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From: Raik G. <rai...@cr...> - 2009-02-04 08:12:23
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Hi Deepak, Deepak Chandran wrote: > Hey Raik, > > The wet-lab group in our lab is growing, so we started thinking about > ways to organize what is located where, etc. And, of course, Brickit > came to mind. However, all the wet-lab people are more acquainted with > MS Windows. I can setup a linux server, but is it possible to have a > local database in Windows? PostgreSQL and Python work in Windows -- what > else does Brickit depend on? The database is supposed to be on the same server anyway. So your wet lab people just need a browser :) Besides, nothing in the Brickit stack is depending on Unix. Python, Django, etc are all available for Windows as well. So, it should definitely be also possible to turn a Windows system into a Brickit server. I don't know why anyone would want to do that but, I guess, living in Seattle can be accepted as excuse ;) Tell me how it goes! Greetings, Raik > > On Tue, Feb 3, 2009 at 3:23 PM, Raik Gruenberg <rai...@cr... > <mailto:rai...@cr...>> wrote: > > Jason Morrison wrote: > > Congrats on the release, Raik! I plan to participate in an iGEM team > > via DIYbio.org this season, so will get a chance to try out > BrickIt. I > > hope to find features that I would like and time to add them, then. > > Hey Jason! > Well, I can assure you, finding missing features will not be any problem > whatsoever... :) > > Greetings, > Raik > > > > > Cheers, > > -Jason > > > > On Tue, Feb 3, 2009 at 5:22 PM, Raik Gruenberg > <rai...@cr... <mailto:rai...@cr...> > > <mailto:rai...@cr... <mailto:rai...@cr...>>> wrote: > > > > Hi all, > > > > the BrickIt development team (currently consisting of: me) > proudly > > presents a > > new release of the portable biobrick management web server > for your > > institute or > > garage: > > http://brickit.wiki.sourceforge.net/ > > > > BrickIt 0.2 constitutes a major overhaul. Both data model and > user > > interface > > have seen a lot of improvements and the underlying python > module has > > been > > refactured to better accommodate future development. There > are also > > several new > > features: At last, it is possible to compose Biobricks from other > > Biobricks, > > Sequencing data can be added to samples, and some more... > > > > Please check out the detailed release notes: > > http://tinyurl.com/ahq2yc > > > > The VMBrickit virtual machine has been updated to 0.2 and Ubuntu > > 8.04 and is > > available for download: > > http://brickit.wiki.sourceforge.net/Virtual+server > > > > I also hope to have a demo web server up and running soon -- > stay tuned. > > > > As most of you know, this is only a tiny side project and doesn't > > receive as > > much of my time as it would deserve. In fact, the next months > won't > > give me much > > chance to push things further. Ironically, we are now at a point > > where one could > > start putting the real fun stuff in -- Biobrick bug-tracking, > sequencing > > analysis, assembly project management, Biobrick relations, > you name it. > > In other words, a little of *your* time can make a real > difference... > > > > Good night and Good luck! > > Raik > > > > -- > > ________________________________ > > > > Dr. Raik Gruenberg > > http://www.raiks.de/contact.html > > ________________________________ > > > > > ------------------------------------------------------------------------------ > > Create and Deploy Rich Internet Apps outside the browser with > > Adobe(R)AIR(TM) > > software. With Adobe AIR, Ajax developers can use existing skills > > and code to > > build responsive, highly engaging applications that combine the > > power of local > > resources and data with the reach of the web. Download the > Adobe AIR > > SDK and > > Ajax docs to start building applications > > today-http://p.sf.net/sfu/adobe-com > > _______________________________________________ > > Brickit-general mailing list > > Bri...@li... > <mailto:Bri...@li...> > > <mailto:Bri...@li... > <mailto:Bri...@li...>> > > https://lists.sourceforge.net/lists/listinfo/brickit-general > > > > > > > > > > -- > > Jason Morrison > > jas...@gm... <mailto:jas...@gm...> > <mailto:jas...@gm... <mailto:jas...@gm...>> > > http://jayunit.net > > (585) 216-5657 > > -- > ________________________________ > > Dr. Raik Gruenberg > http://www.raiks.de/contact.html > ________________________________ > > ------------------------------------------------------------------------------ > Create and Deploy Rich Internet Apps outside the browser with > Adobe(R)AIR(TM) > software. With Adobe AIR, Ajax developers can use existing skills > and code to > build responsive, highly engaging applications that combine the > power of local > resources and data with the reach of the web. Download the Adobe AIR > SDK and > Ajax docs to start building applications > today-http://p.sf.net/sfu/adobe-com > _______________________________________________ > Brickit-general mailing list > Bri...@li... > <mailto:Bri...@li...> > https://lists.sourceforge.net/lists/listinfo/brickit-general > > > > > -- > Deepak -- ________________________________ Dr. Raik Gruenberg http://www.raiks.de/contact.html ________________________________ |
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From: Deepak C. <deepakc@u.washington.edu> - 2009-02-03 23:29:20
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Hey Raik, The wet-lab group in our lab is growing, so we started thinking about ways to organize what is located where, etc. And, of course, Brickit came to mind. However, all the wet-lab people are more acquainted with MS Windows. I can setup a linux server, but is it possible to have a local database in Windows? PostgreSQL and Python work in Windows -- what else does Brickit depend on? On Tue, Feb 3, 2009 at 3:23 PM, Raik Gruenberg <rai...@cr...>wrote: > Jason Morrison wrote: > > Congrats on the release, Raik! I plan to participate in an iGEM team > > via DIYbio.org this season, so will get a chance to try out BrickIt. I > > hope to find features that I would like and time to add them, then. > > Hey Jason! > Well, I can assure you, finding missing features will not be any problem > whatsoever... :) > > Greetings, > Raik > > > > > Cheers, > > -Jason > > > > On Tue, Feb 3, 2009 at 5:22 PM, Raik Gruenberg <rai...@cr... > > <mailto:rai...@cr...>> wrote: > > > > Hi all, > > > > the BrickIt development team (currently consisting of: me) proudly > > presents a > > new release of the portable biobrick management web server for your > > institute or > > garage: > > http://brickit.wiki.sourceforge.net/ > > > > BrickIt 0.2 constitutes a major overhaul. Both data model and user > > interface > > have seen a lot of improvements and the underlying python module has > > been > > refactured to better accommodate future development. There are also > > several new > > features: At last, it is possible to compose Biobricks from other > > Biobricks, > > Sequencing data can be added to samples, and some more... > > > > Please check out the detailed release notes: > > http://tinyurl.com/ahq2yc > > > > The VMBrickit virtual machine has been updated to 0.2 and Ubuntu > > 8.04 and is > > available for download: > > http://brickit.wiki.sourceforge.net/Virtual+server > > > > I also hope to have a demo web server up and running soon -- stay > tuned. > > > > As most of you know, this is only a tiny side project and doesn't > > receive as > > much of my time as it would deserve. In fact, the next months won't > > give me much > > chance to push things further. Ironically, we are now at a point > > where one could > > start putting the real fun stuff in -- Biobrick bug-tracking, > sequencing > > analysis, assembly project management, Biobrick relations, you name > it. > > In other words, a little of *your* time can make a real difference... > > > > Good night and Good luck! > > Raik > > > > -- > > ________________________________ > > > > Dr. Raik Gruenberg > > http://www.raiks.de/contact.html > > ________________________________ > > > > > ------------------------------------------------------------------------------ > > Create and Deploy Rich Internet Apps outside the browser with > > Adobe(R)AIR(TM) > > software. With Adobe AIR, Ajax developers can use existing skills > > and code to > > build responsive, highly engaging applications that combine the > > power of local > > resources and data with the reach of the web. Download the Adobe AIR > > SDK and > > Ajax docs to start building applications > > today-http://p.sf.net/sfu/adobe-com > > _______________________________________________ > > Brickit-general mailing list > > Bri...@li... > > <mailto:Bri...@li...> > > https://lists.sourceforge.net/lists/listinfo/brickit-general > > > > > > > > > > -- > > Jason Morrison > > jas...@gm... <mailto:jas...@gm...> > > http://jayunit.net > > (585) 216-5657 > > -- > ________________________________ > > Dr. Raik Gruenberg > http://www.raiks.de/contact.html > ________________________________ > > > ------------------------------------------------------------------------------ > Create and Deploy Rich Internet Apps outside the browser with > Adobe(R)AIR(TM) > software. With Adobe AIR, Ajax developers can use existing skills and code > to > build responsive, highly engaging applications that combine the power of > local > resources and data with the reach of the web. Download the Adobe AIR SDK > and > Ajax docs to start building applications today- > http://p.sf.net/sfu/adobe-com > _______________________________________________ > Brickit-general mailing list > Bri...@li... > https://lists.sourceforge.net/lists/listinfo/brickit-general > -- Deepak |
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From: Raik G. <rai...@cr...> - 2009-02-03 23:23:24
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Jason Morrison wrote: > Congrats on the release, Raik! I plan to participate in an iGEM team > via DIYbio.org this season, so will get a chance to try out BrickIt. I > hope to find features that I would like and time to add them, then. Hey Jason! Well, I can assure you, finding missing features will not be any problem whatsoever... :) Greetings, Raik > > Cheers, > -Jason > > On Tue, Feb 3, 2009 at 5:22 PM, Raik Gruenberg <rai...@cr... > <mailto:rai...@cr...>> wrote: > > Hi all, > > the BrickIt development team (currently consisting of: me) proudly > presents a > new release of the portable biobrick management web server for your > institute or > garage: > http://brickit.wiki.sourceforge.net/ > > BrickIt 0.2 constitutes a major overhaul. Both data model and user > interface > have seen a lot of improvements and the underlying python module has > been > refactured to better accommodate future development. There are also > several new > features: At last, it is possible to compose Biobricks from other > Biobricks, > Sequencing data can be added to samples, and some more... > > Please check out the detailed release notes: > http://tinyurl.com/ahq2yc > > The VMBrickit virtual machine has been updated to 0.2 and Ubuntu > 8.04 and is > available for download: > http://brickit.wiki.sourceforge.net/Virtual+server > > I also hope to have a demo web server up and running soon -- stay tuned. > > As most of you know, this is only a tiny side project and doesn't > receive as > much of my time as it would deserve. In fact, the next months won't > give me much > chance to push things further. Ironically, we are now at a point > where one could > start putting the real fun stuff in -- Biobrick bug-tracking, sequencing > analysis, assembly project management, Biobrick relations, you name it. > In other words, a little of *your* time can make a real difference... > > Good night and Good luck! > Raik > > -- > ________________________________ > > Dr. Raik Gruenberg > http://www.raiks.de/contact.html > ________________________________ > > ------------------------------------------------------------------------------ > Create and Deploy Rich Internet Apps outside the browser with > Adobe(R)AIR(TM) > software. With Adobe AIR, Ajax developers can use existing skills > and code to > build responsive, highly engaging applications that combine the > power of local > resources and data with the reach of the web. Download the Adobe AIR > SDK and > Ajax docs to start building applications > today-http://p.sf.net/sfu/adobe-com > _______________________________________________ > Brickit-general mailing list > Bri...@li... > <mailto:Bri...@li...> > https://lists.sourceforge.net/lists/listinfo/brickit-general > > > > > -- > Jason Morrison > jas...@gm... <mailto:jas...@gm...> > http://jayunit.net > (585) 216-5657 -- ________________________________ Dr. Raik Gruenberg http://www.raiks.de/contact.html ________________________________ |
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From: Jason M. <jas...@gm...> - 2009-02-03 22:54:36
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Congrats on the release, Raik! I plan to participate in an iGEM team via DIYbio.org this season, so will get a chance to try out BrickIt. I hope to find features that I would like and time to add them, then. Cheers, -Jason On Tue, Feb 3, 2009 at 5:22 PM, Raik Gruenberg <rai...@cr...>wrote: > Hi all, > > the BrickIt development team (currently consisting of: me) proudly presents > a > new release of the portable biobrick management web server for your > institute or > garage: > http://brickit.wiki.sourceforge.net/ > > BrickIt 0.2 constitutes a major overhaul. Both data model and user > interface > have seen a lot of improvements and the underlying python module has been > refactured to better accommodate future development. There are also several > new > features: At last, it is possible to compose Biobricks from other > Biobricks, > Sequencing data can be added to samples, and some more... > > Please check out the detailed release notes: > http://tinyurl.com/ahq2yc > > The VMBrickit virtual machine has been updated to 0.2 and Ubuntu 8.04 and > is > available for download: > http://brickit.wiki.sourceforge.net/Virtual+server > > I also hope to have a demo web server up and running soon -- stay tuned. > > As most of you know, this is only a tiny side project and doesn't receive > as > much of my time as it would deserve. In fact, the next months won't give me > much > chance to push things further. Ironically, we are now at a point where one > could > start putting the real fun stuff in -- Biobrick bug-tracking, sequencing > analysis, assembly project management, Biobrick relations, you name it. > In other words, a little of *your* time can make a real difference... > > Good night and Good luck! > Raik > > -- > ________________________________ > > Dr. Raik Gruenberg > http://www.raiks.de/contact.html > ________________________________ > > > ------------------------------------------------------------------------------ > Create and Deploy Rich Internet Apps outside the browser with > Adobe(R)AIR(TM) > software. With Adobe AIR, Ajax developers can use existing skills and code > to > build responsive, highly engaging applications that combine the power of > local > resources and data with the reach of the web. Download the Adobe AIR SDK > and > Ajax docs to start building applications today- > http://p.sf.net/sfu/adobe-com > _______________________________________________ > Brickit-general mailing list > Bri...@li... > https://lists.sourceforge.net/lists/listinfo/brickit-general > -- Jason Morrison jas...@gm... http://jayunit.net (585) 216-5657 |
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From: Raik G. <rai...@cr...> - 2009-02-03 22:47:24
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Hi all, the BrickIt development team (currently consisting of: me) proudly presents a new release of the portable biobrick management web server for your institute or garage: http://brickit.wiki.sourceforge.net/ BrickIt 0.2 constitutes a major overhaul. Both data model and user interface have seen a lot of improvements and the underlying python module has been refactured to better accommodate future development. There are also several new features: At last, it is possible to compose Biobricks from other Biobricks, Sequencing data can be added to samples, and some more... Please check out the detailed release notes: http://tinyurl.com/ahq2yc The VMBrickit virtual machine has been updated to 0.2 and Ubuntu 8.04 and is available for download: http://brickit.wiki.sourceforge.net/Virtual+server I also hope to have a demo web server up and running soon -- stay tuned. As most of you know, this is only a tiny side project and doesn't receive as much of my time as it would deserve. In fact, the next months won't give me much chance to push things further. Ironically, we are now at a point where one could start putting the real fun stuff in -- Biobrick bug-tracking, sequencing analysis, assembly project management, Biobrick relations, you name it. In other words, a little of *your* time can make a real difference... Good night and Good luck! Raik -- ________________________________ Dr. Raik Gruenberg http://www.raiks.de/contact.html ________________________________ |
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From: <ca...@ar...> - 2008-10-29 02:22:15
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Hello, Is there any good information on using synthetic biology to produce food? thanks, Chris |
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From: Raik G. <rai...@cr...> - 2008-10-28 16:02:15
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PS: once you have installed the development version, the 'new' layout with better views and links can be accessed under http://localhost:8000/registry Greetings, Raik Goksel Misirli wrote: > Hi, > > My name is Goksel Misirli. I'm a PhD student at Newcastle University, UK. > > After our discussions with my tutors,Anil Wipat and Jennifer Hallinan, they > wanted me to setup Brickit and I'm trying to install it to one of our > servers. > > But when I run "python manage.py syncdb" I get the error attached in the > email. It complains about django.core.validators module. > > I checked django files and I could not find validators.py which exist in the > virtual machine installation I downloaded from brickit web site. Virtual > machine installation is ok but the normal installation does not work. > > It looks like brickit does not work with the latest version of Django. Or I > might be missing something else. > > If you could point me at the right direction, I would be grateful. I spent > some time but I could not make it working yet. > > Regards > > Goksel Misirli > > > > > > > ------------------------------------------------------------------------ > -- ________________________________ Dr. Raik Gruenberg http://www.raiks.de/contact.html ________________________________ |
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From: Raik G. <rai...@cr...> - 2008-10-28 16:02:05
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Hi Goksel, nice hearing from some potential brickiters ;-) Which version of brickit are you using? The last official release is quite outdated and should indeed not work with the latest django. If you update django, you also need to update brickit to the latest SVN version: svn co https://brickit.svn.sourceforge.net/svnroot/brickit/trunk brickit Now, the truth is that I am not actually sure whether or not even the latest trunk snapshot works with the latest django either. Right now I am working on a new release which underwent quite a lot of refactoring for easier development, offers some custom forms and views for Biobricks, Vectors and Samples, gives you links between Biobricks and associated samples, tries to support the attachment of sequencing results to samples and adds support for composite biobricks. You can check out the current status of this work like this: "svn co https://brickit.svn.sourceforge.net/svnroot/brickit/branches/devel2 brickitproject" (one line command) If you switch to this branch, you will need to rebuild your database. So the order of installation steps would be: 1) delete your database: dropdb -U partsuser parts 2) create a new empty database: createdb -U admin -O partsuser parts 3) checkout the project: svn co https://brickit.svn.sourceforge.net/svnroot/brickit/branches/devel2 brickitproject 4) put the folder brickitproject into your PYTHONPATH 5) re-populate the database: cd brickitproject/brickit python manage.py syncdb This is a "bleeding edge" snapshot and I haven't yet myself installed it on other machines. You probably will have to adjust the 'MEDIA_FOLDER' (or something like that) in the settings.py. This is the folder where file attachments are stored (only sequencing traces for now). The other caveat is that I am probably going to make at least one last change to the data model before rolling this out as a new official release, so please consider this a preview and don't use it for production purposes yet. If you find the time, it would be great to know whether you can get this development version running on your system. It's also the much better starting point if you want to extend the server -- there are tons of things that need to be improved. Any further questions are most welcome! Pass my best greetings to Anil and Jennifer! Good luck! Raik Goksel Misirli wrote: > Hi, > > My name is Goksel Misirli. I'm a PhD student at Newcastle University, UK. > > After our discussions with my tutors,Anil Wipat and Jennifer Hallinan, they > wanted me to setup Brickit and I'm trying to install it to one of our > servers. > > But when I run "python manage.py syncdb" I get the error attached in the > email. It complains about django.core.validators module. > > I checked django files and I could not find validators.py which exist in the > virtual machine installation I downloaded from brickit web site. Virtual > machine installation is ok but the normal installation does not work. > > It looks like brickit does not work with the latest version of Django. Or I > might be missing something else. > > If you could point me at the right direction, I would be grateful. I spent > some time but I could not make it working yet. > > Regards > > Goksel Misirli > > > > > > > ------------------------------------------------------------------------ > -- ________________________________ Dr. Raik Gruenberg http://www.raiks.de/contact.html ________________________________ |
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From: Raik G. <rai...@cr...> - 2008-07-12 19:43:41
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Hi again, I tried to give a neutral summary of our tele-meeting in my previous mail to the pobol@ group but I am actually not entirely satisfied about the outcome and would like to raise some critics. Sorry for being a bit out of focus and not bringing those up during the call itself... It was excellent to get an overview over the different development efforts -- having a discussion group around these topics was definitely a good idea and perhaps we should broaden it beyond Pobol and registry issues. However, the eventual conclusion was that we all keep on developing our software tools independently and promote Pobol as a connectivity standard. That's less than I had hoped for. To repeat the comment from the review, it's ironic that wet lab synthetic biologists are good at building libraries and exchanging parts against technical and legal odds, whereas their computer colleagues keep on working in closed groups or even alone. I also led slip through some miss-conceptions about BrickIt. The project is not developed "in vacuum" but is actually in real-world use. Even though it right now only handles 200 or so BioBricks and samples, the data model already went through several iterations of modifications and testing to suit our wet lab needs. So, Tim, please have a look at the BrickIt data model! In fact, models.py is the only thing that is really important about the existing code. All the other aspects (project layout, web interface) are just rough attempts to get up and running as quickly as possible. So you are right that one shouldn't use the admin interface for public viewing. In fact, I think one should develop a completely independent set of views and forms (which is how django projects work). The problem is that I don't really have the expertise for that. The devel branch of the svn contains a pretty nice BioBrick view which I tried to merge into the admin interface but that's a rather complicate strategy and one should really start from scratch there. There are also some issues with the JBEI registry architecture though. So you guys are using the Django templating system but refrained from using the Django data API and have some custom XML / mySQL layer underneath. But why? This layout is not more but rather less modular than a pure django solution. For example, if you would use the full django stack, you could rather easily migrate your DB from mySQL to Postgresql or Oracle or whatever whithout changing any of your code (which I actually did with BrickIt). Moreover, the django data API is one of the main advantages of the whole framework. It makes it incredibly intuitive to access the data even for programmers that have never used django before. And given the rising popularity of django and given that Google has chosen the same API for their AppEngine platform, this API is now turning into something like an industry standard (well, or as close as it gets in the splintered world of web development). Chris, Tim, it is really great that you want to open up your registry software -- I would be the first to switch over if the result turns out well. But then you should make it as easy as possible for outside developers to join the project. Yet another custom API creates a high barrier. What I would like to see in the scene is some real software development collaboration. So here are my suggestions: Doug, why don't you guys set up an open source synbio java library? Some of your clotho code about BioBrick handling is certainly of more general use. Tim, we could start the same for the Python side. Of course, even more I would prefer if we could compare the needs and data structure of your JBEI registry and BrickIt and explore whether the two could be merged. Despite the very little time left for programming right now, what I still plan to get done is to finalize the last tweaks to the brickit data model, to clean up the brickit folder structure and then to merge the cleaned devel version back into the trunk. This should give you a better starting point for having another look at it. Sorry about the long discourse! Greetings, Raik -- ________________________________ Dr. Raik Gruenberg http://www.raiks.de/contact.html ________________________________ |
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From: Raik G. <rai...@cr...> - 2008-06-01 20:35:56
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Hi Jason, Jason Morrison wrote: > Raik, > > This is fantastic news - I was actually just looking at the google code > project yesterday (hanging out with some semantic web hackers at > RailsConf) to see if the ontology description was there. I've been > doing some thinking and light hacking on Brickit to expose RDF/XML and > n3 versions of data contained inside. I have next week off, and look > forward to getting some solid time to dig in then. That sounds great! Do you want to have a developer account on the sourceforge project? You could open your own branch or directly check things into the devel branch. My big Biobrick order is going to arrive tomorrow so I am going to be pretty occupied by wet lab work. The minimal brickit plans are to just merge the current devel version (with its much nicer Biobrick view) into the trunk and release it as soon as possible. After that, there won't be much activity from my side for a while. There are anyway some more strategic decisions needed before going on. It's not such a good strategy to expose the Admin interface to normal users. Besides, Brickit is currently using the classic django admin which will be superseeded by the newforms admin branch in the upcoming Django 1.0 . Writing a public interface from scratch (rather than adapting admin) would probably make more sense... if there is the time for that. None of this really affects the RDF/XML export though. Greetings, Raik > > Cheers! > Jason > > On Sun, Jun 1, 2008 at 12:05 PM, Raik Gruenberg <rai...@cr... > <mailto:rai...@cr...>> wrote: > > Hi everyone, > > I've shifted the Pobol ontology files to a new Google Code project > so that we > can track changes and issues: > > http://code.google.com/p/pobol/ > > The initial release contains the ontology in OWL/XML and Turtle > format, plus an > example Biobrick XML file. It has changed with respect to the > previous version 0.1: > > * restrictions clarify which properties are obligatory for certain > classes. For > example, a BiobrickFormat needs exactly one 'prefix', 'suffix', and > one 'self_scar' > > * all sequence-related properties (partSequence, prefix, suffix, > scar) are now > derived from a common dnaSequence ancestor -- this should allow for > some more > general queries and data handling in the future. > > I may not have much time to work on this during the next weeks. > Please review > the wiki and see where you can contribute. It would be great to get more > involvement from people working on the upcoming registries or on > concrete > web/software projects that import / export Biobrick data. Early > coordination can > spare us all a lot of later work and frustration. > > Open issues: > -------------- > (see also http://code.google.com/p/pobol/issues/list) > > * earlier, Jason had suggested to tie the Biobrick Format to the > PhysicalDNA > rather than to a given Biobrick record -- surely worth considering. > Though, it > would be good to know how the MIT registry handles this before > making a decision. > > * The sequenceOntology project provides OWL terms for sequence > features and > locations -- I think it would make sense to already include such feature > properties in the initial pobol draft. > > * Looking at the evolving structure, I would suggest to modify the > BiobrickFamily concept. I'll describe this in a separate mail. > > Greetings, > Raik > > Raik Gruenberg wrote: > > CC to the list for the other Pobol fans ;-) > > Note, this is still very much work in progress. > > /Raik > > > > -------- Original Message -------- > > Subject: pobol first draft > > Date: Sun, 04 May 2008 02:20:30 +0200 > > From: Raik Gruenberg <rai...@cr... > <mailto:rai...@cr...>> > > To: mgaldzic@u.washington.edu <mailto:mgaldzic@u.washington.edu> > > CC: Mackenzie Cowell <mac...@gm... > <mailto:mac...@gm...>>, Jason Morrison > > <jas...@gm... <mailto:jas...@gm...>> > > > > Hi Michael, Mac, Jason, > > > > attached is a first OWL-formatted draft of our minimal ontology: see > > partsrdf.owl. I've written this from scratch as N3 file (see > > partsrdf.n3) and > > converted it to the xml format using the RDF validator at > > http://www.rdfabout.com/demo/validator/ > > > > The owl file loads into Protege and Swoop for perhaps easier > editing. I > > would > > suggest that we continue to ship N3 versions though for better > > readability (they > > say XML was invented as a human readable format, yeah right...). > > > > What is still missing are restrictions, like that a Biobrick must > have > > exactly > > one sequence and format and so on. So far I have just fixed the > range of > > values > > of each property (owl:range) and what kind of properties a class > can have > > (owl:domain, note this goes into the property not the class > definition). > > > > More explanations: "a owl:FunctionalProperty" means this property can > > only occur > > ones per object. And "a owl:InverseFunctionalProperty" means this > > property has > > to be unique for each object. > > > > Apart from the restrictions, I didn't find out yet how to define > a datatype > > "list of Biobrick instances" for the subParts property (aka > > composition). N3 > > allows to formulate lists of values like this: > > > > BBa0102 bbf:subParts (BBa0001 BBa0002). > > > > But I didn't find any documentation how to enforce that in an > ontology. > > Hints > > anyone? > > > > Last note, I changed some property names (dnaSequence rather than > sequence, > > isCircular rather than Circular, subFamilyOf rather than parent) > to better > > conform with informal owl conventions. These are open to debate > of course. > > Ah, and I forgot the selfScar and constraint in Format... > > > > Anyway, work in progress obviously. I've some last traveling to > do starting > > tomorrow and, probably, won't touch these files for the week to come. > > Feel free > > to fill in the missing bits. Could anyone please set up a google code > > project > > for this to get version control? Or this site may be an interesting > > alternative: > > http://www.knoodl.com > > Other ideas? > > > > Greetings, > > Raik > > > > PS: also attached is an incomplete example Biobrick file using this > > ontology in > > N3 and XML format. > > > > > > Michal Galdzicki wrote: > >> i am very impressed as to how well this workshop went. and happy to > >> participate, i will make a better diagram of the pobol class > >> structures and try to explain some of the theory that goes into it. > >> mac: yell at me if i dont post anything by sunday :) > >> > >> It's a pleasure to work with you guys, > >> mike > >> > >> On Wed, Apr 30, 2008 at 9:50 PM, Mackenzie Cowell > <mac...@gm... <mailto:mac...@gm...>> > >> wrote: > >>> Hi Raik, > >>> > >>> I had a great time at the SSSB workshop. I think we accomplished a > >>> lot more > >>> than anyone expected. Michal and I have put up a little bit of info > >>> on the > >>> pobol page on OWW. We still need to fill in the rationale for > all the > >>> classes (my job) and perhaps make a better diagram of the data > model. I > >>> would also like to put together an example xml document of what a > >>> real part > >>> (F2620 or JCA's promoter family?) would look like in pobol format. > >>> > >>> Besides that, what's the next step in moving forward with > >>> implementing pobol > >>> in freebase and in brickit? > >>> > >>> I'll see you on the technical standards list! > >>> > >>> > >>> Mac > >> > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Standards mailing list > > Sta...@bi... <mailto:Sta...@bi...> > > http://biobricks.org/mailman/listinfo/standards_biobricks.org > > -- > ________________________________ > > Dr. Raik Gruenberg > http://www.raiks.de/contact.html > ________________________________ > > _______________________________________________ > Standards mailing list > Sta...@bi... <mailto:Sta...@bi...> > http://biobricks.org/mailman/listinfo/standards_biobricks.org > > > > > -- > Jason Morrison > jas...@gm... <mailto:jas...@gm...> > http://jayunit.net > (585) 216-5657 -- ________________________________ Dr. Raik Gruenberg http://www.raiks.de/contact.html ________________________________ |
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From: Jason M. <jas...@gm...> - 2008-05-14 05:01:42
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Hi Brickiteers, I've added a set of "quick install" instructions for development for OS X 10.5 at <http://brickit.wiki.sourceforge.net/quick+setup+osx>. Much is borrowed from Raik's original Debian/Ubuntu quick install page. If anyone is interested and/or could try them out for a sanity check, that'd be great! (I'm quite new to OS X, and would welcome any suggestions or points where <10.5 instructions would differ). Cheers, Jason -- Jason Morrison jas...@gm... http://jayunit.net (585) 216-5657 |
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From: Raik G. <rai...@cr...> - 2008-04-17 21:11:39
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Hi Reid, sorry, that bit of crucial information was indeed missing on the wiki. I've tried to fill in the gaps: http://brickit.wiki.sourceforge.net/Virtual+server Please, feel free to edit the wiki if you find anything else missing or badly described! So the default login is brickit and the password is brickit, too. There is no root account on Ubuntu systems, you will have to use sudo from the brickit account. BTW, you may also want to check out the development branch, where I have added a real Biobrick View with links to your local samples and the MIT page of that part (if applicable). The instructions for switching are on the same wiki page. After the switch, the old "Edit repository" link won't work. Go to your.server.ip.address/parts instead. Well, if you want to fill in real data right now, you are still better off with the stable branch. Good luck! Raik Reid Williams wrote: > We downloaded the VMware image to try out the software here at UCSF. > Two issues came up. > > First, we don't have the root password for the Ubuntu installation in > the image. We didn't see it on the instructions page and none of the > obvious passwords we tried worked. > Second, on running the image, VMWare complains of a missing iso image > that was used as the CDROM drive. I'm assuming we don't need it but > wanted to mention it anyway. > > We're looking forward to trying out brickit. > thanks, > -reid > > ------------------------------------------------------------------------- > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > Don't miss this year's exciting event. There's still time to save $100. > Use priority code J8TL2D2. > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > _______________________________________________ > Brickit-general mailing list > Bri...@li... > https://lists.sourceforge.net/lists/listinfo/brickit-general > > -- ________________________________ Dr. Raik Gruenberg http://www.raiks.de/contact.html ________________________________ |
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From: Reid W. <eno...@gm...> - 2008-04-17 19:20:35
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We downloaded the VMware image to try out the software here at UCSF. Two issues came up. First, we don't have the root password for the Ubuntu installation in the image. We didn't see it on the instructions page and none of the obvious passwords we tried worked. Second, on running the image, VMWare complains of a missing iso image that was used as the CDROM drive. I'm assuming we don't need it but wanted to mention it anyway. We're looking forward to trying out brickit. thanks, -reid |
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From: Raik G. <rai...@cr...> - 2008-02-06 16:51:35
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The VMBrickit virtual machine has been updated to release 0.1 (svn revision 120 actually, which adds some example data). Note, there is no need to replace a running system, follow the update instructions instead. See: http://brickit.wiki.sourceforge.net/Virtual+server Direct download link: http://serrano.crg.es/vm/vmbrickit_0.1.tar.bz2 Good luck! Raik |
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From: Raik G. <rai...@cr...> - 2008-02-03 19:20:49
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I've bundled the current version of the BrickIt project into a first release for easier download and evaluation. See: http://sourceforge.net/project/showfiles.php?group_id=202085 BrickIt 0.1 corresponds to the version in use at the CRG. The data model has been updated to account for different biobrick formats, to allow for the construction of composite biobricks (Unfortunately, the latter is not yet well supported by the web interface), and to fix some smaller inconsistencies we came across during our daily use. The release is tagged 'release-0.1' in the subversion repository. I will continue to add bugfixes and further improvements to the main ('trunk') development line -- as long as they don't break the existing CRG installation. Anything beyond that (i.e. changes to the data model) will first go into the 'devel' branch and will only be merged back for the next official release. Should there be any changes to the data model, I will include a script with 0.2 to migrate an existing installation without data loss. That means, it should be reasonably save to base your first small production registry on this BrickIt version -- as long as you don't expect anything too fancy... See also the release notes: http://sourceforge.net/project/shownotes.php?group_id=202085&release_id=573615 Questions & comments are, as always, most welcome! Greetings! Raik |
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From: Raik G. <rai...@cr...> - 2007-11-12 09:52:38
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Hi, this mailing list should be our first stop for any brickit-related discussions, questions or suggestions. Join in! Raik -- ________________________________ Dr. Raik Gruenberg http://www.raiks.de/contact.html ________________________________ |
