[Biojava-l] BLAST/Java interface
Patrick McConnell
MCCon012@mc.duke.edu
Mon, 26 Aug 2002 09:23:22 -0400
As far as jar dependencies, it depends on which web services software you
use. It will also depend on whether you want to host web services or not.
For GLUE, the jars your need are:
GLUE-STD.jar
dom.jar
jnet.jar
servlet.jar
Optional dependencies:
jsp.jar and xerces.jar for JSP support
jsse.jar and jcert.jar for SSL support
So, you are looking at anywhere from 4 jars to 8 jars.
Java's Web Services Developer pack includes between 40 and 50 jars. I do
not know how many of these are really needed, and I do not want to try to
figure it out. JWSDP is simply a mess. (One humble progammers opinion)
If you go with Axis, you will have 7 jars:
axis.jar
jaxrpc.jar
saaj.jar
wsdl4j.jar
tt-bytecode.jar
commons-logging.jar
xerces.jar or crimson.jar
However, Axis is still in the beta 3 testing stage. So, I would recommend
against it, except that I know several developers who are using Axis
successfully (and in the hopes that a production version will be released
in the near future).
If this looks like a promising project, I would like to volunteer my time
to help develop web services for BioJava. I have developed many, many web
services for internal use here, which would be good candidates for porting
to BioJava. Also, I am involved in a project for developing web services
to sit atop a grid at the North Carolina Supercomputing Center. We will
also be developing web portals (JSP/servlets) for the web services. These
could also be ported to BioJava. (For instance, I have developed a JSP
script that formats NCBI blast XML to a web page that looks nearly
identicle to NCBI's output.)
Let me know,
-Patrick McConnell
Duke Bioinformatics Shared Resource
"Schreiber, Mark" <mark.schreiber@agresearch.co.nz>@biojava.org on
08/25/2002 04:57:13 PM
Sent by: biojava-l-admin@biojava.org
To: "Brian Gilman" <gilmanb@genome.wi.mit.edu>, "Patrick McConnell"
<MCCon012@mc.duke.edu>, <biojava-l@biojava.org>
cc:
Subject: RE: [Biojava-l] BLAST/Java interface
I think that a web service of BLAST or a binary installation are
preferable to submitting BLAST to NCBI for anything over 30 or so
sequences. You can quite quickly find your domain blocked from NCBI's
web servers if you send large numbers of messages to NCBI. (Speaking
from personal experience).
The question really is can this sort of service be bundled with BioJava
or does it contain so many dependencies that each install would have to
be a custom job? Seems to be getting into the realms of Enterprise
BioJava (don't laugh Brian!)
- Mark
> -----Original Message-----
> From: Brian Gilman [mailto:gilmanb@genome.wi.mit.edu]
> Sent: Saturday, 24 August 2002 2:02 a.m.
> To: Patrick McConnell; biojava-l@biojava.org
> Subject: Re: [Biojava-l] BLAST/Java interface
>
>
> On 8/23/02 9:18 AM, "Patrick McConnell" <MCCon012@mc.duke.edu> wrote:
>
> >
> > ---------------------- Forwarded by Patrick
> McConnell/CanCtr/mc/Duke
> > on 08/23/2002 09:19 AM ---------------------------
> >
> > From: Patrick McConnell on 08/23/2002 08:57 AM
> >
> > To: nathan whitehouse <nlwhitehouse@yahoo.com>
> > cc:
> >
> > Subject: Re: [Biojava-l] BLAST/Java interface (Document
> link: Patrick
> > McConnell)
> >
>
> Hello Patrick et al.
>
> > I have developed a blast web service that takes all of the standard
> > blast parameters and returns NCBI blast XML. I have also generated
> > classes that correspond to the blast XML complex types, so
> you don't
> > even have to know anything about XML.
>
> This is great! If you'd like to take a look at a complete
> analysis framework you can sneak a peak in omnigene's CVS
> repository under analysis and webservice/analysis. The jar
> can built by doing a jar-analysisjob and jar-analysis.
>
> If people would like to discuss how a generic analysis
> service can/has been build I'd be happy to share my thoughts.
> It looks like we are all going to be producing interesting
> services in the near future!!
>
> Ours happens to use a database backend as a queue and EJB's
> to handle the session and transaction layer.
>
> -B
>
> >
> > The web service is developed to be hosted by GLUE, but it
> should not
> > be a problem to port it to another web service container.
> >
> > I have release the source, as well as the compiled Java code. I
> > include the jar for the web services container, so you do
> not need to
> > download anything else to get up and running.
> >
> > See: http://mendel.mc.duke.edu:1755/services/blast/ for full source
> > code and compiled classes.
> >
> > I am currently developing servlets/jsps as a web front-end to this,
> > which will format the XML into an NCBI-like html page.
> Thus, it will
> > be a full package for serving blast.
> >
> > Good luck,
> >
> > -Patrick
> >
> >
> >
> >
> > nathan whitehouse <nlwhitehouse@yahoo.com>@biojava.org on
> 08/22/2002
> > 04:39:05 PM
> >
> > Sent by: biojava-l-admin@biojava.org
> >
> >
> > To: biojava-l@biojava.org
> > cc:
> >
> > Subject: [Biojava-l] BLAST/Java interface
> >
> >
> > Hello people at BioJava,
> >
> > I'm modifying an existing Java applet-servlet used
> > by this lab.
> >
> > People want us to add BLAST to this applet.
> >
> > Anybody know of a good way to do this?
> >
> > Are there convenient BLAST libraries to call from
> > the servlet? We've talked about calling a C or C++
> > library using the JNI. I've looked around and it
> > seems that there's no modularized BLAST lying around
> > that would make this easy.
> > The simple way to do it is just call BLASTAll from
> > the shell with its arguments. But this is a hack; I
> > want to know if there is a better way to pass objects
> > in and out of BLAST.
> >
> > Thanks!
> > Nathan
> >
> > Nathan Whitehouse
> > Shaulsky Lab
> > Baylor College of Medicine
> > Houston, Texas, USA
> >
> > __________________________________________________
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> >
> >
> >
> >
> >
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> >
>
> --
> Brian Gilman <gilmanb@genome.wi.mit.edu>
> Group Leader Medical & Population Genetics Dept.
> MIT/Whitehead Inst. Center for Genome Research
> One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
> phone +1 617 252 1069 / fax +1 617 252 1902
>
> _______________________________________________
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> http://biojava.org/mailman/listinfo/biojava-l
>
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