntry bioEntry = protIter.nextBioEntry();
>>>>     >>      System.out.println (fastaProteinFileName + " == " +
>>>>     accessionId + " =
>>>>     >> " + bioEntry.getAccession());
>>>>     >> }
>>>>     >
>>>>     >
>>>>     > At particular points in my fasta file - I get the following exception:
>>>>     >
>>>>     > 14:53:42,546 ERROR FastaFileProcessing  - File parsing exception (from
>>>>     >> biojava library)
>>>>     >> org.biojava.bio.BioException: Could not read sequence
>>>>     >>     at
>>>>     >>
>>>>     org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
>>>>     >>     at
>>>>     >>
>>>>     org.biojavax.bio.seq.io.RichStreamReader.nextBioEntry(RichStreamReader.java:99)
>>>>     >>     at
>>>>     >>
>>>>     edu.imperial.msc.orthologue.fasta.FastaFileProcessing.getProteinSequenceFromFASTAFile(FastaFileProcessing.java:60)
>>>>     >>     at
>>>>     >>
>>>>     edu.imperial.msc.orthologue.core.OrthologueFinder.getFASTAEntries(OrthologueFinder.java:64)
>>>>     >>     at
>>>>     >>
>>>>     edu.imperial.msc.orthologue.core.OrthologueFinder.<init>(OrthologueFinder.java:51)
>>>>     >>     at
>>>>     >>
>>>>     edu.imperial.msc.orthologue.launcher.OrthologueFinderLauncher.main(OrthologueFinderLauncher.java:60)
>>>>     >> Caused by: java.io.IOException: Mark invalid
>>>>     >>     at java.io.BufferedReader.reset(Unknown Source)
>>>>     >>     at
>>>>     >>
>>>>     org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:202)
>>>>     >>     at
>>>>     >>
>>>>     org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
>>>>     >>     ... 5 more
>>>>     >
>>>>     >
>>>>     > Interestingly if I delete the header portion of the header line (from
>>>>     > type=protein... till the end of the line ...Dgri;)
>>>>     >
>>>>     >> FBpp0145468 type=protein;
>>>>     >>
>>>>     loc=scaffold_15252:join(13219687..13219727,13219972..13220279,13220507..13220798,13220861..13221180,13221286..13221467,13222258..13222629,13226331..13226463,13226531..13226658);
>>>>     >> ID=FBpp0145468; name=Dgri\GH11562-PA; parent=FBgn0119042,FBtr0146976;
>>>>     >> dbxref=FlyBase:FBpp0145468,FlyBase_Annotation_IDs:GH11562-PA;
>>>>     >> MD5=c8dc38c7197a0d3c93c78b08059e2604; length=591; release=r1.3;
>>>>     >> species=Dgri;
>>>>     >>
>>>>     >
>>>>     > It works - but I have a number of these exceptions (and I do not
>>>>     want to
>>>>     > edit the original data).  Mind you I have longer headers in my
>>>>     file which
>>>>     > are parsed OK (strange!).
>>>>     >
>>>>     > Any ideas anyone ?  Alternatively - is there a better way how to
>>>>     get ONE
>>>>     > SINGLE sequence from the whole fasta file give that I have the
>>>>     accession id
>>>>     > (FBpp0145468) ?
>>>>     >
>>>>     > Many Thanks
>>>>     > JP
>>>>     > _______________________________________________
>>>>     > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>     <mailto:Biojava-l at lists.open-bio.org>
>>>>     > http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>     >
>>>>
>>>>     --
>>>>     Richard Holland, BSc MBCS
>>>>     Finance Director, Eagle Genomics Ltd
>>>>     T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>>>>     <mailto:holland at eaglegenomics.com>
>>>>     http://www.eaglegenomics.com/
>>>>
>>>>
>>> -- 
>>> Richard Holland, BSc MBCS
>>> Finance Director, Eagle Genomics Ltd
>>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>>> http://www.eaglegenomics.com/
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
> 
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From harryzs1981 at gmail.com  Wed May  6 13:13:42 2009
From: harryzs1981 at gmail.com (sheng zhao)
Date: Wed, 6 May 2009 15:13:42 +0200
Subject: [Biojava-l] Biojava-doc in chm forma
Message-ID: <3d23b1eb0905060613m643adf87sdef55a05a083dd51@mail.gmail.com>

Hi

Where can I find Biojava-doc in chm format??

Thanks !

harry


From andreas at sdsc.edu  Thu May  7 12:59:32 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 7 May 2009 05:59:32 -0700
Subject: [Biojava-l] SVDSuperimposer
In-Reply-To: <4A02D2E7.9070705@wp.pl>
References: <4A02D2E7.9070705@wp.pl>
Message-ID: <59a41c430905070559v238e0df2p28478d5108dae4a@mail.gmail.com>

Hi Michal,

The SVD superimposer actually does the same Singular Value
Decomposition in both BioJava and BioPython. The difference is that
BioJava also contains a complete alignment algorithm that can
calculate a structure alignment, if the region of similarity between 2
proteins is not known a priori.

See also here:
http://biojava.org/wiki/BioJava:CookBook:PDB:align  and
http://biojava.org/wiki/BioJava:CookBook:PDB:aboutalign

Andreas

On Thu, May 7, 2009 at 5:24 AM, Michal Lorenc <m.t.lorenc at wp.pl> wrote:
> Hello Andreas,
> SVDSuperimposer from BioPython works only with proteins which have the same
> length, but in BioJava it does not matter.
>
> Do you published how SVDSuperimposer in BioJava works or do you know where
> could I found more information?
>
> Thank you in advance.
>
> Best regards,
>
> Michal
>


From raphael.andre.bauer at gmail.com  Fri May  8 13:13:44 2009
From: raphael.andre.bauer at gmail.com (=?UTF-8?Q?Raphael_Andr=C3=A9_Bauer?=)
Date: Fri, 8 May 2009 15:13:44 +0200
Subject: [Biojava-l] SVDSuperimposer
In-Reply-To: <59a41c430905070559v238e0df2p28478d5108dae4a@mail.gmail.com>
References: <4A02D2E7.9070705@wp.pl>
	<59a41c430905070559v238e0df2p28478d5108dae4a@mail.gmail.com>
Message-ID: <9b46aa30905080613o2ea91751sdd086c5d880cc435@mail.gmail.com>

On Thu, May 7, 2009 at 2:59 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Michal,
>
> The SVD superimposer actually does the same Singular Value
> Decomposition in both BioJava and BioPython. The difference is that
> BioJava also contains a complete alignment algorithm that can
> calculate a structure alignment, if the region of similarity between 2
> proteins is not known a priori.
>
> See also here:
> http://biojava.org/wiki/BioJava:CookBook:PDB:align ?and
> http://biojava.org/wiki/BioJava:CookBook:PDB:aboutalign

Maybe it is interesting for you to know that we developed a generic
algorithm for the structural alignment of RNA and proteins called
"LaJolla". The reference implementation is built using BioJava and
released as open source at http://lajolla.sourceforge.net. I think
LaJolla is straight forward to use and modify if you know how to use
Maven and the BioJava core classes.

Btw. The algorithm for the alignment of proteins used by BioJava
yielded sometimes strange results - but I did not do an exhaustive
evaluation. But maybe LaJolla is an alternative in those cases.

Additionally -- if the BioJava project is interested in integrating
LaJolla into BioJava this is really not a problem -- but I do not know
if it blurs the clean toolkit/library character of BioJava.

We are open for all suggestions regarding the algorithm and also
regarding a cooperation with BioJava...

Thanks,

Raphael
@Michal: LaJolla is also partly made in Poland -- so mabye you some
people by chance..

>
> Andreas
>
> On Thu, May 7, 2009 at 5:24 AM, Michal Lorenc <m.t.lorenc at wp.pl> wrote:
>> Hello Andreas,
>> SVDSuperimposer from BioPython works only with proteins which have the same
>> length, but in BioJava it does not matter.
>>
>> Do you published how SVDSuperimposer in BioJava works or do you know where
>> could I found more information?
>>
>> Thank you in advance.
>>
>> Best regards,
>>
>> Michal
>>
> _______________________________________________
> 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 May  8 17:37:41 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 8 May 2009 10:37:41 -0700
Subject: [Biojava-l] SVDSuperimposer
In-Reply-To: <9b46aa30905080613o2ea91751sdd086c5d880cc435@mail.gmail.com>
References: <4A02D2E7.9070705@wp.pl>
	<59a41c430905070559v238e0df2p28478d5108dae4a@mail.gmail.com>
	<9b46aa30905080613o2ea91751sdd086c5d880cc435@mail.gmail.com>
Message-ID: <59a41c430905081037n5b2ce541nc132dbfb2ea49b0a@mail.gmail.com>

Hi Raphael,

Thanks for posting the link to "LaJolla" (funny that you chose this
name, it is the part of the town where my university is located...).
This is very interesting and exactly the kind of applications we are
happy to see BioJava being used for.

Do you want to provide a link back to your project site at
http://biojava.org/wiki/BioJava:BioJavaInside and also add your paper
to the list of papers that are using BioJava?

About the  BioJava algorithm : If you have an example where the
BioJava structure comparison does not give the result you would
expect, could you send it to me so I can take a look ?

Thanks,
Andreas


On Fri, May 8, 2009 at 6:13 AM, Raphael Andr? Bauer
<raphael.andre.bauer at gmail.com> wrote:
> On Thu, May 7, 2009 at 2:59 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Hi Michal,
>>
>> The SVD superimposer actually does the same Singular Value
>> Decomposition in both BioJava and BioPython. The difference is that
>> BioJava also contains a complete alignment algorithm that can
>> calculate a structure alignment, if the region of similarity between 2
>> proteins is not known a priori.
>>
>> See also here:
>> http://biojava.org/wiki/BioJava:CookBook:PDB:align ?and
>> http://biojava.org/wiki/BioJava:CookBook:PDB:aboutalign
>
> Maybe it is interesting for you to know that we developed a generic
> algorithm for the structural alignment of RNA and proteins called
> "LaJolla". The reference implementation is built using BioJava and
> released as open source at http://lajolla.sourceforge.net. I think
> LaJolla is straight forward to use and modify if you know how to use
> Maven and the BioJava core classes.
>
> Btw. The algorithm for the alignment of proteins used by BioJava
> yielded sometimes strange results - but I did not do an exhaustive
> evaluation. But maybe LaJolla is an alternative in those cases.
>
> Additionally -- if the BioJava project is interested in integrating
> LaJolla into BioJava this is really not a problem -- but I do not know
> if it blurs the clean toolkit/library character of BioJava.
>
> We are open for all suggestions regarding the algorithm and also
> regarding a cooperation with BioJava...
>
> Thanks,
>
> Raphael
> @Michal: LaJolla is also partly made in Poland -- so mabye you some
> people by chance..
>
>>
>> Andreas
>>
>> On Thu, May 7, 2009 at 5:24 AM, Michal Lorenc <m.t.lorenc at wp.pl> wrote:
>>> Hello Andreas,
>>> SVDSuperimposer from BioPython works only with proteins which have the same
>>> length, but in BioJava it does not matter.
>>>
>>> Do you published how SVDSuperimposer in BioJava works or do you know where
>>> could I found more information?
>>>
>>> Thank you in advance.
>>>
>>> Best regards,
>>>
>>> Michal
>>>
>> _______________________________________________
>> 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  Mon May 11 04:30:30 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sun, 10 May 2009 21:30:30 -0700
Subject: [Biojava-l] Plans for next biojava release - modularization
Message-ID: <59a41c430905102130v6e878c6bgda582268e02824fe@mail.gmail.com>

Hi,

In case you are not subscribed to biojava-dev: we are having a
discussion about how to organize the code base for the next release of
biojava on the biojava-dev mailing list. If you want to follow this
discussion, but are not subscribed yet, you can do so here:
http://www.biojava.org/mailman/listinfo/biojava-dev

Andreas


From raphael.andre.bauer at gmail.com  Mon May 11 09:10:48 2009
From: raphael.andre.bauer at gmail.com (=?UTF-8?Q?Raphael_Andr=C3=A9_Bauer?=)
Date: Mon, 11 May 2009 11:10:48 +0200
Subject: [Biojava-l] SVDSuperimposer
In-Reply-To: <59a41c430905081037n5b2ce541nc132dbfb2ea49b0a@mail.gmail.com>
References: <4A02D2E7.9070705@wp.pl>
	<59a41c430905070559v238e0df2p28478d5108dae4a@mail.gmail.com> 
	<9b46aa30905080613o2ea91751sdd086c5d880cc435@mail.gmail.com> 
	<59a41c430905081037n5b2ce541nc132dbfb2ea49b0a@mail.gmail.com>
Message-ID: <9b46aa30905110210j5799359s6d72f50dccb3c74f@mail.gmail.com>

On Fri, May 8, 2009 at 7:37 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Raphael,
>
> Thanks for posting the link to "LaJolla" (funny that you chose this
> name, it is the part of the town where my university is located...).
> This is very interesting and exactly the kind of applications we are
> happy to see BioJava being used for.
Well. Phil Bourne and the PDB are there (and I think you are also
somehow connected to both)... I also heard that LaJolla might have
nice beaches, sunny weather and the surf?... So LaJolla definitely is
a good name for a boring structural RNA and protein alignment
algorithm...
>
> Do you want to provide a link back to your project site at
> http://biojava.org/wiki/BioJava:BioJavaInside and also add your paper
> to the list of papers that are using BioJava?
done
>
> About the ?BioJava algorithm : If you have an example where the
> BioJava structure comparison does not give the result you would
> expect, could you send it to me so I can take a look ?
I did not write down the examples (I thought, that the protein
alignment of BioJava is somehow alpha because of "personal
communication of..."). But the examples where simple. If I rediscover
them I will  let you know.

Maybe it is also of help to mention in the source code or on the
webpage of the cookbook: "If our protein alignment alg delivers
strange results please let us now..." or so.. So that users are aware
of submitting strange results...


Thanks,

Raphael

>
> Thanks,
> Andreas
>
>
> On Fri, May 8, 2009 at 6:13 AM, Raphael Andr? Bauer
> <raphael.andre.bauer at gmail.com> wrote:
>> On Thu, May 7, 2009 at 2:59 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> Hi Michal,
>>>
>>> The SVD superimposer actually does the same Singular Value
>>> Decomposition in both BioJava and BioPython. The difference is that
>>> BioJava also contains a complete alignment algorithm that can
>>> calculate a structure alignment, if the region of similarity between 2
>>> proteins is not known a priori.
>>>
>>> See also here:
>>> http://biojava.org/wiki/BioJava:CookBook:PDB:align ?and
>>> http://biojava.org/wiki/BioJava:CookBook:PDB:aboutalign
>>
>> Maybe it is interesting for you to know that we developed a generic
>> algorithm for the structural alignment of RNA and proteins called
>> "LaJolla". The reference implementation is built using BioJava and
>> released as open source at http://lajolla.sourceforge.net. I think
>> LaJolla is straight forward to use and modify if you know how to use
>> Maven and the BioJava core classes.
>>
>> Btw. The algorithm for the alignment of proteins used by BioJava
>> yielded sometimes strange results - but I did not do an exhaustive
>> evaluation. But maybe LaJolla is an alternative in those cases.
>>
>> Additionally -- if the BioJava project is interested in integrating
>> LaJolla into BioJava this is really not a problem -- but I do not know
>> if it blurs the clean toolkit/library character of BioJava.
>>
>> We are open for all suggestions regarding the algorithm and also
>> regarding a cooperation with BioJava...
>>
>> Thanks,
>>
>> Raphael
>> @Michal: LaJolla is also partly made in Poland -- so mabye you some
>> people by chance..
>>
>>>
>>> Andreas
>>>
>>> On Thu, May 7, 2009 at 5:24 AM, Michal Lorenc <m.t.lorenc at wp.pl> wrote:
>>>> Hello Andreas,
>>>> SVDSuperimposer from BioPython works only with proteins which have the same
>>>> length, but in BioJava it does not matter.
>>>>
>>>> Do you published how SVDSuperimposer in BioJava works or do you know where
>>>> could I found more information?
>>>>
>>>> Thank you in advance.
>>>>
>>>> Best regards,
>>>>
>>>> Michal
>>>>
>>> _______________________________________________
>>> 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 jp at javaclass.co.uk  Mon May 11 10:05:43 2009
From: jp at javaclass.co.uk (JP)
Date: Mon, 11 May 2009 11:05:43 +0100
Subject: [Biojava-l] FASTA header, loc attribute question
Message-ID: <4adc29060905110305l392a9792p2aa40590e97c9891@mail.gmail.com>

Hi there at Biojava,

I have two FASTA files - one containing amino acid sequences and the other
containing dna sequences.

In the AA FASTA file I have something like :

>FBpp0077713 type=protein;
loc=2L:join(384551..384894,385701..385746,386308..386576,386703..387270);
ID=FBpp0077713; name=al-PA; parent=FBgn0000061,FBtr0078053;
dbxref=FlyBase:FBpp0077713,GB_protein:AAF51505.1,GB_protein:AAF51505,FlyBase_Annotation_IDs:CG3935-PA,REFSEQ:NP_722629;
MD5=64a866db3e2913b97a2158c2de9d02f6; length=408; release=r5.9;
species=Dmel;
MGISEEIKLEELPQEAKLAHPDAVVLVDRAPGSSAASAGAALTVSMSVSG
GAPSGASGASGGTNSPVSDGNSDCEADEYAPKRKQRRYRTTFTSFQLEEL...
etc etc etc

I would like to parse this header line in particular the loc attribute and
extract it from the entry in the DNA FASTA file (so I get the genomic data
for the protein)

>FBgn0000061 type=gene; loc=2L:378116..387439; ID=FBgn0000061; name=al;
dbxref=FlyBase:FBgn0000061,FlyBase:FBan0003935,FlyBase_Annotation_IDs:CG3935,GB:AE003589,GB_protein:AAF51505,GB:AY121696,GB_protein:AAM52023,GB:BI485174,GB:CZ486795,GB:L08401,GB_protein:AAA28840,UniProt/Swiss-Prot:Q06453,INTERPRO:IPR000047,INTERPRO:IPR001356,INTERPRO:IPR003654,INTERPRO:IPR009057,INTERPRO:IPR012287,bdgpinsituexpr:al,dedb:5830,drsc:FBgn0000061,flight:FBgn0000061,flyatlas:FBgn0000061,flyexpress:FBgn0000061,flygrid:59464,flymine:FBgn0000061,geo:FBgn0000061,hdri:FBgn0000061,if:/gene/aristal.htm,orthologs:ensANOGA:ENSANGP00000011877,orthologs:ensBOSTA:ENSBTAP00000015907,orthologs:ensCANFA:ENSCAFP00000009888,orthologs:ensGALGA:ENSGALP00000005255,orthologs:ensHOMSA:ENSP00000298420,orthologs:ensMACMU:ENSMMUP00000007349,orthologs:ensMONDO:ENSMODP00000008388,orthologs:ensPANTR:ENSPTRP00000004281,orthologs:ensRATNO:ENSRNOP00000027186,orthologs:ensTETNI:GSTENP00015517001,orthologs:graORYSA:Q6YYB8,orthologs:graORYSA:Q8W0T5,orthologs:modCAEEL:WBGene00044330,orthologs:modDANRE:ZDB-GENE-990415-15,orthologs:modMUSMU:MGI:1097716,panther:FBgn0000061;
cyto_range=21C1-21C1; gbunit=AE014134; MD5=0f5568cf13aeb2c7076f11b1ce3d6b2f;
length=9324; release=r5.9; species=Dmel;
GTAGTTTGCTGCCGGCTCTGGAACAGCCCGGTCATCTCGTCGCGTTCGGT
TCCGATTCCGATTCGAATAGTCGAGCTGGGGATACATTGTTGTTTCCGGG
etc etc etc

I understand this is not exactly conventional, but does biojava support the
parsing of the loc attribute ? (join, complement etc.)

Many Thanks
JP



From holland at eaglegenomics.com  Mon May 11 10:27:23 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 11 May 2009 10:27:23 +0000
Subject: [Biojava-l] FASTA header, loc attribute question
In-Reply-To: <4adc29060905110305l392a9792p2aa40590e97c9891@mail.gmail.com>
References: <4adc29060905110305l392a9792p2aa40590e97c9891@mail.gmail.com>
Message-ID: <1242037643.15828.12.camel@buzzybee>

Short answer - no, not directly.

Longer answer - if you can write some code to snip out the Loc string
from the FASTA description line then there is existing code which can
convert the snipped Loc string into a RichLocation, which you can then
apply to the parsed FASTA sequence in order to extract the required
location. The Loc string parser is GenbankLocationParser, part of the
biojavax packages. This assumes that the Loc string conforms to Genbank
format location definitions.

cheers,
Richard

On Mon, 2009-05-11 at 11:05 +0100, JP wrote:
> Hi there at Biojava,
> 
> I have two FASTA files - one containing amino acid sequences and the other
> containing dna sequences.
> 
> In the AA FASTA file I have something like :
> 
> >FBpp0077713 type=protein;
> loc=2L:join(384551..384894,385701..385746,386308..386576,386703..387270);
> ID=FBpp0077713; name=al-PA; parent=FBgn0000061,FBtr0078053;
> dbxref=FlyBase:FBpp0077713,GB_protein:AAF51505.1,GB_protein:AAF51505,FlyBase_Annotation_IDs:CG3935-PA,REFSEQ:NP_722629;
> MD5=64a866db3e2913b97a2158c2de9d02f6; length=408; release=r5.9;
> species=Dmel;
> MGISEEIKLEELPQEAKLAHPDAVVLVDRAPGSSAASAGAALTVSMSVSG
> GAPSGASGASGGTNSPVSDGNSDCEADEYAPKRKQRRYRTTFTSFQLEEL...
> etc etc etc
> 
> I would like to parse this header line in particular the loc attribute and
> extract it from the entry in the DNA FASTA file (so I get the genomic data
> for the protein)
> 
> >FBgn0000061 type=gene; loc=2L:378116..387439; ID=FBgn0000061; name=al;
> dbxref=FlyBase:FBgn0000061,FlyBase:FBan0003935,FlyBase_Annotation_IDs:CG3935,GB:AE003589,GB_protein:AAF51505,GB:AY121696,GB_protein:AAM52023,GB:BI485174,GB:CZ486795,GB:L08401,GB_protein:AAA28840,UniProt/Swiss-Prot:Q06453,INTERPRO:IPR000047,INTERPRO:IPR001356,INTERPRO:IPR003654,INTERPRO:IPR009057,INTERPRO:IPR012287,bdgpinsituexpr:al,dedb:5830,drsc:FBgn0000061,flight:FBgn0000061,flyatlas:FBgn0000061,flyexpress:FBgn0000061,flygrid:59464,flymine:FBgn0000061,geo:FBgn0000061,hdri:FBgn0000061,if:/gene/aristal.htm,orthologs:ensANOGA:ENSANGP00000011877,orthologs:ensBOSTA:ENSBTAP00000015907,orthologs:ensCANFA:ENSCAFP00000009888,orthologs:ensGALGA:ENSGALP00000005255,orthologs:ensHOMSA:ENSP00000298420,orthologs:ensMACMU:ENSMMUP00000007349,orthologs:ensMONDO:ENSMODP00000008388,orthologs:ensPANTR:ENSPTRP00000004281,orthologs:ensRATNO:ENSRNOP00000027186,orthologs:ensTETNI:GSTENP00015517001,orthologs:graORYSA:Q6YYB8,orthologs:graORYSA:Q8W0T5,orthologs:modCAEEL:WBGene00044330,orthologs:modDA!
>  NRE:ZDB-GENE-990415-15,orthologs:modMUSMU:MGI:1097716,panther:FBgn0000061;
> cyto_range=21C1-21C1; gbunit=AE014134; MD5=0f5568cf13aeb2c7076f11b1ce3d6b2f;
> length=9324; release=r5.9; species=Dmel;
> GTAGTTTGCTGCCGGCTCTGGAACAGCCCGGTCATCTCGTCGCGTTCGGT
> TCCGATTCCGATTCGAATAGTCGAGCTGGGGATACATTGTTGTTTCCGGG
> etc etc etc
> 
> I understand this is not exactly conventional, but does biojava support the
> parsing of the loc attribute ? (join, complement etc.)
> 
> Many Thanks
> JP
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/




From thomas.covello at gmail.com  Mon May 11 20:33:43 2009
From: thomas.covello at gmail.com (Thomas Covello)
Date: Mon, 11 May 2009 14:33:43 -0600
Subject: [Biojava-l] NullPointerException when using Viterbi algorithm in
	HMM.
Message-ID: <2e367d7b0905111333o2d074f81if9a34545acb95b5b@mail.gmail.com>

Hello,
I am trying to use a Hidden Markov Model to classify a sequence, and I
am encountering a NullPointerException when I try to use the Viterbi
algorithm. My test case follows - if you want the code I am actually
using I can post it. The stack trace:

java.lang.NullPointerException
        at org.biojava.bio.dp.onehead.SingleDP.viterbi(SingleDP.java:648)
        at org.biojava.bio.dp.onehead.SingleDP.viterbi(SingleDP.java:512)
        at oxytricha_crap.Main.main(Main.java:69)

File: Main.java

package oxytricha_crap;

import org.biojava.bio.seq.*;
import org.biojava.bio.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.dp.*;
import org.biojava.bio.dist.*;
import java.util.*;
import org.biojava.bio.symbol.SymbolList;

public class Main {
    private static Alphabet DNA = DNATools.getDNA();
    private static State IES;
    private static State MDS;
    private static MarkovModel hmm = new SimpleMarkovModel(1, DNA, "MyHMM");

    static {
        try {
            Distribution IES_dist =
                DistributionFactory.DEFAULT.createDistribution(DNA);
            Distribution MDS_dist =
                DistributionFactory.DEFAULT.createDistribution(DNA);
            IES = new SimpleEmissionState("IES", Annotation.EMPTY_ANNOTATION,
                new int [] {1}, IES_dist);
            MDS = new SimpleEmissionState("MDS", Annotation.EMPTY_ANNOTATION,
                new int [] {1}, MDS_dist);
            hmm.addState(IES);
            hmm.addState(MDS);
            hmm.createTransition(MDS, hmm.magicalState());
            hmm.createTransition(hmm.magicalState(), MDS);
            hmm.createTransition(MDS, IES);
            hmm.createTransition(IES, MDS);
            hmm.createTransition(MDS, MDS);
            hmm.createTransition(IES, IES);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }

    public static void main(String[] args) {
        try {
            State currState;
            State lastState = hmm.magicalState();
            Iterator<State> states = Arrays.asList(new State [] {
                MDS, MDS, MDS, IES, IES, IES, MDS, MDS, IES, IES, MDS, MDS,
                MDS, MDS
            }).iterator();
            SymbolList sl = DNATools.createDNA("acgtgtctgagaga");

            HMMTrainer trainer = new SimpleHMMTrainer(hmm);
            trainer.startCycle();
            for (Symbol sym : (List<Symbol>)sl.toList()) {
                currState = states.next();
                if (currState != lastState && lastState != null)
                    trainer.recordTransition(lastState, currState, 1.0);
                trainer.recordEmittedSymbol(currState, sym, 1.0);
                lastState = currState;
            }
            trainer.recordTransition(MDS, hmm.magicalState(), 1.0);

            trainer.completeCycle();

            DP dp = DPFactory.DEFAULT.createDP(hmm);
            SymbolList unknown = DNATools.createDNA("acgtcgtacgtacgtacacaacga");
            StatePath spath = dp.viterbi(new SymbolList [] { unknown },
                ScoreType.PROBABILITY);
        } catch (Exception e) {
            e.printStackTrace();
        }

        System.exit(0);
    }
}


From mauleemacx at gmail.com  Wed May 13 11:21:57 2009
From: mauleemacx at gmail.com (mac LEE)
Date: Wed, 13 May 2009 19:21:57 +0800
Subject: [Biojava-l] biojava on Maven2 repository
Message-ID: <e71c81850905130421v391bf60dna5839f59e33c21db@mail.gmail.com>

Dear All,
Hello. Is it possible to place the biojava jar into the maven 2 repository?

regards,

jack Lee

-- 
Somewhere between heaven and hell
mauleemacx at gmail.com


From raphael.andre.bauer at gmail.com  Wed May 13 13:12:11 2009
From: raphael.andre.bauer at gmail.com (=?UTF-8?Q?Raphael_Andr=C3=A9_Bauer?=)
Date: Wed, 13 May 2009 15:12:11 +0200
Subject: [Biojava-l] biojava on Maven2 repository
In-Reply-To: <e71c81850905130421v391bf60dna5839f59e33c21db@mail.gmail.com>
References: <e71c81850905130421v391bf60dna5839f59e33c21db@mail.gmail.com>
Message-ID: <9b46aa30905130612g194a022eu4fdb30114773b70e@mail.gmail.com>

On Wed, May 13, 2009 at 1:21 PM, mac LEE <mauleemacx at gmail.com> wrote:
> Dear All,
> Hello. Is it possible to place the biojava jar into the maven 2 repository?

You have to install the biojava.jar manually into your local repository:
http://maven.apache.org/guides/mini/guide-3rd-party-jars-local.html

LaJolla is an application that uses that approach too... Maybe the
pom.xml of LaJolla is worth a look to see how it works...:
http://lajolla.svn.sourceforge.net/viewvc/lajolla/trunk/lajolla/pom.xml?revision=350&view=markup

Regards,

Raphael

>
> regards,
>
> jack Lee
>
> --
> Somewhere between heaven and hell
> mauleemacx at gmail.com
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From helpmedicine.savelife at gmail.com  Wed May 13 14:04:18 2009
From: helpmedicine.savelife at gmail.com (helpmedicine savelife)
Date: Wed, 13 May 2009 10:04:18 -0400
Subject: [Biojava-l] biojava on Maven2 repository
In-Reply-To: <9b46aa30905130612g194a022eu4fdb30114773b70e@mail.gmail.com>
References: <e71c81850905130421v391bf60dna5839f59e33c21db@mail.gmail.com>
	<9b46aa30905130612g194a022eu4fdb30114773b70e@mail.gmail.com>
Message-ID: <3d0f70fd0905130704h57eb09b6k33bf067b6f729768@mail.gmail.com>

I agree it is possible by setting up in local repository (I did the same for
my project I am currently working), but now that biojava is being used by
many, I guess it it is a good time to to make it accessible through maven2
by providing the project metadata information to Maven2.

Biojava Team - Is this possible?

Thanks,
Sandya

On Wed, May 13, 2009 at 9:12 AM, Raphael Andr? Bauer <
raphael.andre.bauer at gmail.com> wrote:

> On Wed, May 13, 2009 at 1:21 PM, mac LEE <mauleemacx at gmail.com> wrote:
> > Dear All,
> > Hello. Is it possible to place the biojava jar into the maven 2
> repository?
>
> You have to install the biojava.jar manually into your local repository:
> http://maven.apache.org/guides/mini/guide-3rd-party-jars-local.html
>
> LaJolla is an application that uses that approach too... Maybe the
> pom.xml of LaJolla is worth a look to see how it works...:
>
> http://lajolla.svn.sourceforge.net/viewvc/lajolla/trunk/lajolla/pom.xml?revision=350&view=markup
>
> Regards,
>
> Raphael
>
> >
> > regards,
> >
> > jack Lee
> >
> > --
> > Somewhere between heaven and hell
> > mauleemacx at gmail.com
> > _______________________________________________
> > 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 mauleemacx at gmail.com  Thu May 14 05:50:51 2009
From: mauleemacx at gmail.com (mac LEE)
Date: Thu, 14 May 2009 13:50:51 +0800
Subject: [Biojava-l] biojava on Maven2 repository
In-Reply-To: <3d0f70fd0905130704h57eb09b6k33bf067b6f729768@mail.gmail.com>
References: <e71c81850905130421v391bf60dna5839f59e33c21db@mail.gmail.com>
	<9b46aa30905130612g194a022eu4fdb30114773b70e@mail.gmail.com>
	<3d0f70fd0905130704h57eb09b6k33bf067b6f729768@mail.gmail.com>
Message-ID: <e71c81850905132250x4332497dh708336da0b67a8dd@mail.gmail.com>

Dear All,
I think putting Biojava on central Maven2 repository not only facilitate
current users. It also attracts new users as well, just think of how success
is the BioPerl project resided in CPAN is.  I strongly hope that there will
be central repository soon.
regards,
jack LEE

On Wed, May 13, 2009 at 10:04 PM, helpmedicine savelife <
helpmedicine.savelife at gmail.com> wrote:

> I agree it is possible by setting up in local repository (I did the same
> for
> my project I am currently working), but now that biojava is being used by
> many, I guess it it is a good time to to make it accessible through maven2
> by providing the project metadata information to Maven2.
>
> Biojava Team - Is this possible?
>
> Thanks,
> Sandya
>
> On Wed, May 13, 2009 at 9:12 AM, Raphael Andr? Bauer <
> raphael.andre.bauer at gmail.com> wrote:
>
> > On Wed, May 13, 2009 at 1:21 PM, mac LEE <mauleemacx at gmail.com> wrote:
> > > Dear All,
> > > Hello. Is it possible to place the biojava jar into the maven 2
> > repository?
> >
> > You have to install the biojava.jar manually into your local repository:
> > http://maven.apache.org/guides/mini/guide-3rd-party-jars-local.html
> >
> > LaJolla is an application that uses that approach too... Maybe the
> > pom.xml of LaJolla is worth a look to see how it works...:
> >
> >
> http://lajolla.svn.sourceforge.net/viewvc/lajolla/trunk/lajolla/pom.xml?revision=350&view=markup
> >
> > Regards,
> >
> > Raphael
> >
> > >
> > > regards,
> > >
> > > jack Lee
> > >
> > > --
> > > Somewhere between heaven and hell
> > > mauleemacx at gmail.com
> > > _______________________________________________
> > > 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
> >
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
Somewhere between heaven and hell
mauleemacx at gmail.com



From andreas at sdsc.edu  Thu May 14 13:38:08 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 14 May 2009 06:38:08 -0700
Subject: [Biojava-l] biojava on Maven2 repository
In-Reply-To: <3d0f70fd0905130704h57eb09b6k33bf067b6f729768@mail.gmail.com>
References: <e71c81850905130421v391bf60dna5839f59e33c21db@mail.gmail.com>
	<9b46aa30905130612g194a022eu4fdb30114773b70e@mail.gmail.com>
	<3d0f70fd0905130704h57eb09b6k33bf067b6f729768@mail.gmail.com>
Message-ID: <59a41c430905140638r74554c10wb9c97dddd8f05b6b@mail.gmail.com>

I will have a look at this, once we have mavenized the biojava build
process. In the meanwhile, perhaps somebody could post instructions
how to add biojava to a local maven repository on the wiki?

Andreas



On Wed, May 13, 2009 at 7:04 AM, helpmedicine savelife
<helpmedicine.savelife at gmail.com> wrote:
> I agree it is possible by setting up in local repository (I did the same for
> my project I am currently working), but now that biojava is being used by
> many, I guess it it is a good time to to make it accessible through maven2
> by providing the project metadata information to Maven2.
>
> Biojava Team - Is this possible?
>
> Thanks,
> Sandya
>
> On Wed, May 13, 2009 at 9:12 AM, Raphael Andr? Bauer <
> raphael.andre.bauer at gmail.com> wrote:
>
>> On Wed, May 13, 2009 at 1:21 PM, mac LEE <mauleemacx at gmail.com> wrote:
>> > Dear All,
>> > Hello. Is it possible to place the biojava jar into the maven 2
>> repository?
>>
>> You have to install the biojava.jar manually into your local repository:
>> http://maven.apache.org/guides/mini/guide-3rd-party-jars-local.html
>>
>> LaJolla is an application that uses that approach too... Maybe the
>> pom.xml of LaJolla is worth a look to see how it works...:
>>
>> http://lajolla.svn.sourceforge.net/viewvc/lajolla/trunk/lajolla/pom.xml?revision=350&view=markup
>>
>> Regards,
>>
>> Raphael
>>
>> >
>> > regards,
>> >
>> > jack Lee
>> >
>> > --
>> > Somewhere between heaven and hell
>> > mauleemacx at gmail.com
>> > _______________________________________________
>> > 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
>>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From niall at sgenomics.org  Thu May 14 13:55:31 2009
From: niall at sgenomics.org (Niall Haslam)
Date: Thu, 14 May 2009 15:55:31 +0200
Subject: [Biojava-l] Webservices clients in bio-java
Message-ID: <200905141555.31967.niall@sgenomics.org>

Hi all,

I was wondering if there was any interest in creating a set of maintained 
clients for popular webservices. Depending on how it goes and how feasible it 
is these could be included in biojava. I assume there are plenty of people 
writing and rewriting clients to these things. In the first instance we could 
just set up a repository for example code on using the servers.

I'm sure this would be a useful resource for java programmers. Unless someone 
wants to point me towards a pre-existing resource!

Niall.


From heuermh at acm.org  Thu May 14 16:34:53 2009
From: heuermh at acm.org (Michael Heuer)
Date: Thu, 14 May 2009 12:34:53 -0400 (EDT)
Subject: [Biojava-l] biojava on Maven2 repository
In-Reply-To: <59a41c430905140638r74554c10wb9c97dddd8f05b6b@mail.gmail.com>
Message-ID: <Pine.GSO.4.44.0905141219110.10420-100000@shell3.shore.net>

Hello Andreas,

The biojava jars can be manually uploaded to the central repository.  I
will do this for the 1.7 release.

Once the build migrates to maven, we can set up our own repository that
is mirrored to the central repository.   This is required if we have a
multi-module build, for example.  There may be a maven repo hosted at
open-bio.org already, I think the biomoby folks use one.

   michael


On Thu, 14 May 2009, Andreas Prlic wrote:

> I will have a look at this, once we have mavenized the biojava build
> process. In the meanwhile, perhaps somebody could post instructions
> how to add biojava to a local maven repository on the wiki?
>
> Andreas
>
>
>
> On Wed, May 13, 2009 at 7:04 AM, helpmedicine savelife
> <helpmedicine.savelife at gmail.com> wrote:
> > I agree it is possible by setting up in local repository (I did the same for
> > my project I am currently working), but now that biojava is being used by
> > many, I guess it it is a good time to to make it accessible through maven2
> > by providing the project metadata information to Maven2.
> >
> > Biojava Team - Is this possible?
> >
> > Thanks,
> > Sandya
> >
> > On Wed, May 13, 2009 at 9:12 AM, Raphael Andr? Bauer <
> > raphael.andre.bauer at gmail.com> wrote:
> >
> >> On Wed, May 13, 2009 at 1:21 PM, mac LEE <mauleemacx at gmail.com> wrote:
> >> > Dear All,
> >> > Hello. Is it possible to place the biojava jar into the maven 2
> >> repository?
> >>
> >> You have to install the biojava.jar manually into your local repository:
> >> http://maven.apache.org/guides/mini/guide-3rd-party-jars-local.html
> >>
> >> LaJolla is an application that uses that approach too... Maybe the
> >> pom.xml of LaJolla is worth a look to see how it works...:
> >>
> >> http://lajolla.svn.sourceforge.net/viewvc/lajolla/trunk/lajolla/pom.xml?revision=350&view=markup
> >>
> >> Regards,
> >>
> >> Raphael
> >>
> >> >
> >> > regards,
> >> >
> >> > jack Lee
> >> >
> >> > --
> >> > Somewhere between heaven and hell
> >> > mauleemacx at gmail.com
> >> > _______________________________________________
> >> > 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
> >>
> >
> > _______________________________________________
> > 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 May 15 03:27:05 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 14 May 2009 20:27:05 -0700
Subject: [Biojava-l] biojava on Maven2 repository
In-Reply-To: <Pine.GSO.4.44.0905141219110.10420-100000@shell3.shore.net>
References: <59a41c430905140638r74554c10wb9c97dddd8f05b6b@mail.gmail.com>
	<Pine.GSO.4.44.0905141219110.10420-100000@shell3.shore.net>
Message-ID: <59a41c430905142027g2de44f57s6ef0c48f8c877c17@mail.gmail.com>

That would be helpful, thanks,
Andreas

On Thu, May 14, 2009 at 9:34 AM, Michael Heuer <heuermh at acm.org> wrote:
> Hello Andreas,
>
> The biojava jars can be manually uploaded to the central repository. ?I
> will do this for the 1.7 release.
>
> Once the build migrates to maven, we can set up our own repository that
> is mirrored to the central repository. ? This is required if we have a
> multi-module build, for example. ?There may be a maven repo hosted at
> open-bio.org already, I think the biomoby folks use one.
>
> ? michael
>
>
> On Thu, 14 May 2009, Andreas Prlic wrote:
>
>> I will have a look at this, once we have mavenized the biojava build
>> process. In the meanwhile, perhaps somebody could post instructions
>> how to add biojava to a local maven repository on the wiki?
>>
>> Andreas
>>
>>
>>
>> On Wed, May 13, 2009 at 7:04 AM, helpmedicine savelife
>> <helpmedicine.savelife at gmail.com> wrote:
>> > I agree it is possible by setting up in local repository (I did the same for
>> > my project I am currently working), but now that biojava is being used by
>> > many, I guess it it is a good time to to make it accessible through maven2
>> > by providing the project metadata information to Maven2.
>> >
>> > Biojava Team - Is this possible?
>> >
>> > Thanks,
>> > Sandya
>> >
>> > On Wed, May 13, 2009 at 9:12 AM, Raphael Andr? Bauer <
>> > raphael.andre.bauer at gmail.com> wrote:
>> >
>> >> On Wed, May 13, 2009 at 1:21 PM, mac LEE <mauleemacx at gmail.com> wrote:
>> >> > Dear All,
>> >> > Hello. Is it possible to place the biojava jar into the maven 2
>> >> repository?
>> >>
>> >> You have to install the biojava.jar manually into your local repository:
>> >> http://maven.apache.org/guides/mini/guide-3rd-party-jars-local.html
>> >>
>> >> LaJolla is an application that uses that approach too... Maybe the
>> >> pom.xml of LaJolla is worth a look to see how it works...:
>> >>
>> >> http://lajolla.svn.sourceforge.net/viewvc/lajolla/trunk/lajolla/pom.xml?revision=350&view=markup
>> >>
>> >> Regards,
>> >>
>> >> Raphael
>> >>
>> >> >
>> >> > regards,
>> >> >
>> >> > jack Lee
>> >> >
>> >> > --
>> >> > Somewhere between heaven and hell
>> >> > mauleemacx at gmail.com
>> >> > _______________________________________________
>> >> > 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
>> >>
>> >
>> > _______________________________________________
>> > 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  Sat May 16 19:10:56 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sat, 16 May 2009 12:10:56 -0700
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <200905141555.31967.niall@sgenomics.org>
References: <200905141555.31967.niall@sgenomics.org>
Message-ID: <59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>

Hi Niall.

Which webservices did you have in mind? Something that got recently
discussed on biojava-dev is support Blast webservices...

Andreas

On Thu, May 14, 2009 at 6:55 AM, Niall Haslam <niall at sgenomics.org> wrote:
> Hi all,
>
> I was wondering if there was any interest in creating a set of maintained
> clients for popular webservices. Depending on how it goes and how feasible it
> is these could be included in biojava. I assume there are plenty of people
> writing and rewriting clients to these things. In the first instance we could
> just set up a repository for example code on using the servers.
>
> I'm sure this would be a useful resource for java programmers. Unless someone
> wants to point me towards a pre-existing resource!
>
> Niall.
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From niall at sgenomics.org  Tue May 19 07:36:38 2009
From: niall at sgenomics.org (Niall Haslam)
Date: Tue, 19 May 2009 09:36:38 +0200
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>
References: <200905141555.31967.niall@sgenomics.org>
	<59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>
Message-ID: <200905190936.38541.niall@sgenomics.org>

On Saturday 16 May 2009 21:10, Andreas Prlic wrote:
> Which webservices did you have in mind? Something that got recently
> discussed on biojava-dev is support Blast webservices...

I think BLAST would obviously be one of the main ones to get started with. I 
have a client at the moment which goes as far as fetching the job-id and 
generating a link to the results, which is as much as I need. If I remember 
correctly, the BLAST parser at the moment doesn't deal with the responses 
from the EBI webservices (which I used).

Mark makes a valid point about the choice of technology. I would also 
recommend jax-ws and probably axis2 as the frameworks, but note that some 
clients will probably require axis1_4. Although its not clear which e-mail 
discussion you are referring to - is it one on the biojava-dev mailing list?

A lot of the client code is autogenerated, and I guess one question would be 
should we include this in any repository that we make? I have been using the 
wtp plugin in eclipse and this takes some of the pain out of generating 
clients. Though it does generate some rather large source files.

Niall.


From markjschreiber at gmail.com  Tue May 19 14:05:11 2009
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Tue, 19 May 2009 22:05:11 +0800
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <93b45ca50905190702l2169d7f4qf200ed04f33c17b5@mail.gmail.com>
References: <200905141555.31967.niall@sgenomics.org>
	<59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>
	<200905190936.38541.niall@sgenomics.org>
	<93b45ca50905190702l2169d7f4qf200ed04f33c17b5@mail.gmail.com>
Message-ID: <93b45ca50905190705qec04c48yb7a81c9b0715a50e@mail.gmail.com>

Hi Niall -

There was a recent discussion of generated code on the list. A good solution
for webservices may be to put the wsdl and high level api in the repository
and let jax-ws tools autogenerate the client biolerplate code.

Mark

On 19 May 2009, 3:39 PM, "Niall Haslam" <niall at sgenomics.org> wrote:

On Saturday 16 May 2009 21:10, Andreas Prlic wrote: > Which webservices did
you have in mind? Someth...
I think BLAST would obviously be one of the main ones to get started with. I
have a client at the moment which goes as far as fetching the job-id and
generating a link to the results, which is as much as I need. If I remember
correctly, the BLAST parser at the moment doesn't deal with the responses
from the EBI webservices (which I used).

Mark makes a valid point about the choice of technology. I would also
recommend jax-ws and probably axis2 as the frameworks, but note that some
clients will probably require axis1_4. Although its not clear which e-mail
discussion you are referring to - is it one on the biojava-dev mailing list?

A lot of the client code is autogenerated, and I guess one question would be
should we include this in any repository that we make? I have been using the
wtp plugin in eclipse and this takes some of the pain out of generating
clients. Though it does generate some rather large source files.

Niall. _______________________________________________ Biojava-l mailing
list - Biojava-l at lists.o...


From aaron_b_a at yahoo.com  Wed May 20 01:12:28 2009
From: aaron_b_a at yahoo.com (Aaron Brata Aditama)
Date: Tue, 19 May 2009 18:12:28 -0700 (PDT)
Subject: [Biojava-l] How to write pairwiseAlignment output in my own format?
Message-ID: <248630.13325.qm@web56107.mail.re3.yahoo.com>

There is a default output method in NeedlemanWunsch Class, and it writes output in its own format. How can I write output of paiwire alignment in my own format? For example, I want to get the aligned sequences and the score only.

Aaron Brata Aditama


      


From mike.thon at gmail.com  Thu May 21 18:06:56 2009
From: mike.thon at gmail.com (Michael Thon)
Date: Thu, 21 May 2009 20:06:56 +0200
Subject: [Biojava-l] CRC64Checksum example
Message-ID: <8EEAB8FC-4D9D-4417-90EC-DC9E4329648C@gmail.com>

Hi all - I need to compute a crc64 for some sequences and I thought  
that org.biojavax.utils.CRC64Checksum could do this for me.  Java  
throws a NullPointerException when I try to do:
   crc.update(seq);
where crc is a CRC64Checksum object and seq is a String containing a  
protein sequence.

Does anyone have some example code showing how to compute a crc using  
this class?
Many thanks
Mike Thon


From holland at eaglegenomics.com  Thu May 21 19:11:14 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Thu, 21 May 2009 20:11:14 +0100
Subject: [Biojava-l] CRC64Checksum example
In-Reply-To: <8EEAB8FC-4D9D-4417-90EC-DC9E4329648C@gmail.com>
References: <8EEAB8FC-4D9D-4417-90EC-DC9E4329648C@gmail.com>
Message-ID: <1242933074.29986.16.camel@buzzybee>

Could you provide the line you used to instantiate the CRC64Checksum
object, and the value that you're passing to update(seq), and the full
stacktrace you get when it fails? That'll all help us work out what's
wrong.

cheers,
Richard

On Thu, 2009-05-21 at 20:06 +0200, Michael Thon wrote:
> Hi all - I need to compute a crc64 for some sequences and I thought  
> that org.biojavax.utils.CRC64Checksum could do this for me.  Java  
> throws a NullPointerException when I try to do:
>    crc.update(seq);
> where crc is a CRC64Checksum object and seq is a String containing a  
> protein sequence.
> 
> Does anyone have some example code showing how to compute a crc using  
> this class?
> Many thanks
> Mike Thon
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/




From paolo.romano at istge.it  Wed May 27 16:15:09 2009
From: paolo.romano at istge.it (Paolo Romano)
Date: Wed, 27 May 2009 18:15:09 +0200
Subject: [Biojava-l] NETTAB 2009: Last Call for Participation
Message-ID: <200905271630.n4RGU87M030436@ibm43p.biotech.ist.unige.it>


Last Call for Participation

NETTAB 2009 Workshop on
"Technologies, Tools and Applications for 
Collaborative and Social Bioinformatics Research and Development"
with a Special Session on:
"Methods and Tools for RNA Structure and Functional Analysis"

June 10-13, 2009
Department of Computer Science, University of Catania, Italy

http://www.nettab.org/2009/


KEYNOTE TALKS

RNA WikiProject: Community annotation of RNA families
Alex Bateman, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

Who are you? Managing collaborative digital 
identities in bioinformatics with myExperiment
Duncan Hull, School of Chemistry, University of Manchester, Manchester, UK.

Semantically Integrated eCommunities in 
Biomedicine: Next-Generation Models of Biomedical Communication
Tim Clark, Director of Informatics, MassGeneral 
Institute for Neurodegenerative Disease Neurology 
Research Department, Massachusetts General Hospital, Boston, USA.

Bacterial Phylogeny and Taxonomy in the High-Throughput Sequencing World
Gabriel Valiente, Technical University of 
Catalonia, Department of Software, Barcelona, Spain.

Non coding RNAs (title to be confirmed)
Doron Betel, MSKCC - Computational Biology Center, New York, USA .


SELECTED ORAL COMMUNICATIONS

The DC-THERA Directory: A Knowledge Management 
System to Support Collaboration on Dendritic Cell and Immunology Research
Michaela Guendel, Ciro Scognamiglio, Marco Brandizi and Andrea Splendiani

Bioinformatics Experimentation in a New 
Agent-Based Infrastructure OpenKnowledge
Dietlind Gerloff, Xueping Quan, Adrian de 
Pinninck, Paolo Besana, Siu-wai Leung, Marco Schorlemmer and David Robertson

Abstraction based cooperation for the design of bioinformatics workflows
Fr?d?ric Cadier and Philippe Picouet

Biomedical applications in the EELA-2 Project
Leandro N Ciuffo and Rafael Mayo

Make Histri: collaborative curation of exchange 
histories of bacterial and archaeal type strains
Bert Verslyppe, Paul De Vos, Bernard De Baets and Peter Dawyndt

SBMM Assistant: Social Pathway Annotation
Ismael Navas-Delgado, Alejandro del 
Real-Chicharro, Francisca S?nchez-Jim?nez and Jose F Aldana Montes

GePh-CARD: an information exchange application 
for an Hub & Spoke Network for Skeletal Dysplasias
Marina Mordenti and Luca Sangiorgi

ProDaMa-C: a collaborative web application to 
generate specialized protein structure datasets
Giuliano Armano and Andrea Manconi

RNA tertiary structure prediction with ModeRNA
Magdalena Musielak, Kristian Rother, Tomasz Puton and Janusz M. Bujnicki

Improved heuristic for pairwise RNA secondary structure prediction
Olivier Perriquet and Pedro Barahona

Analysing the microRNA-17-92/Myc/E2F/RB Compound 
Toggle Switch by Theorem Proving
Giampaolo Bella and Pietro Li?

Mapping miRNA genes on human fragile sites and translocation breakpoints
Alfredo Ferro, rosalba giugno, Alessandro Lagan?, 
Alfredo Pulvirenti and Francesco Russo

MicroRNA.gr: A suite of web based tools for elucidating microRNA function
Giorgio L. Papadopoulos, Panagiotis Alexiou, 
Manolis Maragkakis, Martin Reczko and Artemis G. Hatzigeorgiou

miRScape: A Cytoscape Plugin to Annotate Biological Networks with microRNAs
Alfredo Ferro, rosalba giugno, Alessandro Lagan?, 
Misael Mongiov?, Giuseppe Pigola, Alfredo 
Pulvirenti, Gary Bader and Dennis Shasha


POSTERS

A web site supporting collaborative activities 
within the Italian Network for Oncology Bioinformatics
Silvia Giuliani, Elda Rossi, Stefania Parodi and Paolo Romano

Prediction of human targets for viral encoded microRNAs
Alessandro Lagan?, Stefano Forte, Rosalba Giugno, 
Alfredo Pulvirenti and Alfredo Ferro

Genome-wide microRNA target gene identification 
and annotation using multiple prediction algorithms
Dario Corrada, Luciano Milanesi and Daniele Catalucci

Design of highly specific synthetic miRNAs
Alessandro Lagan?, Stefano Forte, Angela Papa, 
Rosalba Giugno, Alfredo Pulvirenti, Dennis Shasha and Alfredo Ferro



NETTAB '09 - Ninth International Workshop on 
Network Tools and Applications in Biology
10-13 June 2009, Catania, Italy
http://www.nettab.org/2009/

Paolo Romano (paolo.romano at istge.it)
Bioinformatics
National Cancer Research Institute (IST)




From jimp at compbio.dundee.ac.uk  Thu May 28 12:29:19 2009
From: jimp at compbio.dundee.ac.uk (James Procter)
Date: Thu, 28 May 2009 13:29:19 +0100
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <93b45ca50905190705qec04c48yb7a81c9b0715a50e@mail.gmail.com>
References: <200905141555.31967.niall@sgenomics.org>	<59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>	<200905190936.38541.niall@sgenomics.org>	<93b45ca50905190702l2169d7f4qf200ed04f33c17b5@mail.gmail.com>
	<93b45ca50905190705qec04c48yb7a81c9b0715a50e@mail.gmail.com>
Message-ID: <4A1E839F.2050700@compbio.dundee.ac.uk>

Hi All.

Mark Schreiber wrote:
> There was a recent discussion of generated code on the list. A good solution
> for webservices may be to put the wsdl and high level api in the repository
> and let jax-ws tools autogenerate the client biolerplate code.

Just to clarify - by high-level API you mean the interface to the code
that takes biojava objects as arguments and translates them into
parameters for the service and vice versa for the results ?

With regard to the recent(ish) discussion about modularisation in BJ3,
I'd suggest that a module is created for each distinct WSDL containing
the glue code for connecting BJ objects with the boilerplate code. The
glue code implements factory methods to generate instances of
appropriate BJ service APIs, which are defined in a core BJ module. This
means that the WSDL + API implementation is decoupled from the BJ
service API.

Does that make sense (and/or am I simply stating the obvious here) ?

Jim.

-- 
-------------------------------------------------------------------
J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.


From willishf at ufl.edu  Thu May 28 13:35:49 2009
From: willishf at ufl.edu (Scooter Willis)
Date: Thu, 28 May 2009 09:35:49 -0400
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <4A1E839F.2050700@compbio.dundee.ac.uk>
References: <200905141555.31967.niall@sgenomics.org>
	<59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>
	<200905190936.38541.niall@sgenomics.org>
	<93b45ca50905190702l2169d7f4qf200ed04f33c17b5@mail.gmail.com>
	<93b45ca50905190705qec04c48yb7a81c9b0715a50e@mail.gmail.com>
	<4A1E839F.2050700@compbio.dundee.ac.uk>
Message-ID: <7ceb4beb0905280635g7bbb028dw9c5d69a9290b5a16@mail.gmail.com>

Jim

I agree. I am planning on doing some testing of  a couple BLAST web services
interfaces(assuming more than one exists) and see what they truly have in
common and see how that would impact a BJ3 front end to multiple providers.
My assumption is that they will be the same. I noticed on the NCBI Blast
implementations the user was required to pass their email address as part of
the web service call. They are concerned with abuse from external processes
and they only allow one sequence per request.

>From wikipedia the following are listed as BLAST resources where more than
one may offer a web service interface. Should BioJava3 try and support more
than one?

Thanks

Scooter

Variations of BLAST

   - WU-BLAST <http://blast.wustl.edu/> ? the original gapping BLAST with
   statistics, developed and maintained by Warren Gish at Washington
   University in St.
Louis<http://en.wikipedia.org/wiki/Washington_University_in_St._Louis>
   - EBI's BLAST Services <http://www.ebi.ac.uk/Tools/blast> ?
EBI's<http://en.wikipedia.org/wiki/European_Bioinformatics_Institute>main
blast services page.
   - FSA-BLAST <http://www.fsa-blast.org/> ? a new, faster but still
   accurate version of NCBI BLAST based on recently published algorithmic
   improvements
   - NBIC mpiBLAST <http://services.nbic.nl:4080/bb/cgi-bin/bb_login.cgi> ?
   at the Netherlands Bioinformatics Centre
   - Parallel BLAST<http://www-users.cs.umn.edu/%7Erangwala/final_bglBLAST.pdf>?
a dual scheduling BLAST tested on the Blue Gene/L
   - mpiBLAST <http://www.mpiblast.org/> ? open-source parallel BLAST
   - A/G BLAST <http://developer.apple.com/darwin/projects/blast/> ?
   implementation for PowerPC G4/G5 processors and Mac OS X, from Apple
   Computer <http://en.wikipedia.org/wiki/Apple_Computer>'s Advanced
   Computation Group<http://en.wikipedia.org/wiki/Advanced_Computation_Group>and
   Genentech <http://en.wikipedia.org/wiki/Genentech>.
   - STRAP <http://3d-alignment.eu/> ? the protein workbench
STRAP<http://www.charite.de/bioinf/strap/>contains a comfortable BLAST
front-end with a cache for BLAST results

 [edit<http://en.wikipedia.org/w/index.php?title=BLAST&action=edit&section=13>
] Commercial versions

   - ThermoBLAST by DNA Software
Inc.<http://dnasoftware.com/ThermoBLAST/tabid/110/Default.aspx>? scans
entire genomes quickly and accurately combing the power of BLAST
   with the most advanced thermodynamics parameters
   - PatternHunter<http://www.bioinformaticssolutions.com/products/ph/index.php>?
an alternative software which provides similar functionality to BLAST
   while claiming increased speed and sensitivity
   - KoriBlast <http://www.korilog.com/products> ? a reliable graphical
   environment dedicated to sequence data mining. KoriBlast combines Blast
   searches with advanced data management capabilities and a state-of-the-art
   graphical user interface.
   - microbial identification BLAST <http://www.sepsitest-blast.de/> ? a
   quality controlled database for in-vitro diagnostics. SepsiTest combines
   broad-range-PCR using ultra-pure reagents with Blast searches in a quality
   controlled environment.




On Thu, May 28, 2009 at 8:29 AM, James Procter <jimp at compbio.dundee.ac.uk>wrote:

> Hi All.
>
> Mark Schreiber wrote:
> > There was a recent discussion of generated code on the list. A good
> solution
> > for webservices may be to put the wsdl and high level api in the
> repository
> > and let jax-ws tools autogenerate the client biolerplate code.
>
> Just to clarify - by high-level API you mean the interface to the code
> that takes biojava objects as arguments and translates them into
> parameters for the service and vice versa for the results ?
>
> With regard to the recent(ish) discussion about modularisation in BJ3,
> I'd suggest that a module is created for each distinct WSDL containing
> the glue code for connecting BJ objects with the boilerplate code. The
> glue code implements factory methods to generate instances of
> appropriate BJ service APIs, which are defined in a core BJ module. This
> means that the WSDL + API implementation is decoupled from the BJ
> service API.
>
> Does that make sense (and/or am I simply stating the obvious here) ?
>
> Jim.
>
> --
> -------------------------------------------------------------------
> J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No. SC015096.
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>



From markjschreiber at gmail.com  Thu May 28 14:11:36 2009
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Thu, 28 May 2009 22:11:36 +0800
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <93b45ca50905280709q6896f96fg598276de20222440@mail.gmail.com>
References: <200905141555.31967.niall@sgenomics.org>
	<59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>
	<200905190936.38541.niall@sgenomics.org>
	<93b45ca50905190702l2169d7f4qf200ed04f33c17b5@mail.gmail.com>
	<93b45ca50905190705qec04c48yb7a81c9b0715a50e@mail.gmail.com>
	<4A1E839F.2050700@compbio.dundee.ac.uk>
	<93b45ca50905280709q6896f96fg598276de20222440@mail.gmail.com>
Message-ID: <93b45ca50905280711q222a0c90ob93a3098ff1b97c7@mail.gmail.com>

By high level API I mean anything not machine generated. That could be
classes that use biojava objects or a more humanized or smarter interface to
the boilerplate code.

- Mark

On 28 May 2009, 2:53 PM, "James Procter" <jimp at compbio.dundee.ac.uk> wrote:

Hi All.

Mark Schreiber wrote: > There was a recent discussion of generated code on
the list. A good solutio...
Just to clarify - by high-level API you mean the interface to the code
that takes biojava objects as arguments and translates them into
parameters for the service and vice versa for the results ?

With regard to the recent(ish) discussion about modularisation in BJ3,
I'd suggest that a module is created for each distinct WSDL containing
the glue code for connecting BJ objects with the boilerplate code. The
glue code implements factory methods to generate instances of
appropriate BJ service APIs, which are defined in a core BJ module. This
means that the WSDL + API implementation is decoupled from the BJ
service API.

Does that make sense (and/or am I simply stating the obvious here) ?

Jim.

--
-------------------------------------------------------------------
J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

_______________________________________________ Biojava-l mailing list -
Biojava-l at lists.open-bio....


From andreas at sdsc.edu  Thu May 28 14:59:17 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 28 May 2009 07:59:17 -0700
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <4A1E839F.2050700@compbio.dundee.ac.uk>
References: <200905141555.31967.niall@sgenomics.org>
	<59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>
	<200905190936.38541.niall@sgenomics.org>
	<93b45ca50905190702l2169d7f4qf200ed04f33c17b5@mail.gmail.com>
	<93b45ca50905190705qec04c48yb7a81c9b0715a50e@mail.gmail.com>
	<4A1E839F.2050700@compbio.dundee.ac.uk>
Message-ID: <59a41c430905280759i503719eaxd2ac64436154be2d@mail.gmail.com>

makes sense and fits to the more detailed discussion we are having on
biojava-dev right now.

A


On Thu, May 28, 2009 at 5:29 AM, James Procter
<jimp at compbio.dundee.ac.uk> wrote:
> Hi All.
>
> Mark Schreiber wrote:
>> There was a recent discussion of generated code on the list. A good solution
>> for webservices may be to put the wsdl and high level api in the repository
>> and let jax-ws tools autogenerate the client biolerplate code.
>
> Just to clarify - by high-level API you mean the interface to the code
> that takes biojava objects as arguments and translates them into
> parameters for the service and vice versa for the results ?
>
> With regard to the recent(ish) discussion about modularisation in BJ3,
> I'd suggest that a module is created for each distinct WSDL containing
> the glue code for connecting BJ objects with the boilerplate code. The
> glue code implements factory methods to generate instances of
> appropriate BJ service APIs, which are defined in a core BJ module. This
> means that the WSDL + API implementation is decoupled from the BJ
> service API.
>
> Does that make sense (and/or am I simply stating the obvious here) ?
>
> Jim.
>
> --
> -------------------------------------------------------------------
> J. B. Procter ?(ENFIN/VAMSAS) ?Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764 ?http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No. SC015096.
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From jimp at compbio.dundee.ac.uk  Thu May 28 15:14:51 2009
From: jimp at compbio.dundee.ac.uk (James Procter)
Date: Thu, 28 May 2009 16:14:51 +0100
Subject: [Biojava-l] Webservices clients in bio-java
In-Reply-To: <7ceb4beb0905280635g7bbb028dw9c5d69a9290b5a16@mail.gmail.com>
References: <200905141555.31967.niall@sgenomics.org>	
	<59a41c430905161210u2b79a402m643eb47704bc06e7@mail.gmail.com>	
	<200905190936.38541.niall@sgenomics.org>	
	<93b45ca50905190702l2169d7f4qf200ed04f33c17b5@mail.gmail.com>	
	<93b45ca50905190705qec04c48yb7a81c9b0715a50e@mail.gmail.com>	
	<4A1E839F.2050700@compbio.dundee.ac.uk>
	<7ceb4beb0905280635g7bbb028dw9c5d69a9290b5a16@mail.gmail.com>
Message-ID: <4A1EAA6B.7020202@compbio.dundee.ac.uk>

Hi Mark, and Scooter.

Mark Schreiber wrote:
> By high level API I mean anything not machine generated. That could be
> classes that use biojava objects or a more humanized or smarter
> interface to the boilerplate code.

ah. yes. that's what I thought. I'd really advocate keeping the Biojava
object adaptor glue for the autogenerated code separate from the core.
This is because (as I'm sure you know) there are no real object design
standards for bioinformatic services (apart from BioMOBY..) - so the
adaptor code is always going to be specific to the WSDL.

Scooter Willis wrote:
> I agree. I am planning on doing some testing of  a couple BLAST web
> services interfaces(assuming more than one exists) and see what they
> truly have in common and see how that would impact a BJ3 front end to
> multiple providers. My assumption is that they will be the same.
Of course, the actual functionality provided by all the servers will be
more or less the same (i.e. inputs and outputs), but servers will differ
in how they wrap the input and result data, how they support parameters,
and how they deal with polling and result retrieval (if they are at all
asynchronous).

 I
> noticed on the NCBI Blast implementations the user was required to pass
> their email address as part of the web service call. They are concerned
> with abuse from external processes and they only allow one sequence per
> request.
Yes. The NCBI has an automatic blacklisting system - too many requests
in a short space of time from a single IP will result in denial of
service for X (24?) hours. I'm not sure how something like Taverna
manages this kind of thing, but I expect this kind of user attribute
will have to be supported in the core web service model - that could
also provide authentication management support too (when users are using
secure or authenticated HTTP connections).


> From wikipedia the following are listed as BLAST resources where more
> than one may offer a web service interface. Should BioJava3 try and
> support more than one?
I would pick the two or three most popular/capable/geographically
widespread services to implement clients for, and then choose your
favourite one to start with (EBI,NCBI, and perhaps one in Japan - e.g.
http://xml.nig.ac.jp/wsdl/Blast.wsdl).

Implementing clients for two or three allows users a nice choice, and
should also capture most variation in the input/output and polling model
that is used. If any more need to be supported, then by then it should
be pretty clear how to go about implementing an API instance for a new WSDL.

You might also want to consider generalising the high-level interface to
non-Blast sequence search services, since they all take and return more
or less the same kind of data and results.

I suspect this discussion should move to the biojava-dev list!

Jim.




From jp at javaclass.co.uk  Thu May 28 18:54:42 2009
From: jp at javaclass.co.uk (JP)
Date: Thu, 28 May 2009 19:54:42 +0100
Subject: [Biojava-l] dN/dS ratio calculation biojava
Message-ID: <4adc29060905281154i6db465edt8c154bb30863296f@mail.gmail.com>

Hi there - is there a class or method which finds the dN/dS ratio
(nonsynonymous/synonymous rate ratio) for two sequences ?

Many Thanks
JP


From ayates at ebi.ac.uk  Fri May 29 08:23:34 2009
From: ayates at ebi.ac.uk (Andy Yates)
Date: Fri, 29 May 2009 09:23:34 +0100
Subject: [Biojava-l] dN/dS ratio calculation biojava
In-Reply-To: <4adc29060905281154i6db465edt8c154bb30863296f@mail.gmail.com>
References: <4adc29060905281154i6db465edt8c154bb30863296f@mail.gmail.com>
Message-ID: <4A1F9B86.6080309@ebi.ac.uk>

Hi JP,

No there isn't a class to calculate dN/dS. At a basic level dN/dS is a
very easy ratio to calculate if you take the very basic approach of
sequences of exact lengths. The basics of it are available from:

http://pubmlst.org/software/analysis/start/manual/dsdn.shtml

The best package I know of to calculate the rates though is codeml. It's
a very awkward program to run but it can be done & will produce the best
results. I can say for sure that the Ensembl Compara team use it to
calculate dN/dS rates for their homologous protein sets.

Hope that helps,

Andy

P.S. I say all of this from personal experience when I wrote a very
basic calculator using BioJava (and I don't know where the code got to).
The amount of work to produce that code vs. running a third party
application just makes it more cost effective to go for the 3rd party app

JP wrote:
> Hi there - is there a class or method which finds the dN/dS ratio
> (nonsynonymous/synonymous rate ratio) for two sequences ?
> 
> Many Thanks
> JP
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From jogoodma at indiana.edu  Tue May 12 20:40:40 2009
From: jogoodma at indiana.edu (Josh Goodman)
Date: Tue, 12 May 2009 20:40:40 -0000
Subject: [Biojava-l] FASTA parsing bug ?
In-Reply-To: <49F822C6.1020809@eaglegenomics.com>
References: <4adc29060904280701q5d3dc760mb018f6b38a9e056f@mail.gmail.com>
	<49F71258.3060103@eaglegenomics.com>
	<4adc29060904280759q4b27a4eembd28974d46199532@mail.gmail.com>
	<49F71EF5.90702@eaglegenomics.com>
	<Pine.LNX.4.64.0904281552580.15441@conger.bio.indiana.edu>
	<49F822C6.1020809@eaglegenomics.com>
Message-ID: <4A09D8DC.1050307@indiana.edu>

Hi all,

I apologize for missing the "next day or so" window but here is my patch.  I'm attaching a patch
file for FastaFormat.java (1.7 tagged branch), the full source file, and a test class.  It seems to
work and performance is on par with the previous approach in my measurements.  One problem that I
couldn't quite figure out a way around is with the guessSymbolTokenization(BufferedInputStream
stream) method.  If the first sequence of the stream has a header length plus first line of sequence
length longer than 2000 characters it will fail to reset properly.

Cheers,
Josh

Richard Holland wrote:
> I'd love to see a proper solution to this that doesn't involve upping
> the read-ahead limit. I was aware that it might be the issue, but had no
> idea why it was not failing for other similar long sequences. I look
> forward to seeing your suggested fix!
> 
> thanks,
> Richard
> 
> Josh Goodman wrote:
>> Hi Richard and JP,
>>
>> I think I can be of some help as I'm the FlyBase developer responsible for 
>> generating these troublesome FASTA files :-).  The cause of this problem 
>> appears to be the description line length for the record FBpp0145470.
>>
>> The trouble lies in org.biojavax.bio.seq.io.FastaFormat in the while loop 
>> at line 196.  Biojava correctly reads in FBpp0145468 but throws an error 
>> when trying to parse FBpp0145469.  There is nothing wrong in FBpp0145469 
>> but when biojava reaches the end of the sequence it reads in the header 
>> for the next record (FBpp0145470).  It then tries to reset the 
>> BufferedReader to the start of FBpp0145470 but that is where the exception 
>> is thrown because line 197 sets the read ahead limit to 500 characters and 
>> the reader.readLine() command exceeds that limit.
>>
>> What isn't obvious to me is why other large definition lines that precede 
>> that line don't throw the same error (e.g. FBpp0157909).  I guess the 
>> javadoc on BufferedReader.mark() does say "may fail" but I assumed it 
>> would be more predictable than that.
>>
>> The file in question can be downloaded from 
>> ftp://ftp.flybase.net/genomes/Drosophila_grimshawi/dgri_r1.3_FB2008_07/fasta/dgri-all-translation-r1.3.fasta.gz.
>>
>> If there is interest in a solution that doesn't involve simply upping the 
>> read ahead limit I can put a patch file together in the next day or so.
>>
>> Cheers,
>> Josh
>>
>> On Tue, 28 Apr 2009, Richard Holland wrote:
>>
>>> You're right, doesn't look like newlines.
>>>
>>> The "Mark invalid" happens when the parser looks too far ahead in the
>>> file attempting to seek out the next valid sequence to parse. I'm not
>>> sure why this is happening.
>>>
>>> I don't have the time to test right now but if you could post the link
>>> to where someone could download the same FASTA as you're using, then it
>>> would make it possible for someone else to investigate in more detail.
>>>
>>> thanks,
>>> Richard
>>>
>>> JP wrote:
>>>> Thanks Richard for your prompt reply.
>>>>
>>>> I will not attach the fasta file I am parsing (12MB) its
>>>> dgri-all-translation-r1.3.fasta from the flybase project.
>>>>
>>>> If the file had any extra new lines I would see them when I loaded it in
>>>> a text editor - no ?
>>>>
>>>> I implemented the whole thing without using Biojava (for this part)
>>>>
>>>>     fr = new FileReader(fastaProteinFileName);
>>>>     br = new BufferedReader(fr);
>>>>     String fastaLine;
>>>>     String startAccession = '>' + accessionId.trim();
>>>>     String fastaEntry = "";
>>>>     boolean record = false;
>>>>     while ((fastaLine = br.readLine()) != null) {
>>>>         fastaLine = fastaLine.trim() + '\n';
>>>>         if (fastaLine.startsWith(startAccession)) {
>>>>             record = true;
>>>>         } else if (record && fastaLine.startsWith(">")) {
>>>>             record = false;
>>>>             break;
>>>>         }
>>>>         if (record) {
>>>>             fastaEntry += fastaLine;
>>>>         }
>>>>     }
>>>>
>>>>
>>>> Notice - I do not use regex - since I'd need to read the whole file and
>>>> then regex upon it (if the record is the first one - I just read that one).
>>>>
>>>> Cheers
>>>> JP
>>>>
>>>>
>>>> On Tue, Apr 28, 2009 at 3:27 PM, Richard Holland
>>>> <holland at eaglegenomics.com <mailto:holland at eaglegenomics.com>> wrote:
>>>>
>>>>     The "Mark invalid" exception is indicating that the parser has gone too
>>>>     far ahead in the file looking for a valid header. I'm not sure why but
>>>>     looking at your original query, there may be extra newlines embedded
>>>>     into your FASTA header line? That would definitely confuse it.
>>>>
>>>>     The parser is not able to currently pull out just one sequence - in
>>>>     effect this is a search facility, which it doesn't have. :(
>>>>
>>>>     thanks,
>>>>     Richard
>>>>
>>>>     JP wrote:
>>>>     > Hi all at BioJava,
>>>>     >
>>>>     > I am trying to parse several FASTA files using the following code:
>>>>     >
>>>>     > fr = new FileReader(fastaProteinFileName);
>>>>     >> br = new BufferedReader(fr);
>>>>     >>
>>>>     >> RichSequenceIterator protIter = IOTools.readFastaProtein(br, null);
>>>>     >> while (protIter.hasNext()) {
>>>>     >>      BioEntry bioEntry = protIter.nextBioEntry();
>>>>     >>      System.out.println (fastaProteinFileName + " == " +
>>>>     accessionId + " =
>>>>     >> " + bioEntry.getAccession());
>>>>     >> }
>>>>     >
>>>>     >
>>>>     > At particular points in my fasta file - I get the following exception:
>>>>     >
>>>>     > 14:53:42,546 ERROR FastaFileProcessing  - File parsing exception (from
>>>>     >> biojava library)
>>>>     >> org.biojava.bio.BioException: Could not read sequence
>>>>     >>     at
>>>>     >>
>>>>     org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
>>>>     >>     at
>>>>     >>
>>>>     org.biojavax.bio.seq.io.RichStreamReader.nextBioEntry(RichStreamReader.java:99)
>>>>     >>     at
>>>>     >>
>>>>     edu.imperial.msc.orthologue.fasta.FastaFileProcessing.getProteinSequenceFromFASTAFile(FastaFileProcessing.java:60)
>>>>     >>     at
>>>>     >>
>>>>     edu.imperial.msc.orthologue.core.OrthologueFinder.getFASTAEntries(OrthologueFinder.java:64)
>>>>     >>     at
>>>>     >>
>>>>     edu.imperial.msc.orthologue.core.OrthologueFinder.<init>(OrthologueFinder.java:51)
>>>>     >>     at
>>>>     >>
>>>>     edu.imperial.msc.orthologue.launcher.OrthologueFinderLauncher.main(OrthologueFinderLauncher.java:60)
>>>>     >> Caused by: java.io.IOException: Mark invalid
>>>>     >>     at java.io.BufferedReader.reset(Unknown Source)
>>>>     >>     at
>>>>     >>
>>>>     org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:202)
>>>>     >>     at
>>>>     >>
>>>>     org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
>>>>     >>     ... 5 more
>>>>     >
>>>>     >
>>>>     > Interestingly if I delete the header portion of the header line (from
>>>>     > type=protein... till the end of the line ...Dgri;)
>>>>     >
>>>>     >> FBpp0145468 type=protein;
>>>>     >>
>>>>     loc=scaffold_15252:join(13219687..13219727,13219972..13220279,13220507..13220798,13220861..13221180,13221286..13221467,13222258..13222629,13226331..13226463,13226531..13226658);
>>>>     >> ID=FBpp0145468; name=Dgri\GH11562-PA; parent=FBgn0119042,FBtr0146976;
>>>>     >> dbxref=FlyBase:FBpp0145468,FlyBase_Annotation_IDs:GH11562-PA;
>>>>     >> MD5=c8dc38c7197a0d3c93c78b08059e2604; length=591; release=r1.3;
>>>>     >> species=Dgri;
>>>>     >>
>>>>     >
>>>>     > It works - but I have a number of these exceptions (and I do not
>>>>     want to
>>>>     > edit the original data).  Mind you I have longer headers in my
>>>>     file which
>>>>     > are parsed OK (strange!).
>>>>     >
>>>>     > Any ideas anyone ?  Alternatively - is there a better way how to
>>>>     get ONE
>>>>     > SINGLE sequence from the whole fasta file give that I have the
>>>>     accession id
>>>>     > (FBpp0145468) ?
>>>>     >
>>>>     > Many Thanks
>>>>     > JP
>>>>     > _______________________________________________
>>>>     > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>     <mailto:Biojava-l at lists.open-bio.org>
>>>>     > http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>     >
>>>>
>>>>     --
>>>>     Richard Holland, BSc MBCS
>>>>     Finance Director, Eagle Genomics Ltd
>>>>     T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>>>>     <mailto:holland at eaglegenomics.com>
>>>>     http://www.eaglegenomics.com/
>>>>
>>>>
>>> -- 
>>> Richard Holland, BSc MBCS
>>> Finance Director, Eagle Genomics Ltd
>>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>>> http://www.eaglegenomics.com/
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
> 
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