[Biojava-l] Fwd: [Fwd: Bio-Informatics Visualization Workshop]

--- Forwarded Message Date: Wed, 10 Apr 2002 11:32:02 -0400 From: "Shneiderman, Ben" <[EMAIL PROTECTED]> To: "'[EMAIL PROTECTED]'" <[EMAIL PROTECTED]>,Faculty<[EMAIL PROTECTED]>,"'[EMAIL PROTECTED]'"<[EMAIL PROTECTED]> Dear Colleagues - please circulate to appropriate people... thanks.. Be

[Biojava-l] Javadoc review

Yesterday I was working on imagemaps using BioJava and wanted to use some structured Annotation. I found some potentially helpful classes, as judged by their names, but they were mostly undocumented. I've added Javadoc, but I could not fully understand the author's intent in some areas (although

Re: [Biojava-l] Javadoc review

Keith James wrote: > Yesterday I was working on imagemaps using BioJava and wanted to use > some structured Annotation. I found some potentially helpful classes, > as judged by their names, but they were mostly undocumented. > > I've added Javadoc, but I could not fully understand the author's >

[Biojava-l] feature property changeability

Hi all, I've checked in a change to the feature interface. It now has getters as well as setters for location, source and type. Additionaly, there are apropreate ChangeType constants on the Feature interface. I have tried to make sure that everything still compiles. This change has implicatio

Re: [Biojava-l] Javadoc review

Keith James wrote: > Yesterday I was working on imagemaps using BioJava and wanted to use > some structured Annotation. I found some potentially helpful classes, > as judged by their names, but they were mostly undocumented. These classes allow you to validate an Annotation object by the values

[Biojava-l] MIAME ER diagram

I was wondering if anyone has constructed an ER diagram for MIAME. Thank you. Regards, Indu _ Send and receive Hotmail on your mobile device: http://mobile.msn.com ___ Biojava-l mailin

Re: [Biojava-l] MIAME ER diagram

On Thu, Apr 11, 2002 at 02:11:50PM +, Indu Shrivastava wrote: > I was wondering if anyone has constructed an ER diagram for MIAME. My understanding is that MIAME has been superceded by MAGE-OM: http://www.mged.org/Workgroups/MAGE/mage.html They offer ER diagrams either in Rose ULM form

Re: [Biojava-l] BioInformatics toolbox.

This is my first time writing to this list, so I think I should introduce myself. My name is Patrick McConnell, and I am a scientific program at the Duke Bioinformatics Shared Resource. We work on a variety of things, but I am currently working on a flexible java framework for high-throughput bat

Re: [Bioperl-l] Re: [Biojava-l] BioInformatics toolbox.

Alex Rolfe wrote: > > A number of people have pointed out that several GUI's exist for > connecting components into pipelines (and I'll add my own- the > biojava-lims code that I've been working on) and that the existing > bio{perl,java} classes could probably be extended or wrapped to fit into

[Biojava-l] translator

Is there a translator tool available in bioperl package which does frame shift & correct translational frame etc. thanks Geetha -Original Message- From: Catherine Letondal [mailto:[EMAIL PROTECTED]] Sent: Thursday, April 11, 2002 3:30 PM To: Alex Rolfe Cc: autopost; [EMAIL PROTECTED]; [E

[Biojava-l] extracting genome sequence from Genbank file

Hello, I have just started using biojava and find it extremely useful. Particularly, I am using it for parsing Genbank files. I took a look at the documentation as well as TestGenbank.java under demos/seq directory to get an idea of how to extract various information from Genbank files. One thi

Re: [Biojava-l] BioInformatics toolbox.

> This is my first time writing to this list, so I think I should introduce > myself. My name is Patrick McConnell, and I am a scientific program at the [snip] Wow. These new AI programs are getting _really_ clever ! :-^ Hi Patrick. Your comments and thoughts are pretty much aligned with mine

RE: [Biojava-l] extracting genome sequence from Genbank file

Hi - The following should do it: File gbFile = new File("myGBFile.gbk"); SequenceIterator si = SeqIOTools.readGenbank( new BufferedReader( new FileReader(gbFile),1024)); Sequence s = si.next(); This returns a sequence iterator that iterates through all the sequences in the GenBan

[Biojava-l] new anoncvs server (was Re: Problems with Biojava CVS)

Tom Hudson wrote: > Using the WebCVS interface, every time I click on help I get the error > message > > /cgi-bin/viewcvs/viewcvs.cgi/biojava-lims/org/biojava/lims//*docroot*/help_dirview.html/biojava-lims/org/biojava/lims/%2Adocroot%2A/help_dirview.html: > unknown location > Hi Tom,

Re: [Biojava-l] new anoncvs server (was Re: Problems with BiojavaCVS)

Maybe it would be a good idea to check out the Web logs to see how often the viewcvs interface is accessed. That might give you an idea of how high a priority to make fixing it. Maybe the biopython folks could have a go :-) ? Yours, Ann --- Ann E. Loraine http://www.loraine.net ___