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From: kumar s <ps_...@ya...> - 2005-02-12 16:02:28
|
Dear group, I am a new member to this group. I have no clue about many thing in MAGE-ML/ontologies. I am reading the docs. now and trying to make sense. However, I have some silly questions to ask, I aplogze for that. 1. I created a database comprising of both raw aswell as processed microarray data (from affy, cDNA, and long oligo). I now want to export the data into MAGE-ML format. Q1. For many of the data fields I do not have information about the classes, fields, in such case, what is the standard. Do I have to leave the that information out? 2. Do I have to write my own parser (I use Python) to create XML files from scratch and then validate the tree structure of the XML file I created 3. Are there any tools available to validate MAGE-ML file I created. Is there a DTD available so that I can use it for writing a validator. 4. If in my database, some provisions are not made that are standard for a MAGE-ML doc. In such case, if I make a MAGE-ML document, will my document be valid for the community and standards OR do I have to change my database schema in such a way that I can make a valid MAGE-ML document. Dear grop, these are the burinig questions I have and could not find an answer. would any one please help me getting some answers. Thank you. Kind regards, Kumar. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com |
From: Diane T. <di...@ca...> - 2002-12-08 21:11:50
|
Hi, Sorry we couldn't make it up this time, we've been busy with several other deadlines. I hope I can provide you enough information to make some progress. Also there's a pymerase mailing list at pym...@li... I'd kind of like to keep this discussion as open as possible as it might be useful for others. Or perhaps it should go into mged-mage-python? > I'm at the MAGE programming jamboree, and am interested in > working on the python side of the toolkit. Too bad you guys couldn't > make it up here! I hope that you can provide me with some > pointers. It looks like there is some python code for parsing XMI > under the mged lib directory, but that further development of > XMI->classes/sql has moved to the pymerase project. (let me know if > I'm wrong here) You're correct. At the last MAGE jambore a programmer from finland translated the perl XMI reader to python. Later I managed to connect pymerase to the XMI reader as an early version of parseXMI. However there were several bugs in that XMI reader that I tried fixing. Eveuntually I got frustrated and figured out how to use the Novosoft UML reader using jython. (the more recent versions of parseXMI in the pymerase.sf.net cvs tree) (A key detail is I'm using the novosoft uml jar file from tigris not from the novosoft sourceforge page. The latest novosoft version is for a later XMI specification and wont work with Argo files. (I'm not sure about the version novosoft consideres "deprecated") http://argouml.tigris.org/source/browse/argouml/lib/ > What I would like to start working on is testing/fixing the code > generation from the MGED xmi model into python classes, and porting > some of the Perl examples to a putative new python MGED tree. Does > this seem like a worthwhile/realistic goal? Have you done work towards > this, and have any tips? The approach I'll take is to get pymerase up > and running, > (getting jython,novosoft uml installed), and to generate the MAGEstk > classes. I haven't tried the XMI reader on something as complex as MAGE, though our more complex project sigoid.sf.net does use some complex XMI constructs there may be a chance that it will generate correctly. Since pymerase originally sprang from the GeneX project, it currently really wants to connect to a postgresql database. This also means that it spends some time trying to define foreign key references (and supporting attributes) to allow objects to be linked together in a relational database. The side effects of this are the construction of some unneeded attributes (see addForeignKeys in parseXMI.py), and quite a bit of extra complexity in the generated classes (the inherited dbAPI base class). The solution that I've been envisioning (but haven't gotten around to yet) was to generate an object model that can interact with a serialization interface. The interface would then call objects responsible for handling the translation of objects to relational tables or to XML documents. Unfortunatly since that may be too complicated for the Jamboree, it may be possible to experiment with the python generated model as long as you don't call the commit method on a generated class. I started stripping down the CreateDBAPI module into CreatePythonAPI, though since we've been orientated toward databases I haven't had time to work on it much recently. > > Let me know if you can offer any guidance. I'll at least put together > a 'pymerase-MAGEstk' > for newbies mini-HOWTO Excellent, documentation is always a good thing... I keep wanting to make a new release of pymerase but keep putting it off because we haven't made documentation yet. Good luck, and feel free to email me with more questions. diane |
From: Gavin S. <she...@ge...> - 2002-10-31 19:54:15
|
Hi Jason, I think it's a bit late for charging registration, both because I say on the web page that the meeting is free, and because I'm not really set up to handle that type of registration, credit cards etc. Were there any lists in particular that you were thinking of? Cheers, Gavin ___________________________________________________________ On 31 Oct 2002, Jason E. Stewart wrote: > "Gavin Sherlock" <she...@ge...> writes: > > > Also, as a general question to the group, does anyone have any > > opinions on any other lists etc that it might be useful to advertize > > the jamboree on? The number of people registered thus far in not > > huge.... > > Hey Gavin, > > Thanks again for organizing this. > > I would suggest advertising the Friday tutorial on some of the general > biosoftware/microarray lists. We want this to be open. If we mention > that Nature and Lancet will be requiring MAGE-ML submission to public > DB's, maybe that will help spark interest. > > Question 1: Are we to the point of requiring a $100 registration fee? > > Question 2: Can we get a sponsor(s) to support a box lunch for the > first day? > > Cheers, > jas. > > > ------------------------------------------------------- > This sf.net email is sponsored by: Influence the future > of Java(TM) technology. Join the Java Community > Process(SM) (JCP(SM)) program now. > http://ads.sourceforge.net/cgi-bin/redirect.pl?sunm0004en > _______________________________________________ > Mged-mage-perl mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage-perl > |
From: Jason E. S. <ja...@op...> - 2002-10-31 18:20:08
|
"Gavin Sherlock" <she...@ge...> writes: > Also, as a general question to the group, does anyone have any > opinions on any other lists etc that it might be useful to advertize > the jamboree on? The number of people registered thus far in not > huge.... Hey Gavin, Thanks again for organizing this. I would suggest advertising the Friday tutorial on some of the general biosoftware/microarray lists. We want this to be open. If we mention that Nature and Lancet will be requiring MAGE-ML submission to public DB's, maybe that will help spark interest. Question 1: Are we to the point of requiring a $100 registration fee? Question 2: Can we get a sponsor(s) to support a box lunch for the first day? Cheers, jas. |
From: Gavin S. <she...@ge...> - 2002-10-31 16:32:15
|
The current hall of fame is so far restricted to: Mohammad shojatalab EBI Angel Pizarro University of Pennsylvania Shawn Handran Axon Instruments, Inc Paul Spellman UC Berkeley Siobhan Pickett Axon Instruments Ronald Taylor University of Colorado Michael Miller Rosetta Biosoftware Add a bunch of SMD'ers, presumably a person or two from Affy, hopefully someone from Agilent, and it's still not a lot. I was hoping for more like 40 on the tutorial day, with ~20-25 during the jamboree, Cheers, Gavin ___________________________________________________________ On Thu, 31 Oct 2002, paul spellman wrote: > Who has registered so far? > > Paul > > > On Thursday, October 31, 2002, at 08:15 AM, Gavin Sherlock wrote: > > > Hi Michael, > > We can certainly devote an hour of Friday to discussing these > > issues concerning the RFP. What time are you expecting to be here on > > the > > Friday? Also, as a general question to the group, does anyone have any > > opinions on any other lists etc that it might be useful to advertize > > the > > jamboree on? The number of people registered thus far in not huge.... > > > > Cheers, > > Gavin > > ___________________________________________________________ > > > > On Wed, 30 Oct 2002, Miller, Michael (Rosetta) wrote: > > > >> Hi Gavin, > >> > >> Before the last OMG meeting I sent out to the mged-mage list a > >> proposed > >> OMG-LSR RFP concerning a Gene Expression Query Service. It was a > >> preliminary draft and I didn't get a lot of feedback outside of the > >> OMG-LSR > >> meeting. > >> > >> I'd like an hour on Friday of the Jamboree to discuss it and get > >> feedback. > >> > >> This is basically the part of the original RFP requirements we didn't > >> do in > >> order to get MAGE completed as a Data Model. I will be mailing out > >> the next > >> draft in a week or two for people to read. There will be a chance to > >> discuss it at the OMG meeting 3rd week of November and then at the > >> Programming Jamboree. Then, if people are happy with it, it can be > >> issued > >> at the January OMG meeting with initial submissions due in the > >> May-July > >> timeframe (later, if we think it seems appropriate to take a little > >> more > >> time). > >> > >> I think the RFP should allow changes to the MAGE model, but that it > >> should > >> stay a pure data model. The Query Service would be an additional > >> model that > >> used the MAGE model as the basis of input and output. But this > >> requirement > >> is certainly open to discussion. > >> > >> The other open question, is the scope of change to the model for this > >> RFP. > >> Do we want a 1.1 (minor fixes), 1.5 (same basic structure but with > >> some big > >> fixes) or a 2.0 (reworking of AuditAndSecurity, Measurement, etc., > >> packages). We can, and probably should, ask for optional new Platform > >> Specific Models for MAGE-OM, that is, XML Schema. > >> > >> Cheers, > >> Michael > >> > >>> -----Original Message----- > >>> From: Gavin Sherlock [mailto:she...@ge...] > >>> Sent: Tuesday, October 29, 2002 11:34 AM > >>> To: Mohammad > >>> Cc: mge...@li...; mic...@eb...; > >>> mge...@li...; > >>> mge...@li...; > >>> mge...@li...; > >>> mge...@li... > >>> Subject: [Mged-ontologies] Re: [Mged-mage] Programming Jamboree > >>> > >>> > >>> Hi Mohammed, > >>> I agree that a more structured agenda is very useful to help > >>> people determine whether they want to be there. I put > >>> something on the > >>> announcement page: > >>> > >>> http://www.dnachip.org/mged/ > >>> > >>> People should feel free to let me (and the list) know their > >>> thoughts, so > >>> we can make the jamboree and tutorial as useful and productive as > >>> possible, > >>> > >>> Cheers, > >>> Gavin > >>> ___________________________________________________________ > >>> > >>> On Tue, 29 Oct 2002, Mohammad wrote: > >>> > >> <snip> > >> > > > > > > > > ------------------------------------------------------- > > This sf.net email is sponsored by: Influence the future > > of Java(TM) technology. Join the Java Community > > Process(SM) (JCP(SM)) program now. > > http://ads.sourceforge.net/cgi-bin/redirect.pl?sunm0004en > > _______________________________________________ > > Mged-mage mailing list > > Mge...@li... > > https://lists.sourceforge.net/lists/listinfo/mged-mage > > > > ------------------------------------------------------- > This sf.net email is sponsored by: Influence the future > of Java(TM) technology. Join the Java Community > Process(SM) (JCP(SM)) program now. > http://ads.sourceforge.net/cgi-bin/redirect.pl?sunm0004en > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > |
From: paul s. <pts...@lb...> - 2002-10-31 16:25:56
|
Who has registered so far? Paul On Thursday, October 31, 2002, at 08:15 AM, Gavin Sherlock wrote: > Hi Michael, > We can certainly devote an hour of Friday to discussing these > issues concerning the RFP. What time are you expecting to be here on > the > Friday? Also, as a general question to the group, does anyone have any > opinions on any other lists etc that it might be useful to advertize > the > jamboree on? The number of people registered thus far in not huge.... > > Cheers, > Gavin > ___________________________________________________________ > > On Wed, 30 Oct 2002, Miller, Michael (Rosetta) wrote: > >> Hi Gavin, >> >> Before the last OMG meeting I sent out to the mged-mage list a >> proposed >> OMG-LSR RFP concerning a Gene Expression Query Service. It was a >> preliminary draft and I didn't get a lot of feedback outside of the >> OMG-LSR >> meeting. >> >> I'd like an hour on Friday of the Jamboree to discuss it and get >> feedback. >> >> This is basically the part of the original RFP requirements we didn't >> do in >> order to get MAGE completed as a Data Model. I will be mailing out >> the next >> draft in a week or two for people to read. There will be a chance to >> discuss it at the OMG meeting 3rd week of November and then at the >> Programming Jamboree. Then, if people are happy with it, it can be >> issued >> at the January OMG meeting with initial submissions due in the >> May-July >> timeframe (later, if we think it seems appropriate to take a little >> more >> time). >> >> I think the RFP should allow changes to the MAGE model, but that it >> should >> stay a pure data model. The Query Service would be an additional >> model that >> used the MAGE model as the basis of input and output. But this >> requirement >> is certainly open to discussion. >> >> The other open question, is the scope of change to the model for this >> RFP. >> Do we want a 1.1 (minor fixes), 1.5 (same basic structure but with >> some big >> fixes) or a 2.0 (reworking of AuditAndSecurity, Measurement, etc., >> packages). We can, and probably should, ask for optional new Platform >> Specific Models for MAGE-OM, that is, XML Schema. >> >> Cheers, >> Michael >> >>> -----Original Message----- >>> From: Gavin Sherlock [mailto:she...@ge...] >>> Sent: Tuesday, October 29, 2002 11:34 AM >>> To: Mohammad >>> Cc: mge...@li...; mic...@eb...; >>> mge...@li...; >>> mge...@li...; >>> mge...@li...; >>> mge...@li... >>> Subject: [Mged-ontologies] Re: [Mged-mage] Programming Jamboree >>> >>> >>> Hi Mohammed, >>> I agree that a more structured agenda is very useful to help >>> people determine whether they want to be there. I put >>> something on the >>> announcement page: >>> >>> http://www.dnachip.org/mged/ >>> >>> People should feel free to let me (and the list) know their >>> thoughts, so >>> we can make the jamboree and tutorial as useful and productive as >>> possible, >>> >>> Cheers, >>> Gavin >>> ___________________________________________________________ >>> >>> On Tue, 29 Oct 2002, Mohammad wrote: >>> >> <snip> >> > > > > ------------------------------------------------------- > This sf.net email is sponsored by: Influence the future > of Java(TM) technology. Join the Java Community > Process(SM) (JCP(SM)) program now. > http://ads.sourceforge.net/cgi-bin/redirect.pl?sunm0004en > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Gavin S. <she...@ge...> - 2002-10-31 16:15:24
|
Hi Michael, We can certainly devote an hour of Friday to discussing these issues concerning the RFP. What time are you expecting to be here on the Friday? Also, as a general question to the group, does anyone have any opinions on any other lists etc that it might be useful to advertize the jamboree on? The number of people registered thus far in not huge.... Cheers, Gavin ___________________________________________________________ On Wed, 30 Oct 2002, Miller, Michael (Rosetta) wrote: > Hi Gavin, > > Before the last OMG meeting I sent out to the mged-mage list a proposed > OMG-LSR RFP concerning a Gene Expression Query Service. It was a > preliminary draft and I didn't get a lot of feedback outside of the OMG-LSR > meeting. > > I'd like an hour on Friday of the Jamboree to discuss it and get feedback. > > This is basically the part of the original RFP requirements we didn't do in > order to get MAGE completed as a Data Model. I will be mailing out the next > draft in a week or two for people to read. There will be a chance to > discuss it at the OMG meeting 3rd week of November and then at the > Programming Jamboree. Then, if people are happy with it, it can be issued > at the January OMG meeting with initial submissions due in the May-July > timeframe (later, if we think it seems appropriate to take a little more > time). > > I think the RFP should allow changes to the MAGE model, but that it should > stay a pure data model. The Query Service would be an additional model that > used the MAGE model as the basis of input and output. But this requirement > is certainly open to discussion. > > The other open question, is the scope of change to the model for this RFP. > Do we want a 1.1 (minor fixes), 1.5 (same basic structure but with some big > fixes) or a 2.0 (reworking of AuditAndSecurity, Measurement, etc., > packages). We can, and probably should, ask for optional new Platform > Specific Models for MAGE-OM, that is, XML Schema. > > Cheers, > Michael > > > -----Original Message----- > > From: Gavin Sherlock [mailto:she...@ge...] > > Sent: Tuesday, October 29, 2002 11:34 AM > > To: Mohammad > > Cc: mge...@li...; mic...@eb...; > > mge...@li...; > > mge...@li...; > > mge...@li...; > > mge...@li... > > Subject: [Mged-ontologies] Re: [Mged-mage] Programming Jamboree > > > > > > Hi Mohammed, > > I agree that a more structured agenda is very useful to help > > people determine whether they want to be there. I put > > something on the > > announcement page: > > > > http://www.dnachip.org/mged/ > > > > People should feel free to let me (and the list) know their > > thoughts, so > > we can make the jamboree and tutorial as useful and productive as > > possible, > > > > Cheers, > > Gavin > > ___________________________________________________________ > > > > On Tue, 29 Oct 2002, Mohammad wrote: > > > <snip> > |
From: Miller, M. (Rosetta) <Michael_Miller@Rosettabio.com> - 2002-10-30 17:29:25
|
Hi Gavin, Before the last OMG meeting I sent out to the mged-mage list a proposed OMG-LSR RFP concerning a Gene Expression Query Service. It was a preliminary draft and I didn't get a lot of feedback outside of the OMG-LSR meeting. I'd like an hour on Friday of the Jamboree to discuss it and get feedback. This is basically the part of the original RFP requirements we didn't do in order to get MAGE completed as a Data Model. I will be mailing out the next draft in a week or two for people to read. There will be a chance to discuss it at the OMG meeting 3rd week of November and then at the Programming Jamboree. Then, if people are happy with it, it can be issued at the January OMG meeting with initial submissions due in the May-July timeframe (later, if we think it seems appropriate to take a little more time). I think the RFP should allow changes to the MAGE model, but that it should stay a pure data model. The Query Service would be an additional model that used the MAGE model as the basis of input and output. But this requirement is certainly open to discussion. The other open question, is the scope of change to the model for this RFP. Do we want a 1.1 (minor fixes), 1.5 (same basic structure but with some big fixes) or a 2.0 (reworking of AuditAndSecurity, Measurement, etc., packages). We can, and probably should, ask for optional new Platform Specific Models for MAGE-OM, that is, XML Schema. Cheers, Michael > -----Original Message----- > From: Gavin Sherlock [mailto:she...@ge...] > Sent: Tuesday, October 29, 2002 11:34 AM > To: Mohammad > Cc: mge...@li...; mic...@eb...; > mge...@li...; > mge...@li...; > mge...@li...; > mge...@li... > Subject: [Mged-ontologies] Re: [Mged-mage] Programming Jamboree > > > Hi Mohammed, > I agree that a more structured agenda is very useful to help > people determine whether they want to be there. I put > something on the > announcement page: > > http://www.dnachip.org/mged/ > > People should feel free to let me (and the list) know their > thoughts, so > we can make the jamboree and tutorial as useful and productive as > possible, > > Cheers, > Gavin > ___________________________________________________________ > > On Tue, 29 Oct 2002, Mohammad wrote: > <snip> |
From: Gavin S. <she...@ge...> - 2002-10-29 19:34:31
|
Hi Mohammed, I agree that a more structured agenda is very useful to help people determine whether they want to be there. I put something on the announcement page: http://www.dnachip.org/mged/ People should feel free to let me (and the list) know their thoughts, so we can make the jamboree and tutorial as useful and productive as possible, Cheers, Gavin ___________________________________________________________ On Tue, 29 Oct 2002, Mohammad wrote: > Hi All, > > Wouldn't it be nice to have a more detail agenda of the programming part? > > > Cheers > -- > /* > * Mohammadreza Shojatalab > * European Bioinformatics Institute Tel: +44 (0)1223 494 669 > * EMBL Outstation Fax: +44 (0)1223 494 468 > * Wellcome Trust Genome Campus E-Mail: sh...@eb... > * Hinxton, Cambridge > * CB10 1SD, UK URL: http://www.ebi.ac.uk/~shoja > */ > > |
From: Mohammad <sh...@eb...> - 2002-10-29 11:48:11
|
Hi All, Wouldn't it be nice to have a more detail agenda of the programming part? Cheers -- /* * Mohammadreza Shojatalab * European Bioinformatics Institute Tel: +44 (0)1223 494 669 * EMBL Outstation Fax: +44 (0)1223 494 468 * Wellcome Trust Genome Campus E-Mail: sh...@eb... * Hinxton, Cambridge * CB10 1SD, UK URL: http://www.ebi.ac.uk/~shoja */ |
From: Gavin S. <she...@ge...> - 2002-10-29 01:54:38
|
Hi all, Sorry for the repost of the message - this is for two reasons. Firstly my stupid registration program was overwriting its file of attendees, rather than appending, so if you've registered, can you reregister please (groan). Secondly I added a couple of extra mailing lists to the recipient list, in a hope of getting a wider distribution. The original email is below: I have put up a web page announcing the next programming jamboree. Hopefully we'll get as many people as the last one, though I understand it's short notice. I would certainly appreciate ideas (and volunteers!) for the tutorial day. I was thinking roughly: MIAME 1hr - Cathy Ball and/or me MAGE-OM most of the day - Paul/Michael/Jason MAGE-stk 1hr - Jason/Michael? depending on who's there. I was also thinking, depending on numbers and tasks, that during the jamboree it may be a good time to try and write use CASE documentation for the model - certainly from SMD's perspective it would help a lot, and we're happy to be involved. The web page is at: http://www.dnachip.org/mged/ The driving directions aren't quite accurate yet..... The best (though not necessarily cheapest) hotels, in terms of location, are the Sheraton in Palo Alto, and the Cardinal. There is a short registration form, so I can get an idea of the number of attendees, so I can get an appropriate room for the tutorial day. For the jamboree proper, we will be limited to 24 Net connections, though everyone doesn't need to be online all the time. To be able to give you an IP address, Stanford does need the hardware address of your laptop's ethernet card, so please put that in the registration form if you're intending on taking part in the jamboree. Look forward to seeing you, and please let me know any suggestions you may have, Cheers, Gavin ___________________________________________________________ Gavin Sherlock Dept. of Genetics Center for Clinical Sciences Research 269 Campus Drive, Room 2255b, Stanford, CA 94305-5166 Tel: 650 498 6012 Fax: 650 723 7016 |
From: Jason E. S. <ja...@op...> - 2002-10-16 01:32:37
|
"Gavin Sherlock" <she...@ge...> writes: I can make it. jas. |
From: Angel P. <an...@sn...> - 2002-10-15 14:45:52
|
Hey gavin, I can make it for the full time. Angel On Mon, 14 Oct 2002, Gavin Sherlock wrote: > Hi all, > Of the few responses that I got from my last email, it seemed that > the most reasonable time to hold the jamboree would be Dec 7th -> 10th, > with a MAGE tutorial on the 6th. Can I get a head count of who could come > on those dates, so I can go ahead and try to set this up, if there's > enough interest. If you're interested, let me know as soon as possible if > it's for the tutorial only, for the programming part only, or for both, so > that I can plan accordingly, > > Cheers, > Gavin > ___________________________________________________________ > > Gavin Sherlock > Dept. of Genetics > Center for Clinical Sciences Research > 269 Campus Drive, > Room 2255b, > Stanford, > CA 94305-5166 > > Tel: 650 498 6012 > Fax: 650 723 7016 > > On Fri, 11 Oct 2002, Gavin Sherlock wrote: > > > Hi all, > > I've done a bit of work to see if we can do it here, and the > > available dates are pretty limited, and all options unfortunately include > > a full weekend. The dates that might work are: > > > > Nov 16th -> 19th > > Dec 7th -> 10th > > Dec 14th -> 17th > > > > Each of these starts on a Saturday - we could have the tutorial day itself > > on the Friday. Does anyone have opinions on these dates? > > > > Cheers, > > Gavin > > ___________________________________________________________ > > > > On 11 Oct 2002, Jason E. Stewart wrote: > > > > > Hey All, > > > > > > I just heard from Brian, and it looks as thought the I3C can't do > > > anything this time around. So we will have to run it ourselves. > > > > > > jas. > > > > > > > > > > > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > Mged-mage-java mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage-java > -- Angel Pizarro Programmer Analyst Center for Bioinformatics an...@pc... |
From: Paul S. <spe...@bd...> - 2002-10-15 14:15:27
|
I can vote for that. Paul On Monday, October 14, 2002, at 05:36 PM, Gavin Sherlock wrote: > Hi all, > Of the few responses that I got from my last email, it seemed that > the most reasonable time to hold the jamboree would be Dec 7th -> 10th, > with a MAGE tutorial on the 6th. Can I get a head count of who could > come > on those dates, so I can go ahead and try to set this up, if there's > enough interest. If you're interested, let me know as soon as > possible if > it's for the tutorial only, for the programming part only, or for > both, so > that I can plan accordingly, > > Cheers, > Gavin > ___________________________________________________________ > > Gavin Sherlock > Dept. of Genetics > Center for Clinical Sciences Research > 269 Campus Drive, > Room 2255b, > Stanford, > CA 94305-5166 > > Tel: 650 498 6012 > Fax: 650 723 7016 > > On Fri, 11 Oct 2002, Gavin Sherlock wrote: > >> Hi all, >> I've done a bit of work to see if we can do it here, and the >> available dates are pretty limited, and all options unfortunately >> include >> a full weekend. The dates that might work are: >> >> Nov 16th -> 19th >> Dec 7th -> 10th >> Dec 14th -> 17th >> >> Each of these starts on a Saturday - we could have the tutorial day >> itself >> on the Friday. Does anyone have opinions on these dates? >> >> Cheers, >> Gavin >> ___________________________________________________________ >> >> On 11 Oct 2002, Jason E. Stewart wrote: >> >>> Hey All, >>> >>> I just heard from Brian, and it looks as thought the I3C can't do >>> anything this time around. So we will have to run it ourselves. >>> >>> jas. >>> >>> >> >> > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > Mged-mage-perl mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage-perl > |
From: Gavin S. <she...@ge...> - 2002-10-15 00:36:05
|
Hi all, Of the few responses that I got from my last email, it seemed that the most reasonable time to hold the jamboree would be Dec 7th -> 10th, with a MAGE tutorial on the 6th. Can I get a head count of who could come on those dates, so I can go ahead and try to set this up, if there's enough interest. If you're interested, let me know as soon as possible if it's for the tutorial only, for the programming part only, or for both, so that I can plan accordingly, Cheers, Gavin ___________________________________________________________ Gavin Sherlock Dept. of Genetics Center for Clinical Sciences Research 269 Campus Drive, Room 2255b, Stanford, CA 94305-5166 Tel: 650 498 6012 Fax: 650 723 7016 On Fri, 11 Oct 2002, Gavin Sherlock wrote: > Hi all, > I've done a bit of work to see if we can do it here, and the > available dates are pretty limited, and all options unfortunately include > a full weekend. The dates that might work are: > > Nov 16th -> 19th > Dec 7th -> 10th > Dec 14th -> 17th > > Each of these starts on a Saturday - we could have the tutorial day itself > on the Friday. Does anyone have opinions on these dates? > > Cheers, > Gavin > ___________________________________________________________ > > On 11 Oct 2002, Jason E. Stewart wrote: > > > Hey All, > > > > I just heard from Brian, and it looks as thought the I3C can't do > > anything this time around. So we will have to run it ourselves. > > > > jas. > > > > > > |
From: Diane T. <di...@ca...> - 2002-09-24 01:23:05
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Hi, I added some new functionality to pymerase recently. The largest change is it's now possible to pass a set of already initialized meta-objects into the readers. This allows initializing information prior to trying to read information out of a particular set of meta-object definitions. I did this because the XMI parser doesn't return inheritence information so I could preconstruct the meta-objects with the right inheritence hierarchy. Also since I'm feeling frustrated with parsing XMI I'm going to be focusing on getting the database compontents working better before going back to it. (If anyone else would like to get XMI working, most of the code is already there, it's just that the XMI reader isn't returning inheritence information (and perhaps cardinality information) correctly. Also I hope to write a graphviz output module to allow rendering things created with the genex table.dtd file format into something that looks like UML. diane |
From: Diane T. <di...@ca...> - 2002-09-03 21:31:30
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"Marcin Swiatek" <Mar...@im...> writes: > Diane, could you please explain to me (or point me to some docs) what is > the status of pymerase. And what is its grand design perhaps too. (We > may want to take this thing off the general mailing list if you think it > won't be interesting for anyone but me). Hi, I just wanted to say that I haven't forgotten you, I just haven't had much time to prepare any extra documentation yet. There is a python orientated list, mged-mage-python, which I've posted some status updates to. So we might want to switch the discussion there. Which has the advantages of not cluttering the main list too much, yet still keeping the discussion publicly accessible. So instead of procrastinating further here's a whirlwind tour. First I'll describe the components of pymerase, followed by a quick description of the generated Object/Relational classes. The pymerase.py defines the main interface to the system currently, both the direct python interface and the command line interface (though Brandon may be moving the command-line interface elsewhere). There's also a tk interface in tkPymerase. The module ClassMembers defines the abstract representation of the objects being defined. There's the base class ClassMembers. Then classes describing attributes of classes ClassAttributes and ClassAssociation. Finally the class representing the information needed to declare a class ClassMetaInfo. Those classes come in different versions one for the version parsing the GeneX table dtd file, and another for the XMI files. The different functionality is to define the additional information needed to encode the objects in a relational database. The GeneX file format provides the information while the XMI parser needs to figure it out. The input modules are defined in pymerase/input, output modules are in pymerase/output. There's some extra utilities in pymerase/util, the most interesting of which are the code to handle forcing variable names to conform to different variable naming conventions. The output format that I most frequently work with is CreateDBAPI and CreateSQL, the first creates the python level objects along with the code to connect to the database. The CreateSQL module creates the sql statements needed to construct the database. Brandon was also working on some code to construct a simple web editor, those output modules are CreateDBEditor and CreateHtmlForms. There's also iPymerase, that if you have ipython installed parses the input files and leaves you in an interpreter to investigate those objects. In the output module there are some subdirectories to contain additional support files for the different output modules. For instance DBAPI has a directory pymerase/output/dbAPI that contains the lower level classes to attach to the database. There was also a first stab at separating the generated objects from the persistence layer checked in as CreatePythonAPI. All of the objects in the generated object model inherit from DBClass (defined in pymerase/output/dbAPI) which handles binding attributes to sql columns. This section needs some further work, right now the object layer and relational layer are too coupled. For instance it's largely assumed that one class corresponds to one table, and that the attribute names are largely the same. DBAPI assumes that an object will have two dictionaries containing the attributes and associations where each element is initialized with a class defining the information needed to pull it out of the database. Currently the attribute and association objects are named Field and ForeignKey, but I'm planning on renaming them soon. The generated objects then have a collection of getter/setter functions which use methods of the class instances contained in the attribute and association dictionaries to actually deal with pulling data out of the database, and caching changes in local memory. Actually writing data requires calling a .commit() funtion. I hope that quick overview helped in some way. diane |
From: Marcin S. <Mar...@im...> - 2002-08-30 19:12:34
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Thanks for the hints. I guess I will take the road more traveled this time and have a close look at the Python MAGEstk. This may be more useful in the long run anyway.=20 Diane, could you please explain to me (or point me to some docs) what is the status of pymerase. And what is its grand design perhaps too. (We may want to take this thing off the general mailing list if you think it won't be interesting for anyone but me). Regards, Marcin > -----Original Message----- > From: Diane Trout [mailto:di...@ca...] > Sent: August 29, 2002 5:52 PM > To: mge...@li... > Cc: mge...@li...; Marcin Swiatek; Jason E. > Stewart > Subject: Re: [Mged-mage] Use Cases, example XML files, example MAGEstk > apps >=20 >=20 > > You may want to coordinate with the MAGEstk Python group,=20 > and see how > > far away they are from having a working version of the=20 > code, and that > > way all the writing of the MAGE-ML could be done for you=20 > automatically > > once you built and populated the appropriate MAGE python=20 > objects. This > > is a lot less error-prone then trying to write MAGE-ML using print > > statements.=20 >=20 >=20 > Well internally we're pushing more for persistent objects than an > object hierarchy to read and write XML files. [...] |
From: Diane T. <di...@ca...> - 2002-08-29 21:52:16
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> You may want to coordinate with the MAGEstk Python group, and see how > far away they are from having a working version of the code, and that > way all the writing of the MAGE-ML could be done for you automatically > once you built and populated the appropriate MAGE python objects. This > is a lot less error-prone then trying to write MAGE-ML using print > statements. Well internally we're pushing more for persistent objects than an object hierarchy to read and write XML files. The components I'm currently trying to get working * Get XMI parsing working correctly * Split the persistence layer from the object layer * Implement auto-generation of primary/foreign key information for the relational layer. To make it easier for other people to contribute code I'm also trying to: * Improve documentation * Make clearly defined APIs. Unfortunately this means that the code needed to traverse the object hierarchy and write out the XML files is pretty far down on my to do list. (And probably separate enough from the internals of this tool to make a great project for someone else to take on.) For some background on where we're currently at. Pymerase (the name we've been using for the python tool that implements MAGEstk) started off as a tool to generate an object hierarchy to provide a python API to GeneX 2. So it can currently parse the general table definition xml files developed for GeneX 2 and from that generate: * objects that are tightly tied to the database. * sql create table statements. * prototype web interface to the database. (Thanks to Brandon) (We have used the tool to develop prototypes for systems other than GeneX or Mage, check the lib/Python/pymerase/examples directory in the MGED/MAGEstk CVS tree). I've gotten close to getting pymerase to generate things from the XMI file. (Just a few more bugs...) It is worth pointing out that there is a tension on the where I need to spend my time developing pymerase, internally we want persistent objects, while mage needs the object hierarchy without the tight coupling to the database. So it might be a little while before I get a chance to fully decouple it. diane |
From: Brandon K. <ki...@ca...> - 2002-08-17 00:59:13
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Hi All, There is going to be a change in how pymerase is run by command line and gui... Both of which are being moved into /lib/Python/pymerase/bin/pymerase. I have just checked that file in, but it currently has a bug that doesn't display the available input/output modules available in the command line interface. The GUI part works just fine. type [path]/lib/Python/pymerase/bin/pymerase --help for command line help type [path]/lib/Python/pymerase/bin/pymerase --gui to launch the gui For now, I am leaving the command line interface in /lib/Python/pymerase/pymerase.py and the gui in /lib/Python/pymerase/tkPymerase.py. I want to make sure the new program is stable before I remove those features. Stay tuned for future updates! -Brandon |
From: Diane T. <di...@ca...> - 2002-08-15 00:24:18
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Hi, pymerase now supports differing name mangling conventions for different output modules. Currently CreateDBAPI and CreateSQL have been updated to support this feature. Additionally DBAPI will peek at SQL's name mangling convention so all the variable access to the sql database uses the same convention that used for the sql create table statements. Look at pymerase/examples/school/TestSchool.py to see how it works. The current default will be to have the DBAPI use CapWord conventions for getters & setters, while the internal variables that are communicating with the sql database will be using the underscore_word convention. diane |
From: Brandon K. <ki...@ca...> - 2002-08-13 02:08:15
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Hi All, I've checked in a new version of tkPymerase! I've added the following: - Menus - Load/Save settings options under the file menu - About Dialog Box (quickly made, needs improvement) Todo: - Fix up about dialog box - Add Help Dialog Box - Add more documentation - Come up with more improvements -Brandon |
From: Brandon K. <ki...@ca...> - 2002-08-08 02:50:53
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Hi All, I've committed tkPymerase.py which is a Tk front end (GUI) for running pymerase. Check it out! =o) Current Features Include: -Basic error checking (Won't launch a pymerase job if an parameter is missing). -Displays Information in command prompt while running. -Can't run iPymerase with other output modules (de-selects options when chosen) -Saves settings used when launch complete. (saves settings under /home/{USER}/.tkPymerase) Future Features: -Menu (File --> Load Settings; Save Settings; Quit) -Load and Save settings from file (once feature is added, settings files will be added to examples) -Make it clear that iPymerase can't be run with other output modules. -Add support for Name Manglers as they become available. -Brandon King |
From: Diane T. <di...@ca...> - 2002-07-02 01:18:46
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Two example databases have been added to the pymerase directory hierarchy under examples/. One is a quick example of representing the relationship between students, dorms, classes, faculty, and staff. (examples/school) The other richer example is a model of cellular chemical reactions. (examples/ReactionDB). Documentation for setting up pymerase is located in pymerase/README, what's needed to run the examples is in examples/README.example diane |
From: Diane T. <di...@ca...> - 2002-07-01 22:42:50
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Hi, I decided to convert the dbAPI to be a bit more consistant with the new default naming convention. get_objects is now getObjects, get_all_objects is getAllObjects, and you can probably guess what is now getObjectsWhere. I hope that future changes are just additions and not renaming calls. diane |