<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Peter,<br><br>Good to see some activity on the BioCocoa list!<br><br>As far as I know, CVS can no longer be used to get access to the latest version of BioCocoa.<br>You should use SVN to get at the latest source code.<br><br>Best wishes,<br><br>Peter<br><br><br><br><br>On 28 Jan 2008, at 03:04, Koen van der Drift wrote:<br><br><blockquote type="cite">Hi Peter,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I'm not sure about the cvs error, but we've switched to using svn, see<br></blockquote><blockquote type="cite">instructions here on how to get the source code from the repository:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><a href="http://www.bioinformatics.org/biococoa/wiki/pmwiki.php?n=Main.UsingSubversion">http://www.bioinformatics.org/biococoa/wiki/pmwiki.php?n=Main.UsingSubversion</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">As Alex explained, there is not much activity going on with BioCocoa<br></blockquote><blockquote type="cite">right now, but new blood is always welcome! I've also included Peter<br></blockquote><blockquote type="cite">Schols's name, since he was the original developer of BioCocoa, and<br></blockquote><blockquote type="cite">may be able to help you out with your cvs errors.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">cheers,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">- Koen<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Jan 27, 2008, at 8:25 PM, Alexander Griekspoor wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hi Peter,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Unfortunately the BioCocoa project is no longer (very) active due to<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">a lack of time and to some extent need by the core developers. That<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">doesn't mean it's completely dead but what is missing is one or two<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">people who very actively like to push the project forward and which<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">have a need for a BioCocoa framework and the time to develop it. So<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">for instance it's indeed not pushed forward to 10.5, but you should<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">be easily able to checkout the project change the target SDK to 10.4<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">or 10.5 in XCode.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I don't know what formats Vector NTI support, and what it is you<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">wish to convert exactly. We have a simple GCK read method but it<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">only takes the sequence (not the vector map). Since the GCK file<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">format is closed (and binary) it won't be easy to get all data out<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">that you might wish, unless you're only interested in the raw<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">sequence.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">If you are still interested Koen should probably be able to help you<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">out with the CVS issue.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Finally, regarding 4Peaks and contigs, we'd love to do that one day<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">if time permits, we'll do our best.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Best wishes,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Alex & Tom<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Mek & Tosj<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">On 26 jan 2008, at 16:57, Peter Ulvskov wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">----------------------------------------------------------------------------<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">The following message was sent to you via the Bioinformatics.Org<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">email form.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">The sender is user Peter Ulvskov <<a href="mailto:p.ulvskov@dias.kvl.dk">p.ulvskov@dias.kvl.dk</a>>.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">To report abuse, please forward this message to <<a href="mailto:abuse@bioinformatics.org">abuse@bioinformatics.org</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">----------------------------------------------------------------------------<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Dear Alexander,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I hope that you can spare the time for a few questions:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I have signed up at bioinformatics.org because of BioCocoa. My new<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">username/password works fine for login, but I am rejected when I do<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">this:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">export CVSROOT=':ext:<a href="mailto:Ulvskov@bioinformatics.org">Ulvskov@bioinformatics.org</a>:/cvsroot'<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">cvs checkout BioCocoa -P<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">...and enter my password<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Does it take more than signing up at bioinformatics.org to download<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">BioCocoa?<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I then did the download manually, and got the 10.3.9 SDK error,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">which raises<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">the question whether BioCocoa is an active project? Are efforts<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">being made at<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">moving BioCocoa forward to 10.5? What does it entail changing the<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">SDK to<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Leopard (in other words, can I do this myself)?<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Finally, the problem I wanted to solve using BioCocoa is writing a<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">file<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">conversion utility which will convert Gene Construction Kit files<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">to Vector NTI<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">files. Is it correct that BioCocoa will help me get there?<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">By the way, one of the reasons why Vector NTI is making its way<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">into the lab<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">(under Windows XP (ouch!) on our Intel Macs) is the need for a contig<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">assembly program. Judging from your FAQ-page at Mekentosj, this is<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">one of<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">the most frequently requested features for 4Peaks. Any chance that<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">you will<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">be swayed by the prayers?<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Thanks for your time, best regards,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Peter<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">(My Bioinformatics.Org username is Ulvskov.)<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">__________________________________________________<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">D O T E A S Y - "Join the web hosting revolution!"<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> <a href="http://www.doteasy.com">http://www.doteasy.com</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">**********************************************<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> ** Alexander Griekspoor PhD **<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">**********************************************<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> mekentosj.com<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> EnzymeX - To cut or not to cut<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">2006 Winner of the Apple Design Awards<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Best Mac OS X Scientific Solution<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> <a href="http://www.mekentosj.com/enzymex">http://www.mekentosj.com/enzymex</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">**********************************************<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Biococoa-dev mailing list<br></blockquote><blockquote type="cite"><a href="mailto:Biococoa-dev@bioinformatics.org">Biococoa-dev@bioinformatics.org</a><br></blockquote><blockquote type="cite"><a href="http://www.bioinformatics.org/mailman/listinfo/biococoa-dev">http://www.bioinformatics.org/mailman/listinfo/biococoa-dev</a><br></blockquote><br></body></html>