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[Biojava-l] (no subject)

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[Biojava-l] Re: [Bioperl-l] Re: Biojava-l digest, Vol 1 #611 - 2 msgs

autopost wrote: > Are there any open source projects that are working towards creating tools > or a suite of applications for BioInformatics rather than creating a > library/SDK? We want to find a group that is interested (or is already) > creating pre-built tools > > BioPerl and BioJava are

Re: [Biojava-l] Re: Biojava-l digest, Vol 1 #611 - 2 msgs

On Fri, 5 Apr 2002, autopost wrote: > Are there any open source projects that are working towards creating tools > or a suite of applications for BioInformatics rather than creating a > library/SDK? We want to find a group that is interested (or is already) > creating pre-built tools > > Bio

[Biojava-l] Re: [Bioperl-l] Re: Biojava-l digest, Vol 1 #611 - 2 msgs

Hi, The suggestion you made is because you did not know the broad band philosophy of BioXXX. Bioperl and some other sister projects have originally been based on 'open' philosophy. Object oriented Bioperl is a very significant part of it, however, the general Bioperl encompasses it. (Bioperl is

[Biojava-l] Re: Biojava-l digest, Vol 1 #611 - 2 msgs

Are there any open source projects that are working towards creating tools or a suite of applications for BioInformatics rather than creating a library/SDK? We want to find a group that is interested (or is already) creating pre-built tools BioPerl and BioJava are great libraries. I would th

[Biojava-l] ORF Hunting

Is there any methods in biojava that predict open reading frames? I looked through the javadocs and I couldn't find any. I just want all the ORFs, I don't want to do gene prediction. -John ___ Biojava-l mailing list - [EMAIL PROTECTED] http://bi

Re: [Biojava-l] Convince us to use BioJava (and come to the next bootcamp)

On Fri, 5 Apr 2002, Tom Hudson wrote: > A research group here at UNCW is starting a couple of bioinformatics > projects in Java. I said, "look here, there's this open-source group on > the web that's created a huge amount of code already, let's use it!" > > The responses I've gotten have been

[Biojava-l] Alignment files?

Hello Everyone, I've got some msf alignment files (generated by clustalw) I'm trying to parse, but org.biojava.bio.seq.io.MSFAlignmentFormat chokes on them and org.biojava.bio.program.sax.SequenceAlignmentSAXParser doesn't parse MSF files, it only parses Clustal and Needle. I was thinking

Re: [Biojava-l] Convince us to use BioJava (and come to the next bootcamp)

> "Tom" == Tom Hudson <[EMAIL PROTECTED]> writes: Tom> A research group here at UNCW is starting a couple of Tom> bioinformatics projects in Java. I said, "look here, there's Tom> this open-source group on the web that's created a huge amount Tom> of code already, let's use it!" T

[Biojava-l] Convince us to use BioJava (and come to the next bootcamp)

A research group here at UNCW is starting a couple of bioinformatics projects in Java. I said, "look here, there's this open-source group on the web that's created a huge amount of code already, let's use it!" The responses I've gotten have been on the order of "Eww, 600+ classes. I can write

Re: [Biojava-l] Framework VI Expression of Interest

On Fri, 5 Apr 2002, Jean-Marie Buerstedde wrote: > > I think there is ample opportunity to obtain funding for a biojava > initiative and it seems to be advantageous to get as many as possible > centers and people involved. One idea among others could be to propose > JAVA and especially J2EE a

Re: [Biojava-l] biojava-acedb - recent version?

Hi Ben, I don't think we ever got the ace->sequence bridge working fully. It was done before the days of the feature projection framework, when life was even more complicated. The package for retrieving ace objects should all work fine though. Initialy, you could 'hide' the org.acedb.sequence pac

[Biojava-l] Framework VI Expression of Interest

The first guidelines for the new European framework VI are now available (http://www.cordis.lu/fp6). There are a number of differences to previous frameworks with emphasis on bigger consortia for integrated projects and so-called networks of excellence. One of the main emphasis is on bioinform

Re: [Biojava-l] FeatureHolder.containsFeature()

> "Mark" == Schreiber, Mark <[EMAIL PROTECTED]> writes: >> Could I propose that with regard to DB-backed persistent >> objects, Feature objects store the unique id of the feature >> within them and containsFeature only returns true if the >> feature of that unique ID is a chil