It's down until chris gets to the datacenter.
On Fri, 14 May 2004, Thomas Down wrote:
> I'm not getting any response from the WebCVS machine at the moment.
> Other open-bio sites are working fine, so I guess it's not a network
> problem. Anybody else know about this?
>
> Thomas.
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev@biojava.org
> http://biojava.org/mailman/listinfo/biojava-dev
>
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From bruno.aranda at ebiointel.com Fri May 14 08:31:59 2004
From: bruno.aranda at ebiointel.com (Bruno Aranda - eBioIntel)
Date: Fri May 14 08:35:48 2004
Subject: [Biojava-dev] SNP analyses in Biojava2
Message-ID: <3080.212.170.16.36.1084537919.squirrel@central.ebiointel.com>
Hello everybody,
We are endeavouring a project about SNP and related stuff and, of course,
it will be using BioJava. It is a long term project and we are now in
early design. What I would like it to do is to analyze the SNPs with
summary statistics, neutrality tests, coalescent and other things. As we
are just in the earliest thoughts and it will be using J2SE 1.5 I think
that all this SNP api would be a good contribution to Biojava 2. So, is
there any specification about, for instance, how to do statistical
equation classes in Biojava 2 (just the classes with the equations to
process statistics)... it is too early for this? Of course I can do it
aside BioJava but, if I make all these classes with the bjv2 phylosophy,
then it will be easier to include them...
Any appreciation is welcome,
Bruno Aranda
From matthew_pocock at yahoo.co.uk Fri May 14 09:05:28 2004
From: matthew_pocock at yahoo.co.uk (Matthew Pocock)
Date: Fri May 14 09:19:06 2004
Subject: [Biojava-dev] SNP analyses in Biojava2
In-Reply-To: <3080.212.170.16.36.1084537919.squirrel@central.ebiointel.com>
References: <3080.212.170.16.36.1084537919.squirrel@central.ebiointel.com>
Message-ID: <40A4C418.3090505@yahoo.co.uk>
Hi,
Bruno Aranda - eBioIntel wrote:
>Hello everybody,
>
>We are endeavouring a project about SNP and related stuff and, of course,
>it will be using BioJava. It is a long term project and we are now in
>early design. What I would like it to do is to analyze the SNPs with
>summary statistics, neutrality tests, coalescent and other things. As we
>are just in the earliest thoughts and it will be using J2SE 1.5 I think
>that all this SNP api would be a good contribution to Biojava 2. So, is
>
>
Sounds interesting. SNPs are definitely something I'd like us to support
- biojava 2 is about data integration and handling many more types of
data, so SNPs are a good example.
>there any specification about, for instance, how to do statistical
>equation classes in Biojava 2 (just the classes with the equations to
>process statistics)... it is too early for this? Of course I can do it
>
>
We don't have anything yet. This is a perfect time to find out what
people would need. For example, what classes do you want to see? What
API would you like to talk to for the statistical equations? Would you
like to be able to pass in a string like "p(x) = p(x | y)" and have it
produce code? Would you pass around Strategy objects for different
probability distributions? And so on.
>aside BioJava but, if I make all these classes with the bjv2 phylosophy,
>then it will be easier to include them...
>
>
Agreed. At the moment I've got basic data integration and query working,
and a 1st cut at the biological features API. Everything else is up for
grabs. The core design principles are now in the README on the trunk,
and scatterd on different package.html files in the source.
Matthew
>Any appreciation is welcome,
>
>Bruno Aranda
>
>
>_______________________________________________
>biojava-dev mailing list
>biojava-dev@biojava.org
>http://biojava.org/mailman/listinfo/biojava-dev
>
>
>
From matthew.pocock at ncl.ac.uk Fri May 14 11:20:02 2004
From: matthew.pocock at ncl.ac.uk (Matthew Pocock)
Date: Fri May 14 11:23:53 2004
Subject: [Biojava-dev] bjv2 alpha 2
Message-ID: <40A4E3A2.4030508@ncl.ac.uk>
Hi,
I've just rolled out bjv2 alpha 2 - shelob. This is both a feature and
performance enhancement release. Get it from subversion at:
http://www.derkholm.net/svn/repos/bjv2/branches/shelob
As always, the development version is at:
http://www.derkholm.net/svn/repos/bjv2/trunk
features:
* gff support
* guts for allowing both gff and to be viewed as a stream of features
or sequences
* schema support on queryables
performance:
* elide away unnecisary object creation - 10x speed improvement
* adaptive indexing - data sources work out what questions you ask &
build indexes
* starting to do query optimization through the query and integration
layers - 320 sec query down to 6 sec!! I think this has replaced an n*n
scaling with a log(n) scaling. Pure objects would be constant-time
though - still some way to go
miscelanei:
* now requires the /newest/ javac - the javac bundled with java 1.5
beta1 was buggy
* more documentation - design and user docs
An example script:
import org.bjv2.seq.Sequence;
import org.bjv2.seq.Sequences;
import org.bjv2.seq.io.IO;
import org.bjv2.symbol.SymbolList;
import org.bjv2.gql.Queryable;
import java.io.File;
/**
* Demonstration of integrating multiple files.
*
* Use: IntegrateSequences seqFile1, seqFile2, ...
*
* The files can be any biological sequence/feature format files -
currently gff & embl are supported.
* The output will be a list of all sequences, and the number of
features on the sequence, regardless of
* whether the feature was annotated in the same file that the sequence
was defined in.
*
* @author Matthew Pocock
*/
public class IntegrateSequences
{
public static void main(String[] args)
throws Throwable
{
// load all the data in
for(String arg: args) {
File seqFile = new File(arg);
System.out.println("Loading: " + seqFile);
IO.loadSequence(seqFile);
}
System.out.println("All sequences: ");
// get the queryable with all the sequence data in
// this will be made prettier for alpha3
Queryable allSeqs = (Queryable)
Sequences.defaultContext().getMapping().image(
Sequences.getIdentifiers().get(Sequences.Domains.SEQUENCE));
System.out.println("\t" + allSeqs);
// loop over all sequences, printing out the sequence length & the
number of features
for(Sequence seq: allSeqs) {
System.out.println("\t" + seq.getIdentifier());
SymbolList symL = seq.getSymbolList();
if(symL != null) {
System.out.println("\t\tlength: " + symL.length());
}
System.out.println("\t\tfeatures: " + seq.getFeatures().size());
}
}
}
From heuermh at acm.org Fri May 14 11:09:34 2004
From: heuermh at acm.org (Michael Heuer)
Date: Fri May 14 11:55:21 2004
Subject: [Biojava-dev] SNP analyses in Biojava2
In-Reply-To: <3080.212.170.16.36.1084537919.squirrel@central.ebiointel.com>
Message-ID:
On Fri, 14 May 2004, Bruno Aranda - eBioIntel wrote:
> We are endeavouring a project about SNP and related stuff and, of course,
> it will be using BioJava. It is a long term project and we are now in
> early design. What I would like it to do is to analyze the SNPs with
> summary statistics, neutrality tests, coalescent and other things. As we
> are just in the earliest thoughts and it will be using J2SE 1.5 I think
> that all this SNP api would be a good contribution to Biojava 2. So, is
> there any specification about, for instance, how to do statistical
> equation classes in Biojava 2 (just the classes with the equations to
> process statistics)... it is too early for this? Of course I can do it
> aside BioJava but, if I make all these classes with the bjv2 phylosophy,
> then it will be easier to include them...
Take a look at the COLT library
> http://dsd.lbl.gov/~hoschek/colt/
the commons-math library
> http://jakarta.apache.org/commons/math
or perhaps making calls out to the R statistical package
> http://www.r-project.org
I don't think the biojava or bjv2 library is the right place for the
statistics classes. SNP api on the other hand ...
michael
From taoxu at bioinformatics.ubc.ca Fri May 14 13:33:07 2004
From: taoxu at bioinformatics.ubc.ca (Tao Xu)
Date: Fri May 14 13:37:34 2004
Subject: [Biojava-dev] Feature at position 0
Message-ID: <34ce131723.3172334ce1@cmmt.ubc.ca>
I have noticed that the in the nightly build, no Exception is thrown.
I guess it just simply ignored the features at position 0, as David
suggested.
I tend to like the idea of relax the location constraint. Another
approach might be create a RelaxLocation class.
Regards,
Tao
----- Original Message -----
From: Matthew Pocock
Date: Friday, May 14, 2004 3:21 am
Subject: Re: [Biojava-dev] Feature at position 0
> I think for the sake of useability, we could either relax the
> location
> constraint to allow point locations at 0, or in the sp parser, re-
> write
> these as <1 - what do people think?
>
> Matthew
>
> Tao Xu wrote:
>
> >Hi there,
> >
> >I am trying to use SeqIOTools.readSwissport() to process a
> SwissProt flat file. An Exception is thrown whenever a feature at
> position 0 is encountered. The user manual from UniProt/SwissProt
> says that a feature at position 0 means the initiator methionine
> was cleaved off.
> >This happens quite often ( at least a few persent of the
> SwissProt records has this line "FT INIT_MET 0 0". I
> googled and found your message. Is there a solution to this
> problem now? Thanks a lot for your help.
> >
> >Regards,
> >
> >Tao
> >
> >On Wednesday 15 Oct 2003 2:11 pm, Mark Southern wrote:
> >
> >
> >>This is a real world example.
> >>
> >>Swissprot ID KAP3_RAT (AC P12369) is an example of a sequence
> with a
> >>feature entry at sequence location 0:
> >>
> >>FT INIT_MET 0 0 BY SIMILARITY.
> >>
> >>
> >>This raises an IllegalArgumentException when the sequence is
> read in via
> >>SeqIOTools.fileToBiojava (see below).
> >>
> >>I don't know how oftem this would come up but its definitely a
> situation>>that isn't handled at the moment. Thoughts anyone?
> >>
> >>
> >>
> >Hmm, this one could be a problem - our coordinate system starts
> from one.
> >What do they mean by position 0? A cleaved methionine that's
> gone alreadY?
> >
> >Maybe our code ought to have the option to skip these silently?
> >
> >Regards,
> >David Huen
> >
> >
> >
> >------------------------------------------------------------------
> ------
> >
> >_______________________________________________
> >biojava-dev mailing list
> >biojava-dev@biojava.org
> >http://biojava.org/mailman/listinfo/biojava-dev
> >
> >
>
>
From autobuilder at derkholm.net Sat May 15 00:11:20 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Sat May 15 00:06:17 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1084594280347.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040515
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From autobuilder at derkholm.net Sun May 16 00:11:15 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Sun May 16 00:06:09 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <5450181.1084680675868.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040516
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From irfan at t-online.de Sun May 16 04:53:28 2004
From: irfan at t-online.de (abdenace)
Date: Sun May 16 14:05:43 2004
Subject: [Biojava-dev] =?windows-1251?b?zuHz9+Xt6OU=?=
Message-ID: <200405161805.i4GI5cKr002801@portal.open-bio.org>
????????? ???????!
?????????? ??? 20.05 ????????????? ? ??????????? ??????-?????? ?? ???? : ??????? ?????????????? ????????.
??????? ?????????????: ???????????? ?? ?????? ? ??????????, ????????????? ???????????
????????, ???????????? ?? ??????????? ???????????, ?????????? ?????????????, ???????????? ??
??????? ????????.
????????? ????????:
1. ?????? ????????????? ???????? ?? ?????? ? ? ??????.
??????, ?????????? ?? ????????? ????????????? ???????. ??????? ????????????? ?????????
??????? ?? ????????????? ???????. ??????? ??????????? ????? ? ???????.
2. ????????????? ??????? ??????????? ????????.
??????? ?????? ????? ????????. ??????????????? ?????? ??????? ????????. ????????? ?????????
????? ???????? ???????????. ???????.
3. ????????????? ??????? ???????? ????????.
??????? ?????? ????? ????????. ??????????????? ?????? ??????? ???????? ??? ????????.
??????????? ???????? ???????? ????? ????????.
4. ????????????? ??????? ????????? ????????.
??????? ?????? ????? ???????? . ??????????????? ??????. ??????????? ???????? ???????? ?????
?????????. ???????.
5. ????????????? ??????? ??????????? ????????.
??????? ?????? ????? ????????. ??????????????? ??????. ??????????? ???????? ???????? ??????
????????????. ???????
??????? ?????? ?????????? ????????.
6. ??????-?????: "???????????? ?????????? ???????? ??????? ????????????? ????????. ???????? ?
???? ????????".
??????? ????. ?????????? ????????????? ???????? ??????? ? ??????????? ???????????
?????????????? ???????.
???????? ???????????? ??? ?????? ? ??????? ?????????????. ?????????? ??? ??? ????????.
????????? ?????? ???? ??????? ??????? ?????? ??? ?????? ????????
????????? ???????
3900 ??????, ? ?.?. ???. ????? ?????? ????? (???????? ???
???????????). ? ????? ????? ??????: ??????? ?
???????????,??????????? ????????
????-?????, ????.
??????-????? ???????? ? ?????? (?. ?????????????).????? ?????????? ? 10 ?? 17.30.
??????????? ?????????? ???????????.
??????? ??? ??????? 747-71-88
From faq3 at cn.1618.net Sun May 16 15:25:52 2004
From: faq3 at cn.1618.net (faq3@cn.1618.net)
Date: Sun May 16 15:29:35 2004
Subject: [Biojava-dev] Software for Search-Engine, Mail, DNS, and more
Message-ID: <008601c43b7b$99ffa260$0301a8c0@1618.net>
http://cn.1618.net
http://hk.1618.net
http://tw.1618.net
http://us.1618.net
ftp://1618NETSOFTWARE:E171BB2D873546689C770BCBE415B3F6@ftp.1618.net
SORRY: this message is created by robot!!!
From seki at sesmail.com Mon May 17 16:14:19 2004
From: seki at sesmail.com (Rookie D. Discouragements)
Date: Sun May 16 16:38:01 2004
Subject: [Biojava-dev] Have a nice day! //your souls. You need not fear,
you need not despair, when
Message-ID: <100101c43b82$ba4df4f1$12ba754f@sesmail.com>
Get easy money! http://members.lycos.co.uk/lancer131/1/
---
In like manner, vice, while confined to certain limits, which
From autobuilder at derkholm.net Mon May 17 00:10:58 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Mon May 17 00:05:43 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <5450181.1084767059106.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040517
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From td2 at sanger.ac.uk Mon May 17 18:08:12 2004
From: td2 at sanger.ac.uk (Thomas Down)
Date: Mon May 17 18:11:46 2004
Subject: Pre-release soon? (was Re: [Biojava-dev] FeatureFilter.OverlapsExtent)
In-Reply-To: <40A49F32.1020805@yahoo.co.uk>
References: <81CA6F2E-A57D-11D8-8F19-000A95C8B056@sanger.ac.uk>
<40A49F32.1020805@yahoo.co.uk>
Message-ID:
On 14 May 2004, at 11:28, Matthew Pocock wrote:
>
> My bad. I added it to fix some rendering glitches with CDS features
> without an exon in the visible range. As long as it is semantically
> equivalent to ShadowOverlapsLocation, then do the switch. Can you make
> sure there's a factory method on FeatureTools for the shadow ones?
This is done now.
I'm trying to get the javadoc tidied up a bit ready for a 1.4pre1
release. It's quite a while since 1.3 now, lots of things have
improved, and the latest versions of dazzle, biojava-ensembl, and
probably lots of other stuff currently only work with the HEAD.
I'm currently planning to put out 1.4pre1 at the end of this week.
Does anyone have any objections to that timing?
Thomas.
From autobuilder at derkholm.net Tue May 18 00:10:58 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Tue May 18 00:05:26 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1084853458586.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040518
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
The following files were modified in the last 24 hours:
* biojava-live/src/org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.java
* biojava-live/src/org/biojava/bio/seq/DNATools.java
* biojava-live/src/org/biojava/bio/seq/FeatureFilter.java
* biojava-live/src/org/biojava/bio/seq/FilterUtils.java
* biojava-live/src/org/biojava/bio/seq/GeneticCodes.java
* biojava-live/src/org/biojava/bio/seq/NucleotideTools.java
* biojava-live/src/org/biojava/bio/seq/ProteinTools.java
* biojava-live/src/org/biojava/bio/seq/RNATools.java
* biojava-live/src/org/biojava/bio/seq/SequenceTools.java
A patch file reflecting these changes is available from
http://www.derkholm.net/autobuild/patches/
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From cadfredhyt at oddpost.com Tue May 18 22:15:53 2004
From: cadfredhyt at oddpost.com (cadfredhyt@oddpost.com)
Date: Tue May 18 23:58:41 2004
Subject: [Biojava-dev] Federal Provincial Subsidies
Message-ID: <957501c43d47$366927d0$468186ef@cadfredhyt>
Canada Books
26 Bellevue
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Qc, Canada
J0R 1B0
450-224-9275
Legal Deposit-National Library of Canada
ISBN 2-922870-05-7
The Canadian Subsidy Directory 2004 edition is available.
This publication contains more than 2600 listings of grants
and loans offered by government departments, foundations
and associations.
The publication is sold for $69.95
To obtain a copy please call: 450-224-9275
From autobuilder at derkholm.net Wed May 19 00:11:00 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Wed May 19 00:05:18 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1084939860874.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040519
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From bruno_dev at ebiointel.com Wed May 19 08:23:33 2004
From: bruno_dev at ebiointel.com (Bruno Aranda - Dev)
Date: Wed May 19 08:27:09 2004
Subject: [Biojava-dev] More about SNPs in BioJava 2
Message-ID: <4509.192.168.53.9.1084969413.squirrel@192.168.53.100>
Hello again,
I've been thinking about the SNP stuff. In order to work with SNPs it
would be useful before have a good api for alignments. From the
alignments we can find segregating sites (polymorphic sites), and
calculate some biological statistics from it as, to name few:
- Polymorphism measures:
Number of segregating sites (S) Nei 1987
Number of segregating sites per nucleotide
Theta θ per site (estimated from S)
Minimum number of mutations (η) Tajima 1996
Minimum number of mutations η per site
Theta θ per site (estimated from η)
Theta θ per DNA sequence (estimated from S) Tajima 1993
Variance of θ per DNA sequence (estimated from S) - without
recombination
Standard deviation of θ per DNA sequence (estimated from S) -
without recombination
Variance of θ per DNA sequence (estimated from S) - free
recombination
[...]
- Synonymous-Nonsynonimous
Number of Synonymous differences Nei and Gojobori 1986
Number of Non-synonymous differences
Number of Synonymous positions
Number of Non-synonymous positions
Number of synonymous polymorphisms per synonymous site
Number of non-synonymous polymorphisms per non-synonymous site
Number of synonymous polymorphisms per synonymous site - with
Jukes&Cantor correction
Number of non-synonymous polymorphisms per non-synonymous site -
with
Jukes&Cantor correction
Variance of Ks (Jukes&Cantor)
Variance of Ka (Jukes&Cantor)
[...]
We can also do pairwise comparisons between polymorphic sites and
calculate Linkage Disequilibriums (more equations here, like D'
(Lewontin), R, R2 (Hill, Robertson), distance between both comparing
sites, and so on...).
All (or most) of these equations are only applied in this field of
biology, and you cannot find them in libraries as colt or apache commons
math... Of course you can calculate some other basic probabilities like
Chi square and Fisher distributions from another packages. Moreover this
equations are pretty simple and use often the same variables. I guess
that the best strategy here would be use some Objects. For example we
could have:
PolymorphismCalculator polyCalc = new
PolymorphismCalculatior(alignment); int segregatingSites =
polyCalc.calculateSegregatingSites();
....
.... or something like this. The biological functions would be in
Strategy Objects for different models and biostatistics, but I am sure
that better ideas will come about this :)
We could also get the SNP objects form an alignment using some
utilities...
SNP[] snps = SNPTools.retrieveFromAlignment(alignment);
A SNP would be a Symbol composed by AtomicSymbols, and some
annotations...
Well, but alignments are not the only source for SNPs. For example, we
can get the SNPS from the NCBI in a few formats, being this kind of
Fasta the most used I think:
>gnl|dbSNP|ss12724475|allelePos=632|totalLen=659|PIGGENOME|P1|taxid=9823|mol=cDNA|snpclass=1|alleles='T/A'
CATCATTGAGCTACTTGCCCTTCGGAGCAGGACCCCGCTCTTGCGTAGGG
GAGATGCTAGCCCGCCAGGAGCTCTTCCTCTTCACGGCTGGATTGCTGCA
GAGGTTCGACCTGGAGCTCCCAGATGATGGGCAGCTACCCTGTCTCGTGG
GCAACCCCAGTTTGGTCCTGCAGATAGATCCTTTCAAAGTGAAGATCAAG
GAGCGCCAGGCCTGGAAGGAAGCCCACACTG
W
AGGGGAGTACCTCCTGACTCCACCCTG
The SNP here is the W ambigous symbol.
Well, this is an overall idea about SNPs... more focused on SNP
calculations. It would be useful to have more opinions about this and
other aspects of SNPs...
Bruno
From jason at cgt.duhs.duke.edu Wed May 19 21:29:15 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Wed May 19 21:32:54 2004
Subject: [Biojava-dev] More about SNPs in BioJava 2
In-Reply-To: <4509.192.168.53.9.1084969413.squirrel@192.168.53.100>
References: <4509.192.168.53.9.1084969413.squirrel@192.168.53.100>
Message-ID:
I've done quite a few of these in bioperl.
Many of the distance methods came from the EMBOSS code or phylip code.
You are more than welcome to steal liberally from Bio::PopGen code in
bioperl (live CVS code not release code as there are some bug fixes).
-jason
On Wed, 19 May 2004, Bruno Aranda - Dev wrote:
> Hello again,
>
> I've been thinking about the SNP stuff. In order to work with SNPs it
> would be useful before have a good api for alignments. From the
> alignments we can find segregating sites (polymorphic sites), and
> calculate some biological statistics from it as, to name few:
>
> - Polymorphism measures:
> Number of segregating sites (S) Nei 1987
> Number of segregating sites per nucleotide
> Theta θ per site (estimated from S)
> Minimum number of mutations (η) Tajima 1996
> Minimum number of mutations η per site
> Theta θ per site (estimated from η)
> Theta θ per DNA sequence (estimated from S) Tajima 1993
> Variance of θ per DNA sequence (estimated from S) - without
> recombination
> Standard deviation of θ per DNA sequence (estimated from S) -
> without recombination
> Variance of θ per DNA sequence (estimated from S) - free
> recombination
>
> [...]
>
> - Synonymous-Nonsynonimous
> Number of Synonymous differences Nei and Gojobori 1986
> Number of Non-synonymous differences
> Number of Synonymous positions
> Number of Non-synonymous positions
> Number of synonymous polymorphisms per synonymous site
> Number of non-synonymous polymorphisms per non-synonymous site
> Number of synonymous polymorphisms per synonymous site - with
> Jukes&Cantor correction
> Number of non-synonymous polymorphisms per non-synonymous site -
> with
> Jukes&Cantor correction
> Variance of Ks (Jukes&Cantor)
> Variance of Ka (Jukes&Cantor)
>
> [...]
>
> We can also do pairwise comparisons between polymorphic sites and
> calculate Linkage Disequilibriums (more equations here, like D'
> (Lewontin), R, R2 (Hill, Robertson), distance between both comparing
> sites, and so on...).
>
> All (or most) of these equations are only applied in this field of
> biology, and you cannot find them in libraries as colt or apache commons
> math... Of course you can calculate some other basic probabilities like
> Chi square and Fisher distributions from another packages. Moreover this
> equations are pretty simple and use often the same variables. I guess
> that the best strategy here would be use some Objects. For example we
> could have:
>
> PolymorphismCalculator polyCalc = new
> PolymorphismCalculatior(alignment); int segregatingSites =
> polyCalc.calculateSegregatingSites();
> ....
>
> .... or something like this. The biological functions would be in
> Strategy Objects for different models and biostatistics, but I am sure
> that better ideas will come about this :)
>
> We could also get the SNP objects form an alignment using some
> utilities...
>
> SNP[] snps = SNPTools.retrieveFromAlignment(alignment);
>
> A SNP would be a Symbol composed by AtomicSymbols, and some
> annotations...
>
> Well, but alignments are not the only source for SNPs. For example, we
> can get the SNPS from the NCBI in a few formats, being this kind of
> Fasta the most used I think:
>
> >gnl|dbSNP|ss12724475|allelePos=632|totalLen=659|PIGGENOME|P1|taxid=9823|mol=cDNA|snpclass=1|alleles='T/A'
> CATCATTGAGCTACTTGCCCTTCGGAGCAGGACCCCGCTCTTGCGTAGGG
> GAGATGCTAGCCCGCCAGGAGCTCTTCCTCTTCACGGCTGGATTGCTGCA
> GAGGTTCGACCTGGAGCTCCCAGATGATGGGCAGCTACCCTGTCTCGTGG
> GCAACCCCAGTTTGGTCCTGCAGATAGATCCTTTCAAAGTGAAGATCAAG
> GAGCGCCAGGCCTGGAAGGAAGCCCACACTG
> W
> AGGGGAGTACCTCCTGACTCCACCCTG
>
> The SNP here is the W ambigous symbol.
>
> Well, this is an overall idea about SNPs... more focused on SNP
> calculations. It would be useful to have more opinions about this and
> other aspects of SNPs...
>
>
> Bruno
>
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev@biojava.org
> http://biojava.org/mailman/listinfo/biojava-dev
>
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From autobuilder at derkholm.net Thu May 20 00:10:58 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Thu May 20 00:05:05 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <5450181.1085026258459.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040520
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
The following files were modified in the last 24 hours:
* biojava-live/src/org/biojava/bio/program/das/dasalignment/Alignment.java
* biojava-live/src/org/biojava/bio/program/das/dasalignment/DASAlignmentCall.java
* biojava-live/src/org/biojava/bio/program/das/dasalignment/DASAlignmentClient.java
* biojava-live/src/org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.java
* biojava-live/src/org/biojava/bio/program/das/dasalignment/DASException.java
* biojava-live/src/org/biojava/bio/program/das/dasalignment/MSDMappingReader.java
* biojava-live/src/org/biojava/bio/program/das/dasalignment/MSD_Mapping_ContentHandler.java
* biojava-live/src/org/biojava/bio/program/das/dasstructure/DASStructureCall.java
* biojava-live/src/org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.java
* biojava-live/src/org/biojava/bio/structure/AminoAcid.java
* biojava-live/src/org/biojava/bio/structure/AtomImpl.java
* biojava-live/src/org/biojava/bio/structure/Calc.java
* biojava-live/src/org/biojava/bio/structure/Chain.java
* biojava-live/src/org/biojava/bio/structure/ChainImpl.java
* biojava-live/src/org/biojava/bio/structure/Group.java
* biojava-live/src/org/biojava/bio/structure/GroupIterator.java
* biojava-live/src/org/biojava/bio/structure/Hetatom.java
* biojava-live/src/org/biojava/bio/structure/Structure.java
* biojava-live/src/org/biojava/bio/structure/StructureImpl.java
A patch file reflecting these changes is available from
http://www.derkholm.net/autobuild/patches/
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From autobuilder at derkholm.net Fri May 21 00:11:13 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Fri May 21 00:05:30 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <5450181.1085112674054.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040521
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From matthew_pocock at yahoo.co.uk Fri May 21 11:54:33 2004
From: matthew_pocock at yahoo.co.uk (Matthew Pocock)
Date: Fri May 21 11:58:13 2004
Subject: [Biojava-dev] bjv2 alpha 3
Message-ID: <40AE2639.3020806@yahoo.co.uk>
Hi,
I'ts that time again. I've committed alpha 3 - scylla to svn. This adds
support for flat-file indexing and mapping between Java and RDF. It also
introduces some direct requirements for build tools that are only
available on Java 1.5 beta 2 - but with any luck that should be comming
out soon.
Get it while it's hot at:
http://www.derkholm.net/svn/repos/bjv2/branches/scylla
As always, the development version is at:
http://www.derkholm.net/svn/repos/bjv2/trunk
Features:
org.bjv2.io.index:
Indexing API that supports any file format understood by org.bjv2.io
automatically.
Currently there is one implementation of this API. Implementations
should be easy to write for things like SRS.
org.bjv2.rdf:
API for representing Java classes and objects as RDFS and RDF.
This supports a fully pluggable architecture, so that multiple
classes can be mapped to the same RDF type, properties can be explicitly
mapped to RDF properties, and instances can be checked for metaData
fields (e.g. Feature.getType() can result in different RDFS documents
being produced for features with different types, or an instance of
Annotation or Map may have a schema that contains information about
which properties are present).
@Utility annotation
This flags a class as being a utility class. This means that it must
expose only static fields and methods, and must not be instantiable.
More coding-style validators will follow.
Matthew
From heuermh at acm.org Fri May 21 12:44:02 2004
From: heuermh at acm.org (Michael Heuer)
Date: Fri May 21 12:55:25 2004
Subject: [Biojava-dev] bjv2 alpha 3
In-Reply-To: <40AE2639.3020806@yahoo.co.uk>
Message-ID:
On Fri, 21 May 2004, Matthew Pocock wrote:
> org.bjv2.rdf:
> API for representing Java classes and objects as RDFS and RDF.
> This supports a fully pluggable architecture, so that multiple
> classes can be mapped to the same RDF type, properties can be explicitly
> mapped to RDF properties, and instances can be checked for metaData
> fields (e.g. Feature.getType() can result in different RDFS documents
> being produced for features with different types, or an instance of
> Annotation or Map may have a schema that contains information about
> which properties are present).
Sounds interesting, but what can we use this for?
> @Utility annotation
> This flags a class as being a utility class. This means that it must
> expose only static fields and methods, and must not be instantiable.
> More coding-style validators will follow.
While this pattern is good coding style, it causes problems in certian
environments that require no-arg constructors.
Most (if not all) of the apache projects now include a constructor like
/**
* XxxUtils should not normally be instantiated. This
* constructor is public to permit tools that require a JavaBean
* instance to operate.
*/
public XxxUtils()
{
// empty
}
in utility classes. See e.g.
> http://jakarta.apache.org/commons/lang/apidocs/org/apache/commons/lang/ArrayUtils.html
michael
From autobuilder at derkholm.net Sat May 22 00:11:07 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Sat May 22 00:08:05 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <5450181.1085199067479.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040522
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
The following files were modified in the last 24 hours:
* biojava-live/src/org/biojava/bio/structure/io/PDBFileReader.java
* biojava-live/src/org/biojava/bio/structure/io/PDBSRSReader.java
* biojava-live/src/org/biojava/bio/structure/io/StructureIO.java
A patch file reflecting these changes is available from
http://www.derkholm.net/autobuild/patches/
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From td2 at sanger.ac.uk Sat May 22 07:52:11 2004
From: td2 at sanger.ac.uk (Thomas Down)
Date: Sat May 22 07:55:36 2004
Subject: [Biojava-dev] Distribution serialization
Message-ID: <75DE2104-ABE6-11D8-B9D9-000A95C8B056@sanger.ac.uk>
I've just had another hack at distribution serialization -- this clears
up some rather fragile contracts between different classes, and allows
IndexedNthOrderDistributions to be usably serialized.
I hope this won't affect anyone too much (you're not using
serialization for long-term data storage, are you?), but if you've got
your own Distribution implementations which extend
AbstractDistribution, and need to serialize them, you might have to
make a few changes -- look at SimpleDistribution for an example.
Thomas.
From autobuilder at derkholm.net Sun May 23 00:10:57 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Sun May 23 00:05:50 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <5450181.1085285457956.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040523
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
The following files were modified in the last 24 hours:
* biojava-live/src/org/biojava/bio/dist/AbstractDistribution.java
* biojava-live/src/org/biojava/bio/dist/AbstractOrderNDistribution.java
* biojava-live/src/org/biojava/bio/dist/IndexedNthOrderDistribution.java
* biojava-live/src/org/biojava/bio/dist/SimpleDistribution.java
* biojava-live/src/org/biojava/bio/symbol/SimpleAtomicSymbol.java
A patch file reflecting these changes is available from
http://www.derkholm.net/autobuild/patches/
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From mark.schreiber at group.novartis.com Sun May 23 21:21:54 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Sun May 23 21:25:27 2004
Subject: [Biojava-dev] bjv2 alpha 3
Message-ID:
>> @Utility annotation
>> This flags a class as being a utility class. This means that it
must
>> expose only static fields and methods, and must not be instantiable.
>> More coding-style validators will follow.
>
>While this pattern is good coding style, it causes problems in certian
>environments that require no-arg constructors.
>
>Most (if not all) of the apache projects now include a constructor like
>
> /**
> * XxxUtils should not normally be instantiated. This
> * constructor is public to permit tools that require a JavaBean
> * instance to operate.
> */
> public XxxUtils()
> {
> // empty
> }
>
>in utility classes. See e.g.
>
> http://jakarta.apache.org/commons/lang/apidocs/org/apache/commons/lang/ArrayUtils.html
>
> michael
This is not a bad idea. If you ever try to make a GUI application based on
BioJava using an IDE you pretty quickly come unstuck on the more non-bean
like elements, the *Tools being the biggest problems. A public constructor
on a utility class is not really a problem other than possibly creating
more than one copy in the VM and adding a bit of cruft.
It would be nice if more of BioJava could be made into valid beans.
Unfortunately this does render all of the elegant singletons invalid. If
only java had a keyword for a constructor that could be called only by the
VM to create a bean. I suspect such a thing would cause all kinds of
security problems though.
- Mark
From autobuilder at derkholm.net Mon May 24 00:11:04 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Mon May 24 00:04:19 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <5450181.1085371864399.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040524
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From matthew_pocock at yahoo.co.uk Mon May 24 09:02:02 2004
From: matthew_pocock at yahoo.co.uk (Matthew Pocock)
Date: Mon May 24 09:05:37 2004
Subject: [Biojava-dev] bjv2 alpha 3
In-Reply-To:
References:
Message-ID: <40B1F24A.1080108@yahoo.co.uk>
Queue brain-dump... Utility methods are primarily intended for dumb
users - dumb coder users. A different mechanism may be more appropreate
for dumb drag-n-droppers. I am assuming from what you have said that
bean editors let you do quasi-illegal things like invoking static
methods relative to instances. I've no problem with 'skinning' bjv2 for
a different user group. What if we had some magic like this:
Object tool = new ToolFactory().makeTool(Utility.class)
This returns a 1st class object with non-static methods that alias to
the static tools methods on Utility.class and is serializable - would
this help?
What's the standard pattern for exposing processes through beans? I'd
feel much happier if this level of logic was handled in a workflow
language e.g. Taverna could be adapted so that all utility classes
become processors. That way dumb d-n-d users realy don't have to look at
any of the code.
>It would be nice if more of BioJava could be made into valid beans.
>Unfortunately this does render all of the elegant singletons invalid. If
>only java had a keyword for a constructor that could be called only by the
>VM to create a bean. I suspect such a thing would cause all kinds of
>security problems though.
>
>- Mark
>
>
>_______________________________________________
>biojava-dev mailing list
>biojava-dev@biojava.org
>http://biojava.org/mailman/listinfo/biojava-dev
>
>
>
From heuermh at acm.org Mon May 24 15:16:55 2004
From: heuermh at acm.org (Michael Heuer)
Date: Mon May 24 15:53:36 2004
Subject: [Biojava-dev] bjv2 alpha 3
In-Reply-To: <40B1F24A.1080108@yahoo.co.uk>
Message-ID:
On Mon, 24 May 2004, Matthew Pocock wrote:
> Queue brain-dump... Utility methods are primarily intended for dumb
> users - dumb coder users. A different mechanism may be more appropreate
> for dumb drag-n-droppers. I am assuming from what you have said that
> bean editors let you do quasi-illegal things like invoking static
> methods relative to instances. I've no problem with 'skinning' bjv2 for
> a different user group. What if we had some magic like this:
>
> Object tool = new ToolFactory().makeTool(Utility.class)
>
> This returns a 1st class object with non-static methods that alias to
> the static tools methods on Utility.class and is serializable - would
> this help?
That is nifty but doesn't help with the public default constructor
problem. Most reflective code won't be able to figure out factory
construction methods automatically.
There was a long debate on the commons-dev mailing list in 2002 and a
long second round of debate in 2003 that maybe isn't worth rehashing
here. In the end the community decided to go with public constructors
documented against normal use, so that is what I was suggesting.
michael
> What's the standard pattern for exposing processes through beans? I'd
> feel much happier if this level of logic was handled in a workflow
> language e.g. Taverna could be adapted so that all utility classes
> become processors. That way dumb d-n-d users realy don't have to look at
> any of the code.
>
> >It would be nice if more of BioJava could be made into valid beans.
> >Unfortunately this does render all of the elegant singletons invalid. If
> >only java had a keyword for a constructor that could be called only by the
> >VM to create a bean. I suspect such a thing would cause all kinds of
> >security problems though.
> >
> >- Mark
>
From randell.mmasonge at rapt.nl Mon May 24 18:35:49 2004
From: randell.mmasonge at rapt.nl (Randell M. Mason)
Date: Mon May 24 18:41:46 2004
Subject: [Biojava-dev] Get your medicines from us.
Message-ID: <40B278C5.33E06FA1@rapt.nl>
Cheap Viagra and other drugs such as Soma, Lìpitor, Celebrex,
Valìum, Xanax, and more.
We believe ordering medìcation should be as simple
as ordering anything else on the Net.
No doctor consultatìon needed. Safe, private and easy.
Shipped to the whole world. Look here and save:
http://4hbedomain.com/
The link below is for people who hate adv....
http://4hbedomain.com/o.php
From autobuilder at derkholm.net Tue May 25 00:11:03 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Tue May 25 00:04:06 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <5450181.1085458264026.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040525
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
The following files were modified in the last 24 hours:
* biojava-live/src/org/biojava/bio/structure/GroupIterator.java
A patch file reflecting these changes is available from
http://www.derkholm.net/autobuild/patches/
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From mark.schreiber at group.novartis.com Tue May 25 04:42:50 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Tue May 25 04:46:22 2004
Subject: [Biojava-dev] bjv2 alpha 3
Message-ID:
Hey! I prefer to think of myself as a lazy drag n dropper than a dumb drag
n dropper :)
But serioulsy, there are other good reasons to have a beany version of
things. Interoperability with JAXB and other bean centric APIs springs to
mind. Threre are lots of cool things that can be done with beans and
reflection all of which happily violate the principle of encapsulation and
are quasi illegal but are cool none the less.
Matthew Pocock
Sent by: biojava-dev-bounces@portal.open-bio.org
05/24/2004 09:02 PM
To: Mark Schreiber/GP/Novartis@PH
cc: biojava-dev-bounces@portal.open-bio.org, Biojava-dev
, Michael Heuer
Subject: Re: [Biojava-dev] bjv2 alpha 3
Queue brain-dump... Utility methods are primarily intended for dumb
users - dumb coder users. A different mechanism may be more appropreate
for dumb drag-n-droppers. I am assuming from what you have said that
bean editors let you do quasi-illegal things like invoking static
methods relative to instances. I've no problem with 'skinning' bjv2 for
a different user group. What if we had some magic like this:
Object tool = new ToolFactory().makeTool(Utility.class)
This returns a 1st class object with non-static methods that alias to
the static tools methods on Utility.class and is serializable - would
this help?
What's the standard pattern for exposing processes through beans? I'd
feel much happier if this level of logic was handled in a workflow
language e.g. Taverna could be adapted so that all utility classes
become processors. That way dumb d-n-d users realy don't have to look at
any of the code.
>It would be nice if more of BioJava could be made into valid beans.
>Unfortunately this does render all of the elegant singletons invalid. If
>only java had a keyword for a constructor that could be called only by
the
>VM to create a bean. I suspect such a thing would cause all kinds of
>security problems though.
>
>- Mark
>
>
>_______________________________________________
>biojava-dev mailing list
>biojava-dev@biojava.org
>http://biojava.org/mailman/listinfo/biojava-dev
>
>
>
_______________________________________________
biojava-dev mailing list
biojava-dev@biojava.org
http://biojava.org/mailman/listinfo/biojava-dev
From Russell.Smithies at agresearch.co.nz Tue May 25 17:03:24 2004
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue May 25 17:06:57 2004
Subject: [Biojava-dev] JNIReg
Message-ID:
Has anyone used JNIReg from http://www.trustice.com/java/jnireg/ to
write registry keys before?
I need to write and read a few reg keys to the Windows registry but it
has even less documentation than Biojava :-(
Has anyone got some old code lying about or can anyone suggest a better
way to do this?
I think it can also be done using reflection and properties but not sure
how.
Thanx
Russell Smithies
Bioinformatics Software Developer
AgResearch Invermay
Private Bag 50034
Puddle Alley
Mosgiel
New Zealand
Tel: +64 3 489 9171
Fax: +64 3 489 3739
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================
From autobuilder at derkholm.net Wed May 26 00:11:03 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Wed May 26 00:03:59 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <5450181.1085544664124.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040526
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From melisa at seznam.cz Wed May 26 00:23:19 2004
From: melisa at seznam.cz (iris)
Date: Wed May 26 00:37:37 2004
Subject: [Biojava-dev] =?windows-1251?b?zuHz9+Xt6OU=?=
Message-ID: <200405260437.i4Q4bSKr013087@portal.open-bio.org>
????????? ???????!
?????????? ??? 31 ??? ???????
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?? ??????????? ???? ??????????? ?????? ????????, ??????? ?? ???????????? ????????? ?
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??????? ????????.
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??????????? ????????.
? ?????????, ????????? ???????? ?????????? ?????? ?????? ??????????????, ??? ???????????
????????? ????????? ?????????? ? ?????????? ?????????.
?????????? ???????? ???????????? ????????? ?????????:
1. ????????? ?????????
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- ?????????? ???? ?????????
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- ???????? ???, ????????? ?????????. ?????????? ????????.
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- ?????? ?????????? ???????? ? ?????????.
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- ???????? ??????? ?????????.
- ?????? ??????????? ?? ?????????? ?????
- ????? ???????? ???????, ?????????? ?????? ????????? ???????.
- ????????? ?????????? ???????? ???????, ????????? ??????????? ???????.
- ??????????. ??????????, ?????????????? ? ???????? ????????.
- ????????? ? ????????.
4. ?????? ???????????? ????????. ???????? ?????????? ???????? ???????.
?? ????????? ???????? ????????? ??????:
- ?????????? ??????????? ? ???????????? ?????, ?????????? ?? ?????????
- ???????????? ? ????????? ???? ?????????? ? ????????? ?????????????? ? ??????? ? ???????
????????
- ?????? ???????? ?????? ?????????? ? ????????????? ?? ? ????? ????????? ?????????
- ????????? ??????????? ????????? ???, ????? ????????? ???????????? ???????????
- ????????? ????? ? ???? ??? ??????? ??? ?????????? ?????????.
????????? ??????? ? ???????????
3900 ??????, ? ?.?. ???. ????? ?????? ????? (???????? ???
???????????). ? ????????? ??????: ??????? ?
???????????,??????????? ????????
????-?????, ????.
??????-????? ???????? ? ?????? (?. ?????????????).?????? - ? 10 ????? ? ????????? - ? 17.30 - 18.00.
??? ??????? ? ???????? ??????????
????????????????.
???? ?? ?? ?????? ???????? ??????-????? ??
?????????? ??? ?????????? ?????? ?? ?????
???????????.?
??????????????? ??????????? ???????????
????????. ?????????
???????????? ???????????? 2600 ???. ?
?.?. ???
??????? ??? ??????? 788-73-28
From marketingdirecto at eyou.com Wed May 26 04:06:37 2004
From: marketingdirecto at eyou.com (marketingdirecto@eyou.com)
Date: Wed May 26 04:12:03 2004
Subject: [Biojava-dev] I,05/22
Message-ID: <200405260811.i4Q8BtKr015311@portal.open-bio.org>
Dear Sir,
we have been in the field of diesel fuel injection
systems for quite a few years.(CHINA)
Recently we have developed a new kind of h&r,
"CH-D90101A=AM Bosch number HD90101A"Its unit price is USD150/pc.And
we also adjust the unit price of Nozzle , Plunger to USD4~8/pc
respectively.
We tell you that we will update our VE h&r
(hydraulic heads for the VE distributor pump) list in our
homepages.Thirty more models will be added.And the minimum
order will be 10pcs a model.
we give the unity quotation of VE distributor head:
3-cyl:USD:55/1pcs
4-cyl:USD:40~50/1pcs
5-cyl:USD:60/1pcs
6-cyl:USD:45~50/1pcs
We can ship the following three models to you within 6~8 weeks. after
we receive your payment.
If you feel interested in our products,please advise the details about
what you need,such model name,part number,quantity and so on.We are always
within your touch.
Thanks and best regards
Looking forward to our favorable cooperation.
Hope to hear from you soon.
(NIPPON DENSO)
D00-0143
D00-0242
D00-0262
D00-0371
D00-0432
D00-1030
D00-1060
D00-1090
D00-1210
D00-1220
D00-1230
D00-1240
D00-1250
D00-1330
D00-1331
D00-1600
D40-0080
ZEXEL
Z00-2220
Z00-3320
Z00-4520
Z00-5521
Z00-8821
Z00-9720
Z01-0520
Z01-2120
Z02-0820
Z02-0920
Z02-1420
Z02-4020
Z02-4320
Z02-3820
Z03-2820
Z03-3120
Z03-3520
Z04-1520
Z04-2200
Z05-1920
Z30-1420
BOSCH
A 333 320
A 333 323
A 334 313
A 334 327
A 334 565
A 334 337
A 334 378
A 334 424
A 334 475
A 334 485
A 334 494
A 334 496
A 334 580
A 334 590
A 334 564
A 334 565
A 334 575
A 334 592
A 334 595
A 334 596
A 334 603
A 334 604
A 334 606
A 334 617
A 334 675
A 334 678
A 334 720
A 334 780
A 334 798
A 334 859
A 334 874
A 334 899
A 334 946
A 335 345
B 335 022
A 336 335
A 336 352
A 336 364
A 336 403
A 336 423
A 336 464
A 336 480
A 336 528
A 336 608
A 336 614
A 336 626
A 336 632
B 334 050
B 334 021
B 336 013
We have a large number of nozzle, plunger and delivery valve
in stock.Here is a list of part of them.
"
"
NOZZLE
093400-1310 DN0SD193
093400-1710 DLLA160SND171
093400-2280 DNOSD228
093400-5210 DNOPD21
093400-5571 ND-DN4PD57
093400-5590 ND-DLLA150P59
093400-7690 ND-DN10PDN129
093400-7700 ND-DN10PDN130
DNOSD261
DNOSD220
DNOSD293
DLLA150P205
DLLA150S1070
105000-108 NP-DNOSD211
105000-1130 NP-DN4SD24
10500-1650 NP-DNOSD2110
105000-1080 NP-DNOSD211
105000-1360 NP-DN4SD24
105000-1730 NP-DNOSD21
105000-1740 NP-DNOSD193
105000-1760
105000-2280 NP-DNOSDN228
105007-1120 NP-DNOPDN112
105007-1130 NP-DN0PDN113
105007-1210 NP-DNOPDN121
105015-2780 NP-DLLA166S374NP6
105015-3280 NP-DLLA150S328NP52
105015-3520 DLLA150S384NP73
105015-3650 NP-DLLA151S354N86
105015-3670 NP-DLLA160S354NP88
105015-3850 NP-DLLA150S334N385
105015-4130 NP-DLLA154S324N413
105015-4170 NP-DLLA137S374N417
105015-4190 DLLA154S334N419
105015-4220 NP-DLLA160S295N422
105015-4330 NP-DLLA105S304N433
105015-4730 NP-DLLA148S324N473
105015-5070 NP-DLLA160S325N507
105015-6130 NP-DLLA142SN613
105015-6380 DLLA158SN638
105015-8690 DLLA158SN869
105015-8860 NP-DLLA148SN886
105017-0070 NP-DLLA154PN007
105017-0090 NP-DLLA152PN009
105017-0630 NP-DLLA152PN063
105017-0670 DLLA154PN067
105017-0100 DLLA160PN010
105017-0210 DLLA150PN021
105017-0211/10 DLLA150PN021
105017-0900 DLLA152PN009
105017-1160 NP-DLLA154PN116
105017-1180 DLLA155PN118
105007-1210 NP-DNOPDN121
105017-1780 DLLA153PN178
0 433 271 740
0 433 271 047 DLLA150S187
0 433 271 045 DLLA150S186
0 433 171 031 DLLA150P30
0 433 171 050 DLLA160P50
0 433 171 059 DLLA150P59
0 433 171 104 DLLA150P115
0 433 171 149 DLLA146P166
0 433 171 137 DLLA146P154
0 433 171 161 DLLA144P184
0 433 171 172 DLLA154P206
0 433 171 231 DLLA150P326
0 433 171 435 DLLA145P574
0 433 171 444 DLLA150P585
0 433 175 048 DSLA145P300
0 433 271 045 DLLA150S186
0 433 271 047 DLLA150S187
0 433 271 361 DLLA150S739
0 433 271 404 DLLA142S792
0 433 271 874 DLLA150S739
0 466 171 003 DLL-A160P3
NP-DLL154S284N393
NP-DLL160S 354NP88
6801128
6801118
PLUNGER LIST:
131101-7020 0-4
131101-7520 0-9
A17
131151-2720 A43
131151-3220 A44
131151-5820 A74
131151-7320 A89
A98
131152-1420 A138
A147
131152-2220 A148
131152-3120 A158
131152-3320 A160
131152-5620 A188
131153-1220 A196
131152-8520 A226
131153-8920 A768
A722
134101-1420 P2
134101-1520 P3
P4
134101-1820 P6
134101-3820 P25
134101-6320 P48
134101-6420 P49
Delivery valve
146430-1420
131160-1920 02A
131160-2220 05A
131160-2920 12A
131160-3620 20A
134110-0120 P1
134110-0520 P4
134110-0920 P8
134110-4520 P44
131110-0620 161S2
134110-0920 P8
134110-4520 P44
134110-7420 P73
131110-2920 A9
131110-3920 A20
131110-4720 A28
131110-5120 A32
131110-5220 A33
131110-5920 A40
13110-6820 A49
131110-7720 A58
131110-7820 A59
131110-9420 A75
131160-0420 A85
1 468 532 247 A247
146430-0020 VE1
146430-1420 VE15
"
marketingdirecto@eyou.com
From tamal at t-online.de Wed May 26 22:01:15 2004
From: tamal at t-online.de (cesar)
Date: Wed May 26 22:11:58 2004
Subject: [Biojava-dev] =?windows-1251?b?zuHz9+Xt6OU=?=
Message-ID: <200405270211.i4R2BmKr026664@portal.open-bio.org>
????????? ???????!
?????????? ??? 3 ???? ???????? ? ??????????? ??????-?????? ??
???? : ????? ??????????????? ??????????
??????? ????????????? ??????? ???????????, ????????? ?????????????, ????????????? ???6????????.
????????? ????????.
1. ??????? ??????????????? ?????????. ???????? ? ????????????: ????????? ?????????,
??????????????? ???????, ??????????????? ??????????. ??? ?????????, ???? ?????????
???????????????? ?? ???????? ?????????? ??????????? ??????? ? ????? ????? ???????????????
?????????.
2. ????? ? ????? ??????????????? ????????? ??? ????? ????????? ??????? ??
???????
3. ???? ??????????? ? ??????? ???????? ??????????????? ????????? ??? ????? ???????????????.
?????? ??????????????? ????????? ? ????????? ?????.
4. ????????? ???????? ???????? ??????? ? ?????????????? ??????? ? ??????????????? ?????????.
?????????? ??????????? ? ????????? ?? ? ????????? ?????
5. ????????? ???? ???????? ?? ?????? ??????????????? ?????????
6. ??????????? ?????????? ????? ???????? ??????????????? ?????????, ????????? ? ????????????
?? 1 ?????? 2002 ?.
7. ????????????? ????????? ???????? ??? ????? ??????????????? ????????? ? ????????, ?????????
? ??? ?????????????
8. ?????????? ? ?????? ??????? ???????? ??????????????? ????????? ????????? ??????? ?
????????, ???????? ??????? ?? ?????? ? ????????? ?????.
C???????? ??????? ? ??????-??????
3900 ??????, c ?????? ???. ????? ?????? ????? (???????? ???
???????????). ? ????? ????? ??????: ??????? ? ?????? ??????,?????????????? ???????? ?????????
????-?????, ????.
??????-????? ???????? ? ?????? (?. ?????????????).?????? - ? 10 ????? ? ????????? - ? 17.30 - 18.00.
??? ??????? ? ???????? ??????????
????????????????.
???? ???? ??????? ? ??????????? ?????????? ??
?????????? ??? ?????????? ?????? ?? ?????
????? ? ?????? ??????-???????.? ??????????? ??????????? ???????????
????????. ?????????
???????????? ???????????? 2600 ???. ? ???
??????? ??? ??????? 788-7328
From autobuilder at derkholm.net Thu May 27 00:10:58 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Thu May 27 00:03:34 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1085631058809.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040527
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From cornelius_arringtonfa at cuba-solidarity.org.uk Thu May 27 00:01:08 2004
From: cornelius_arringtonfa at cuba-solidarity.org.uk (Cornelius Arrington)
Date: Thu May 27 00:04:49 2004
Subject: [Biojava-dev] Very powerful weightloss now available.
Message-ID: <1e1c01c4439f$93618f05$09d7f2f6@hull-college.ac.uk>
Hello, I have a special_offer for you...
WANT TO LOSE WEIGHT?
The most powerful weightloss is now available
without prescription. All natural Adipren720
100% Money Back Guarant?e!
- Lose up to 19% Total Body Weight.
- Up to 300% more Weight Loss while dieting.
- Loss of 20-35% abdominal Fat.
- Reduction of 40-70% overall Fat under skin.
- Increase metabolic rate by 76.9% without Exercise.
- Boost your Confidence level and Self Esteem.
- Burns calorized fat.
- Suppresses appetite for sugar.
Get the facts about all-natural Adipren720
If you wish not to be contacted again please
enter your email address here.
From johnnie.mullen_ut at siak.ch Thu May 27 12:54:16 2004
From: johnnie.mullen_ut at siak.ch (Johnnie I. Mullen)
Date: Thu May 27 12:58:13 2004
Subject: [Biojava-dev] Get medicines here, great prices.
Message-ID:
Hello, I have a great offer for you...
One of the cheapest medication sites on the internet is
available for you without prescription.
We have Viagra, Cialis, Soma, Meridia, Propecia, Lipitor,
Xanax, Valium, Celebrex, and more.
-100% Money Back Guarant?e!
-No Consultation.
-No Prior Prescription needed.
-No appointments.
-No Waiting Rooms.
-No embarassment.
-Private & Confidential.
-Discreet Packaging.
-Huge savings.
-Shipped to the whole world.
Your order will be packaged discreetly for your
privacy and protection.
http://4hbedomain.com/
If you don't want to be contacted again,
enter your email address here:
http://4hbedomain.com/o.php
From autobuilder at derkholm.net Fri May 28 00:11:14 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Fri May 28 00:03:36 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1085717474542.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040528
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From t.youngbi at heineken.nl Fri May 28 09:39:28 2004
From: t.youngbi at heineken.nl (Teresa Young)
Date: Fri May 28 09:44:27 2004
Subject: [Biojava-dev] Very powerful weightloss now available.
Message-ID:
Hello, I have a special_offer for you...
WANT TO LOSE WEIGHT?
The most powerful weightloss is now available
without prescription. All natural Adipren720
100% Money Back Guarant?e!
- Lose up to 19% Total Body Weight.
- Up to 300% more Weight Loss while dieting.
- Loss of 20-35% abdominal Fat.
- Reduction of 40-70% overall Fat under skin.
- Increase metabolic rate by 76.9% without Exercise.
- Boost your Confidence level and Self Esteem.
- Burns calorized fat.
- Suppresses appetite for sugar.
Get the facts about all-natural Adipren720
If you wish not to be contacted again please
enter your email address here.
From autobuilder at derkholm.net Sat May 29 00:11:04 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Sat May 29 00:03:29 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1085803864469.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040529
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
The following files were modified in the last 24 hours:
* biojava-live/src/org/biojava/bio/structure/Atom.java
* biojava-live/src/org/biojava/bio/structure/AtomImpl.java
* biojava-live/src/org/biojava/bio/structure/AtomIterator.java
* biojava-live/src/org/biojava/bio/structure/Calc.java
* biojava-live/src/org/biojava/bio/structure/Group.java
* biojava-live/src/org/biojava/bio/structure/Hetatom.java
* biojava-live/src/org/biojava/bio/structure/Structure.java
* biojava-live/src/org/biojava/bio/structure/StructureImpl.java
* biojava-live/src/org/biojava/bio/structure/io/PDBFileReader.java
A patch file reflecting these changes is available from
http://www.derkholm.net/autobuild/patches/
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From janelle_townsend_md at coopergroup.co.uk Sat May 29 23:04:07 2004
From: janelle_townsend_md at coopergroup.co.uk (Janelle Townsend)
Date: Sat May 29 23:10:01 2004
Subject: [Biojava-dev] Get medicines here, great prices.
Message-ID: <4e0001c445f2$8f72b37e$4d45a35b@voxpop.fr>
Hello, I have a great offer for you...
One of the cheapest medication sites on the internet is
available for you without prescription.
We have Viagra, Cialis, Soma, Meridia, Propecia, Lipitor,
Xanax, Valium, Celebrex, and more.
-100% Money Back Guarant?e!
-No Consultation.
-No Prior Prescription needed.
-No appointments.
-No Waiting Rooms.
-No embarassment.
-Private & Confidential.
-Discreet Packaging.
-Huge savings.
-Shipped to the whole world.
Your order will be packaged discreetly for your
privacy and protection.
http://r1g4t2you.com/
If you don't want to be contacted again,
enter your email address here:
http://r1g4t2you.com/o.php
From autobuilder at derkholm.net Sun May 30 00:11:02 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Sun May 30 00:03:22 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1085890262966.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040530
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
The following files were modified in the last 24 hours:
* biojava-live/src/org/biojava/bio/symbol/SoftMaskedAlphabet.java
* biojava-live/tests/org/biojava/bio/symbol/TestSoftMaskedAlphabet.java
A patch file reflecting these changes is available from
http://www.derkholm.net/autobuild/patches/
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From pjkerr_qg at ridgecrest.ca.us Sun May 30 05:37:52 2004
From: pjkerr_qg at ridgecrest.ca.us (Patricia J. Kerr)
Date: Sun May 30 02:38:46 2004
Subject: [Biojava-dev] Very powerful weightloss now available.
Message-ID: <3cc801c44629$d59d7897$c6c218bb@2.dk>
Hello, I have a special_offer for you...
WANT TO LOSE WEIGHT?
The most powerful weightloss is now available
without prescription. All natural Adipren720
100% Money Back Guarant?e!
- Lose up to 19% Total Body Weight.
- Up to 300% more Weight Loss while dieting.
- Loss of 20-35% abdominal Fat.
- Reduction of 40-70% overall Fat under skin.
- Increase metabolic rate by 76.9% without Exercise.
- Boost your Confidence level and Self Esteem.
- Burns calorized fat.
- Suppresses appetite for sugar.
Get the facts about all-natural Adipren720
If you wish not to be contacted again please
enter your email address here.
From fred at exsel.co.uk Sun May 30 23:50:13 2004
From: fred at exsel.co.uk (=?Windows-1251?B?1/Ph5e3q7iDC4Ovl7fLo7eA=?=)
Date: Sun May 30 23:49:22 2004
Subject: [Biojava-dev] Re:
Message-ID: <200405310349.i4V3nFKr017996@portal.open-bio.org>
? ???? e-mail ???????? ????????? ????????? ?? ?????? ? ????????? ? ??????? ??????? ?????? ? ???.
???????????? ?????????? ? ??????????:
1. ??????? ???????? ????????.
2. ???? ?????? ?????????? ? ????? ????? ????????????.
3. ??????????? ?????? ?????????? ???????? (??????? ???????? ???????, ?????????? ??????? ????? ? ?????, ?????? webmoney).
4. ?????? ???????? (e-mail, ICQ).
5. ?????? HTML
6. ??????? ????????: ??????????, ?????????????, ????????????? ? ?????????????.
7. ??????? 23-35 ???.
?? ???????? ?????????????? ??????? ?????????? ?????? ?? - ICQ 349071146
From autobuilder at derkholm.net Mon May 31 00:10:59 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Mon May 31 00:02:43 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1085976660029.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20040531
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net