From charles.parnot at stanford.edu Sun Apr 3 03:29:40 2005 From: charles.parnot at stanford.edu (Charles PARNOT) Date: Sat, 2 Apr 2005 23:29:40 -0800 Subject: [Biococoa-dev] Test-BCFoundation Message-ID: I worked on the tests for BCFoundation: * updated target name to follow the guidelines + renaming of the prefix header and info.plist --> now 'Test - BCFoundation' * rewrote the tests for BCSequenceDNA initializers to also test symbol sets * uncovered a bug in BCAbstractSequence initializers --> yeah! Tests are useful ;-) * the other subclasses will follow... * everything else too... charles -- Help science go fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford/ Charles Parnot charles.parnot at stanford.edu Room B157 in Beckman Center 279, Campus Drive Stanford University Stanford, CA 94305 (USA) Tel +1 650 725 7754 Fax +1 650 725 8021 From a.griekspoor at nki.nl Sun Apr 3 04:42:20 2005 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Sun, 3 Apr 2005 10:42:20 +0200 Subject: [Biococoa-dev] Test-BCFoundation In-Reply-To: References: Message-ID: <16ae2606b5e413e477e72b78a96fa98e@nki.nl> Great! For those not having seen this one, there's a great new article on OCUnit testing from Apple: http://developer.apple.com/tools/unittest.html And there's more exciting news to tell, but I'm first going to enjoy the sun a bit, I have a exhausting week behind me, and the weather is just perfect today, sorry ;-) Cheers, Alex On 3-apr-05, at 9:29, Charles PARNOT wrote: > I worked on the tests for BCFoundation: > > * updated target name to follow the guidelines + renaming of the > prefix header and info.plist > --> now 'Test - BCFoundation' > > * rewrote the tests for BCSequenceDNA initializers to also test symbol > sets > > * uncovered a bug in BCAbstractSequence initializers --> yeah! Tests > are useful ;-) > > * the other subclasses will follow... > > * everything else too... > > charles > > -- > Help science go fast forward: > http://cmgm.stanford.edu/~cparnot/xgrid-stanford/ > > Charles Parnot > charles.parnot at stanford.edu > > Room B157 in Beckman Center > 279, Campus Drive > Stanford University > Stanford, CA 94305 (USA) > > Tel +1 650 725 7754 > Fax +1 650 725 8021 > _______________________________________________ > 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 MacOS X: The power of UNIX with the simplicity of the Mac *************************************************************** From charles.parnot at stanford.edu Mon Apr 4 01:21:34 2005 From: charles.parnot at stanford.edu (Charles PARNOT) Date: Sun, 3 Apr 2005 22:21:34 -0700 Subject: [Biococoa-dev] Test-BCFoundation In-Reply-To: <16ae2606b5e413e477e72b78a96fa98e@nki.nl> References: <16ae2606b5e413e477e72b78a96fa98e@nki.nl> Message-ID: At 10:42 AM +0200 4/3/05, Alexander Griekspoor wrote: >Great! >For those not having seen this one, there's a great new article on OCUnit testing from Apple: >http://developer.apple.com/tools/unittest.html > >And there's more exciting news to tell, but I'm first going to enjoy the sun a bit, I have a exhausting week behind me, and the weather is just perfect today, sorry ;-) > >Cheers, >Alex News, news, come on, tell us! Less exciting news, more down to earth: * added tests for BCSequenceRNA * uncovered a bug in BCSymbolset, rnaSymbolSet --> yeah! Tests are useful again :-) * the other subclasses will follow... * everything else too... charles -- Help science go fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford/ Charles Parnot charles.parnot at stanford.edu Room B157 in Beckman Center 279, Campus Drive Stanford University Stanford, CA 94305 (USA) Tel +1 650 725 7754 Fax +1 650 725 8021 From kvddrift at earthlink.net Mon Apr 4 05:49:29 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 4 Apr 2005 05:49:29 -0400 Subject: [Biococoa-dev] Test-BCFoundation In-Reply-To: References: Message-ID: <2e3944259f571bbe80107356b2685c11@earthlink.net> On Apr 3, 2005, at 3:29 AM, Charles PARNOT wrote: > * updated target name to follow the guidelines + renaming of the > prefix header and info.plist > --> now 'Test - BCFoundation' > Thanks for that Charles. One question, maybe we should create a Test directory at the root level of BioCocoa, instead of inside BCFoundation? cheers, - Koen. From charles.parnot at stanford.edu Mon Apr 4 13:25:35 2005 From: charles.parnot at stanford.edu (Charles PARNOT) Date: Mon, 4 Apr 2005 09:25:35 -0800 Subject: [Biococoa-dev] Test-BCFoundation In-Reply-To: <2e3944259f571bbe80107356b2685c11@earthlink.net> References: <2e3944259f571bbe80107356b2685c11@earthlink.net> Message-ID: At 5:49 -0400 4/4/05, Koen van der Drift wrote: >On Apr 3, 2005, at 3:29 AM, Charles PARNOT wrote: > >>* updated target name to follow the guidelines + renaming of the prefix header and info.plist >> --> now 'Test - BCFoundation' >> > >Thanks for that Charles. One question, maybe we should create a Test directory at the root level of BioCocoa, instead of inside BCFoundation? > >cheers, > >- Koen. I initially decided to hide it in BCFoundation, but I see how a 'Test' directory would nicely mirror a 'Demo' folder... I will make the move. I will also rename the framework 'TestBCFoundation.framework' instead of 'Test - BCFoundation': no more space character (that stopped me for a while, stupid CLI!) charles -- Help science go fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford/ Charles Parnot charles.parnot at stanford.edu Room B157 in Beckman Center 279, Campus Drive Stanford University Stanford, CA 94305 (USA) Tel +1 650 725 7754 Fax +1 650 725 8021 From a.griekspoor at nki.nl Mon Apr 4 18:30:11 2005 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Tue, 5 Apr 2005 00:30:11 +0200 Subject: [BioCocoa-dev] BioCocoa meeting Message-ID: <3fae1ef84043c28c079f38cc7f0e5b64@nki.nl> Hi everybody, Here's the news I was talking about. Robert Kehrer at Apple responded to our question about a WWDC2005 BioCocoa meeting with the email below. Personally I think it's a great idea to join the BioHackathon with the BioCocoa team, of course as it coincides with the WWDC we can meet up there as well. That is, I still haven't heard about a potential sponsorship. I'll try to bring up that subject again if we know more about the BioHackathon. I discussed this off-list with Peter already, and he would like to join the BioHackaThon as well. Now I would like to know a few things and ask you guys if the following is a good idea. First, who would be interested to join this BioHackaThon if this were possible. It would be a great opportunity to really hack away with BioCocoa and do lots of work (starting at the WWDC already of course). Why would you like to join, or why wouldn't you. Second, I propose to contact the organizers of the BioHackathon as soon as possible to see what the possibilities are, costs, etc. We have been thinking in terms of the OpenBio organization already. It might be (way) too early to really join, but it might be the perfect opportunity to introduce ourselves, discuss with those people what our and their options are, and meet a lot of people with lots of experience and attract perhaps a few enthusiastic people from this field. If you all agree, I can do the same thing with Peter again and send an email to the people mentioned by Robert Kehrer. Let's then see how things evolve.... Cheers, Alex > Alexander, > > The Apple and the OpenBio community are planning a BioHackaThon 2005 > to be in conjunction with the WWDC 2005. > > Plans would include: > 1) A kick-off reception on Sunday June 5th to welcome the OpenBio > attendees > 2) WWDC attendance by as many OpenBio community luminaries as possible > 3) A 4-5 day BioHackathon on the Apple Campus in Cupertino immediately > following the WWDC > > Community leaders are currently identifying the appropriate attendees > and seeking travel and lodging funding. I expect that key people from > each of the various Bio* groups would be in attendance and see no > reason that BioCocoa couldn't be included if that project is > officially part of the OpenBio community. > > The BioHackathon organizers include Susanna Lewis, Cyrus Harmon, Steve > Chervitz and Jason Stajich (cc'ed). You should contact them to > investigate the participation of the BioCocoa team. > --- > Robert Kehrer > strategic alliance mgr, sciences ??| ??worldwide developer relations > > > On Mar 13, 2005, at 5:29 AM, Alexander Griekspoor wrote: > >> Dear Robert, >> >> It was a great pleasure to meet you during WWDC 2004 right after the >> ceremony of the design awards and during the science lunches. Back >> then >> you told me that I could contact you whenever I needed your help with >> anything related to our programs and with this mail I want to make >> use >> of this promise ;-) >> >> Right after last year's meeting I got in contact with Peter Schols >> from >> Belgium who wrote a Cocoa framework - called BioCocoa - for reading >> and >> writing biological sequences. Around the same time he made his >> framework open source at BioInformatics.org, and I joined his team to >> help further development also with the idea to use it in our apps. >> After some discussions I proposed to broaden the general idea behind >> BioCocoa to a more general Bio framework, encompassing much more than >> sequenceIO alone. At the last WWDC, I spoke the guy from BioPerl >> about this >> and he was enthusiastic about the idea of a BioCocoa sister back >> then. >> This was exactly the idea we had in mind, and we set out to develop >> this great and powerful BioCocoa framework leveraging all the good >> things from Cocoa. Soon after, we managed to recruit a few more >> enthusiastic mac bioprogrammers. It turned out that all of us were >> reinventing the wheel time after time again for our programs, and >> having a great Cocoa based foundation would not only help all of us >> and >> save us much time, it will also increase the number of bio-apps for >> Mac >> OS X! >> >> Right now, our team consists of 8 enthusiastic programmers and things >> are starting to look really good! The core foundation begins to take >> shape, and it promises very much. Take a look at our mailinglist >> traffic and see how much effort everyone is putting into this, >> impressive and fun to see. >> A few weeks ago I proposed on the list to organize a meeting at the >> next WWDC. For us it would be a week where we would not only meet >> each >> other for the first time, but also a week where we discuss the >> directions and future of the framework much more productively. >> Additionally all of us could learn about the new stuff in Tiger and >> see >> how this fits in our framework (Did I say CoreData?!!!). Such a >> meeting >> would propel our efforts tremendously. It's about this subject that >> Peter and I would like to ask your help and at the same time do a >> proposal. >> >> First the help, some of the team will go for sure to the WWDC, us >> included >> (definitely addicted ;-). Possible because we're students and hope to >> get a scholarship. We'll pay for our own trip and hotel costs just >> because we JUST NEED to be there! Except for propably one person who >> can't take the time off from his job, everyone would like to go, they >> might be able to get to San Francisco, and find a place to stay, but >> not everyone can afford to pay the $1600 registration fee (remember >> your salary back then? ;-). So our question is a simple and bold one, >> would it be possible for Apple to sponsor our initiative and >> framework >> development with a WWDC ticket for those who do not manage to get or >> meet the criteria for a student scholarship? >> >> To give you an idea about how much "sponsorship" we're talking here, >> this is the BioCocoa team: >> Peter from Belgium has applied for a scholarship >> Mek & Tosj from The Netherlands have applied for a scholarship >> Jim Balhoff from the states has applied for a scholarship >> Philipp Seibel from Germany has applied for a scholarship >> Vincent Merckx from Belgium has applied for a scholarship >> >> Then we have: >> Charles Parnot (the one from XGrid at stanford) from Stanford >> John Timmer (who developed the plugin system in 4Peaks) from NY >> Todd Harris (who's also part of BioPerl) from Cold Spring Harbor. >> >> The sponsorship would thus be 3-5 WWDC tickets (if we all get the >> scholarships of course). >> >> So what's in it for Apple? Well, Apple is advertising all over the >> web >> in the past week that (Bio)Science is one of its main markets, that >> Macs are big in biosciences and genomics (which they are!) and that >> Mac >> OS X can play a key role as a development platform. At the same time, >> one of the truly great things with respect to programming is >> definitely >> the power of Cocoa. Yet we have BioRuby, BioPerl, BioJava, but no >> BioCocoa! We hope to fill this gap, ideally (and this I admit is >> really >> in the future) something that will grow into a real sister/brother >> project under the Open Bio organisation. BioCocoa will benefit us as >> programmers but it will also be a major selling point for Apple to >> promote Mac OS X in the scientific community. >> >> Finally, in this light we would like to hear if you're interested in >> the following proposal. What do you think of organising a scientific >> meeting around BioCocoa at WWDC05 (if there are any scitech meetings >> of >> course) where we present our framework to the other scientists >> around? >> It would be a great way to interest more mac science programmers for >> our initiative and also a great opportunity to discuss what the needs >> are in this respect of scientists using the mac. >> >> You find more info on BioCocoa at: >> http://bioinformatics.org/project/?group_id=318? (bioinformatics.org, >> mailinglist + CVS) >> http://bioinformatics.org/biococoa/?? (original framework) >> >> What we do plan to have before the WWDC is a website dedicated to the >> new version of the framework, documentation about the architecture of >> the BioCocoa foundation, a simple demonstration application showing >> what the framework can do. >> >> Looking forward to your response, and see you hopefully at WWDC 2005! >> On behalf of the complete BioCocoa team, >> Alexander Griekspoor >> Peter Schols. >> ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 E-mail: a.griekspoor at nki.nl AIM: mekentosj at mac.com Web: http://www.mekentosj.com EnzymeX - To cut or not to cut http://www.mekentosj.com/enzymex ********************************************************* -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 9110 bytes Desc: not available URL: From kvddrift at earthlink.net Mon Apr 4 18:44:51 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 4 Apr 2005 18:44:51 -0400 Subject: [BioCocoa-dev] BioCocoa meeting In-Reply-To: <3fae1ef84043c28c079f38cc7f0e5b64@nki.nl> References: <3fae1ef84043c28c079f38cc7f0e5b64@nki.nl> Message-ID: <39a169282de43f6e950e436b48a590ef@earthlink.net> Great news Alex, I guess I need to find a new job with more vacation days :D - Koen. On Apr 4, 2005, at 6:30 PM, Alexander Griekspoor wrote: > Hi everybody, > > Here's the news I was talking about. Robert Kehrer at Apple responded > to our question about a WWDC2005 BioCocoa meeting with the email > below. > Personally I think it's a great idea to join the BioHackathon with the > BioCocoa team, of course as it coincides with the WWDC we can meet up > there as well. That is, I still haven't heard about a potential > sponsorship. I'll try to bring up that subject again if we know more > about the BioHackathon. > I discussed this off-list with Peter already, and he would like to > join the BioHackaThon as well. Now I would like to know a few things > and ask you guys if the following is a good idea. > First, who would be interested to join this BioHackaThon if this were > possible. It would be a great opportunity to really hack away with > BioCocoa and do lots of work (starting at the WWDC already of course). > Why would you like to join, or why wouldn't you. > Second, I propose to contact the organizers of the BioHackathon as > soon as possible to see what the possibilities are, costs, etc. We > have been thinking in terms of the OpenBio organization already. It > might be (way) too early to really join, but it might be the perfect > opportunity to introduce ourselves, discuss with those people what our > and their options are, and meet a lot of people with lots of > experience and attract perhaps a few enthusiastic people from this > field. If you all agree, I can do the same thing with Peter again and > send an email to the people mentioned by Robert Kehrer. Let's then see > how things evolve.... > Cheers, > Alex > > >> Alexander, >> >> The Apple and the OpenBio community are planning a BioHackaThon 2005 >> to be in conjunction with the WWDC 2005. >> >> Plans would include: >> 1) A kick-off reception on Sunday June 5th to welcome the OpenBio >> attendees >> 2) WWDC attendance by as many OpenBio community luminaries as >> possible >> 3) A 4-5 day BioHackathon on the Apple Campus in Cupertino >> immediately following the WWDC >> >> Community leaders are currently identifying the appropriate attendees >> and seeking travel and lodging funding. I expect that key people from >> each of the various Bio* groups would be in attendance and see no >> reason that BioCocoa couldn't be included if that project is >> officially part of the OpenBio community. >> >> The BioHackathon organizers include Susanna Lewis, Cyrus Harmon, >> Steve Chervitz and Jason Stajich (cc'ed). You should contact them to >> investigate the participation of the BioCocoa team. >> --- >> Robert Kehrer >> strategic alliance mgr, sciences ??| ??worldwide developer relations >> >> >> On Mar 13, 2005, at 5:29 AM, Alexander Griekspoor wrote: >> >>> Dear Robert, >>> >>> It was a great pleasure to meet you during WWDC 2004 right after the >>> ceremony of the design awards and during the science lunches. Back >>> then >>> you told me that I could contact you whenever I needed your help >>> with >>> anything related to our programs and with this mail I want to make >>> use >>> of this promise ;-) >>> >>> Right after last year's meeting I got in contact with Peter Schols >>> from >>> Belgium who wrote a Cocoa framework - called BioCocoa - for reading >>> and >>> writing biological sequences. Around the same time he made his >>> framework open source at BioInformatics.org, and I joined his team >>> to >>> help further development also with the idea to use it in our apps. >>> After some discussions I proposed to broaden the general idea behind >>> BioCocoa to a more general Bio framework, encompassing much more >>> than >>> sequenceIO alone. At the last WWDC, I spoke the guy from BioPerl >>> about this >>> and he was enthusiastic about the idea of a BioCocoa sister back >>> then. >>> This was exactly the idea we had in mind, and we set out to develop >>> this great and powerful BioCocoa framework leveraging all the good >>> things from Cocoa. Soon after, we managed to recruit a few more >>> enthusiastic mac bioprogrammers. It turned out that all of us were >>> reinventing the wheel time after time again for our programs, and >>> having a great Cocoa based foundation would not only help all of us >>> and >>> save us much time, it will also increase the number of bio-apps for >>> Mac >>> OS X! >>> >>> Right now, our team consists of 8 enthusiastic programmers and >>> things >>> are starting to look really good! The core foundation begins to take >>> shape, and it promises very much. Take a look at our mailinglist >>> traffic and see how much effort everyone is putting into this, >>> impressive and fun to see. >>> A few weeks ago I proposed on the list to organize a meeting at the >>> next WWDC. For us it would be a week where we would not only meet >>> each >>> other for the first time, but also a week where we discuss the >>> directions and future of the framework much more productively. >>> Additionally all of us could learn about the new stuff in Tiger and >>> see >>> how this fits in our framework (Did I say CoreData?!!!). Such a >>> meeting >>> would propel our efforts tremendously. It's about this subject that >>> Peter and I would like to ask your help and at the same time do a >>> proposal. >>> >>> First the help, some of the team will go for sure to the WWDC, us >>> included >>> (definitely addicted ;-). Possible because we're students and hope >>> to >>> get a scholarship. We'll pay for our own trip and hotel costs just >>> because we JUST NEED to be there! Except for propably one person who >>> can't take the time off from his job, everyone would like to go, >>> they >>> might be able to get to San Francisco, and find a place to stay, but >>> not everyone can afford to pay the $1600 registration fee (remember >>> your salary back then? ;-). So our question is a simple and bold >>> one, >>> would it be possible for Apple to sponsor our initiative and >>> framework >>> development with a WWDC ticket for those who do not manage to get or >>> meet the criteria for a student scholarship? >>> >>> To give you an idea about how much "sponsorship" we're talking here, >>> this is the BioCocoa team: >>> Peter from Belgium has applied for a scholarship >>> Mek & Tosj from The Netherlands have applied for a scholarship >>> Jim Balhoff from the states has applied for a scholarship >>> Philipp Seibel from Germany has applied for a scholarship >>> Vincent Merckx from Belgium has applied for a scholarship >>> >>> Then we have: >>> Charles Parnot (the one from XGrid at stanford) from Stanford >>> John Timmer (who developed the plugin system in 4Peaks) from NY >>> Todd Harris (who's also part of BioPerl) from Cold Spring Harbor. >>> >>> The sponsorship would thus be 3-5 WWDC tickets (if we all get the >>> scholarships of course). >>> >>> So what's in it for Apple? Well, Apple is advertising all over the >>> web >>> in the past week that (Bio)Science is one of its main markets, that >>> Macs are big in biosciences and genomics (which they are!) and that >>> Mac >>> OS X can play a key role as a development platform. At the same >>> time, >>> one of the truly great things with respect to programming is >>> definitely >>> the power of Cocoa. Yet we have BioRuby, BioPerl, BioJava, but no >>> BioCocoa! We hope to fill this gap, ideally (and this I admit is >>> really >>> in the future) something that will grow into a real sister/brother >>> project under the Open Bio organisation. BioCocoa will benefit us as >>> programmers but it will also be a major selling point for Apple to >>> promote Mac OS X in the scientific community. >>> >>> Finally, in this light we would like to hear if you're interested in >>> the following proposal. What do you think of organising a scientific >>> meeting around BioCocoa at WWDC05 (if there are any scitech >>> meetings of >>> course) where we present our framework to the other scientists >>> around? >>> It would be a great way to interest more mac science programmers for >>> our initiative and also a great opportunity to discuss what the >>> needs >>> are in this respect of scientists using the mac. >>> >>> You find more info on BioCocoa at: >>> http://bioinformatics.org/project/?group_id=318? (bioinformatics.org, >>> mailinglist + CVS) >>> http://bioinformatics.org/biococoa/?? (original framework) >>> >>> What we do plan to have before the WWDC is a website dedicated to >>> the >>> new version of the framework, documentation about the architecture >>> of >>> the BioCocoa foundation, a simple demonstration application showing >>> what the framework can do. >>> >>> Looking forward to your response, and see you hopefully at WWDC >>> 2005! >>> On behalf of the complete BioCocoa team, >>> Alexander Griekspoor >>> Peter Schols. >>> > ********************************************************* > ** Alexander Griekspoor ** > ********************************************************* > The Netherlands Cancer Institute > Department of Tumorbiology (H4) > Plesmanlaan 121, 1066 CX, Amsterdam > Tel: + 31 20 - 512 2023 > Fax: + 31 20 - 512 2029 > E-mail: a.griekspoor at nki.nl > AIM: mekentosj at mac.com > Web: http://www.mekentosj.com > > EnzymeX - To cut or not to cut > http://www.mekentosj.com/enzymex > > ********************************************************* > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From jtimmer at bellatlantic.net Mon Apr 4 20:34:20 2005 From: jtimmer at bellatlantic.net (John Timmer) Date: Mon, 04 Apr 2005 20:34:20 -0400 Subject: [BioCocoa-dev] BioCocoa meeting In-Reply-To: <3fae1ef84043c28c079f38cc7f0e5b64@nki.nl> Message-ID: Hey all - I?m not sure if I?ll be able to get out to California for an extended stay around then, but I?d love to if it can be arranged. Maybe an actual invitation from apple would make it easier to arrange! Anything I can do to help out, let me know, but otherwise, you seem to be handling things nicely. It sounds like a great opportunity. I?m checking out OpenBio now, and they seem like a pretty straightforward operation. The only potential issue is that they seem to be exclusively cross-platform stuff, but I guess we?d just have to ask about our stuff. Thanks for you work on this - JT > > Hi everybody, > > Here's the news I was talking about. Robert Kehrer at Apple responded to our > question about a WWDC2005 BioCocoa meeting with the email below. > Personally I think it's a great idea to join the BioHackathon with the > BioCocoa team, of course as it coincides with the WWDC we can meet up there as > well. That is, I still haven't heard about a potential sponsorship. I'll try > to bring up that subject again if we know more about the BioHackathon. > I discussed this off-list with Peter already, and he would like to join the > BioHackaThon as well. Now I would like to know a few things and ask you guys > if the following is a good idea. > First, who would be interested to join this BioHackaThon if this were > possible. It would be a great opportunity to really hack away with BioCocoa > and do lots of work (starting at the WWDC already of course). Why would you > like to join, or why wouldn't you. > Second, I propose to contact the organizers of the BioHackathon as soon as > possible to see what the possibilities are, costs, etc. We have been thinking > in terms of the OpenBio organization already. It might be (way) too early to > really join, but it might be the perfect opportunity to introduce ourselves, > discuss with those people what our and their options are, and meet a lot of > people with lots of experience and attract perhaps a few enthusiastic people > from this field. If you all agree, I can do the same thing with Peter again > and send an email to the people mentioned by Robert Kehrer. Let's then see how > things evolve.... > Cheers, > Alex > _______________________________________________ This mind intentionally left blank -------------- next part -------------- An HTML attachment was scrubbed... URL: From jtimmer at bellatlantic.net Tue Apr 5 11:17:49 2005 From: jtimmer at bellatlantic.net (John Timmer) Date: Tue, 05 Apr 2005 11:17:49 -0400 Subject: [Biococoa-dev] BCSymbol flexibility Message-ID: Just wanted to confirm something that I can do in about 5 minutes is a good idea before doing it: Part of the point of making the symbol definitions .plists was that they'd be extremely easy to extend. For performance reasons, so far we've simply added ivars for everything in the .plist, but that may not be necessary in all cases. For some cases, or for convenience, it may be worthwhile to simply leave some information stored in the dictionary that's used to initialize the symbol. Right now, however, to get access to that information, a user would have to grab the dictionary, then query it directly. It seems a better idea to simply add a "valueForKey:" method to BCSymbol, and use that to return the value out of the dictionary. Does anyone think that doing so is a bad idea? JT _______________________________________________ This mind intentionally left blank From biococoa at bioworxx.com Tue Apr 5 11:28:00 2005 From: biococoa at bioworxx.com (Philipp Seibel) Date: Tue, 5 Apr 2005 17:28:00 +0200 Subject: [Biococoa-dev] BCSymbol flexibility In-Reply-To: References: Message-ID: <58315c0e3526b39c61551b808512e000@bioworxx.com> Am 05.04.2005 um 17:17 schrieb John Timmer: > Just wanted to confirm something that I can do in about 5 minutes is a > good > idea before doing it: > > Part of the point of making the symbol definitions .plists was that > they'd > be extremely easy to extend. For performance reasons, so far we've > simply > added ivars for everything in the .plist, but that may not be > necessary in > all cases. For some cases, or for convenience, it may be worthwhile to > simply leave some information stored in the dictionary that's used to > initialize the symbol. > > Right now, however, to get access to that information, a user would > have to > grab the dictionary, then query it directly. It seems a better idea to > simply add a "valueForKey:" method to BCSymbol, and use that to return > the > value out of the dictionary. i agree, but this has to be well documented ;-) Phil > Does anyone think that doing so is a bad idea? > > JT > > > _______________________________________________ > This mind intentionally left blank > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > > Philipp Seibel Lehrstuhl f?r Bioinformatik Biozentrum, Am Hubland Universit?t W?rzburg philipp.seibel at biozentrum.uni-wuerzburg.de From a.griekspoor at nki.nl Tue Apr 5 11:41:25 2005 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Tue, 5 Apr 2005 17:41:25 +0200 Subject: [Biococoa-dev] BCSymbol flexibility In-Reply-To: <58315c0e3526b39c61551b808512e000@bioworxx.com> References: <58315c0e3526b39c61551b808512e000@bioworxx.com> Message-ID: > Am 05.04.2005 um 17:17 schrieb John Timmer: > >> Just wanted to confirm something that I can do in about 5 minutes is >> a good >> idea before doing it: > [snippet] >> Does anyone think that doing so is a bad idea? >> >> JT >> > > i agree, but this has to be well documented ;-) > > Phil Same here, good idea... Alex ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com 4Peaks - For Peaks, Four Peaks. 2004 Winner of the Apple Design Awards Best Mac OS X Student Product http://www.mekentosj.com/4peaks ********************************************************* From jtimmer at bellatlantic.net Tue Apr 5 18:23:44 2005 From: jtimmer at bellatlantic.net (John Timmer) Date: Tue, 05 Apr 2005 18:23:44 -0400 Subject: [Biococoa-dev] BCSymbol flexibility In-Reply-To: <58315c0e3526b39c61551b808512e000@bioworxx.com> Message-ID: > > i agree, but this has to be well documented ;-) > Okay, let me know how its documentation looks. I added header doc for symbolInfo while I was at it. JT _______________________________________________ This mind intentionally left blank From kvddrift at earthlink.net Tue Apr 5 19:37:39 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 5 Apr 2005 19:37:39 -0400 Subject: [Biococoa-dev] Re: BCFoundation Test In-Reply-To: References: Message-ID: <2a7f505351ce3b8dc44e950164060d6b@earthlink.net> All, I added a new test class to test sequence properties. I will fill it in later, but for it to work you will need the latest OCUnit (v40). This will add the possibility to test two floats within a given accuracy. cheers, - Koen. From kvddrift at earthlink.net Tue Apr 5 20:24:43 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 5 Apr 2005 20:24:43 -0400 Subject: [Biococoa-dev] BCSymbol flexibility In-Reply-To: References: Message-ID: <2879c3387b94b3b4ae35e6bdba2c656f@earthlink.net> On Apr 5, 2005, at 6:23 PM, John Timmer wrote: > Okay, let me know how its documentation looks. I added header doc for > symbolInfo while I was at it. > Looks good. Maybe you can add a line that points to the string definitions in BCStringDefinitions.h, which should be used as key. - Koen. From kvddrift at earthlink.net Tue Apr 5 20:43:44 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 5 Apr 2005 20:43:44 -0400 Subject: [Biococoa-dev] Apple bio seminars Message-ID: <82cf33e86a3000b1f5a0cde5e2467b74@earthlink.net> Hi, On this page you can find some science related webcasted seminars. Registration is free. http://seminars.apple.com/seminarsonline/ - Koen. From charles.parnot at stanford.edu Wed Apr 6 01:54:54 2005 From: charles.parnot at stanford.edu (Charles PARNOT) Date: Tue, 5 Apr 2005 22:54:54 -0700 Subject: [Biococoa-dev] Test-BCFoundation In-Reply-To: <2a7f505351ce3b8dc44e950164060d6b@earthlink.net> References: <2a7f505351ce3b8dc44e950164060d6b@earthlink.net> <16ae2606b5e413e477e72b78a96fa98e@nki.nl> Message-ID: At 7:37 PM -0400 4/5/05, Koen van der Drift wrote: >All, > >I added a new test class to test sequence properties. I will fill it in later, but for it to work you will need the latest OCUnit (v40). This will add the possibility to test two floats within a given accuracy. > >cheers, > >- Koen. Works well, nice! More work done tonight too: * added tests for BCSequenceProtein * uncovered a bug in BCAminoAcid, symbolForChar --> yeah! Tests are useful again again, whaowww :-) * still BCSequence to do * everything else too... * renaming + relocation of Tests still on my mind... charles -- Help science go fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford/ Charles Parnot charles.parnot at stanford.edu Room B157 in Beckman Center 279, Campus Drive Stanford University Stanford, CA 94305 (USA) Tel +1 650 725 7754 Fax +1 650 725 8021 From jtimmer at bellatlantic.net Wed Apr 6 13:27:07 2005 From: jtimmer at bellatlantic.net (John Timmer) Date: Wed, 06 Apr 2005 13:27:07 -0400 Subject: [Biococoa-dev] More on CoreData Message-ID: In case anyone missed it, Apple finally put the overview article on CoreData up: http://developer.apple.com/macosx/tiger/coredata.html This finally allows me the liberty of making a few more comments on the problems we'll have supporting both this and earlier OS versions at the same time. The first is that all the objects that go into a CoreData store have to be subclasses of NSManagedObject. This class isn't going to exist in any previous versions of the OS. The second is that many of the classes we rely on (ie - NSArrays) aren't native CoreData objects. This means that, in order to stick an array into an NSManagedObject subclass in a saveable manner, we'd have to first convert it to data via NSCoding, or use its string representation. There's three ways I can imagine handling things: Create a "dummy" NSManagedObject subclass that's used to prevent compiler errors when built on < 10.4. This seems like an awkward solution, but would allow us to start building CoreData compatibility into the basic classes, like Symbols and Sequences. Since the class won't actually be NSManaged object, we can override some methods in our subclasses without worrying that they'll ever be called on earlier OS versions. Create a separate framework that allows conversion between our standard classes and CoreData compatible ones. This would at least allow a collection of BioCocoa objects to be shuffled into and out of a CoreData persistent store, but wouldn't allow the use of some of the more advanced CoreData features, like relationships, etc. in our classes. Give up and make BioCocoa 10.4 only, or at least provide a 10.4 only fork. That's clearly the best from the feature perspective, but will clearly limit our audience. There may be other options, and once the NDA comes off, I'm sure the Cocoa-dev mailing list will be full of people looking for (and hopefully creating) solutions to similar problems. Anyway, I thought you guys would be interested (I could tell by Alex's email to Apple that he is ;), and it's always better to start major design discussions sooner rather than later. John _______________________________________________ This mind intentionally left blank From jtimmer at bellatlantic.net Fri Apr 8 13:37:13 2005 From: jtimmer at bellatlantic.net (John Timmer) Date: Fri, 08 Apr 2005 13:37:13 -0400 Subject: [Biococoa-dev] Weighted sequence score In-Reply-To: Message-ID: I'm looking into implementing the weighted sequence score that I mentioned earlier. Two questions about the design of this that I'd appreciate input on. The first is rather simple: The easiest way to set up the scoring is to have an array of dictionaries. Given a symbol and a position, you grab the dictionary at that position, and get an NSNumber out of it based on the symbol, or nil, which gets converted to the user's defined default. Very easy to code, but it does not seem that efficient - lots of object messaging and looking things up. Does anyone have an alternate suggestion on how to structure this? The second thing is that this problem is clearly "embarrassingly parallel", meaning that it's a great candidate for threading. I though it might be a good example case on how to properly and safely set up threads, so that we can use it as an example as we expand the framework. To keep the complexity out of the way of users, I was hoping to define a public class definition in the header that provided a civilized interface to the actual processing, plus offered either simulated synchronous execution or asynchronous execution with a callback. The actual objects that would perform the threaded processing would be defined in a private interface in the .m file. Does this sound like a good idea? Any alternate suggestions? Looking forward to your input - John _______________________________________________ This mind intentionally left blank From kvddrift at earthlink.net Fri Apr 8 20:34:48 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 8 Apr 2005 20:34:48 -0400 Subject: [Biococoa-dev] More on CoreData In-Reply-To: References: Message-ID: Hi, I read the article, and it looks like a cool new feature to me. Not sure yet how useful it will be to BioCocoa. I think it will be more beneficial for developers who use BioCocoa for their own app and want to save datastructures. Although we do have IO classes, they are bound by the various sequence formats that are available. Other than taking over the accessors right now I don't see much more advantages. Of course, I don't have a seed, so you guys who have Tiger previews might know more about this than I do ;-) However, if we decide to implement it, which is fine with me, than we should try to find a way that we at least keep supporting 10.3.x. The jump from 10.2.8 to 10.4 seems alittle bit too big. Also as you said, there will be ampel discussion in the cocoadev mailing lists on how to use existing datastructures with an NSManagedObject. I would say let's wait what comes out of that after the Tiger has been released. cheers, - Koen. On Apr 6, 2005, at 1:27 PM, John Timmer wrote: > In case anyone missed it, Apple finally put the overview article on > CoreData > up: > http://developer.apple.com/macosx/tiger/coredata.html > > This finally allows me the liberty of making a few more comments on the > problems we'll have supporting both this and earlier OS versions at > the same > time. > > The first is that all the objects that go into a CoreData store have > to be > subclasses of NSManagedObject. This class isn't going to exist in any > previous versions of the OS. > > The second is that many of the classes we rely on (ie - NSArrays) > aren't > native CoreData objects. This means that, in order to stick an array > into > an NSManagedObject subclass in a saveable manner, we'd have to first > convert > it to data via NSCoding, or use its string representation. > > > There's three ways I can imagine handling things: > > Create a "dummy" NSManagedObject subclass that's used to prevent > compiler > errors when built on < 10.4. This seems like an awkward solution, but > would > allow us to start building CoreData compatibility into the basic > classes, > like Symbols and Sequences. Since the class won't actually be > NSManaged > object, we can override some methods in our subclasses without > worrying that > they'll ever be called on earlier OS versions. > > Create a separate framework that allows conversion between our standard > classes and CoreData compatible ones. This would at least allow a > collection of BioCocoa objects to be shuffled into and out of a > CoreData > persistent store, but wouldn't allow the use of some of the more > advanced > CoreData features, like relationships, etc. in our classes. > > Give up and make BioCocoa 10.4 only, or at least provide a 10.4 only > fork. > That's clearly the best from the feature perspective, but will clearly > limit > our audience. > > > There may be other options, and once the NDA comes off, I'm sure the > Cocoa-dev mailing list will be full of people looking for (and > hopefully > creating) solutions to similar problems. > > Anyway, I thought you guys would be interested (I could tell by Alex's > email > to Apple that he is ;), and it's always better to start major design > discussions sooner rather than later. > > John > > _______________________________________________ > This mind intentionally left blank > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > From charles.parnot at stanford.edu Sat Apr 9 13:50:35 2005 From: charles.parnot at stanford.edu (Charles PARNOT) Date: Sat, 9 Apr 2005 10:50:35 -0700 Subject: [Biococoa-dev] More on CoreData In-Reply-To: References: Message-ID: Thanks for the pointer! The CoreData concepts have started to sink in my brain... I am not sure I grab all of it yet, but I hope these discussions will help. It seems we have two related issues at this point if we want to support CoreData: (1) The existing code does not fully support it (2) How do we make the code both 10.2 and 10.4 compatible Regarding point (1), you mention NSArray as a potential issue. Let's try to make a more exhaustive list: NSDictionary, NSSet, ..??.. Probably others. There is one point that is also unclear to me. NSArray seems to be covered by the one-to-many relationship between entities. Can that be translated into an NSArray concept? A related question is performance, when we are dealing with large NSArray of NSSymbol. Related to that, I can see how NSManagedObject subclasses can add behavior, but how does one add costum properties? Just adding ivars? Is it then just a matter of having KVC support? How is coding supported, just NSCoding? Or should all object ivars be subclasses of NSManagedObject? How does the NSManagedObject class know that properties have been added? Can we create a NSManagedArray class to wrap NSArray? Regarding point (2), the mock NSManagedObject is a very good way of doing it. An alternative is a: #define NSManagedObject NSObject for the 10.2/10.3 build. Of course, on top of that, you still want the CoreData implementation to be transparent to earlier systems. It is also fairly easy to add #ifdef around code that we don't want to compile in the 10.2/10.3 build. If we use of precompiler tags , then we get two different bundles, one for each version of the system. Either way, in general, I think we should have full CoreData support and intermediary solutions that give up some of its functionality are not worth the trouble. Finally, I think Koen raised a good point: it is still unclear to me how the user would want to use CoreData with the BioCocoa framework? It is the following: we providing NSManagedObject subclasses to the user, so the user can then use them transparently to implement its own CoreData solution in the application? thanks for your feedback on all these questions, John! charles At 1:27 PM -0400 4/6/05, John Timmer wrote: >In case anyone missed it, Apple finally put the overview article on CoreData >up: >http://developer.apple.com/macosx/tiger/coredata.html > >This finally allows me the liberty of making a few more comments on the >problems we'll have supporting both this and earlier OS versions at the same >time. > >The first is that all the objects that go into a CoreData store have to be >subclasses of NSManagedObject. This class isn't going to exist in any >previous versions of the OS. > >The second is that many of the classes we rely on (ie - NSArrays) aren't >native CoreData objects. This means that, in order to stick an array into >an NSManagedObject subclass in a saveable manner, we'd have to first convert >it to data via NSCoding, or use its string representation. > > >There's three ways I can imagine handling things: > >Create a "dummy" NSManagedObject subclass that's used to prevent compiler >errors when built on < 10.4. This seems like an awkward solution, but would >allow us to start building CoreData compatibility into the basic classes, >like Symbols and Sequences. Since the class won't actually be NSManaged >object, we can override some methods in our subclasses without worrying that >they'll ever be called on earlier OS versions. > >Create a separate framework that allows conversion between our standard >classes and CoreData compatible ones. This would at least allow a >collection of BioCocoa objects to be shuffled into and out of a CoreData >persistent store, but wouldn't allow the use of some of the more advanced >CoreData features, like relationships, etc. in our classes. > >Give up and make BioCocoa 10.4 only, or at least provide a 10.4 only fork. >That's clearly the best from the feature perspective, but will clearly limit >our audience. > > >There may be other options, and once the NDA comes off, I'm sure the >Cocoa-dev mailing list will be full of people looking for (and hopefully >creating) solutions to similar problems. > >Anyway, I thought you guys would be interested (I could tell by Alex's email >to Apple that he is ;), and it's always better to start major design >discussions sooner rather than later. > >John -- Help science go fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford/ Charles Parnot charles.parnot at stanford.edu Room B157 in Beckman Center 279, Campus Drive Stanford University Stanford, CA 94305 (USA) Tel +1 650 725 7754 Fax +1 650 725 8021 From jtimmer at bellatlantic.net Sat Apr 9 14:58:01 2005 From: jtimmer at bellatlantic.net (John Timmer) Date: Sat, 09 Apr 2005 14:58:01 -0400 Subject: [Biococoa-dev] More on CoreData In-Reply-To: Message-ID: > Regarding point (1), you mention NSArray as a potential issue. Let's try to > make a more exhaustive list: NSDictionary, NSSet, ..??.. Probably others. > There is one point that is also unclear to me. NSArray seems to be covered by > the one-to-many relationship between entities. Can that be translated into an > NSArray concept? A related question is performance, when we are dealing with > large NSArray of NSSymbol. Well, I thought this part was under NDA, but it's all over the Cocoa-dev mailing list now, and the list-mom hasn't cut in to stop it. The problem is that relationships to other objects are stored in sets. You have to do all the management if you want to order them. For example, to make a sequence array, you'd have to insert a "holder" object that contains a position value and a reference to the appropriate symbol, and then re-create the array when you woke the sequence out of the store. See below for some thoughts on using NSCoding for the array. > Related to that, I can see how NSManagedObject subclasses can add behavior, > but how does one add costum properties? Just adding ivars? Is it then just a > matter of having KVC support? How is coding supported, just NSCoding? Or > should all object ivars be subclasses of NSManagedObject? How does the > NSManagedObject class know that properties have been added? Can we create a > NSManagedArray class to wrap NSArray? For any simple values, you can just treat any Core Data object as a dictionary, using "valueForKey" and "setValue:forKey:" as setters and getters. Since named methods get tried first, you can override the default behavior simply by making an NSManagedObject subclass and handling specific values with "myValue" and "setMyValue:" methods. You can use that to handle some more elaborate behavior. For example, you can have a value that's "dateOfBirth", and use that in a "ageInWeeks" method without having to create a new value. You can also have a "notesAsRTF" value which holds NSData, and then a "notesString" method that extracts only the NSString using the data. NSCoding would work the same way, including for arrays, as long as you don't need to preserve relationships to objects in the coded ones. > Finally, I think Koen raised a good point: it is still unclear to me how the > user would want to use CoreData with the BioCocoa framework? It is the > following: we providing NSManagedObject subclasses to the user, so the user > can then use them transparently to implement its own CoreData solution in the > application? There's several ways I could imagine doing it - ranging from making everything a core data object to just making BCSequence one. That actually may be the best way to handle it. It would actually help make the features work, as a feature could easily refer to the specific sequence, and all that could be preserved between saves. Since we already have easy methods for storing/retrieving the actual sequence as strings and sequence types as ints, it becomes fairly easy to store things as strings/scalars, and still provide a BioCocoa face to the world. This might allow us to make a specialized NSManagedObject class for pre-10.4 systems that handles saving to files in a way that's analogous to CoreData. Since we only need to get it to work for a single class, it might be relatively painless. _______________________________________________ This mind intentionally left blank From peter.schols at bio.kuleuven.ac.be Tue Apr 12 06:15:39 2005 From: peter.schols at bio.kuleuven.ac.be (Peter Schols) Date: Tue, 12 Apr 2005 12:15:39 +0200 Subject: [Biococoa-dev] Compiling problems and how to solve them Message-ID: Dear listers, This message is probably NOT useful for anyone who succeeded in compiling the latest BioCocoa version from our CVS server. However, for people new to the project, this might be of interest: If you experience problems when compiling the latest version of BC, make sure you install the Mac OS 10.2.x and Mac OS 10.3.x SDKs from the Xcode CD. I don't think these SDKs are installed by default. However, they are required to properly compile BC. After installing them, make sure that BioCocoa links to the right SDK in the Xcode project: - Select the BioCocoa target from the list of targets - Click Get Info and then select the build tab - Make sure the SDKROOT property points to a valid SDK path That should fix any (pre)compiler errors. Maybe we could add this to the HTML dev documentation? Many thanks to Alex who provided me with the solution to this problem! Peter From kvddrift at earthlink.net Tue Apr 12 20:17:38 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 12 Apr 2005 20:17:38 -0400 Subject: [Biococoa-dev] Compiling problems and how to solve them In-Reply-To: References: Message-ID: <7e9119498c0bcae4089247bdc51db18d@earthlink.net> On Apr 12, 2005, at 6:15 AM, Peter Schols wrote: > Maybe we could add this to the HTML dev documentation? > Done :) - Koen. From charles.parnot at stanford.edu Fri Apr 22 02:15:08 2005 From: charles.parnot at stanford.edu (Charles PARNOT) Date: Thu, 21 Apr 2005 23:15:08 -0700 Subject: [Biococoa-dev] more tests on sequence classes Message-ID: Hey all! Just to let you know I manage to add little pieces of code every 2-3 days in the past 2 weeks, and I am all done with the sequence class tests! I now need to strike that from my Todo list :-) charles -- Help science go fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford/ Charles Parnot charles.parnot at stanford.edu Room B157 in Beckman Center 279, Campus Drive Stanford University Stanford, CA 94305 (USA) Tel +1 650 725 7754 Fax +1 650 725 8021 From kvddrift at earthlink.net Fri Apr 22 07:18:16 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 22 Apr 2005 07:18:16 -0400 Subject: [Biococoa-dev] more tests on sequence classes In-Reply-To: References: Message-ID: Thanks Charles, Great work. Good to see some life on the list. I guess everyone is getting ready for Tiger. Charles, would you mind moving the Tests directory out of BCFoundation ? cheers, - Koen. On Apr 22, 2005, at 2:15 AM, Charles PARNOT wrote: > Hey all! > Just to let you know I manage to add little pieces of code every 2-3 > days in the past 2 weeks, and I am all done with the sequence class > tests! I now need to strike that from my Todo list :-) > > charles > > -- > Help science go fast forward: > http://cmgm.stanford.edu/~cparnot/xgrid-stanford/ > > Charles Parnot > charles.parnot at stanford.edu > > Room B157 in Beckman Center > 279, Campus Drive > Stanford University > Stanford, CA 94305 (USA) > > Tel +1 650 725 7754 > Fax +1 650 725 8021 > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > From jtimmer at bellatlantic.net Fri Apr 22 13:00:21 2005 From: jtimmer at bellatlantic.net (John Timmer) Date: Fri, 22 Apr 2005 13:00:21 -0400 Subject: [Biococoa-dev] more tests on sequence classes In-Reply-To: Message-ID: Let me add my appreciations to Charles for this bit of work, and thanks for the bugs he fixed using it. JT > Hey all! > Just to let you know I manage to add little pieces of code every 2-3 > days in the past 2 weeks, and I am all done with the sequence class > tests! I now need to strike that from my Todo list :-) > > charles _______________________________________________ This mind intentionally left blank From charles.parnot at stanford.edu Sun Apr 24 19:41:45 2005 From: charles.parnot at stanford.edu (Charles PARNOT) Date: Sun, 24 Apr 2005 16:41:45 -0700 Subject: [Biococoa-dev] more tests on sequence classes In-Reply-To: References: Message-ID: At 7:18 AM -0400 4/22/05, Koen van der Drift wrote: >Thanks Charles, > >Great work. Good to see some life on the list. I guess everyone is getting ready for Tiger. > >Charles, would you mind moving the Tests directory out of BCFoundation ? > >cheers, > >- Koen. > done! charles -- Help science go fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford/ Charles Parnot charles.parnot at stanford.edu Room B157 in Beckman Center 279, Campus Drive Stanford University Stanford, CA 94305 (USA) Tel +1 650 725 7754 Fax +1 650 725 8021 From charles.parnot at stanford.edu Wed Apr 27 01:25:36 2005 From: charles.parnot at stanford.edu (Charles PARNOT) Date: Tue, 26 Apr 2005 22:25:36 -0700 Subject: [Biococoa-dev] dev docs on unit test Message-ID: Like the title said, I added some pointers on test units... and stroke it from my todo list. I may be a bit busy with the Tiger transition for a while, + papers writing, so expect my contributions to be a bit less frequent in the next 2 weeks ;-) charles -- Help science go fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford/ Charles Parnot charles.parnot at stanford.edu Room B157 in Beckman Center 279, Campus Drive Stanford University Stanford, CA 94305 (USA) Tel +1 650 725 7754 Fax +1 650 725 8021 From peter.schols at bio.kuleuven.be Thu Apr 28 12:35:18 2005 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Thu, 28 Apr 2005 18:35:18 +0200 Subject: [Biococoa-dev] I/O classes Message-ID: <30e5e0e09d7e9221e7a642a09492b757@bio.kuleuven.be> Dear listers, In the coming weeks, I'll finally have some time to resume my BioCocoa work. Much has changed since I checked out the project last time and I must say that I'm very impressed with the quality and the amount of work being done. Congratulations on a job well done! I've started BioCocoa as a very small framework just to parse and write sequence file formats, so the main focus of my BC work will be on the I/O classes. I have noticed that Koen has already updated BCReader to the new architecture and it's now aptly called BCSequenceReader. If I'm right, BCCreator has not been modified yet so it seems that I'll be doing this. As some of you may know, I recently implemented Cocoa code for a lot more bioinformatics file formats (such as BEAST XML, Hennig86, Nona, Plain/Raw and TNT). If it's OK with you guys, I could add this implementation to the I/O classes. Any ideas/comments are welcome. Most of these formats are from the Phylogeny world, the area I'm working in. Additionally, for one of my own projects, I'm working on classes to perform BLAST queries and return the results. They are far from finished but if they seem useful, I'm willing to 'donate' them to the BC project. Anyway, as soon as I have done some real work, I'll post the .h and .m files on the list so everyone can review them as I don't want to mess with the CVS repository and commit something that breaks existing code ;-) Peter From kvddrift at earthlink.net Thu Apr 28 20:10:08 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 28 Apr 2005 20:10:08 -0400 Subject: [Biococoa-dev] I/O classes In-Reply-To: <30e5e0e09d7e9221e7a642a09492b757@bio.kuleuven.be> References: <30e5e0e09d7e9221e7a642a09492b757@bio.kuleuven.be> Message-ID: <7a05e434d18071a2d0bcf88c64d4b0ac@earthlink.net> Hi Peter, Good to see you back! Right now BCSequenceReader is far from finished, I only added a few methods (for the simple file formats ;-). The other methods in that class are still from the old BCReader class. I think we still need to carefully decide on how we are going to implement the datastructure, regarding annotations, features, and sequence sets. Feel free to start implementing the new methods, but I think we should also revive that discussion here. It would be a waste of efforts if you did a lot of work, but then later found that you are using a different datastorage approach. cheers, - Koen. On Apr 28, 2005, at 12:35 PM, Peter Schols wrote: > Dear listers, > > In the coming weeks, I'll finally have some time to resume my BioCocoa > work. Much has changed since I checked out the project last time and I > must say that I'm very impressed with the quality and the amount of > work being done. Congratulations on a job well done! > > I've started BioCocoa as a very small framework just to parse and > write sequence file formats, so the main focus of my BC work will be > on the I/O classes. I have noticed that Koen has already updated > BCReader to the new architecture and it's now aptly called > BCSequenceReader. If I'm right, BCCreator has not been modified yet so > it seems that I'll be doing this. As some of you may know, I recently > implemented Cocoa code for a lot more bioinformatics file formats > (such as BEAST XML, Hennig86, Nona, Plain/Raw and TNT). If it's OK > with you guys, I could add this implementation to the I/O classes. Any > ideas/comments are welcome. Most of these formats are from the > Phylogeny world, the area I'm working in. > > Additionally, for one of my own projects, I'm working on classes to > perform BLAST queries and return the results. They are far from > finished but if they seem useful, I'm willing to 'donate' them to the > BC project. > > Anyway, as soon as I have done some real work, I'll post the .h and .m > files on the list so everyone can review them as I don't want to mess > with the CVS repository and commit something that breaks existing code > ;-) > > Peter > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > From peter.schols at bio.kuleuven.be Sat Apr 30 10:35:17 2005 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Sat, 30 Apr 2005 16:35:17 +0200 Subject: [Biococoa-dev] I/O classes In-Reply-To: <7a05e434d18071a2d0bcf88c64d4b0ac@earthlink.net> References: <30e5e0e09d7e9221e7a642a09492b757@bio.kuleuven.be> <7a05e434d18071a2d0bcf88c64d4b0ac@earthlink.net> Message-ID: <8380f49a9565ff1d123401449c0445cd@bio.kuleuven.be> Hi Koen, Good point about the datastructure discussion. Most of the I/O formats we support now, don't have annotation possibilities, but we should definitely think about a way to handle sequence sets, as most of these file formats are just that. I'll see what I can come up with and I'll post any ideas on the list. Best wishes, Peter On 29 Apr 2005, at 02:10, Koen van der Drift wrote: > Hi Peter, > > Good to see you back! > > Right now BCSequenceReader is far from finished, I only added a few > methods (for the simple file formats ;-). The other methods in that > class are still from the old BCReader class. I think we still need to > carefully decide on how we are going to implement the datastructure, > regarding annotations, features, and sequence sets. Feel free to start > implementing the new methods, but I think we should also revive that > discussion here. It would be a waste of efforts if you did a lot of > work, but then later found that you are using a different datastorage > approach. > > cheers, > > - Koen. > > > > > On Apr 28, 2005, at 12:35 PM, Peter Schols wrote: > >> Dear listers, >> >> In the coming weeks, I'll finally have some time to resume my >> BioCocoa work. Much has changed since I checked out the project last >> time and I must say that I'm very impressed with the quality and the >> amount of work being done. Congratulations on a job well done! >> >> I've started BioCocoa as a very small framework just to parse and >> write sequence file formats, so the main focus of my BC work will be >> on the I/O classes. I have noticed that Koen has already updated >> BCReader to the new architecture and it's now aptly called >> BCSequenceReader. If I'm right, BCCreator has not been modified yet >> so it seems that I'll be doing this. As some of you may know, I >> recently implemented Cocoa code for a lot more bioinformatics file >> formats (such as BEAST XML, Hennig86, Nona, Plain/Raw and TNT). If >> it's OK with you guys, I could add this implementation to the I/O >> classes. Any ideas/comments are welcome. Most of these formats are >> from the Phylogeny world, the area I'm working in. >> >> Additionally, for one of my own projects, I'm working on classes to >> perform BLAST queries and return the results. They are far from >> finished but if they seem useful, I'm willing to 'donate' them to the >> BC project. >> >> Anyway, as soon as I have done some real work, I'll post the .h and >> .m files on the list so everyone can review them as I don't want to >> mess with the CVS repository and commit something that breaks >> existing code ;-) >> >> Peter >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> >