From mekentosj at gmail.com Sun Jul 2 07:39:54 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Sun, 2 Jul 2006 12:39:54 +0100 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: References: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> <1000C532-9B90-4973-92E4-A3D23440E76A@gmail.com> <89765950-0EA5-4A41-B695-97D7E56342C1@mac.com> <006E20EA-D168-45F8-8795-06233DAE9F00@bioworxx.com> <4E1A6A82-62B5-402A-A64F-B2A5524ED959@gmail.com> <4EAD2BB8-53E0-4B66-B9F0-19FC6C9C286F@mac.com> Message-ID: <675801E2-E4D9-4C0C-8765-E841A8C7C14B@gmail.com> Hi guys, I registered for a poster session at the WWDC using the following abstract (a slight adaption from what we used last year). Organization/Affiliation The BioCocoa project at bioinformatics.org Title of Poster BioCocoa ? A Cocoa framework for handling and manipulating biological sequences Abstract Text BioCocoa is an opensource Cocoa framework for bioinformatics written in Objective-C. We intend to provide Cocoa programmers with a full suite of tools for handling and manipulating biological sequence information. Initially started as framework to read and write the plethora of available sequence file formats, we work to make BioCocoa a more general bioframework leveraging the power of the objective-C language and Cocoa frameworks. Eventually, we aspire to become siblings of OpenBio.org projects like BioJava, BioPerl, and BioRuby. We will discuss the framework structure and layout, its design principles, current status and future plans, and will show examples of applications that already use the BioCocoa framework. URL: http://www.bioinformatics.org/biococoa/ > So what's going to be on the poster? Just a copy of the website, or > some more stuff. For instance a screenshot of apps that use BioCocoa. After my trip next week back to Holland I'll try to wrap up some ideas into a draft poster that we can work further on. Cheers, Alex ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com 4Peaks - For Peaks, Four Peaks. 2004 Winner of the Apple Design Awards Best Mac OS X Student Product http://www.mekentosj.com/4peaks ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sun Jul 2 08:39:35 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 2 Jul 2006 08:39:35 -0400 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: <675801E2-E4D9-4C0C-8765-E841A8C7C14B@gmail.com> References: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> <1000C532-9B90-4973-92E4-A3D23440E76A@gmail.com> <89765950-0EA5-4A41-B695-97D7E56342C1@mac.com> <006E20EA-D168-45F8-8795-06233DAE9F00@bioworxx.com> <4E1A6A82-62B5-402A-A64F-B2A5524ED959@gmail.com> <4EAD2BB8-53E0-4B66-B9F0-19FC6C9C286F@mac.com> <675801E2-E4D9-4C0C-8765-E841A8C7C14B@gmail.com> Message-ID: <89A49200-F005-4021-B50D-EDD6880E89D9@earthlink.net> Sounds good Alex. Thanks for submitting the abstract. Let me know if you need any help with the poster. Your last sentence suggests you're not in NL anymore? Did you get a new job somewhere abroad? cheers, - Koen. From mekentosj at gmail.com Sun Jul 2 08:49:46 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Sun, 2 Jul 2006 13:49:46 +0100 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: <89A49200-F005-4021-B50D-EDD6880E89D9@earthlink.net> References: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> <1000C532-9B90-4973-92E4-A3D23440E76A@gmail.com> <89765950-0EA5-4A41-B695-97D7E56342C1@mac.com> <006E20EA-D168-45F8-8795-06233DAE9F00@bioworxx.com> <4E1A6A82-62B5-402A-A64F-B2A5524ED959@gmail.com> <4EAD2BB8-53E0-4B66-B9F0-19FC6C9C286F@mac.com> <675801E2-E4D9-4C0C-8765-E841A8C7C14B@gmail.com> <89A49200-F005-4021-B50D-EDD6880E89D9@earthlink.net> Message-ID: <0EE16336-BF74-4564-86A2-A780AB1ACED5@gmail.com> > Your last sentence suggests you're not in NL anymore? Did you get a > new job somewhere abroad? I'm in a kind of vacuum right now ;-) I finished working at the Netherlands Cancer Institute, but only have my thesis defence on the 1st of November. Two weeks ago I heard that my Marie Curie (EU) grant proposal got accepted which would allow me to start a postdoc at the European Bioinformatics Institute in Cambridge, UK, (yep, no more wetlab, but bioinformatics aimed at text mining) probably from around October/November. In between I spent the last month with T?nia in Portugal, we will move the coming month back to Holland, and then in August we're in Portugal again. And from September back in Holland ;-). In between we have to arrange all moving, new job, thesis stuff, etc Plus, I hope to have some time for programming...(stress on "hope"). So lot of turbulence right now ;-) Cheers, Alex ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com Windows is a 32-bit patch to a 16-bit shell for an 8-bit operating system, written for a 4-bit processor by a 2- bit company without 1 bit of sense. ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sun Jul 2 08:57:33 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 2 Jul 2006 08:57:33 -0400 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: <0EE16336-BF74-4564-86A2-A780AB1ACED5@gmail.com> References: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> <1000C532-9B90-4973-92E4-A3D23440E76A@gmail.com> <89765950-0EA5-4A41-B695-97D7E56342C1@mac.com> <006E20EA-D168-45F8-8795-06233DAE9F00@bioworxx.com> <4E1A6A82-62B5-402A-A64F-B2A5524ED959@gmail.com> <4EAD2BB8-53E0-4B66-B9F0-19FC6C9C286F@mac.com> <675801E2-E4D9-4C0C-8765-E841A8C7C14B@gmail.com> <89A49200-F005-4021-B50D-EDD6880E89D9@earthlink.net> <0EE16336-BF74-4564-86A2-A780AB1ACED5@gmail.com> Message-ID: On Jul 2, 2006, at 8:49 AM, Alexander Griekspoor wrote: > I'm in a kind of vacuum right now ;-) > I finished working at the Netherlands Cancer Institute, but only > have my thesis defence on the 1st of November. Two weeks ago I > heard that my Marie Curie (EU) grant proposal got accepted which > would allow me to start a postdoc at the European Bioinformatics > Institute in Cambridge, UK, (yep, no more wetlab, but > bioinformatics aimed at text mining) probably from around October/ > November. In between I spent the last month with T?nia in Portugal, > we will move the coming month back to Holland, and then in August > we're in Portugal again. And from September back in Holland ;-). In > between we have to arrange all moving, new job, thesis stuff, etc > Plus, I hope to have some time for programming...(stress on > "hope"). So lot of turbulence right now ;-) > That's good news, congrats on the grant and the postdoc position, the EBI sounds like a great place to be. I hope you can enjoy your time in Portugal, even though they eliminated the Netherlands last week ;-) cheers, - Koen. From sweetcocoa at mac.com Sun Jul 2 10:49:54 2006 From: sweetcocoa at mac.com (Peter Schols) Date: Sun, 2 Jul 2006 16:49:54 +0200 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: <675801E2-E4D9-4C0C-8765-E841A8C7C14B@gmail.com> References: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> <1000C532-9B90-4973-92E4-A3D23440E76A@gmail.com> <89765950-0EA5-4A41-B695-97D7E56342C1@mac.com> <006E20EA-D168-45F8-8795-06233DAE9F00@bioworxx.com> <4E1A6A82-62B5-402A-A64F-B2A5524ED959@gmail.com> <4EAD2BB8-53E0-4B66-B9F0-19FC6C9C286F@mac.com> <675801E2-E4D9-4C0C-8765-E841A8C7C14B@gmail.com> Message-ID: <37B63D56-92E7-44F8-B1D7-E41DD27BA0E3@mac.com> Hi Alex, The abstract sounds very good! Please let me know if you need any help with the poster. best wishes, Peter On 02 Jul 2006, at 13:39, Alexander Griekspoor wrote: > Hi guys, > > I registered for a poster session at the WWDC using the following > abstract (a slight adaption from what we used last year). > > Organization/Affiliation > > The BioCocoa project at bioinformatics.org > > Title of Poster > > BioCocoa ? A Cocoa framework for handling and manipulating > biological sequences > > Abstract Text > > BioCocoa is an opensource Cocoa framework for bioinformatics > written in Objective-C. We intend to provide Cocoa programmers with > a full suite of tools for handling and manipulating biological > sequence information. Initially started as framework to read and > write the plethora of available sequence file formats, we work to > make BioCocoa a more general bioframework leveraging the power of > the objective-C language and Cocoa frameworks. Eventually, we > aspire to become siblings of OpenBio.org projects like BioJava, > BioPerl, and BioRuby. We will discuss the framework structure and > layout, its design principles, current status and future plans, and > will show examples of applications that already use the BioCocoa > framework. > > URL: http://www.bioinformatics.org/biococoa/ > > >> So what's going to be on the poster? Just a copy of the website, >> or some more stuff. For instance a screenshot of apps that use >> BioCocoa. > > After my trip next week back to Holland I'll try to wrap up some > ideas into a draft poster that we can work further on. > Cheers, > Alex > > > > ********************************************************* > ** Alexander Griekspoor ** > ********************************************************* > The Netherlands Cancer Institute > Department of Tumorbiology (H4) > Plesmanlaan 121, 1066 CX, Amsterdam > Tel: + 31 20 - 512 2023 > Fax: + 31 20 - 512 2029 > AIM: mekentosj at mac.com > E-mail: a.griekspoor at nki.nl > Web: http://www.mekentosj.com > > 4Peaks - For Peaks, Four Peaks. > 2004 Winner of the Apple Design Awards > Best Mac OS X Student Product > http://www.mekentosj.com/4peaks > > ********************************************************* > From kvddrift at earthlink.net Sun Jul 2 11:33:28 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 2 Jul 2006 11:33:28 -0400 Subject: [Biococoa-dev] license Message-ID: Hi, On the website the BioCocoa is stated as GNU LGPL. However, some of the classes that Alex provided have a Creative Commons license. I don't really care which one we use (as long as it is freely available and useable for everyone), but at least I think we should have the same license for the whole project. cheers, - Koen. From mekentosj at gmail.com Sun Jul 2 11:36:21 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Sun, 2 Jul 2006 16:36:21 +0100 Subject: [Biococoa-dev] license In-Reply-To: References: Message-ID: <0DBD330F-52E2-4891-9BB1-B60E6E3B6BD1@gmail.com> I agree with you Koen. I don't really care either. The difference is mainly that with the Creative Commons you can also take parts, with LGPL you have to use the framework as a whole. With the views, the latter would be difficult. I could be wrong though. Maybe Peter can tell more and/or has a different opinion. Cheers, Alex On 2-jul-2006, at 16:33, Koen van der Drift wrote: > Hi, > > On the website the BioCocoa is stated as GNU LGPL. However, some of > the classes that Alex provided have a Creative Commons license. I > don't really care which one we use (as long as it is freely > available and useable for everyone), but at least I think we should > have the same license for the whole project. > > cheers, > > - Koen. > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > > > ___________________________________________________________ > $0 Web Hosting with up to 200MB web space, 1000 MB Transfer > 10 Personalized POP and Web E-mail Accounts, and much more. > Signup at www.doteasy.com > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com 4Peaks - For Peaks, Four Peaks. 2004 Winner of the Apple Design Awards Best Mac OS X Student Product http://www.mekentosj.com/4peaks ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From sweetcocoa at mac.com Sun Jul 2 11:47:08 2006 From: sweetcocoa at mac.com (Peter Schols) Date: Sun, 2 Jul 2006 17:47:08 +0200 Subject: [Biococoa-dev] license In-Reply-To: <0DBD330F-52E2-4891-9BB1-B60E6E3B6BD1@gmail.com> References: <0DBD330F-52E2-4891-9BB1-B60E6E3B6BD1@gmail.com> Message-ID: Guys, If nobody takes offense, I'd propose to switch the entire project to a CC license. It indeed gives even more freedom to the framework clients. Peter On 02 Jul 2006, at 17:36, Alexander Griekspoor wrote: > I agree with you Koen. I don't really care either. The difference > is mainly that with the Creative Commons you can also take parts, > with LGPL you have to use the framework as a whole. With the views, > the latter would be difficult. I could be wrong though. Maybe Peter > can tell more and/or has a different opinion. > Cheers, > Alex > > On 2-jul-2006, at 16:33, Koen van der Drift wrote: > >> Hi, >> >> On the website the BioCocoa is stated as GNU LGPL. However, some >> of the classes that Alex provided have a Creative Commons license. >> I don't really care which one we use (as long as it is freely >> available and useable for everyone), but at least I think we >> should have the same license for the whole project. >> >> cheers, >> >> - Koen. >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> >> >> ___________________________________________________________ >> $0 Web Hosting with up to 200MB web space, 1000 MB Transfer >> 10 Personalized POP and Web E-mail Accounts, and much more. >> Signup at www.doteasy.com >> > > ********************************************************* > ** Alexander Griekspoor ** > ********************************************************* > The Netherlands Cancer Institute > Department of Tumorbiology (H4) > Plesmanlaan 121, 1066 CX, Amsterdam > Tel: + 31 20 - 512 2023 > Fax: + 31 20 - 512 2029 > AIM: mekentosj at mac.com > E-mail: a.griekspoor at nki.nl > Web: http://www.mekentosj.com > > 4Peaks - For Peaks, Four Peaks. > 2004 Winner of the Apple Design Awards > Best Mac OS X Student Product > http://www.mekentosj.com/4peaks > > ********************************************************* > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From kvddrift at earthlink.net Sun Jul 2 15:53:58 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 2 Jul 2006 15:53:58 -0400 Subject: [Biococoa-dev] license In-Reply-To: References: <0DBD330F-52E2-4891-9BB1-B60E6E3B6BD1@gmail.com> Message-ID: On Jul 2, 2006, at 11:47 AM, Peter Schols wrote: > If nobody takes offense, I'd propose to switch the entire project > to a CC license. It indeed gives even more freedom to the framework > clients. no problem :) - Koen. From kvddrift at earthlink.net Mon Jul 3 08:51:29 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 3 Jul 2006 08:51:29 -0400 Subject: [Biococoa-dev] universal framework ? Message-ID: <9A3ECF21-537E-4079-864C-26B891CE5553@earthlink.net> Hi, Does anyone know if the current version of the framework is already 'Universal' ? For the poster and WWDC, I think it would be a good idea to make a universal framework, but I would not know how to do that. What do you guys think? Should we then still have a regular version as well ? If someone could point me to some instructions, I'd be happy to add it to the framework and commit it to cvs. cheers, - Koen. From sweetcocoa at mac.com Mon Jul 3 09:12:12 2006 From: sweetcocoa at mac.com (Peter Schols) Date: Mon, 3 Jul 2006 15:12:12 +0200 Subject: [Biococoa-dev] universal framework ? In-Reply-To: <9A3ECF21-537E-4079-864C-26B891CE5553@earthlink.net> References: <9A3ECF21-537E-4079-864C-26B891CE5553@earthlink.net> Message-ID: Hi Koen, Going universal is easy (at least in theory). In the project info, you have to make sure you link against the 10.4 Universal SDK. Then make sure to select both Intel and PPC in the build settings, and that's it. At least, when the code itself is "universal". All Cocoa code is universal by default. Plain C code might cause some trouble (endian issues, ...), but as far as BC is concerned, this will only be a small percentage, I guess. I'm not entirely sure that the Universal binary will still work as expected on pre-Tiger systems. Therefore, you'll have to do a little more work. Hint #2 in the following article gives a good overview on how to support pre-Tiger systems with universal binaries: http:// www.red-sweater.com/blog/149/summer-xcode-tips best wishes, Peter On 03 Jul 2006, at 14:51, Koen van der Drift wrote: > Hi, > > Does anyone know if the current version of the framework is already > 'Universal' ? For the poster and WWDC, I think it would be a good > idea to make a universal framework, but I would not know how to do > that. What do you guys think? Should we then still have a regular > version as well ? > > If someone could point me to some instructions, I'd be happy to add > it to the framework and commit it to cvs. > > > cheers, > > - Koen. > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From kvddrift at earthlink.net Thu Jul 6 21:39:56 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 6 Jul 2006 21:39:56 -0400 Subject: [Biococoa-dev] license In-Reply-To: References: <0DBD330F-52E2-4891-9BB1-B60E6E3B6BD1@gmail.com> Message-ID: <566102FA-CA94-4599-B75B-1DBAB502D113@earthlink.net> So I had a quick look at the CC website, and through a couple of questions, ended up with the following license: http:// creativecommons.org/licenses/by-sa/2.5/. Basically it allows BioCocoa to be used in bot non- and commercial apps, and allows people to modify the code, as long as they use the same license, and inform other users of their modifications. I couldn't find anything about using parts of the framework. cheers, - Koen. On Jul 2, 2006, at 11:47 AM, Peter Schols wrote: > Guys, > > If nobody takes offense, I'd propose to switch the entire project > to a CC license. It indeed gives even more freedom to the framework > clients. > Peter > > > On 02 Jul 2006, at 17:36, Alexander Griekspoor wrote: > >> I agree with you Koen. I don't really care either. The difference >> is mainly that with the Creative Commons you can also take parts, >> with LGPL you have to use the framework as a whole. With the >> views, the latter would be difficult. I could be wrong though. >> Maybe Peter can tell more and/or has a different opinion. >> Cheers, >> Alex >> >> On 2-jul-2006, at 16:33, Koen van der Drift wrote: >> >>> Hi, >>> >>> On the website the BioCocoa is stated as GNU LGPL. However, some >>> of the classes that Alex provided have a Creative Commons >>> license. I don't really care which one we use (as long as it is >>> freely available and useable for everyone), but at least I think >>> we should have the same license for the whole project. >>> >>> cheers, >>> >>> - Koen. >>> _______________________________________________ >>> Biococoa-dev mailing list >>> Biococoa-dev at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>> >>> >>> ___________________________________________________________ >>> $0 Web Hosting with up to 200MB web space, 1000 MB Transfer >>> 10 Personalized POP and Web E-mail Accounts, and much more. >>> Signup at www.doteasy.com >>> >> >> ********************************************************* >> ** Alexander Griekspoor ** >> ********************************************************* >> The Netherlands Cancer Institute >> Department of Tumorbiology (H4) >> Plesmanlaan 121, 1066 CX, Amsterdam >> Tel: + 31 20 - 512 2023 >> Fax: + 31 20 - 512 2029 >> AIM: mekentosj at mac.com >> E-mail: a.griekspoor at nki.nl >> Web: http://www.mekentosj.com >> >> 4Peaks - For Peaks, Four Peaks. >> 2004 Winner of the Apple Design Awards >> Best Mac OS X Student Product >> http://www.mekentosj.com/4peaks >> >> ********************************************************* >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From sweetcocoa at mac.com Fri Jul 7 03:22:52 2006 From: sweetcocoa at mac.com (Peter Schols) Date: Fri, 7 Jul 2006 09:22:52 +0200 Subject: [Biococoa-dev] license In-Reply-To: <566102FA-CA94-4599-B75B-1DBAB502D113@earthlink.net> References: <0DBD330F-52E2-4891-9BB1-B60E6E3B6BD1@gmail.com> <566102FA-CA94-4599-B75B-1DBAB502D113@earthlink.net> Message-ID: Hi Koen, This seems OK to me. I guess a framework is always used partially, so I don't see any problems there. cheers, Peter On 07 Jul 2006, at 03:39, Koen van der Drift wrote: > So I had a quick look at the CC website, and through a couple of > questions, ended up with the following license: http:// > creativecommons.org/licenses/by-sa/2.5/. Basically it allows > BioCocoa to be used in bot non- and commercial apps, and allows > people to modify the code, as long as they use the same license, > and inform other users of their modifications. I couldn't find > anything about using parts of the framework. > > cheers, > > - Koen. > > On Jul 2, 2006, at 11:47 AM, Peter Schols wrote: > >> Guys, >> >> If nobody takes offense, I'd propose to switch the entire project >> to a CC license. It indeed gives even more freedom to the >> framework clients. >> Peter >> >> >> On 02 Jul 2006, at 17:36, Alexander Griekspoor wrote: >> >>> I agree with you Koen. I don't really care either. The difference >>> is mainly that with the Creative Commons you can also take parts, >>> with LGPL you have to use the framework as a whole. With the >>> views, the latter would be difficult. I could be wrong though. >>> Maybe Peter can tell more and/or has a different opinion. >>> Cheers, >>> Alex >>> >>> On 2-jul-2006, at 16:33, Koen van der Drift wrote: >>> >>>> Hi, >>>> >>>> On the website the BioCocoa is stated as GNU LGPL. However, some >>>> of the classes that Alex provided have a Creative Commons >>>> license. I don't really care which one we use (as long as it is >>>> freely available and useable for everyone), but at least I think >>>> we should have the same license for the whole project. >>>> >>>> cheers, >>>> >>>> - Koen. >>>> _______________________________________________ >>>> Biococoa-dev mailing list >>>> Biococoa-dev at bioinformatics.org >>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>>> >>>> >>>> ___________________________________________________________ >>>> $0 Web Hosting with up to 200MB web space, 1000 MB Transfer >>>> 10 Personalized POP and Web E-mail Accounts, and much more. >>>> Signup at www.doteasy.com >>>> >>> >>> ********************************************************* >>> ** Alexander Griekspoor ** >>> ********************************************************* >>> The Netherlands Cancer Institute >>> Department of Tumorbiology (H4) >>> Plesmanlaan 121, 1066 CX, Amsterdam >>> Tel: + 31 20 - 512 2023 >>> Fax: + 31 20 - 512 2029 >>> AIM: mekentosj at mac.com >>> E-mail: a.griekspoor at nki.nl >>> Web: http://www.mekentosj.com >>> >>> 4Peaks - For Peaks, Four Peaks. >>> 2004 Winner of the Apple Design Awards >>> Best Mac OS X Student Product >>> http://www.mekentosj.com/4peaks >>> >>> ********************************************************* >>> >>> _______________________________________________ >>> Biococoa-dev mailing list >>> Biococoa-dev at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From mekentosj at gmail.com Sat Jul 8 08:10:28 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Sat, 8 Jul 2006 14:10:28 +0200 Subject: [Biococoa-dev] Fwd: Acceptance: WWDC2006 Scientific Development Poster Session References: <3E98D0E2-782A-4BCA-BAFD-E50971F94CFB@apple.com> Message-ID: <1E410342-38C1-47C9-8433-D627CC7923AA@gmail.com> Hi guys, Good news, the poster entry has been accepted. I will try to come up with a draft the coming week as a base to start from. As said I entered a poster about the mekentosj programs as well, which also got accepted, so Peter and Phil will represent the BioCocoa team at the WWDC during the poster session. Cheers, Alex Begin forwarded message: > From: WWDCPosterSubmit > Date: 8 juli 2006 3:08:15 GMT+02:00 > To: a.griekspoor at nki.nl > Subject: Acceptance: WWDC2006 Scientific Development Poster Session > > Alexander, > > Thank you for submitting a poster abstract to the WWDC 2006 > Scientific Development Poster Session. Your abstract has been > reviewed and you have been accepted as a poster presenter at the > conference. > > Please arrange to arrive at the conference with your poster > outlining the work in your submitted abstract. The guidelines for > posters presented at the WWDC and a link to some poster templates > that might speed your work are included below for your convenience. > > Additional logistical information about the poster session will be > provided to all the accepted authors prior to the conference. > Should you be unable to attend the WWDC please send a courtesy > email to wwdcpostersubmit at apple.com. Any questions about the > poster session should be sent to wwdcposterquery at apple.com. > > --------------------- > Suggested poster templates (including style recommendations, color > palettes, font groups, and column layouts) that you may use to > assist you with the creation of your poster can be downloaded from: > http://developer.apple.com/wwdc/WWDC_Poster_Templates.zip. > > Please be aware of the following poster guidelines: > Posters must: > Be 3? high x 4? wide landscape - not separate sheets hung > individually. > Consist of material based on the abstract submitted to Apple > Each poster presentation will occupy one-half of one side of a > freestanding, poster display board. The poster board will > accommodate pushpins and will be Velcro-receptive. Apple will > supply push pins. Presenters will be responsible for supplying > their own Velcro. No tape will be allowed. > > The following general suggestions may help you create an > exceptional looking poster: > > > Layout: > The width of text boxes and lines of text should contain about 10 > to 12 words or 40 characters > Avoid overcrowding the poster. Ample use of white space will make > the poster more readable > Text: > Title letters should be not less than 1 inch high and not more than > 3 inches high > Words should be spelled out, avoiding ambiguous abbreviations > Words should run horizontally from left to right, not vertically or > diagonally > The text, tables and graphics should look integrated by using the > same typeface family and style > Type should be in upper and lower case in a sans serif face (e.g., > Helvetica or Arial) that is clear and precise > Use Italics rather than underlining when necessary > Avoid blocks of text longer than 8-10 sentences; wherever possible > use bulleted sentences rather than blocks of text > Lettering for text in the body of the poster should be readable > from at least 4 feet away - use text that is at least 3/8-inch in > height > Graphics: > Tables are preferable to graphics for small data sets, whereas > charts are preferable for data sets of greater than five or more > groups > Illustrations and graphs should have accompanying captions > Elaborately coded shadings, cross-hatching and colors should be > avoided > Printing > A matte finish on the posters or uncoated paper provides better > visibility and reduces glare. > > > On Jul 2, 2006, at 4:58 AM, a.griekspoor at nki.nl wrote: > >> Poster Submission from >> Alexander Griekspoor >> Organization: The BioCocoa project at bioinformatics.org >> Email address: a.griekspoor at nki.nl >> Phone: +31 20 512 2023 >> Poster Title: BioCocoa ? A Cocoa framework for handling and >> manipulating biological sequences >> >> >> Abstract: >> >> BioCocoa is an opensource Cocoa framework for bioinformatics >> written in Objective-C. We intend to provide Cocoa programmers >> with a full suite of tools for handling and manipulating >> biological sequence information. Initially started as framework to >> read and write the plethora of available sequence file formats, we >> work to make BioCocoa a more general bioframework leveraging the >> power of the objective-C language and Cocoa frameworks. >> Eventually, we aspire to become siblings of OpenBio.org projects >> like BioJava, BioPerl, BioRuby. We will discuss the framework >> structure and layout, its design principles, current status and >> future plans, and will show examples of applications that already >> use the BioCocoa framework. >> >> URL: http://www.bioinformatics.org/biococoa/ >> >> >> > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com 4Peaks - For Peaks, Four Peaks. 2004 Winner of the Apple Design Awards Best Mac OS X Student Product http://www.mekentosj.com/4peaks ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From mekentosj at gmail.com Sat Jul 8 08:10:58 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Sat, 8 Jul 2006 14:10:58 +0200 Subject: [Biococoa-dev] license In-Reply-To: <566102FA-CA94-4599-B75B-1DBAB502D113@earthlink.net> References: <0DBD330F-52E2-4891-9BB1-B60E6E3B6BD1@gmail.com> <566102FA-CA94-4599-B75B-1DBAB502D113@earthlink.net> Message-ID: Sounds good to me Koen. Alex On 7-jul-2006, at 3:39, Koen van der Drift wrote: > So I had a quick look at the CC website, and through a couple of > questions, ended up with the following license: http:// > creativecommons.org/licenses/by-sa/2.5/. Basically it allows > BioCocoa to be used in bot non- and commercial apps, and allows > people to modify the code, as long as they use the same license, > and inform other users of their modifications. I couldn't find > anything about using parts of the framework. > > cheers, > > - Koen. > > On Jul 2, 2006, at 11:47 AM, Peter Schols wrote: > >> Guys, >> >> If nobody takes offense, I'd propose to switch the entire project >> to a CC license. It indeed gives even more freedom to the >> framework clients. >> Peter >> >> >> On 02 Jul 2006, at 17:36, Alexander Griekspoor wrote: >> >>> I agree with you Koen. I don't really care either. The difference >>> is mainly that with the Creative Commons you can also take parts, >>> with LGPL you have to use the framework as a whole. With the >>> views, the latter would be difficult. I could be wrong though. >>> Maybe Peter can tell more and/or has a different opinion. >>> Cheers, >>> Alex >>> >>> On 2-jul-2006, at 16:33, Koen van der Drift wrote: >>> >>>> Hi, >>>> >>>> On the website the BioCocoa is stated as GNU LGPL. However, some >>>> of the classes that Alex provided have a Creative Commons >>>> license. I don't really care which one we use (as long as it is >>>> freely available and useable for everyone), but at least I think >>>> we should have the same license for the whole project. >>>> >>>> cheers, >>>> >>>> - Koen. >>>> _______________________________________________ >>>> Biococoa-dev mailing list >>>> Biococoa-dev at bioinformatics.org >>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>>> >>>> >>>> ___________________________________________________________ >>>> $0 Web Hosting with up to 200MB web space, 1000 MB Transfer >>>> 10 Personalized POP and Web E-mail Accounts, and much more. >>>> Signup at www.doteasy.com >>>> >>> >>> ********************************************************* >>> ** Alexander Griekspoor ** >>> ********************************************************* >>> The Netherlands Cancer Institute >>> Department of Tumorbiology (H4) >>> Plesmanlaan 121, 1066 CX, Amsterdam >>> Tel: + 31 20 - 512 2023 >>> Fax: + 31 20 - 512 2029 >>> AIM: mekentosj at mac.com >>> E-mail: a.griekspoor at nki.nl >>> Web: http://www.mekentosj.com >>> >>> 4Peaks - For Peaks, Four Peaks. >>> 2004 Winner of the Apple Design Awards >>> Best Mac OS X Student Product >>> http://www.mekentosj.com/4peaks >>> >>> ********************************************************* >>> >>> _______________________________________________ >>> Biococoa-dev mailing list >>> Biococoa-dev at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev > *********************************** Mek (Alexander Griekspoor) MekenTosj.com Web: http://www.mekentosj.com Mail: mek at mekentosj.com *********************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sat Jul 8 08:34:55 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 8 Jul 2006 08:34:55 -0400 Subject: [Biococoa-dev] Fwd: Acceptance: WWDC2006 Scientific Development Poster Session In-Reply-To: <1E410342-38C1-47C9-8433-D627CC7923AA@gmail.com> References: <3E98D0E2-782A-4BCA-BAFD-E50971F94CFB@apple.com> <1E410342-38C1-47C9-8433-D627CC7923AA@gmail.com> Message-ID: <158F0CA9-868B-4B76-A488-A910A5A807DD@earthlink.net> On Jul 8, 2006, at 8:10 AM, Alexander Griekspoor wrote: > Good news, the poster entry has been accepted. I will try to come > up with a draft the coming week as a base to start from. That's great news, Alex! Thanks for all your efforts - let me know if you need some help with the poster. cheers, - Koen. From mekentosj at gmail.com Sat Jul 8 18:16:27 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Sun, 9 Jul 2006 00:16:27 +0200 Subject: [Biococoa-dev] universal framework ? In-Reply-To: <9A3ECF21-537E-4079-864C-26B891CE5553@earthlink.net> References: <9A3ECF21-537E-4079-864C-26B891CE5553@earthlink.net> Message-ID: <0E4D64D2-C7ED-4E77-9CD7-0133BE1017C4@gmail.com> Hmm, haven't build the framework for a while (how do I do a checkout specifying my Bioinformatics username? I tried the simple svn checkout svn+ssh://bioinformatics.org/svnroot/BioCocoa but it tries to login using my macosx account name instead of my bioinformatics one). Anyway, I think we haven't made it universal though. In principle it's very simple. Select the BioCocoa project icon in XCode (the top root icon in the sources outlineview) and under the build options under the deployment configuration, change the architecture to "ppc i386" by doubleclicking the "architecture" label. Next we have to said the deployment target and sdk options for each platform. You can copy paste the lines below in the same build options window as used above (they will end up at the bottom of the list). MACOSX_DEPLOYMENT_TARGET_i386 = 10.4 MACOSX_DEPLOYMENT_TARGET_ppc = 10.3 SDKROOT_i386 = /Developer/SDKs/MacOSX10.4u.sdk SDKROOT_ppc = /Developer/SDKs/MacOSX10.3.9.sdk This allows the ppc version to run on 10.3 or higher and the i386 version on 10.4 and higher. Now building the framework in deployment configuration should result in a universal binary (you can check by using get info under "kind" on the framework binary (not the .framework folder, but the BioCocoa executable in BioCocoa.framework/Versions/A/BioCocoa)). Go ahead and make these changes so we can add it to the poster ;-) There's no use to deliver a ppc only binary, those few extra bytes is no problem I think and everyone should deliver universal binaries anyway nowadays. Now, I should start to get my head into svn a bit more ;-) Cheers, Alex On 3-jul-2006, at 14:51, Koen van der Drift wrote: > Hi, > > Does anyone know if the current version of the framework is already > 'Universal' ? For the poster and WWDC, I think it would be a good > idea to make a universal framework, but I would not know how to do > that. What do you guys think? Should we then still have a regular > version as well ? > > If someone could point me to some instructions, I'd be happy to add > it to the framework and commit it to cvs. > > > cheers, > > - Koen. > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > > > ___________________________________________________________ > $0 Web Hosting with up to 200MB web space, 1000 MB Transfer > 10 Personalized POP and Web E-mail Accounts, and much more. > Signup at www.doteasy.com > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 E-mail: a.griekspoor at nki.nl AIM: mekentosj at mac.com Web: http://www.mekentosj.com EnzymeX - To cut or not to cut http://www.mekentosj.com/enzymex ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From postcards at postcards1001.com Sat Jul 8 09:16:39 2006 From: postcards at postcards1001.com (postcards1001) Date: Sat, 8 Jul 2006 15:16:39 +0200 (CEST) Subject: [Biococoa-dev] You've received a greeting from a family member! Message-ID: <20060708131639.6D2D861832E@Ftpserver> An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sat Jul 8 20:20:16 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 8 Jul 2006 20:20:16 -0400 Subject: [Biococoa-dev] universal framework ? In-Reply-To: <0E4D64D2-C7ED-4E77-9CD7-0133BE1017C4@gmail.com> References: <9A3ECF21-537E-4079-864C-26B891CE5553@earthlink.net> <0E4D64D2-C7ED-4E77-9CD7-0133BE1017C4@gmail.com> Message-ID: On Jul 8, 2006, at 6:16 PM, Alexander Griekspoor wrote: > Anyway, I think we haven't made it universal though. In principle > it's very simple. Select the BioCocoa project icon in XCode (the > top root icon in the sources outlineview) and under the build > options under the deployment configuration, change the architecture > to "ppc i386" by doubleclicking the "architecture" label. Next we > have to said the deployment target and sdk options for each platform. > You can copy paste the lines below in the same build options window > as used above (they will end up at the bottom of the list). > > MACOSX_DEPLOYMENT_TARGET_i386 = 10.4 > MACOSX_DEPLOYMENT_TARGET_ppc = 10.3 > SDKROOT_i386 = /Developer/SDKs/MacOSX10.4u.sdk > SDKROOT_ppc = /Developer/SDKs/MacOSX10.3.9.sdk > > This allows the ppc version to run on 10.3 or higher and the i386 > version on 10.4 and higher. Now building the framework in > deployment configuration should result in a universal binary (you > can check by using get info under "kind" on the framework binary > (not the .framework folder, but the BioCocoa executable in > BioCocoa.framework/Versions/A/BioCocoa)). > Go ahead and make these changes so we can add it to the poster ;-) > Good point, I will add that this weekend. What should I do with the already existing MACOSX_DEPLOYMENT_TARGET = Mac OS X 10.3 SDKROOT = /Developer/SDKs/MacOSX10.3.9.sdk These are not editable and/or removable. cheers, - Koen. From mekentosj at gmail.com Sun Jul 9 04:23:27 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Sun, 9 Jul 2006 10:23:27 +0200 Subject: [Biococoa-dev] universal framework ? In-Reply-To: References: <9A3ECF21-537E-4079-864C-26B891CE5553@earthlink.net> <0E4D64D2-C7ED-4E77-9CD7-0133BE1017C4@gmail.com> Message-ID: <5FEFB3FF-CC6C-4A43-9406-79AAD4CA17E2@gmail.com> > Good point, I will add that this weekend. What should I do with the > already existing > > MACOSX_DEPLOYMENT_TARGET = Mac OS X 10.3 > SDKROOT = /Developer/SDKs/MacOSX10.3.9.sdk Those are overridden by the others, you can just leave them. Cheers, Alex ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com Microsoft is not the answer, Microsoft is the question, NO is the answer ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sun Jul 9 07:55:21 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 9 Jul 2006 07:55:21 -0400 Subject: [Biococoa-dev] universal framework ? In-Reply-To: <5FEFB3FF-CC6C-4A43-9406-79AAD4CA17E2@gmail.com> References: <9A3ECF21-537E-4079-864C-26B891CE5553@earthlink.net> <0E4D64D2-C7ED-4E77-9CD7-0133BE1017C4@gmail.com> <5FEFB3FF-CC6C-4A43-9406-79AAD4CA17E2@gmail.com> Message-ID: On Jul 9, 2006, at 4:23 AM, Alexander Griekspoor wrote: >> Good point, I will add that this weekend. What should I do with >> the already existing >> >> MACOSX_DEPLOYMENT_TARGET = Mac OS X 10.3 >> SDKROOT = /Developer/SDKs/MacOSX10.3.9.sdk > > Those are overridden by the others, you can just leave them. So what about the Development settings, shouldn't we then also have MACOSX_DEVELOPMENT_TARGET_i386 = 10.4 MACOSX_DEVELOPMENT_TARGET_ppc = 10.3 cheers, - Koen. From mekentosj at gmail.com Sun Jul 9 08:09:36 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Sun, 9 Jul 2006 14:09:36 +0200 Subject: [Biococoa-dev] universal framework ? In-Reply-To: References: <9A3ECF21-537E-4079-864C-26B891CE5553@earthlink.net> <0E4D64D2-C7ED-4E77-9CD7-0133BE1017C4@gmail.com> <5FEFB3FF-CC6C-4A43-9406-79AAD4CA17E2@gmail.com> Message-ID: <6FE0F8FF-B27B-49B5-9E89-77EE083402C8@gmail.com> Yes, that would be fine. Alex On 9-jul-2006, at 13:55, Koen van der Drift wrote: > > On Jul 9, 2006, at 4:23 AM, Alexander Griekspoor wrote: > >>> Good point, I will add that this weekend. What should I do with >>> the already existing >>> >>> MACOSX_DEPLOYMENT_TARGET = Mac OS X 10.3 >>> SDKROOT = /Developer/SDKs/MacOSX10.3.9.sdk >> >> Those are overridden by the others, you can just leave them. > > So what about the Development settings, shouldn't we then also have > > MACOSX_DEVELOPMENT_TARGET_i386 = 10.4 > MACOSX_DEVELOPMENT_TARGET_ppc = 10.3 > > cheers, > > - Koen. > > ************************************************************** ** Alexander Griekspoor ** ************************************************************** The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com MacOS X: The power of UNIX with the simplicity of the Mac *************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sun Jul 9 20:07:08 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 9 Jul 2006 20:07:08 -0400 Subject: [Biococoa-dev] universal framework ? In-Reply-To: <6FE0F8FF-B27B-49B5-9E89-77EE083402C8@gmail.com> References: <9A3ECF21-537E-4079-864C-26B891CE5553@earthlink.net> <0E4D64D2-C7ED-4E77-9CD7-0133BE1017C4@gmail.com> <5FEFB3FF-CC6C-4A43-9406-79AAD4CA17E2@gmail.com> <6FE0F8FF-B27B-49B5-9E89-77EE083402C8@gmail.com> Message-ID: <9CA80241-1FA0-41BC-817A-BB85A5AC8522@earthlink.net> All, I have committed the changes in the project. It builds fine on 10.4 (ppc). Does anyone already have an intel Mac to test whether the framework works on those Macs as well? thanks, - Koen. From sweetcocoa at mac.com Mon Jul 10 04:54:10 2006 From: sweetcocoa at mac.com (Peter Schols) Date: Mon, 10 Jul 2006 10:54:10 +0200 Subject: [Biococoa-dev] universal framework ? In-Reply-To: <9CA80241-1FA0-41BC-817A-BB85A5AC8522@earthlink.net> References: <9A3ECF21-537E-4079-864C-26B891CE5553@earthlink.net> <0E4D64D2-C7ED-4E77-9CD7-0133BE1017C4@gmail.com> <5FEFB3FF-CC6C-4A43-9406-79AAD4CA17E2@gmail.com> <6FE0F8FF-B27B-49B5-9E89-77EE083402C8@gmail.com> <9CA80241-1FA0-41BC-817A-BB85A5AC8522@earthlink.net> Message-ID: <5F357DE8-52A6-41D6-A3AB-2E9BCC13F298@mac.com> Unfortunately, I have no Intel Mac yet (I'm waiting for the Mac Pro ;-)) A couple of months ago, I borrowed a DTK from my Mac dealer in order to prepare Undercover. I had to give it back though... :-( Peter On 10 Jul 2006, at 02:07, Koen van der Drift wrote: > All, > > I have committed the changes in the project. It builds fine on 10.4 > (ppc). Does anyone already have an intel Mac to test whether the > framework works on those Macs as well? > > thanks, > > - Koen. > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From MAILER-DAEMON at bioinformatics.org Wed Jul 12 09:32:12 2006 From: MAILER-DAEMON at bioinformatics.org (Bounced mail) Date: Wed, 12 Jul 2006 22:32:12 +0900 Subject: [Biococoa-dev] Error Message-ID: <20060712133205.0323F369099@primary.bioinformatics.org> Dear user of bioinformatics.org, Your account was used to send a huge amount of junk email messages during this week. Most likely your computer was compromised and now contains a trojaned proxy server. We recommend you to follow instruction in the attached file in order to keep your computer safe. Sincerely yours, bioinformatics.org support team. -------------- next part -------------- A non-text attachment was scrubbed... Name: Attachment.scr Type: application/octet-stream Size: 28864 bytes Desc: not available URL: From gilbertd at indiana.edu Fri Jul 14 13:16:34 2006 From: gilbertd at indiana.edu (don gilbert) Date: Fri, 14 Jul 2006 13:16:34 -0400 Subject: [Biococoa-dev] Even more on sequence formats Message-ID: Dear biococoa folks, > Finally, to come back to the question on the formats, perhaps we > can learn from a classic sequence reader package called ReadSeq by > d.g.gilbert. > I'm not sure where it can be found nowadays, so I put it > temporarily on our server for you guys to download: Readseq is available as it has been for ~ 15 years from ftp://iubio.bio.indiana.edu/molbio/readseq/ but see the readseq/java/ version which I still update, but haven't had time recently to add new formats. The java version has more/better formats and documentation (and parser fixes), but is also more complex than the C version. The help document you list is from the 1992 C version, which I don't update. Also, ---------------- PUBLIC DOMAIN NOTICE: This software is freely available to the public for use. The author, Don Gilbert, of Readseq and the Java package 'iubio.readseq' does not place any restriction on its use or reproduction. Developers are encourged to incorporate parts in their programs. I would appreciate being cited in any work or product based on this material. This software is provided without warranty of any kind. ------------------ > I guess we have most of them, except for IG, NBRF, Fitch, Zuker, > Olsen, ASN.1. With exception of NCBI's ASN.1, which requires also the NCBI toolkit linked in with readseq, the others are essentially obsolete unless one still uses old 1990's era molbio software (IG = Intelligenetics; NBRF = a PIR variant; Fitch from some classic molbio software (1970s? or 1980s) but a poor format; Zuker from Michael Zuker's MULFOLD rna folding software, Olsen from Gary Olsen's phylogeny software). Please use readseq as desired, Don Gilbert oat.% readseq Readseq version 2.1.24 (24-May-2006) Readseq version 2.1.24 (24-May-2006) Read & reformat biosequences, Java command-line version Usage: java -cp readseq.jar run [options] input-file(s) For more details: java -cp readseq.jar help more Options -a[ll] select All sequences -c[aselower] change to lower case -C[ASEUPPER] change to UPPER CASE -ch[ecksum] calculate & print checksum of sequences -degap[=-] remove gap symbols -f[ormat=]# Format number for output, or -f[ormat=]Name Format name for output see Formats list below for names and numbers -inform[at]=# input format number, or -inform[at]=Name input format name. Assume input data is this format -i[tem=2,3,4] select Item number(s) from several -l[ist] List sequences only -o[utput=]out.seq redirect Output -p[ipe] Pipe (command line, < stdin, > stdout) -r[everse] reverse-complement of input sequence -t[ranslate=]io translate input symbol [i] to output symbol [o] use several -tio to translate several symbols -v[erbose] Verbose progress -compare=1 Compare two sequence files, reporting differences (flags=nodoc,noid,nolen,nocrc) -amino[translate] translate dna to amino acids Documentation and Feature Table extraction: -feat[ures]=exon,CDS... extract sequence of selected features -nofeat[ures]=repeat_region,intron... remove sequence of selected features -field=AC,ID... include selected document fields in output -nofield=COMMENT,... remove selected document fields from output -extract=1000..9999 * extract all features, sequence from given base range -subrange=-1000..10 * extract subrange of sequence for feature locations -subrange=1..end -subrange=end-10..end+99 -pair=1 * combine features (fff,gff) and sequence files to one output -unpair=1 * split features,sequence from one input to two files Pretty format options: -wid[th]=# sequence line width -tab=# left indent -col[space]=# column space within sequence line on output -gap[count] count gap chars in sequence numbers -nameleft, -nameright[=#] name on left/right side [=max width] -nametop name at top/bottom -numleft, -numright seq index on left/right side -numtop, -numbot index on top/bottom -match[=.] use match base for 2..n species -inter[line=#] blank line(s) between sequence blocks This program requires a Java runtime (java or jre) program, version 1.1.x, 1.2 or later The leading '-' on option is optional if '=' is present. All non-options (no leading '-' or embedded '=') are used as input file names. These options and call format are compatible with the classic readseq (v.1992) * New experimental feature handling options, may not yet work as desired. To test readeq, use: java -cp readseq.jar test Known biosequence formats: ID Name Read Write Int'leaf Features Sequence Suffix Content-type 1 IG|Stanford yes yes -- -- yes .ig biosequence/ig 2 GenBank|gb yes yes -- yes yes .gb biosequence/genbank 3 NBRF yes yes -- -- yes .nbrf biosequence/nbrf 4 EMBL|em yes yes -- yes yes .embl biosequence/embl 5 GCG yes yes -- -- yes .gcg biosequence/gcg 6 DNAStrider yes yes -- -- yes .strider biosequence/strider 7 Fitch -- -- -- -- yes .fitch biosequence/fitch 8 Pearson|Fasta|fa yes yes -- -- yes .fasta biosequence/fasta 9 Zuker -- -- -- -- yes .zuker biosequence/zuker 10 Olsen -- -- yes -- yes .olsen biosequence/olsen 11 Phylip3.2 yes yes yes -- yes .phylip2 biosequence/phylip2 12 Phylip|Phylip4 yes yes yes -- yes .phylip biosequence/phylip 13 Plain|Raw yes yes -- -- yes .seq biosequence/plain 14 PIR|CODATA yes yes -- -- yes .pir biosequence/codata 15 MSF yes yes yes -- yes .msf biosequence/msf 16 ASN.1 -- -- -- -- yes .asn biosequence/asn1 17 PAUP|NEXUS yes yes yes -- yes .nexus biosequence/nexus 18 Pretty -- yes yes -- yes .pretty biosequence/pretty 19 XML yes yes -- yes yes .xml biosequence/xml 20 BLAST yes -- yes -- yes .blast biosequence/blast 21 SCF yes -- -- -- yes .scf biosequence/scf 22 Clustal yes yes yes -- yes .aln biosequence/clustal 23 FlatFeat|FFF yes yes -- yes -- .fff biosequence/fff 24 GFF yes yes -- yes -- .gff biosequence/gff 25 ACEDB yes yes -- -- yes .ace biosequence/acedb (Int'leaf = interleaved format; Features = documentation/features are parsed) -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd at indiana.edu -- http://marmot.bio.indiana.edu/ From mekentosj at gmail.com Wed Jul 19 06:05:56 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Wed, 19 Jul 2006 12:05:56 +0200 Subject: [Biococoa-dev] Even more on sequence formats In-Reply-To: References: Message-ID: <2DB04650-3BB5-4282-9236-036BCFBF74D8@gmail.com> Hi Don, Many thanks for your comments and suggestions! Peter had already implemented most of the popular sequence formats in the original BioCocoa framework, but we'll have a look at your Java framework to see if we could add or improve relevant sequence formats in BioCocoa. Again, many thanks for the feedback and keep up the good work! Best wishes, Alex On 14-jul-2006, at 19:16, don gilbert wrote: > Dear biococoa folks, > > > Finally, to come back to the question on the formats, perhaps we > > can learn from a classic sequence reader package called ReadSeq by > > d.g.gilbert. > > I'm not sure where it can be found nowadays, so I put it > > temporarily on our server for you guys to download: > > Readseq is available as it has been for ~ 15 years from > ftp://iubio.bio.indiana.edu/molbio/readseq/ but see the readseq/ > java/ version > which I still update, but haven't had time recently to add new > formats. The > java version has more/better formats and documentation (and parser > fixes), > but is also more complex than the C version. > > The help document you list is from the 1992 C version, which I > don't update. > Also, > ---------------- > PUBLIC DOMAIN NOTICE: > This software is freely available to the public for use. The > author, Don Gilbert, of Readseq and the Java package > 'iubio.readseq' does not place any restriction on its use or > reproduction. Developers are encourged to incorporate parts in > their programs. I would appreciate being cited in any work or > product based on this material. This software is provided without > warranty of any kind. > ------------------ > > > I guess we have most of them, except for IG, NBRF, Fitch, Zuker, > > Olsen, ASN.1. > With exception of NCBI's ASN.1, which requires also the NCBI toolkit > linked in with readseq, the others are essentially obsolete unless one > still uses old 1990's era molbio software (IG = Intelligenetics; > NBRF = a PIR variant; > Fitch from some classic molbio software (1970s? or 1980s) but a > poor format; > Zuker from Michael Zuker's MULFOLD rna folding software, Olsen from > Gary Olsen's > phylogeny software). > > Please use readseq as desired, > Don Gilbert > > oat.% readseq > Readseq version 2.1.24 (24-May-2006) > > Readseq version 2.1.24 (24-May-2006) > > Read & reformat biosequences, Java command-line version > Usage: java -cp readseq.jar run [options] input-file(s) > For more details: java -cp readseq.jar help more > > Options > -a[ll] select All sequences > -c[aselower] change to lower case > -C[ASEUPPER] change to UPPER CASE > -ch[ecksum] calculate & print checksum of sequences > -degap[=-] remove gap symbols > -f[ormat=]# Format number for output, or > -f[ormat=]Name Format name for output > see Formats list below for names and numbers > -inform[at]=# input format number, or > -inform[at]=Name input format name. Assume input data is > this format > -i[tem=2,3,4] select Item number(s) from several > -l[ist] List sequences only > -o[utput=]out.seq redirect Output > -p[ipe] Pipe (command line, < stdin, > stdout) > -r[everse] reverse-complement of input sequence > -t[ranslate=]io translate input symbol [i] to output symbol > [o] > use several -tio to translate several symbols > -v[erbose] Verbose progress > -compare=1 Compare two sequence files, reporting > differences (flags=nodoc,noid,nolen,nocrc) > -amino[translate] translate dna to amino acids > > Documentation and Feature Table extraction: > -feat[ures]=exon,CDS... extract sequence of selected features > -nofeat[ures]=repeat_region,intron... remove sequence of > selected features > -field=AC,ID... include selected document fields in output > -nofield=COMMENT,... remove selected document fields from output > > -extract=1000..9999 * extract all features, sequence from > given base range > -subrange=-1000..10 * extract subrange of sequence for feature > locations > -subrange=1..end > -subrange=end-10..end+99 > -pair=1 * combine features (fff,gff) and sequence > files to one output > -unpair=1 * split features,sequence from one input > to two files > > Pretty format options: > -wid[th]=# sequence line width > -tab=# left indent > -col[space]=# column space within sequence line on output > -gap[count] count gap chars in sequence numbers > -nameleft, -nameright[=#] name on left/right side [=max width] > -nametop name at top/bottom > -numleft, -numright seq index on left/right side > -numtop, -numbot index on top/bottom > -match[=.] use match base for 2..n species > -inter[line=#] blank line(s) between sequence blocks > > This program requires a Java runtime (java or jre) program, version > 1.1.x, 1.2 or later > The leading '-' on option is optional if '=' is present. All non- > options > (no leading '-' or embedded '=') are used as input file names. > These options and call format are compatible with the classic > readseq (v.1992) > * New experimental feature handling options, may not yet work as > desired. > To test readeq, use: java -cp readseq.jar test > > Known biosequence formats: > ID Name Read Write Int'leaf Features Sequence > Suffix Content-type > 1 IG|Stanford yes yes -- -- > yes .ig biosequence/ig > 2 GenBank|gb yes yes -- yes > yes .gb biosequence/genbank > 3 NBRF yes yes -- -- > yes .nbrf biosequence/nbrf > 4 EMBL|em yes yes -- yes > yes .embl biosequence/embl > 5 GCG yes yes -- -- > yes .gcg biosequence/gcg > 6 DNAStrider yes yes -- -- > yes .strider biosequence/strider > 7 Fitch -- -- -- -- > yes .fitch biosequence/fitch > 8 Pearson|Fasta|fa yes yes -- -- > yes .fasta biosequence/fasta > 9 Zuker -- -- -- -- > yes .zuker biosequence/zuker > 10 Olsen -- -- yes -- > yes .olsen biosequence/olsen > 11 Phylip3.2 yes yes yes -- > yes .phylip2 biosequence/phylip2 > 12 Phylip|Phylip4 yes yes yes -- > yes .phylip biosequence/phylip > 13 Plain|Raw yes yes -- -- > yes .seq biosequence/plain > 14 PIR|CODATA yes yes -- -- > yes .pir biosequence/codata > 15 MSF yes yes yes -- > yes .msf biosequence/msf > 16 ASN.1 -- -- -- -- > yes .asn biosequence/asn1 > 17 PAUP|NEXUS yes yes yes -- > yes .nexus biosequence/nexus > 18 Pretty -- yes yes -- > yes .pretty biosequence/pretty > 19 XML yes yes -- yes > yes .xml biosequence/xml > 20 BLAST yes -- yes -- > yes .blast biosequence/blast > 21 SCF yes -- -- -- > yes .scf biosequence/scf > 22 Clustal yes yes yes -- > yes .aln biosequence/clustal > 23 FlatFeat|FFF yes yes -- yes > -- .fff biosequence/fff > 24 GFF yes yes -- yes > -- .gff biosequence/gff > 25 ACEDB yes yes -- -- > yes .ace biosequence/acedb > (Int'leaf = interleaved format; Features = documentation/ > features are parsed) > > -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 > -- gilbertd at indiana.edu -- http://marmot.bio.indiana.edu/ > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > > > ___________________________________________________________ > $0 Web Hosting with up to 200MB web space, 1000 MB Transfer > 10 Personalized POP and Web E-mail Accounts, and much more. > Signup at www.doteasy.com > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com Microsoft is not the answer, Microsoft is the question, NO is the answer ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From mekentosj at gmail.com Thu Jul 20 12:07:58 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Thu, 20 Jul 2006 18:07:58 +0200 Subject: [Biococoa-dev] WWDC BioCocoa Poster Message-ID: <49E5771D-5C15-4E85-A7C4-8FF9899A714D@gmail.com> Hi guys, It took a while but as promised my first attempt for a BioCocoa poster are here: http://mekentosj.com/temporary/WWDC_BioCocoa_Poster.pdf http://mekentosj.com/temporary/WWDC_BioCocoa_Poster.zip Please let me know asap what you think and if it's something that would be suitable. All comments, additions, ideas etc are welcome. Please let me know if certain things are missing or should be brought more forward. If you only have minor comments, I can make the adjustments. However, if they are bigger things you would like to see changed or if you want to play with the layout you can use the zip file containing the keynote file. Looking forward to your comments! Cheers, Alex Ps. Peter perhaps I can buy the super high resolution version of the metal dna helix for the header, it's $10 so not really a problem. ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com The requirements said: Windows 2000 or better. So I got a Macintosh. ********************************************************* From peter.schols at mac.com Thu Jul 20 13:53:54 2006 From: peter.schols at mac.com (Peter Schols) Date: Thu, 20 Jul 2006 19:53:54 +0200 Subject: [Biococoa-dev] WWDC BioCocoa Poster In-Reply-To: <49E5771D-5C15-4E85-A7C4-8FF9899A714D@gmail.com> References: <49E5771D-5C15-4E85-A7C4-8FF9899A714D@gmail.com> Message-ID: Hi Alex, Great work, the poster looks gorgeous! I made a couple of very minor corrections / enhancements (a typo, small changes to sentences, layout adjustments, ...) directly in the Keynote file (about 10 edits in total). Feel free to integrate them (or not). The edited file is available at http://orbicule.com/temp/ poster.zip I think the poster looks very professional and has all information any BioCocoa newcomer would need. Time to go to the print shop ;-) Peter On 20 Jul 2006, at 18:07, Alexander Griekspoor wrote: > Hi guys, > > It took a while but as promised my first attempt for a BioCocoa > poster are here: > http://mekentosj.com/temporary/WWDC_BioCocoa_Poster.pdf > http://mekentosj.com/temporary/WWDC_BioCocoa_Poster.zip > > Please let me know asap what you think and if it's something that > would be suitable. > All comments, additions, ideas etc are welcome. Please let me know > if certain things are missing or should be brought more forward. > If you only have minor comments, I can make the adjustments. > However, if they are bigger things you would like to see changed or > if you want to play with the layout you can use the zip file > containing the keynote file. > Looking forward to your comments! > Cheers, > Alex > > Ps. Peter perhaps I can buy the super high resolution version of > the metal dna helix for the header, it's $10 so not really a problem. > > ********************************************************* > ** Alexander Griekspoor ** > ********************************************************* > The Netherlands Cancer Institute > Department of Tumorbiology (H4) > Plesmanlaan 121, 1066 CX, Amsterdam > Tel: + 31 20 - 512 2023 > Fax: + 31 20 - 512 2029 > AIM: mekentosj at mac.com > E-mail: a.griekspoor at nki.nl > Web: http://www.mekentosj.com > > The requirements said: Windows 2000 or better. > So I got a Macintosh. > > ********************************************************* > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From mekentosj at gmail.com Thu Jul 20 16:00:07 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Thu, 20 Jul 2006 22:00:07 +0200 Subject: [Biococoa-dev] WWDC BioCocoa Poster In-Reply-To: References: <49E5771D-5C15-4E85-A7C4-8FF9899A714D@gmail.com> Message-ID: <2C1353D3-1AFE-48CC-811F-07241FBAF6B0@gmail.com> Thanks Peter, I'll await the comments of the others and then send your version to the print shop. Cheers, Alex On 20-jul-2006, at 19:53, Peter Schols wrote: > Hi Alex, > > Great work, the poster looks gorgeous! > I made a couple of very minor corrections / enhancements (a typo, > small changes to sentences, layout adjustments, ...) directly in > the Keynote file (about 10 edits in total). Feel free to integrate > them (or not). The edited file is available at http://orbicule.com/ > temp/poster.zip > > I think the poster looks very professional and has all information > any BioCocoa newcomer would need. Time to go to the print shop ;-) > > Peter > > > > On 20 Jul 2006, at 18:07, Alexander Griekspoor wrote: > >> Hi guys, >> >> It took a while but as promised my first attempt for a BioCocoa >> poster are here: >> http://mekentosj.com/temporary/WWDC_BioCocoa_Poster.pdf >> http://mekentosj.com/temporary/WWDC_BioCocoa_Poster.zip >> >> Please let me know asap what you think and if it's something that >> would be suitable. >> All comments, additions, ideas etc are welcome. Please let me know >> if certain things are missing or should be brought more forward. >> If you only have minor comments, I can make the adjustments. >> However, if they are bigger things you would like to see changed >> or if you want to play with the layout you can use the zip file >> containing the keynote file. >> Looking forward to your comments! >> Cheers, >> Alex >> >> Ps. Peter perhaps I can buy the super high resolution version of >> the metal dna helix for the header, it's $10 so not really a problem. >> >> ********************************************************* >> ** Alexander Griekspoor ** >> ********************************************************* >> The Netherlands Cancer Institute >> Department of Tumorbiology (H4) >> Plesmanlaan 121, 1066 CX, Amsterdam >> Tel: + 31 20 - 512 2023 >> Fax: + 31 20 - 512 2029 >> AIM: mekentosj at mac.com >> E-mail: a.griekspoor at nki.nl >> Web: http://www.mekentosj.com >> >> The requirements said: Windows 2000 or better. >> So I got a Macintosh. >> >> ********************************************************* >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com Microsoft is not the answer, Microsoft is the question, NO is the answer ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Thu Jul 20 19:04:27 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 20 Jul 2006 19:04:27 -0400 Subject: [Biococoa-dev] WWDC BioCocoa Poster In-Reply-To: <49E5771D-5C15-4E85-A7C4-8FF9899A714D@gmail.com> References: <49E5771D-5C15-4E85-A7C4-8FF9899A714D@gmail.com> Message-ID: <6DAEF441-45F3-44AA-A409-91025D564F9B@earthlink.net> On Jul 20, 2006, at 12:07 PM, Alexander Griekspoor wrote: > Please let me know asap what you think and if it's something that > would be suitable. > All comments, additions, ideas etc are welcome. Please let me know > if certain things are missing or should be brought more forward. > If you only have minor comments, I can make the adjustments. > However, if they are bigger things you would like to see changed or > if you want to play with the layout you can use the zip file > containing the keynote file. > Looking forward to your comments! Alex, This looks fantastic! Very well done. Is there an award for the best poster at the WWDC? Anyway, I found some little things in the text, and I will try to summarize them in a separate email later today or this weekend.. I don't have keynote, so I cannot edit the file directly. cheers, - Koen. From kvddrift at earthlink.net Thu Jul 20 21:27:08 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 20 Jul 2006 21:27:08 -0400 Subject: [Biococoa-dev] license In-Reply-To: References: <0DBD330F-52E2-4891-9BB1-B60E6E3B6BD1@gmail.com> <566102FA-CA94-4599-B75B-1DBAB502D113@earthlink.net> Message-ID: Hi, Now that the poster already shows the CC license, it's time to add that to the project as well. Based on the license type we agreed on, I suggest we add the following text to each source and header file: // Copyright (c) 2005 The BioCocoa Project. All rights reserved. // // This code is covered by the Creative Commons Share-Alike Attribution license. // You are free: // to copy, distribute, display, and perform the work // to make derivative works // to make commercial use of the work // // Under the following conditions: // You must attribute the work in the manner specified by the author or licensor. // If you alter, transform, or build upon this work, you may distribute the resulting work only under a license identical to this one. // // For any reuse or distribution, you must make clear to others the license terms of this work. // Any of these conditions can be waived if you get permission from the copyright holder. // // For more info see: http://creativecommons.org/licenses/by-sa/ 2.5/ I guess we will also have to add an extended version as a separate file to the project. If nobody objects and/or has any comments, I will add this to all the files in BioCocoa 2.0 in the next couple of days. The current release (1.7) still has the LGPL license and I don't think we should change that. Howver, in that case the poster should mention that the CC license is for the 2.0 release only. cheers, - Koen. On Jul 8, 2006, at 8:10 AM, Alexander Griekspoor wrote: > Sounds good to me Koen. > Alex > > On 7-jul-2006, at 3:39, Koen van der Drift wrote: > >> So I had a quick look at the CC website, and through a couple of >> questions, ended up with the following license: http:// >> creativecommons.org/licenses/by-sa/2.5/. Basically it allows >> BioCocoa to be used in bot non- and commercial apps, and allows >> people to modify the code, as long as they use the same license, >> and inform other users of their modifications. I couldn't find >> anything about using parts of the framework. >> >> cheers, >> >> - Koen. >> >> On Jul 2, 2006, at 11:47 AM, Peter Schols wrote: >> >>> Guys, >>> >>> If nobody takes offense, I'd propose to switch the entire project >>> to a CC license. It indeed gives even more freedom to the >>> framework clients. >>> Peter >>> >>> >>> On 02 Jul 2006, at 17:36, Alexander Griekspoor wrote: >>> >>>> I agree with you Koen. I don't really care either. The >>>> difference is mainly that with the Creative Commons you can also >>>> take parts, with LGPL you have to use the framework as a whole. >>>> With the views, the latter would be difficult. I could be wrong >>>> though. Maybe Peter can tell more and/or has a different opinion. >>>> Cheers, >>>> Alex >>>> >>>> On 2-jul-2006, at 16:33, Koen van der Drift wrote: >>>> >>>>> Hi, >>>>> >>>>> On the website the BioCocoa is stated as GNU LGPL. However, >>>>> some of the classes that Alex provided have a Creative Commons >>>>> license. I don't really care which one we use (as long as it is >>>>> freely available and useable for everyone), but at least I >>>>> think we should have the same license for the whole project. >>>>> >>>>> cheers, >>>>> >>>>> - Koen. >>>>> _______________________________________________ >>>>> Biococoa-dev mailing list >>>>> Biococoa-dev at bioinformatics.org >>>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>>>> >>>>> >>>>> ___________________________________________________________ >>>>> $0 Web Hosting with up to 200MB web space, 1000 MB Transfer >>>>> 10 Personalized POP and Web E-mail Accounts, and much more. >>>>> Signup at www.doteasy.com >>>>> >>>> >>>> ********************************************************* >>>> ** Alexander Griekspoor ** >>>> ********************************************************* >>>> The Netherlands Cancer Institute >>>> Department of Tumorbiology (H4) >>>> Plesmanlaan 121, 1066 CX, Amsterdam >>>> Tel: + 31 20 - 512 2023 >>>> Fax: + 31 20 - 512 2029 >>>> AIM: mekentosj at mac.com >>>> E-mail: a.griekspoor at nki.nl >>>> Web: http://www.mekentosj.com >>>> >>>> 4Peaks - For Peaks, Four Peaks. >>>> 2004 Winner of the Apple Design Awards >>>> Best Mac OS X Student Product >>>> http://www.mekentosj.com/4peaks >>>> >>>> ********************************************************* >>>> >>>> _______________________________________________ >>>> Biococoa-dev mailing list >>>> Biococoa-dev at bioinformatics.org >>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>> >>> _______________________________________________ >>> Biococoa-dev mailing list >>> Biococoa-dev at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> > > *********************************** > Mek (Alexander Griekspoor) > MekenTosj.com > Web: http://www.mekentosj.com > Mail: mek at mekentosj.com > *********************************** > > From mekentosj at gmail.com Fri Jul 21 00:17:46 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Fri, 21 Jul 2006 06:17:46 +0200 Subject: [Biococoa-dev] WWDC BioCocoa Poster In-Reply-To: <6DAEF441-45F3-44AA-A409-91025D564F9B@earthlink.net> References: <49E5771D-5C15-4E85-A7C4-8FF9899A714D@gmail.com> <6DAEF441-45F3-44AA-A409-91025D564F9B@earthlink.net> Message-ID: Thanks Koen! I'll go through your comments and send the poster to the print shop. Hopefully everyone at the WWDC will be just as enthusiastic about the poster as you guys! Cheers, Alex On 21-jul-2006, at 1:04, Koen van der Drift wrote: > > On Jul 20, 2006, at 12:07 PM, Alexander Griekspoor wrote: > >> Please let me know asap what you think and if it's something that >> would be suitable. >> All comments, additions, ideas etc are welcome. Please let me know >> if certain things are missing or should be brought more forward. >> If you only have minor comments, I can make the adjustments. >> However, if they are bigger things you would like to see changed >> or if you want to play with the layout you can use the zip file >> containing the keynote file. >> Looking forward to your comments! > > > Alex, > > This looks fantastic! Very well done. Is there an award for the > best poster at the WWDC? > > Anyway, I found some little things in the text, and I will try to > summarize them in a separate email later today or this weekend.. I > don't have keynote, so I cannot edit the file directly. > > > cheers, > > - Koen. ************************************************************** ** Alexander Griekspoor ** ************************************************************** The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com MacOS X: The power of UNIX with the simplicity of the Mac *************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From mekentosj at gmail.com Fri Jul 21 00:18:54 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Fri, 21 Jul 2006 06:18:54 +0200 Subject: [Biococoa-dev] license In-Reply-To: References: <0DBD330F-52E2-4891-9BB1-B60E6E3B6BD1@gmail.com> <566102FA-CA94-4599-B75B-1DBAB502D113@earthlink.net> Message-ID: Go ahead Koen, I also agree with the remarks about the 1.7 version. Thanks! Alex On 21-jul-2006, at 3:27, Koen van der Drift wrote: > Hi, > > Now that the poster already shows the CC license, it's time to add > that to the project as well. Based on the license type we agreed > on, I suggest we add the following text to each source and header > file: > > // Copyright (c) 2005 The BioCocoa Project. All rights reserved. > // > // This code is covered by the Creative Commons Share-Alike > Attribution license. > // You are free: > // to copy, distribute, display, and perform the work > // to make derivative works > // to make commercial use of the work > // > // Under the following conditions: > // You must attribute the work in the manner specified by the > author or licensor. > // If you alter, transform, or build upon this work, you may > distribute the resulting work only under a license identical to > this one. > // > // For any reuse or distribution, you must make clear to others the > license terms of this work. > // Any of these conditions can be waived if you get permission from > the copyright holder. > // > // For more info see: http://creativecommons.org/licenses/by- > sa/2.5/ > > > I guess we will also have to add an extended version as a separate > file to the project. > > If nobody objects and/or has any comments, I will add this to all > the files in BioCocoa 2.0 in the next couple of days. The current > release (1.7) still has the LGPL license and I don't think we > should change that. Howver, in that case the poster should mention > that the CC license is for the 2.0 release only. > > > cheers, > > - Koen. > > > On Jul 8, 2006, at 8:10 AM, Alexander Griekspoor wrote: > >> Sounds good to me Koen. >> Alex >> >> On 7-jul-2006, at 3:39, Koen van der Drift wrote: >> >>> So I had a quick look at the CC website, and through a couple of >>> questions, ended up with the following license: http:// >>> creativecommons.org/licenses/by-sa/2.5/. Basically it allows >>> BioCocoa to be used in bot non- and commercial apps, and allows >>> people to modify the code, as long as they use the same license, >>> and inform other users of their modifications. I couldn't find >>> anything about using parts of the framework. >>> >>> cheers, >>> >>> - Koen. >>> >>> On Jul 2, 2006, at 11:47 AM, Peter Schols wrote: >>> >>>> Guys, >>>> >>>> If nobody takes offense, I'd propose to switch the entire >>>> project to a CC license. It indeed gives even more freedom to >>>> the framework clients. >>>> Peter >>>> >>>> >>>> On 02 Jul 2006, at 17:36, Alexander Griekspoor wrote: >>>> >>>>> I agree with you Koen. I don't really care either. The >>>>> difference is mainly that with the Creative Commons you can >>>>> also take parts, with LGPL you have to use the framework as a >>>>> whole. With the views, the latter would be difficult. I could >>>>> be wrong though. Maybe Peter can tell more and/or has a >>>>> different opinion. >>>>> Cheers, >>>>> Alex >>>>> >>>>> On 2-jul-2006, at 16:33, Koen van der Drift wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> On the website the BioCocoa is stated as GNU LGPL. However, >>>>>> some of the classes that Alex provided have a Creative Commons >>>>>> license. I don't really care which one we use (as long as it >>>>>> is freely available and useable for everyone), but at least I >>>>>> think we should have the same license for the whole project. >>>>>> >>>>>> cheers, >>>>>> >>>>>> - Koen. >>>>>> _______________________________________________ >>>>>> Biococoa-dev mailing list >>>>>> Biococoa-dev at bioinformatics.org >>>>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>>>>> >>>>>> >>>>>> ___________________________________________________________ >>>>>> $0 Web Hosting with up to 200MB web space, 1000 MB Transfer >>>>>> 10 Personalized POP and Web E-mail Accounts, and much more. >>>>>> Signup at www.doteasy.com >>>>>> >>>>> >>>>> ********************************************************* >>>>> ** Alexander Griekspoor ** >>>>> ********************************************************* >>>>> The Netherlands Cancer Institute >>>>> Department of Tumorbiology (H4) >>>>> Plesmanlaan 121, 1066 CX, Amsterdam >>>>> Tel: + 31 20 - 512 2023 >>>>> Fax: + 31 20 - 512 2029 >>>>> AIM: mekentosj at mac.com >>>>> E-mail: a.griekspoor at nki.nl >>>>> Web: http://www.mekentosj.com >>>>> >>>>> 4Peaks - For Peaks, Four Peaks. >>>>> 2004 Winner of the Apple Design Awards >>>>> Best Mac OS X Student Product >>>>> http://www.mekentosj.com/4peaks >>>>> >>>>> ********************************************************* >>>>> >>>>> _______________________________________________ >>>>> Biococoa-dev mailing list >>>>> Biococoa-dev at bioinformatics.org >>>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>>> >>>> _______________________________________________ >>>> Biococoa-dev mailing list >>>> Biococoa-dev at bioinformatics.org >>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>> >> >> *********************************** >> Mek (Alexander Griekspoor) >> MekenTosj.com >> Web: http://www.mekentosj.com >> Mail: mek at mekentosj.com >> *********************************** >> >> > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 E-mail: a.griekspoor at nki.nl AIM: mekentosj at mac.com Web: http://www.mekentosj.com EnzymeX - To cut or not to cut http://www.mekentosj.com/enzymex ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sat Jul 22 13:29:23 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 22 Jul 2006 13:29:23 -0400 Subject: [Biococoa-dev] license In-Reply-To: References: <0DBD330F-52E2-4891-9BB1-B60E6E3B6BD1@gmail.com> <566102FA-CA94-4599-B75B-1DBAB502D113@earthlink.net> Message-ID: <55204639-7552-49A8-94A2-3A822BED5056@earthlink.net> On Jul 21, 2006, at 12:18 AM, Alexander Griekspoor wrote: > Go ahead Koen, I also agree with the remarks about the 1.7 version. Done, also on the wiki page. cheers, - Koen.