From mek at mekentosj.com Fri Jun 2 11:31:19 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Fri, 2 Jun 2006 17:31:19 +0200 Subject: [Biococoa-dev] WWDC Scientific Poster Session In-Reply-To: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> References: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> Message-ID: <770285AE-FE98-46CB-9CEC-85A4B0B527C6@mekentosj.com> Hi Guys, Sorry for the late reply. As said, we are not going in august unfortunately, but it would be great if you guys could do the poster! I'm also curious to the new site design Peter has done. Way to go! Cheers, Alex On 27-mei-2006, at 10:52, Peter Schols wrote: > Hi Phil and others, > > I will attend for sure and I agree that we should aim to submit a > BioCocoa poster. Are we the only two attending? > I was thinking that we could re-use the website text (from the new > website that should be ready by WWDC). This brings me to the > website and its status: a couple of weeks ago, I worked on a front > page and CSS layout which is 99% ready. The only thing that's > needed is an introductory text. I'll try to come up with something. > If somebody on the list has any ideas, feel free to submit... > > Peter > > > > > > On 27 May 2006, at 10:34, Philipp Seibel wrote: > >> Hey, >> >> i just read about the new poster session at WWDC http:// >> developer.apple.com/wwdc/science_poster.html. I think we should >> take this opportunity to present biococoa again. >> What do you think? >> Am i right that peter is the only one except from me who is >> attending this year? >> >> @peter: do you attend for sure? >> >> cheers, >> Phil >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > > _______________________________________________ > 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 Windows vs Mac 65 million years ago, there were more dinosaurs than humans. Where are the dinosaurs now? ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From mek at mekentosj.com Wed Jun 21 17:54:03 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Wed, 21 Jun 2006 22:54:03 +0100 Subject: [Biococoa-dev] WWDC Scientific Poster Session In-Reply-To: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> References: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> Message-ID: <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> Hi guys, There's a fairly big chance I could still make an appearance at the WWDC! Not definitive yet, but I'll let you guys know as soon as it is. How are we doing with a BioCocoa poster? Cheers, Alex On 27-mei-2006, at 9:52, Peter Schols wrote: > Hi Phil and others, > > I will attend for sure and I agree that we should aim to submit a > BioCocoa poster. Are we the only two attending? > I was thinking that we could re-use the website text (from the new > website that should be ready by WWDC). This brings me to the > website and its status: a couple of weeks ago, I worked on a front > page and CSS layout which is 99% ready. The only thing that's > needed is an introductory text. I'll try to come up with something. > If somebody on the list has any ideas, feel free to submit... > > Peter > > > > > > On 27 May 2006, at 10:34, Philipp Seibel wrote: > >> Hey, >> >> i just read about the new poster session at WWDC http:// >> developer.apple.com/wwdc/science_poster.html. I think we should >> take this opportunity to present biococoa again. >> What do you think? >> Am i right that peter is the only one except from me who is >> attending this year? >> >> @peter: do you attend for sure? >> >> cheers, >> Phil >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > > _______________________________________________ > 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 LabAssistant - Get your life organized! http://www.mekentosj.com/labassistant ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From peter.schols at mac.com Thu Jun 22 12:24:23 2006 From: peter.schols at mac.com (peter.schols at mac.com) Date: Thu, 22 Jun 2006 18:24:23 +0200 Subject: [Biococoa-dev] WWDC Scientific Poster Session In-Reply-To: <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> References: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> Message-ID: Hi Alex, Great to hear you can probably make it to WWDC! That way, you can receive the ADA yourself ;-)) Well, the BioCocoa poster is still in a conceptual phase... (nothing has been done yet, except for downloading the templates ;-)) I'm currently too busy with the BC homepage.... you will hear about this very soon. So if anyone feels tempted to play around with Keynote, please go ahead! cheers, Peter On 21 Jun 2006, at 23:54, Alexander Griekspoor wrote: > Hi guys, > > There's a fairly big chance I could still make an appearance at the > WWDC! Not definitive yet, but I'll let you guys know as soon as it is. > How are we doing with a BioCocoa poster? > Cheers, > Alex > > On 27-mei-2006, at 9:52, Peter Schols wrote: > >> Hi Phil and others, >> >> I will attend for sure and I agree that we should aim to submit a >> BioCocoa poster. Are we the only two attending? >> I was thinking that we could re-use the website text (from the new >> website that should be ready by WWDC). This brings me to the >> website and its status: a couple of weeks ago, I worked on a front >> page and CSS layout which is 99% ready. The only thing that's >> needed is an introductory text. I'll try to come up with >> something. If somebody on the list has any ideas, feel free to >> submit... >> >> Peter >> >> >> >> >> >> On 27 May 2006, at 10:34, Philipp Seibel wrote: >> >>> Hey, >>> >>> i just read about the new poster session at WWDC http:// >>> developer.apple.com/wwdc/science_poster.html. I think we should >>> take this opportunity to present biococoa again. >>> What do you think? >>> Am i right that peter is the only one except from me who is >>> attending this year? >>> >>> @peter: do you attend for sure? >>> >>> cheers, >>> Phil >>> _______________________________________________ >>> Biococoa-dev mailing list >>> Biococoa-dev at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>> >> >> >> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >> >> _______________________________________________ >> 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 > > LabAssistant - Get your life organized! > http://www.mekentosj.com/labassistant > > ********************************************************* > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From peter.schols at mac.com Thu Jun 22 12:38:31 2006 From: peter.schols at mac.com (peter.schols at mac.com) Date: Thu, 22 Jun 2006 18:38:31 +0200 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> References: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> Message-ID: Hi, It sounds unbelievable, but I finally managed to complete the CSS design for our homepage. 'Complete' is a bit euphemistic here because the home page still needs some work and tweaking, but before doing so, I'd like to get your advice. I have created two designs and they can be viewed at: http://bioinformatics.org/biococoa/Option1/ http://bioinformatics.org/biococoa/Option2/ It would be great to hear from the list which design we should continue with. Of course, I'm also very interested in your feedback on the contents and layout. Cheers, Peter From ttenzin at gmail.com Thu Jun 22 18:57:30 2006 From: ttenzin at gmail.com (Tenzin Togden) Date: Thu, 22 Jun 2006 23:57:30 +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> Message-ID: Hello. I've been quiet throughout this year. Recently took a break and have been playing with CSS a bit myself, so one thing I can do is give feedback. Option 1 : First impression - a lotus flower, perfect ... I can't help this reaction, I practice buddhist medicine and the plant symbolises a lot. Clarity, and memories of having worked with stunningly beautiful plants, in the Himalaya.. Colours, a green, natural look ... also perfect. Sometimes I spend so much time up to my elbows in code I forget that the large bundles of alphanumerics, collection of frameworks, apps, and sometimes very pretty visual output all go towards healing, and if we don't see a plant or patient for months, we're still practicing a form of medicine :) This option works for me, and would be consistent with CSS I am using, although personally I would have chose a lighter grey background, somewhere around #e0e0e0, #d9d9d9 and #cccccc. Option 2 : First impression - technology, science fiction almost. Well, this is what biotechnology is, a medical science where people understand nature at it's highest levels, and create or synthesize anew, medicines and living beings, using highly complex machines to do so :) This has a clinical, lab feel that will appeal to many.I personally prefer a slightly darker, NeXT - Rhapsodesque shade of blue, but that's me. In both cases the Biococoa text in the header graphic doesn't survive rescaling so well, for small screen rendering on cellphone and pda, but the body text is perfectly readable. If I'd had to design a header or logo for BioCocoa myself, I would have started with the name itself, and be trying to mix a photo of a coffee plant, with renders of the most visually interesting molecules from it. Possibly with a fixed background image for the body, of a lot of ASCII DNA code ala the original BioCocoa icon and logo, in white on light off-white grey. Again, that's just me. Off topic ... Hello everyone, the reason you don't hear from me is I am not good enough at programming to create for myself GNUstep makefiles from XCode or .proj. I use the Biococoa Sequence Converter, and look forward to NIB support in GNUstep improving to include XCode. Or I learn enough about makefiles to do that myself but this will take time as will understanding the framework enough to make good use of it. Let alone contribute. Or I get a Mac capable of running OSX when I can afford it :) I'm currently looking for biotech journalist work to finance my own research. Tenzin -------------- next part -------------- An HTML attachment was scrubbed... URL: From charles.parnot at gmail.com Fri Jun 23 03:07:16 2006 From: charles.parnot at gmail.com (Charles Parnot) Date: Fri, 23 Jun 2006 00:07:16 -0700 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: References: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> Message-ID: Frankly, I love both headers and styles. Very neat! charles On Jun 22, 2006, at 9:38 AM, peter.schols at mac.com wrote: > Hi, > > It sounds unbelievable, but I finally managed to complete the CSS > design for our homepage. > 'Complete' is a bit euphemistic here because the home page still > needs some work and tweaking, but before doing so, I'd like to get > your advice. I have created two designs and they can be viewed at: > http://bioinformatics.org/biococoa/Option1/ > http://bioinformatics.org/biococoa/Option2/ > > It would be great to hear from the list which design we should > continue with. Of course, I'm also very interested in your feedback > on the contents and layout. > > Cheers, > > Peter > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev -- Xgrid-at-Stanford Help science move fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford Charles Parnot charles.parnot at gmail.com From charles.parnot at gmail.com Fri Jun 23 03:10:09 2006 From: charles.parnot at gmail.com (Charles Parnot) Date: Fri, 23 Jun 2006 00:10:09 -0700 Subject: [Biococoa-dev] WWDC Scientific Poster Session In-Reply-To: <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> References: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> Message-ID: <8DEC71FE-9BEB-4BEB-A290-E2F4448FCA6C@gmail.com> That would be exxxxxcellent news! charles talking of good news, V?ronique and I just had a third kid June 21st, her name is Victoria... Sister Madeleine (5) and brother Oscar (2.5) are very happy too, it seems :-) On Jun 21, 2006, at 2:54 PM, Alexander Griekspoor wrote: > Hi guys, > > There's a fairly big chance I could still make an appearance at the > WWDC! Not definitive yet, but I'll let you guys know as soon as it is. > How are we doing with a BioCocoa poster? > Cheers, > Alex > > On 27-mei-2006, at 9:52, Peter Schols wrote: > >> Hi Phil and others, >> >> I will attend for sure and I agree that we should aim to submit a >> BioCocoa poster. Are we the only two attending? >> I was thinking that we could re-use the website text (from the new >> website that should be ready by WWDC). This brings me to the >> website and its status: a couple of weeks ago, I worked on a front >> page and CSS layout which is 99% ready. The only thing that's >> needed is an introductory text. I'll try to come up with >> something. If somebody on the list has any ideas, feel free to >> submit... >> >> Peter >> >> >> >> >> >> On 27 May 2006, at 10:34, Philipp Seibel wrote: >> >>> Hey, >>> >>> i just read about the new poster session at WWDC http:// >>> developer.apple.com/wwdc/science_poster.html. I think we should >>> take this opportunity to present biococoa again. >>> What do you think? >>> Am i right that peter is the only one except from me who is >>> attending this year? >>> >>> @peter: do you attend for sure? >>> >>> cheers, >>> Phil >>> _______________________________________________ >>> Biococoa-dev mailing list >>> Biococoa-dev at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>> >> >> >> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >> >> _______________________________________________ >> 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 > > LabAssistant - Get your life organized! > http://www.mekentosj.com/labassistant > > ********************************************************* > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev -- Xgrid-at-Stanford Help science move fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford Charles Parnot charles.parnot at gmail.com From peter.schols at mac.com Fri Jun 23 03:54:44 2006 From: peter.schols at mac.com (Peter Schols) Date: Fri, 23 Jun 2006 09:54:44 +0200 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: References: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> Message-ID: Thanks! Peter On 23 Jun 2006, at 09:07, Charles Parnot wrote: > Frankly, I love both headers and styles. Very neat! > > charles > > > On Jun 22, 2006, at 9:38 AM, peter.schols at mac.com wrote: > >> Hi, >> >> It sounds unbelievable, but I finally managed to complete the CSS >> design for our homepage. >> 'Complete' is a bit euphemistic here because the home page still >> needs some work and tweaking, but before doing so, I'd like to get >> your advice. I have created two designs and they can be viewed at: >> http://bioinformatics.org/biococoa/Option1/ >> http://bioinformatics.org/biococoa/Option2/ >> >> It would be great to hear from the list which design we should >> continue with. Of course, I'm also very interested in your >> feedback on the contents and layout. >> >> Cheers, >> >> Peter >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev > > -- > Xgrid-at-Stanford > Help science move fast forward: > http://cmgm.stanford.edu/~cparnot/xgrid-stanford > > Charles Parnot > charles.parnot at gmail.com > > > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From peter.schols at mac.com Fri Jun 23 04:20:11 2006 From: peter.schols at mac.com (Peter Schols) Date: Fri, 23 Jun 2006 10:20:11 +0200 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: References: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> Message-ID: <5DF77226-3AC8-48DF-A171-6B392C6DD8B1@mac.com> Hi Tenzin, Thanks for your comments on the CSS layouts! I'm pretty sure it will become easier to bring Cocoa projects to GNUStep over the coming months, thanks to NIB improvements Apple will introduce. That way, Xcode projects could maybe even directly opened by the GORM All the best, Peter On 23 Jun 2006, at 00:31, Tenzin Togden wrote: > Hello. > > I've been quiet throughout this year. > Recently took a break and have been playing with CSS a bit myself, > so one thing I can do is give feedback. > > Option 1 : > > First impression - a lotus flower, perfect ... I can't help this > reaction, > I practice buddhist medicine and the plant symbolises a lot. > Clarity, and memories of having worked with stunningly beautiful > plants, > in the Himalaya.. Colours, a green, natural look ... also perfect. > > Sometimes I spend so much time up to my elbows in code I forget that > the large bundles of alphanumerics, collection of frameworks, apps, > and sometimes very pretty visual output all go towards healing, > and if we don't see a plant or patient for months, > we're still practicing a form of medicine :) > > This option works for me, and would be consistent with CSS I am using, > although personally I would have chose a lighter grey background, > somewhere around #e0e0e0, #d9d9d9 and #cccccc. > > Option 2 : > > First impression - technology, science fiction almost. > Well, this is what biotechnology is, a medical science where people > understand nature at it's highest levels, and create or synthesize > anew, > medicines and living beings, using highly complex machines to do so :) > > This has a clinical, lab feel that will appeal to many.I personally > prefer > a slightly darker, NeXT - Rhapsodesque shade of blue, but that's me. > > In both cases the Biococoa text in the header graphic doesn't survive > rescaling so well, for small screen rendering on cellphone and pda, > but the body text is perfectly readable. > > If I'd had to design a header or logo for BioCocoa myself, > I would have started with the name itself, and be trying to mix a > photo > of a coffee plant, with renders of the most visually interesting > molecules from it. > Possibly with a fixed background image for the body, of a lot of > ASCII DNA code > ala the original BioCocoa icon and logo, in white on light off- > white grey. > > Again, that's just me. > > > Off topic ... > > Hello everyone, > the reason you don't hear from me is I am not good enough at > programming > to create for myself GNUstep makefiles from XCode or .proj. > > I use the Biococoa Sequence Converter, and look forward to NIB > support in GNUstep improving to include XCode. > > Or I learn enough about makefiles to do that myself but this will > take time > as will understanding the framework enough to make good use of it. > Let alone contribute. > > Or I get a Mac capable of running OSX when I can afford it :) > > I'm currently looking for biotech journalist work to finance my own > research. > > Tenzin > > From kvddrift at earthlink.net Mon Jun 26 00:07:24 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 26 Jun 2006 00:07:24 -0400 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: References: <48074E16-515D-409C-A98B-00B1FF3F9A05@bio.kuleuven.be> <38C6635C-309B-4DD3-A007-8726383B56C6@mekentosj.com> Message-ID: On Jun 22, 2006, at 12:38 PM, peter.schols at mac.com wrote: > Hi, > > It sounds unbelievable, but I finally managed to complete the CSS > design for our homepage. > 'Complete' is a bit euphemistic here because the home page still > needs some work and tweaking, but before doing so, I'd like to get > your advice. I have created two designs and they can be viewed at: > http://bioinformatics.org/biococoa/Option1/ > http://bioinformatics.org/biococoa/Option2/ > > It would be great to hear from the list which design we should > continue with. Of course, I'm also very interested in your feedback > on the contents and layout. I like the second version better. I am not sure what the relation of the flower is with biococoa. cheers, - Koen. From mekentosj at gmail.com Mon Jun 26 06:49:30 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Mon, 26 Jun 2006 11:49:30 +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> Message-ID: <1000C532-9B90-4973-92E4-A3D23440E76A@gmail.com> Hi Peter, Looks very good!! I too prefer option 2 much over option 1, the DNA picture is awesome, where did you get that from? I.a.w. can it also be used for more BioCocoa promotion stuff like the poster? If so, do you have it at higher resolution, than if you send it I will try to do an initial setup of the poster in the same style as option 2. Cheers, Alex On 26-jun-2006, at 5:07, Koen van der Drift wrote: > > On Jun 22, 2006, at 12:38 PM, peter.schols at mac.com wrote: > >> Hi, >> >> It sounds unbelievable, but I finally managed to complete the CSS >> design for our homepage. >> 'Complete' is a bit euphemistic here because the home page still >> needs some work and tweaking, but before doing so, I'd like to get >> your advice. I have created two designs and they can be viewed at: >> http://bioinformatics.org/biococoa/Option1/ >> http://bioinformatics.org/biococoa/Option2/ >> >> It would be great to hear from the list which design we should >> continue with. Of course, I'm also very interested in your >> feedback on the contents and layout. > > I like the second version better. I am not sure what the relation > of the flower is with biococoa. > > 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 LabAssistant - Get your life organized! http://www.mekentosj.com/labassistant ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From gorazd_1957 at yahoo.ca Mon Jun 26 08:48:41 2006 From: gorazd_1957 at yahoo.ca (Gorazd Krosl) Date: Mon, 26 Jun 2006 08:48:41 -0400 Subject: [Biococoa-dev] Error in tarball link in subversion repository Message-ID: <599D2C27-E85D-4F0F-AA03-4DEFFC6261F3@yahoo.ca> Hi, I have recently subscribed to BioCocoa mailing list, since my profession is in research and I know some (not much) programming in Cocoa. I was browsing subversion repository (http://bioinformatics.org/ websvn/listing.php?repname=BioCocoa) and when I clicked to Tarball link (http://bioinformatics.org/websvn/dl.php? repname=BioCocoa&path=&rev=0&isdir=1) the following error message appeared: "Parse error: parse error, unexpected '(', expecting ')' in /mnt/nfs0/www/html/websvn/dl.php on line 32". As I can see from browsing subversion repository, the version of BioCocoa is quite different from the one that I can download normally. I tried to checkout svn as per advice on the page http:// bioinformatics.org/biococoa/Option2/ (which I quite like) but it requires password. Thanks for reading and keep up the good work. I would really like to see the source, in a hope that I can contribute in some small way. Gorazd __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From mekentosj at gmail.com Mon Jun 26 08:54:18 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Mon, 26 Jun 2006 13:54:18 +0100 Subject: [Biococoa-dev] Error in tarball link in subversion repository In-Reply-To: <599D2C27-E85D-4F0F-AA03-4DEFFC6261F3@yahoo.ca> References: <599D2C27-E85D-4F0F-AA03-4DEFFC6261F3@yahoo.ca> Message-ID: <34B16165-B02C-45FF-AEBD-78C829C91B56@gmail.com> Hi Gorazd, Welcome to the list, great to hear there's more interest in BioCocoa. Perhaps Koen, Charles or Peter can comment on the issue with SVN, they're more experienced. Cheers, Alex On 26-jun-2006, at 13:48, Gorazd Krosl wrote: > Hi, > I have recently subscribed to BioCocoa mailing list, since my > profession is in research and I know some (not much) programming in > Cocoa. > I was browsing subversion repository (http://bioinformatics.org/ > websvn/listing.php?repname=BioCocoa) and when I clicked to Tarball > link (http://bioinformatics.org/websvn/dl.php? > repname=BioCocoa&path=&rev=0&isdir=1) the following error message > appeared: "Parse error: parse error, unexpected '(', expecting ')' > in /mnt/nfs0/www/html/websvn/dl.php on line 32". > > As I can see from browsing subversion repository, the version of > BioCocoa is quite different from the one that I can download > normally. I tried to checkout svn as per advice on the page http:// > bioinformatics.org/biococoa/Option2/ (which I quite like) but it > requires password. > > Thanks for reading and keep up the good work. I would really like > to see the source, in a hope that I can contribute in some small way. > > Gorazd > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection > aroundhttp:// > mail.yahoo.com_______________________________________________ > 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 MacOS X: The power of UNIX with the simplicity of the Mac *************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From sweetcocoa at mac.com Mon Jun 26 12:18:27 2006 From: sweetcocoa at mac.com (Peter Schols) Date: Mon, 26 Jun 2006 18:18:27 +0200 Subject: [Biococoa-dev] Error in tarball link in subversion repository In-Reply-To: <599D2C27-E85D-4F0F-AA03-4DEFFC6261F3@yahoo.ca> References: <599D2C27-E85D-4F0F-AA03-4DEFFC6261F3@yahoo.ca> Message-ID: <6C7A59E6-27A2-479E-B4AF-880EAC4AD3C2@mac.com> Hi Gorazd, Thanks for your interest in the project! I'm aware of this tarball issue: it's a problem we will have to discuss with the bioinformatics.org admin. It might be the easiest to become a team member. Just send me your bioinformatics.org username and I'll add you to the BioCocoa team. If you don't already have a username, you can get one for free @ bioinformatics.org. best wishes, Peter On 26 Jun 2006, at 14:48, Gorazd Krosl wrote: > Hi, > I have recently subscribed to BioCocoa mailing list, since my > profession is in research and I know some (not much) programming in > Cocoa. > I was browsing subversion repository (http://bioinformatics.org/ > websvn/listing.php?repname=BioCocoa) and when I clicked to Tarball > link (http://bioinformatics.org/websvn/dl.php? > repname=BioCocoa&path=&rev=0&isdir=1) the following error message > appeared: "Parse error: parse error, unexpected '(', expecting ')' > in /mnt/nfs0/www/html/websvn/dl.php on line 32". > > As I can see from browsing subversion repository, the version of > BioCocoa is quite different from the one that I can download > normally. I tried to checkout svn as per advice on the page http:// > bioinformatics.org/biococoa/Option2/ (which I quite like) but it > requires password. > > Thanks for reading and keep up the good work. I would really like > to see the source, in a hope that I can contribute in some small way. > > Gorazd > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection > aroundhttp:// > mail.yahoo.com_______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From peter.schols at mac.com Mon Jun 26 12:33:18 2006 From: peter.schols at mac.com (Peter Schols) Date: Mon, 26 Jun 2006 18:33:18 +0200 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: <1000C532-9B90-4973-92E4-A3D23440E76A@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> Message-ID: <89765950-0EA5-4A41-B695-97D7E56342C1@mac.com> Hi Alex, > Looks very good!! I too prefer option 2 much over option 1, Since an overwhelming majority seems to be in favor of option 2, I'll stick with that one ;-) > the DNA picture is awesome, where did you get that from? I.a.w. can > it also be used for more BioCocoa promotion stuff like the poster? Yep, with the poster in mind (and other promotional gadgets such as t- shirts, caps, ...) I purchased the high-res version at istockphoto.com. > If so, do you have it at higher resolution, than if you send it I > will try to do an initial setup of the poster in the same style as > option 2. I'll send you the image (in a separate email). It would be great if you could have a first go at the poster Thanks! Peter From mekentosj at gmail.com Mon Jun 26 12:35:17 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Mon, 26 Jun 2006 17:35:17 +0100 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: <89765950-0EA5-4A41-B695-97D7E56342C1@mac.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> Message-ID: Great Peter, I'll give it a try. Cheers, Alex On 26-jun-2006, at 17:33, Peter Schols wrote: > Hi Alex, > >> Looks very good!! I too prefer option 2 much over option 1, > > Since an overwhelming majority seems to be in favor of option 2, > I'll stick with that one ;-) > >> the DNA picture is awesome, where did you get that from? I.a.w. >> can it also be used for more BioCocoa promotion stuff like the >> poster? > > Yep, with the poster in mind (and other promotional gadgets such as > t-shirts, caps, ...) I purchased the high-res version at > istockphoto.com. > >> If so, do you have it at higher resolution, than if you send it I >> will try to do an initial setup of the poster in the same style as >> option 2. > > I'll send you the image (in a separate email). > It would be great if you could have a first go at the poster > > Thanks! > > Peter > > > ********************************************************* ** 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 ttenzin at gmail.com Mon Jun 26 13:12:53 2006 From: ttenzin at gmail.com (Tenzin Togden) Date: Mon, 26 Jun 2006 18:12:53 +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> Message-ID: If chemical graphics are needed, for posters et cetera, let me know. I have experience in chemical graphics,design and DTP. Since looking at option 1, I decided for amusement to experiment with some renders, of 1CT9 from Lotus Japonica,Oryza Sativa and others. They can be seen here : http://synthesis.dyndns.org/tenzin/bioinformatics/mol/1CT9ch.png http://synthesis.dyndns.org/tenzin/bioinformatics/mol/1CT9ch2.png http://synthesis.dyndns.org/tenzin/bioinformatics/mol/1CT9ch3.png These can be freely used for BioCocoa graphics if desired, or I could render anything particularly wanted. Tenzin From sweetcocoa at mac.com Mon Jun 26 14:18:12 2006 From: sweetcocoa at mac.com (Peter Schols) Date: Mon, 26 Jun 2006 20:18:12 +0200 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> Message-ID: Looks great, they could be used for the poster. Thanks! Peter On 26 Jun 2006, at 19:12, Tenzin Togden wrote: > If chemical graphics are needed, for posters et cetera, let me know. > > I have experience in chemical graphics,design and DTP. > > Since looking at option 1, I decided for amusement to experiment with > some renders, of 1CT9 from Lotus Japonica,Oryza Sativa and others. > > They can be seen here : > > http://synthesis.dyndns.org/tenzin/bioinformatics/mol/1CT9ch.png > > http://synthesis.dyndns.org/tenzin/bioinformatics/mol/1CT9ch2.png > > http://synthesis.dyndns.org/tenzin/bioinformatics/mol/1CT9ch3.png > > These can be freely used for BioCocoa graphics if desired, > or I could render anything particularly wanted. > > Tenzin > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From gorazd_1957 at yahoo.ca Mon Jun 26 16:57:46 2006 From: gorazd_1957 at yahoo.ca (Gorazd Krosl) Date: Mon, 26 Jun 2006 16:57:46 -0400 Subject: [Biococoa-dev] Error in tarball link in subversion repository In-Reply-To: <34B16165-B02C-45FF-AEBD-78C829C91B56@gmail.com> References: <599D2C27-E85D-4F0F-AA03-4DEFFC6261F3@yahoo.ca> <34B16165-B02C-45FF-AEBD-78C829C91B56@gmail.com> Message-ID: <9692267E-29A5-43D3-9F22-52FE9AA142CA@yahoo.ca> Hi Alexander, Thank you for the welcome. Peter has kindly explained to me what the issues are with the tarball download and advised me to join the group. Now I just hope that I will be able to contribute in some small way. Cheers, Gorazd On 26-Jun-06, at 8:54 AM, Alexander Griekspoor wrote: > Hi Gorazd, > Welcome to the list, great to hear there's more interest in > BioCocoa. Perhaps Koen, Charles or Peter can comment on the issue > with SVN, they're more experienced. > Cheers, > Alex > > On 26-jun-2006, at 13:48, Gorazd Krosl wrote: > >> Hi, >> I have recently subscribed to BioCocoa mailing list, since my >> profession is in research and I know some (not much) programming >> in Cocoa. >> I was browsing subversion repository (http://bioinformatics.org/ >> websvn/listing.php?repname=BioCocoa) and when I clicked to Tarball >> link (http://bioinformatics.org/websvn/dl.php? >> repname=BioCocoa&path=&rev=0&isdir=1) the following error message >> appeared: "Parse error: parse error, unexpected '(', expecting ')' >> in /mnt/nfs0/www/html/websvn/dl.php on line 32". >> >> As I can see from browsing subversion repository, the version of >> BioCocoa is quite different from the one that I can download >> normally. I tried to checkout svn as per advice on the page http:// >> bioinformatics.org/biococoa/Option2/ (which I quite like) but it >> requires password. >> >> Thanks for reading and keep up the good work. I would really like >> to see the source, in a hope that I can contribute in some small way. >> >> Gorazd >> >> __________________________________________________ >> Do You Yahoo!? >> Tired of spam? Yahoo! Mail has the best spam protection >> aroundhttp:// >> mail.yahoo.com_______________________________________________ >> 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 > > MacOS X: The power of UNIX with the simplicity of the Mac > > *************************************************************** > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From kvddrift at earthlink.net Mon Jun 26 19:15:05 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 26 Jun 2006 19:15:05 -0400 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> Message-ID: <1BF725BD-0327-4A53-8C21-285FA17D3CDA@earthlink.net> On Jun 26, 2006, at 1:12 PM, Tenzin Togden wrote: > These can be freely used for BioCocoa graphics if desired, > or I could render anything particularly wanted. Great pictures! I am not sure if they should be used with BioCocoa, we may give the impression that BioCocoa can be used to render pdb files ;-) Of course, that could always be an extension of BioCocoa if some one feels the urge to work on that. I believe that Phillip already started on some classes for pdb files. cheers, - Koen. From gorazd_1957 at yahoo.ca Wed Jun 28 06:50:34 2006 From: gorazd_1957 at yahoo.ca (Gorazd Krosl) Date: Wed, 28 Jun 2006 06:50:34 -0400 (EDT) Subject: [Biococoa-dev] svn and beginner questions Message-ID: <20060628105034.41919.qmail@web51113.mail.yahoo.com> Hi, As a new member and beginner with svn, I have a few (probably dumb) questions. I have been able to download the project using svn svn+ssh://.... however, using the svnX is not permitting me to do it. It is returning "access denied" error despite I have provided it with my user name and password. I am probably missing something very obvious, so any pointers will be greatly appreciated. Second, since this is my very first time working in a collaboration, I would like to know what is the proper procedure when I for instance create new class or something simmilar and would like to put it in for a group to see. Do I commit directly, ask Peter for permission (review) or what? Sorry for these questions, but as you can see, I am a beginner. You do not need to hold my hand, just point me to where policies are written. Thanks for patience and have a nice day, Gorazd __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From biococoa at bioworxx.com Wed Jun 28 12:52:53 2006 From: biococoa at bioworxx.com (Philipp Seibel) Date: Wed, 28 Jun 2006 18:52:53 +0200 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> Message-ID: <006E20EA-D168-45F8-8795-06233DAE9F00@bioworxx.com> Hey Alex, hey Peter, i had nearly no second to think about my WWDC attendance until now. Just read the latest news on the list. @alex: If you need some help with the poster just tell me what i can do. btw. it would be great to see you at the WWDC :-) @all: did anybody allready thought about the abstract? k thats it for the moment, i just wanted to give a beep ;-) cheers, Phil Am 26.06.2006 um 18:35 schrieb Alexander Griekspoor: > Great Peter, > I'll give it a try. > Cheers, > Alex > > On 26-jun-2006, at 17:33, Peter Schols wrote: > >> Hi Alex, >> >>> Looks very good!! I too prefer option 2 much over option 1, >> >> Since an overwhelming majority seems to be in favor of option 2, >> I'll stick with that one ;-) >> >>> the DNA picture is awesome, where did you get that from? I.a.w. >>> can it also be used for more BioCocoa promotion stuff like the >>> poster? >> >> Yep, with the poster in mind (and other promotional gadgets such >> as t-shirts, caps, ...) I purchased the high-res version at >> istockphoto.com. >> >>> If so, do you have it at higher resolution, than if you send it I >>> will try to do an initial setup of the poster in the same style >>> as option 2. >> >> I'll send you the image (in a separate email). >> It would be great if you could have a first go at the poster >> >> Thanks! >> >> Peter >> >> >> > > ********************************************************* > ** 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. > > ********************************************************* > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From sweetcocoa at mac.com Wed Jun 28 15:20:35 2006 From: sweetcocoa at mac.com (Peter Schols) Date: Wed, 28 Jun 2006 21:20:35 +0200 Subject: [Biococoa-dev] svn and beginner questions In-Reply-To: <20060628105034.41919.qmail@web51113.mail.yahoo.com> References: <20060628105034.41919.qmail@web51113.mail.yahoo.com> Message-ID: <3AE962BC-FB35-4F53-8F01-C63D3DD2E090@mac.com> Hi Gorazd, Have you tried checking out code through the command line (using the terminal)? best wishes, Peter On 28 Jun 2006, at 12:50, Gorazd Krosl wrote: > Hi, > As a new member and beginner with svn, I have a few > (probably dumb) questions. I have been able to > download the project using svn svn+ssh://.... however, > using the svnX is not permitting me to do it. It is > returning "access denied" error despite I have > provided it with my user name and password. I am > probably missing something very obvious, so any > pointers will be greatly appreciated. > Second, since this is my very first time working in a > collaboration, I would like to know what is the proper > procedure when I for instance create new class or > something simmilar and would like to put it in for a > group to see. Do I commit directly, ask Peter for > permission (review) or what? > Sorry for these questions, but as you can see, I am a > beginner. You do not need to hold my hand, just point > me to where policies are written. > > Thanks for patience and have a nice day, > Gorazd > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From gorazd_1957 at yahoo.ca Wed Jun 28 16:27:22 2006 From: gorazd_1957 at yahoo.ca (Gorazd Krosl) Date: Wed, 28 Jun 2006 16:27:22 -0400 Subject: [Biococoa-dev] svn and beginner questions In-Reply-To: <3AE962BC-FB35-4F53-8F01-C63D3DD2E090@mac.com> References: <20060628105034.41919.qmail@web51113.mail.yahoo.com> <3AE962BC-FB35-4F53-8F01-C63D3DD2E090@mac.com> Message-ID: <3D221EFE-99C3-4357-96CD-525CEF3A1DCD@yahoo.ca> Hi Peter, Yes and it worked no problem. The only funny thing was, that the server asked me for a password 2 times if I remember correctly. And I am quite certain that I typed it in correctly, since I typed it "one finger at the time." Anyway, I have the project and I can learn svn commands, I boookmarked the svn red-bean book in Safari to have it handy. One question though, is XCode communicating with my "working copy" or with repository on bioinformatics? If I add to repository through XCode for instance, is it adding locally or on the site as well? I don't want to make a mess there until I am sure I am doing it right. Thanks and have a nice day, Gorazd On 28-Jun-06, at 3:20 PM, Peter Schols wrote: > Hi Gorazd, > > Have you tried checking out code through the command line (using > the terminal)? > best wishes, > > Peter > > > On 28 Jun 2006, at 12:50, Gorazd Krosl wrote: > >> Hi, >> As a new member and beginner with svn, I have a few >> (probably dumb) questions. I have been able to >> download the project using svn svn+ssh://.... however, >> using the svnX is not permitting me to do it. It is >> returning "access denied" error despite I have >> provided it with my user name and password. I am >> probably missing something very obvious, so any >> pointers will be greatly appreciated. >> Second, since this is my very first time working in a >> collaboration, I would like to know what is the proper >> procedure when I for instance create new class or >> something simmilar and would like to put it in for a >> group to see. Do I commit directly, ask Peter for >> permission (review) or what? >> Sorry for these questions, but as you can see, I am a >> beginner. You do not need to hold my hand, just point >> me to where policies are written. >> >> Thanks for patience and have a nice day, >> Gorazd >> >> __________________________________________________ >> Do You Yahoo!? >> Tired of spam? Yahoo! Mail has the best spam protection around >> http://mail.yahoo.com >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From charles.parnot at gmail.com Wed Jun 28 16:34:51 2006 From: charles.parnot at gmail.com (Charles Parnot) Date: Wed, 28 Jun 2006 13:34:51 -0700 Subject: [Biococoa-dev] svn and beginner questions In-Reply-To: <3D221EFE-99C3-4357-96CD-525CEF3A1DCD@yahoo.ca> References: <20060628105034.41919.qmail@web51113.mail.yahoo.com> <3AE962BC-FB35-4F53-8F01-C63D3DD2E090@mac.com> <3D221EFE-99C3-4357-96CD-525CEF3A1DCD@yahoo.ca> Message-ID: Until you commit anything, Xcode will not touch the repository. I would recommand to not use Xcode for commits, but rather the command- line or svnX. There are a few quirks with Xcode (last time I checked, though, was several months ago) and the CLI or svnX give you a better understanding of what happens. charles On Jun 28, 2006, at 1:27 PM, Gorazd Krosl wrote: > Hi Peter, > Yes and it worked no problem. The only funny thing was, that the > server asked me for a password 2 times if I remember correctly. And > I am quite certain that I typed it in correctly, since I typed it > "one finger at the time." Anyway, I have the project and I can > learn svn commands, I boookmarked the svn red-bean book in Safari > to have it handy. One question though, is XCode communicating with > my "working copy" or with repository on bioinformatics? If I add to > repository through XCode for instance, is it adding locally or on > the site as well? I don't want to make a mess there until I am sure > I am doing it right. > > Thanks and have a nice day, > Gorazd > > On 28-Jun-06, at 3:20 PM, Peter Schols wrote: > >> Hi Gorazd, >> >> Have you tried checking out code through the command line (using >> the terminal)? >> best wishes, >> >> Peter >> >> >> On 28 Jun 2006, at 12:50, Gorazd Krosl wrote: >> >>> Hi, >>> As a new member and beginner with svn, I have a few >>> (probably dumb) questions. I have been able to >>> download the project using svn svn+ssh://.... however, >>> using the svnX is not permitting me to do it. It is >>> returning "access denied" error despite I have >>> provided it with my user name and password. I am >>> probably missing something very obvious, so any >>> pointers will be greatly appreciated. >>> Second, since this is my very first time working in a >>> collaboration, I would like to know what is the proper >>> procedure when I for instance create new class or >>> something simmilar and would like to put it in for a >>> group to see. Do I commit directly, ask Peter for >>> permission (review) or what? >>> Sorry for these questions, but as you can see, I am a >>> beginner. You do not need to hold my hand, just point >>> me to where policies are written. >>> >>> Thanks for patience and have a nice day, >>> Gorazd >>> >>> __________________________________________________ >>> Do You Yahoo!? >>> Tired of spam? Yahoo! Mail has the best spam protection around >>> http://mail.yahoo.com >>> _______________________________________________ >>> Biococoa-dev mailing list >>> Biococoa-dev at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection > aroundhttp:// > mail.yahoo.com_______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev -- Xgrid-at-Stanford Help science move fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford Charles Parnot charles.parnot at gmail.com From mekentosj at gmail.com Thu Jun 29 05:10:56 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Thu, 29 Jun 2006 10:10:56 +0100 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: <006E20EA-D168-45F8-8795-06233DAE9F00@bioworxx.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> Message-ID: <4E1A6A82-62B5-402A-A64F-B2A5524ED959@gmail.com> Hi Phil, It will sure be a pleasure again. Things are almost arranged for my trip, looks promising! I still have an abstract of last year, shall I register with that one? I'll try to have a look at the poster this weekend. Cheers and see you in august! Alex On 28-jun-2006, at 17:52, Philipp Seibel wrote: > Hey Alex, hey Peter, > > i had nearly no second to think about my WWDC attendance until now. > Just read the latest news on the list. > > @alex: If you need some help with the poster just tell me what i > can do. > btw. it would be great to see you at the WWDC :-) > > @all: did anybody allready thought about the abstract? > > k thats it for the moment, i just wanted to give a beep ;-) > > cheers, > > Phil > > Am 26.06.2006 um 18:35 schrieb Alexander Griekspoor: > >> Great Peter, >> I'll give it a try. >> Cheers, >> Alex >> >> On 26-jun-2006, at 17:33, Peter Schols wrote: >> >>> Hi Alex, >>> >>>> Looks very good!! I too prefer option 2 much over option 1, >>> >>> Since an overwhelming majority seems to be in favor of option 2, >>> I'll stick with that one ;-) >>> >>>> the DNA picture is awesome, where did you get that from? I.a.w. >>>> can it also be used for more BioCocoa promotion stuff like the >>>> poster? >>> >>> Yep, with the poster in mind (and other promotional gadgets such >>> as t-shirts, caps, ...) I purchased the high-res version at >>> istockphoto.com. >>> >>>> If so, do you have it at higher resolution, than if you send it >>>> I will try to do an initial setup of the poster in the same >>>> style as option 2. >>> >>> I'll send you the image (in a separate email). >>> It would be great if you could have a first go at the poster >>> >>> Thanks! >>> >>> Peter >>> >>> >>> >> >> ********************************************************* >> ** 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. >> >> ********************************************************* >> >> >> _______________________________________________ >> 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 sweetcocoa at mac.com Thu Jun 29 13:42:04 2006 From: sweetcocoa at mac.com (Peter Schols) Date: Thu, 29 Jun 2006 19:42:04 +0200 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: <4E1A6A82-62B5-402A-A64F-B2A5524ED959@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> Message-ID: <4EAD2BB8-53E0-4B66-B9F0-19FC6C9C286F@mac.com> On 29 Jun 2006, at 11:10, Alexander Griekspoor wrote: > I still have an abstract of last year, shall I register with that one? Great idea > I'll try to have a look at the poster this weekend. Even better ;-) peter From kvddrift at earthlink.net Fri Jun 30 08:30:50 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 30 Jun 2006 08:30:50 -0400 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: <4EAD2BB8-53E0-4B66-B9F0-19FC6C9C286F@mac.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> Message-ID: On Jun 29, 2006, at 1:42 PM, Peter Schols wrote: >> I'll try to have a look at the poster this weekend. > > Even better ;-) 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. - Koen. From james.balhoff at duke.edu Fri Jun 30 10:28:29 2006 From: james.balhoff at duke.edu (Jim Balhoff) Date: Fri, 30 Jun 2006 10:28:29 -0400 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: On Jun 30, 2006, at 8:30 AM, Koen van der Drift wrote: > 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. My friend Olivier Fedrigo has released an application using BioCocoa (I think the "old" version): You guys might also be interested in the structure viewer he's got in there, using VTK. - Jim ____________________________________________ James P. Balhoff National Evolutionary Synthesis Center Duke University 2024 West Main St., Suite A200 Durham, NC 27705 USA From sweetcocoa at mac.com Fri Jun 30 10:44:22 2006 From: sweetcocoa at mac.com (Peter Schols) Date: Fri, 30 Jun 2006 16:44:22 +0200 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: <530AC979-6C9A-487F-82F7-71042C4CFB7C@mac.com> Hi Jim, Thanks for the link, looks quite useful for a couple of researchers I know. Also, it's great to see BioCocoa-based apps being released! best wishes, Peter On 30 Jun 2006, at 16:28, Jim Balhoff wrote: > On Jun 30, 2006, at 8:30 AM, Koen van der Drift wrote: > >> 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. > > My friend Olivier Fedrigo has released an application using > BioCocoa (I think the "old" version): > > > > You guys might also be interested in the structure viewer he's got > in there, using VTK. > > - Jim > > > > ____________________________________________ > James P. Balhoff > National Evolutionary Synthesis Center > Duke University > 2024 West Main St., Suite A200 > Durham, NC 27705 > USA > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From kvddrift at earthlink.net Fri Jun 30 10:59:18 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 30 Jun 2006 10:59:18 -0400 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: <530AC979-6C9A-487F-82F7-71042C4CFB7C@mac.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> <530AC979-6C9A-487F-82F7-71042C4CFB7C@mac.com> Message-ID: <3C9DFAC2-D6C6-49F8-A3E9-9BB6910AFBAD@earthlink.net> I am also working on an app that uses BioCocoa, but it is still in (early) development. I will put some screenshots on a website today or tomorrow. - Koen. On Jun 30, 2006, at 10:44 AM, Peter Schols wrote: > Hi Jim, > > Thanks for the link, looks quite useful for a couple of researchers > I know. > Also, it's great to see BioCocoa-based apps being released! > > best wishes, > > Peter > > On 30 Jun 2006, at 16:28, Jim Balhoff wrote: > >> On Jun 30, 2006, at 8:30 AM, Koen van der Drift wrote: >> >>> 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. >> >> My friend Olivier Fedrigo has released an application using >> BioCocoa (I think the "old" version): >> >> >> >> You guys might also be interested in the structure viewer he's got >> in there, using VTK. >> >> - Jim >> >> >> >> ____________________________________________ >> James P. Balhoff >> National Evolutionary Synthesis Center >> Duke University >> 2024 West Main St., Suite A200 >> Durham, NC 27705 >> USA >> >> >> _______________________________________________ >> 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 Jun 30 11:01:15 2006 From: sweetcocoa at mac.com (Peter Schols) Date: Fri, 30 Jun 2006 17:01:15 +0200 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: <3C9DFAC2-D6C6-49F8-A3E9-9BB6910AFBAD@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> <530AC979-6C9A-487F-82F7-71042C4CFB7C@mac.com> <3C9DFAC2-D6C6-49F8-A3E9-9BB6910AFBAD@earthlink.net> Message-ID: <0C59C5CF-F597-402B-91AE-37129C1097F4@mac.com> Now we know why you proposed to add screenshots to the poster ;-)) I'd be very interested to see them! peter On 30 Jun 2006, at 16:59, Koen van der Drift wrote: > I am also working on an app that uses BioCocoa, but it is still in > (early) development. I will put some screenshots on a website today > or tomorrow. > > - Koen. > > > On Jun 30, 2006, at 10:44 AM, Peter Schols wrote: > >> Hi Jim, >> >> Thanks for the link, looks quite useful for a couple of >> researchers I know. >> Also, it's great to see BioCocoa-based apps being released! >> >> best wishes, >> >> Peter >> >> On 30 Jun 2006, at 16:28, Jim Balhoff wrote: >> >>> On Jun 30, 2006, at 8:30 AM, Koen van der Drift wrote: >>> >>>> 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. >>> >>> My friend Olivier Fedrigo has released an application using >>> BioCocoa (I think the "old" version): >>> >>> >>> >>> You guys might also be interested in the structure viewer he's >>> got in there, using VTK. >>> >>> - Jim >>> >>> >>> >>> ____________________________________________ >>> James P. Balhoff >>> National Evolutionary Synthesis Center >>> Duke University >>> 2024 West Main St., Suite A200 >>> Durham, NC 27705 >>> USA >>> >>> >>> _______________________________________________ >>> 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 kvddrift at earthlink.net Fri Jun 30 11:32:54 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 30 Jun 2006 11:32:54 -0400 Subject: [Biococoa-dev] BioCocoa homepage In-Reply-To: <0C59C5CF-F597-402B-91AE-37129C1097F4@mac.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> <530AC979-6C9A-487F-82F7-71042C4CFB7C@mac.com> <3C9DFAC2-D6C6-49F8-A3E9-9BB6910AFBAD@earthlink.net> <0C59C5CF-F597-402B-91AE-37129C1097F4@mac.com> Message-ID: On Jun 30, 2006, at 11:01 AM, Peter Schols wrote: > Now we know why you proposed to add screenshots to the poster ;-)) > I'd be very interested to see them! Heheheheh :-) Here's already a link: http://home.earthlink.net/~kvddrift/id.html Just a teaser so far, I will add some screenshots later, now I'm watching Ger-Arg. cheers, - Koen.