From: Tim R. <ra...@eb...> - 2007-03-19 09:30:11
|
Hi Gavin, I agree with Michael - this is the way I'd code what you've described in MAGE-TAB. The only addition I'd suggest is to add a Label column with the label names. A single Labeled Extract can have many Labels; this differs from tab2mage, where a separate LE is created for each label. You should end up with two rows per hybridization. I've checked, and the current parser implementation will support this arrangement (although I don't know if the accompanying data file parser copes with idat files as yet). As mentioned in my previous email, the feature extraction protocol currently has to be combined with the scanning protocol; we may want to consider how to fix that at the jamboree. Cheers, Tim -- On Sun, 18 Mar 2007, Miller, Michael D (Rosetta) wrote: > hi gavin, > > i'm not that familiar with the genotyping protocols, so this may be off > base, but i would think one could use the 'Labeled Extract Name' column > in the order where the labeling occurred. > > the tiffs i would imagine would be in the 'Image' column with perhaps a > Comment column to specify which image it was. > > if i understand right, the idat files are the Feature Extracted data > that's been collapsed per bead type from the raw data, so there could be > a 'Scan Name' column with two 'Array Data File' columns for the two idat > files, again with a Comment column for each to differentiate which was > which. > > tim discussed some issues around the feature extraction protocol in his > 3/16 e-mail which might be relevant. > > but i'm not sure what meaning the tiff files would have since the idat > files are per bead type, not per bead? > > cheers, > michael > >> -----Original Message----- >> From: mge...@li... >> [mailto:mge...@li...] On Behalf >> Of Gavin Sherlock >> Sent: Saturday, March 17, 2007 2:37 PM >> To: Tim Rayner >> Cc: mged-mage2; MGED-mage >> Subject: [Mged-mage2] MAGE-TAB Illumina question >> >> Hi Tim, >> >> Do you have any example MAGE-TAB files for Illumina Genotyping? >> Because there is no sample labeling per se, but instead 2 labels are >> incorporated during an allele specific extension step, after which >> you get 2 tiffs (one for each channel) and 2 idat files, I was a >> little unsure how exactly to deal with this in the sdrf file. Any >> pointers would be appreciated, >> >> Cheers, >> Gavin >> >> -------------------------------------------------------------- >> ----------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the >> chance to share your >> opinions on IT & business topics through brief surveys-and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge >> &CID=DEVDEV >> _______________________________________________ >> Mged-MAGE2 mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage2 >> >> > > |
From: Don M. <dM...@ge...> - 2007-03-21 22:13:05
|
Hi friends, We're looking forward to seeing and meeting with you in next week in =20 sunny California. Current forecasts are for a cloudy Tuesday, but a =20= sunny remainder of the week in the upper 60's. Here's my current list of attendees and agenda. Please let me know =20 if you wish to contribute any more bodies or agenda items! Regards, Don Maier MAGE Jamboree: March 27 - 30 Stanford University: Clark Center, Rm. 362 Attendees: 1) Cathy Ball (SMD) 2) Cate Beauheim (Stanford) 3) Alvis Brazma (EBI) 4) Steve Chervitz (Affymetrix) 5) Junmin Liu (U. Penn) 6) Don Maier (SMD) 7) Tim Rayner (EBI) 8) Ugis Sarkans (EBI) 9) Paul Spellman (Lawrence Berkeley National Laboratory) 10) Joe White (Dana-Farber/Harvard Cancer Center) Agenda: 1) Tim =96 Final version of MAGE-TAB 2) Alvis/Ugis =96 MAGE-TAB object model: a) Possible move to FUGE-TAB b) Discussion of basic concepts (no formal proposal yet). 3) Don =96 The =93one-parser=94 requirement and how to satisfy it for = =20 MAGE-TAB: a) There is thought to be a strong requirement to have exactly =20 one MAGE-TAB parser in one body of code in one language that can be =20 used from either a Java or a Perl programming environment. =20 Satisfying this requirement would ensure that MAGE-TAB never destroys =20= itself on the shoals of disagreeing acceptors. b) Proposal for how to satisfy this requirement.= |
From: Junmin L. <ju...@pc...> - 2007-03-23 16:17:00
|
Hi, Don and Jamboree attendees, Since last Oct., for one of the requirement of our in-house data loading=20 pipeline, we developed an extendable framework MR_Ti and a set of=20 toolkits to help loading MIAMI-compliant documents in different formats=20 into our GUS schema. Chris has suggested me to present this on the=20 Jamboree to get feedback and to see if it can be useful to the=20 communities. Note MAGE-Tab is part of our pipeline, we have started to generate and=20 load MAGE-Tabs to GUS, we will also like to show public the files we=20 have and make sure they are exchangable and compliant with MAGE-Tab spec.= =20 1.0 release. Thanks, ---junmin On Wed, 21 Mar 2007, Don Maier wrote: > Hi friends, > > We're looking forward to seeing and meeting with you in next week in sunn= y=20 > California. Current forecasts are for a cloudy Tuesday, but a sunny=20 > remainder of the week in the upper 60's. > > Here's my current list of attendees and agenda. Please let me know if y= ou=20 > wish to contribute any more bodies or agenda items! > > Regards, > Don Maier > > > MAGE Jamboree: March 27 - 30 > Stanford University: Clark Center, Rm. 362 > > Attendees: > > 1) Cathy Ball (SMD) > 2) Cate Beauheim (Stanford) > 3) Alvis Brazma (EBI) > 4) Steve Chervitz (Affymetrix) > 5) Junmin Liu (U. Penn) > 6) Don Maier (SMD) > 7) Tim Rayner (EBI) > 8) Ugis Sarkans (EBI) > 9) Paul Spellman (Lawrence Berkeley National Laboratory) > 10) Joe White (Dana-Farber/Harvard Cancer Center) > > > Agenda: > > 1) Tim =96 Final version of MAGE-TAB > > 2) Alvis/Ugis =96 MAGE-TAB object model: > > a) Possible move to FUGE-TAB > > b) Discussion of basic concepts (no formal proposal yet). > > 3) Don =96 The =93one-parser=94 requirement and how to satisfy it for = MAGE-TAB: > > a) There is thought to be a strong requirement to have exactly one=20 > MAGE-TAB parser in one body of code in one language that can be used from= =20 > either a Java or a Perl programming environment. Satisfying this require= ment=20 > would ensure that MAGE-TAB never destroys itself on the shoals of disagre= eing=20 > acceptors. > > b) Proposal for how to satisfy this requirement. |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2007-03-23 16:55:49
|
hi junmin, that's great work, if i could get a copy of the presentation when it's ready, that would be much appreciated. hi don, > > a) There is thought to be a strong requirement to have=20 > exactly one=20 > > MAGE-TAB parser in one body of code in one language that=20 > can be used from=20 > > either a Java or a Perl programming environment. =20 > Satisfying this requirement=20 > > would ensure that MAGE-TAB never destroys itself on the=20 > shoals of disagreeing=20 > > acceptors. i think this is a great requirement, similar to the OMG compliancy section, but i have one caveat with the wording. yes, we definitely should have as a goal a definitive MAGE-TAB parser that has a mode that verifies that a set of files is MAGE-TAB compliant (including resolving the references between the files). And it should have a mode that developers could certainly use as the basis of their import implementation. > exactly one=20 > > MAGE-TAB parser in one body of code in one language that=20 > can be used from=20 > > either a Java or a Perl programming environment. =20 my caveat is that there is no problem having more than one, often for efficiency reasons for an application there would be a parser tuned to specific database schema and additional application rules for standard, compliant MAGE-TAB files (for instance, the application rules might restrict MAGE-TAB to require certain columns for the application that in general aren't required). i would change the wording to: > exactly one official validating MAGE-TAB parser in one body of code in one language that=20 > can also be used from=20 > > either a Java or a Perl programming environment by any import application. note that if it is in one language there will be by necessity, i think, a bit of an impedance using it in a different language. cheers, michael =20 > -----Original Message----- > From: mge...@li...=20 > [mailto:mge...@li...] On Behalf=20 > Of Junmin Liu > Sent: Friday, March 23, 2007 9:17 AM > To: Don Maier > Cc: mged-mage2; MGED-mage > Subject: Re: [Mged-mage2] MGED Jamboree next week - March 27-30! >=20 > Hi, Don and Jamboree attendees, > Since last Oct., for one of the requirement of our in-house=20 > data loading=20 > pipeline, we developed an extendable framework MR_Ti and a set of=20 > toolkits to help loading MIAMI-compliant documents in=20 > different formats=20 > into our GUS schema. Chris has suggested me to present this on the=20 > Jamboree to get feedback and to see if it can be useful to the=20 > communities. >=20 > Note MAGE-Tab is part of our pipeline, we have started to=20 > generate and=20 > load MAGE-Tabs to GUS, we will also like to show public the files we=20 > have and make sure they are exchangable and compliant with=20 > MAGE-Tab spec.=20 > 1.0 release. >=20 > Thanks, > ---junmin >=20 >=20 >=20 > On Wed, 21 Mar 2007, Don Maier wrote: >=20 > > Hi friends, > > > > We're looking forward to seeing and meeting with you in=20 > next week in sunny=20 > > California. Current forecasts are for a cloudy Tuesday,=20 > but a sunny=20 > > remainder of the week in the upper 60's. > > > > Here's my current list of attendees and agenda. Please=20 > let me know if you=20 > > wish to contribute any more bodies or agenda items! > > > > Regards, > > Don Maier > > > > > > MAGE Jamboree: March 27 - 30 > > Stanford University: Clark Center, Rm. 362 > > > > Attendees: > > > > 1) Cathy Ball (SMD) > > 2) Cate Beauheim (Stanford) > > 3) Alvis Brazma (EBI) > > 4) Steve Chervitz (Affymetrix) > > 5) Junmin Liu (U. Penn) > > 6) Don Maier (SMD) > > 7) Tim Rayner (EBI) > > 8) Ugis Sarkans (EBI) > > 9) Paul Spellman (Lawrence Berkeley National Laboratory) > > 10) Joe White (Dana-Farber/Harvard Cancer Center) > > > > > > Agenda: > > > > 1) Tim - Final version of MAGE-TAB > > > > 2) Alvis/Ugis - MAGE-TAB object model: > > > > a) Possible move to FUGE-TAB > > > > b) Discussion of basic concepts (no formal proposal yet). > > > > 3) Don - The "one-parser" requirement and how to satisfy=20 > it for MAGE-TAB: > > > > a) There is thought to be a strong requirement to have=20 > exactly one=20 > > MAGE-TAB parser in one body of code in one language that=20 > can be used from=20 > > either a Java or a Perl programming environment. =20 > Satisfying this requirement=20 > > would ensure that MAGE-TAB never destroys itself on the=20 > shoals of disagreeing=20 > > acceptors. > > > > b) Proposal for how to satisfy this requirement. >=20 |
From: Don M. <dM...@ge...> - 2007-03-23 17:31:04
|
Hi Michael, Thank you for your enthusiastic support for the "one-parser" requirement -- at least, in your initial statement about it. Two comments about your comments: i) There likely will be a performance tradeoff. In my view, any modest performance cost is utterly trivial compared to the gain in solving this problem once and for everyone. Of course, there were those who invoked the specter of performance to justify continuing continuing careers in assembly language programming. ii) The architecture of a push parser makes it possible to perform any set of "custom" actions that are conjoined with the parse. This includes performing operations on your favorite database and flagging constructs that an installation prefers not to support. There *is* a problem, a really big problem, with having more than one parser. Two is too many. I hope that I can clearly convey this to the group. Regards, Don M. On Mar 23, 2007, at 9:55 AM, Miller, Michael D (Rosetta) wrote: > hi junmin, > > that's great work, if i could get a copy of the presentation when it's > ready, that would be much appreciated. > > hi don, > >>> a) There is thought to be a strong requirement to have >> exactly one >>> MAGE-TAB parser in one body of code in one language that >> can be used from >>> either a Java or a Perl programming environment. >> Satisfying this requirement >>> would ensure that MAGE-TAB never destroys itself on the >> shoals of disagreeing >>> acceptors. > > i think this is a great requirement, similar to the OMG compliancy > section, but i have one caveat with the wording. > > yes, we definitely should have as a goal a definitive MAGE-TAB parser > that has a mode that verifies that a set of files is MAGE-TAB > compliant > (including resolving the references between the files). And it should > have a mode that developers could certainly use as the basis of their > import implementation. > >> exactly one >>> MAGE-TAB parser in one body of code in one language that >> can be used from >>> either a Java or a Perl programming environment. > > my caveat is that there is no problem having more than one, often for > efficiency reasons for an application there would be a parser tuned to > specific database schema and additional application rules for > standard, > compliant MAGE-TAB files (for instance, the application rules might > restrict MAGE-TAB to require certain columns for the application > that in > general aren't required). > > i would change the wording to: > >> exactly one official validating MAGE-TAB parser in one body of >> code in > one language that >> can also be used from >>> either a Java or a Perl programming environment by any import > application. > > note that if it is in one language there will be by necessity, i > think, > a bit of an impedance using it in a different language. > > cheers, > michael > > >> -----Original Message----- >> From: mge...@li... >> [mailto:mge...@li...] On Behalf >> Of Junmin Liu >> Sent: Friday, March 23, 2007 9:17 AM >> To: Don Maier >> Cc: mged-mage2; MGED-mage >> Subject: Re: [Mged-mage2] MGED Jamboree next week - March 27-30! >> >> Hi, Don and Jamboree attendees, >> Since last Oct., for one of the requirement of our in-house >> data loading >> pipeline, we developed an extendable framework MR_Ti and a set of >> toolkits to help loading MIAMI-compliant documents in >> different formats >> into our GUS schema. Chris has suggested me to present this on the >> Jamboree to get feedback and to see if it can be useful to the >> communities. >> >> Note MAGE-Tab is part of our pipeline, we have started to >> generate and >> load MAGE-Tabs to GUS, we will also like to show public the files we >> have and make sure they are exchangable and compliant with >> MAGE-Tab spec. >> 1.0 release. >> >> Thanks, >> ---junmin >> >> >> >> On Wed, 21 Mar 2007, Don Maier wrote: >> >>> Hi friends, >>> >>> We're looking forward to seeing and meeting with you in >> next week in sunny >>> California. Current forecasts are for a cloudy Tuesday, >> but a sunny >>> remainder of the week in the upper 60's. >>> >>> Here's my current list of attendees and agenda. Please >> let me know if you >>> wish to contribute any more bodies or agenda items! >>> >>> Regards, >>> Don Maier >>> >>> >>> MAGE Jamboree: March 27 - 30 >>> Stanford University: Clark Center, Rm. 362 >>> >>> Attendees: >>> >>> 1) Cathy Ball (SMD) >>> 2) Cate Beauheim (Stanford) >>> 3) Alvis Brazma (EBI) >>> 4) Steve Chervitz (Affymetrix) >>> 5) Junmin Liu (U. Penn) >>> 6) Don Maier (SMD) >>> 7) Tim Rayner (EBI) >>> 8) Ugis Sarkans (EBI) >>> 9) Paul Spellman (Lawrence Berkeley National Laboratory) >>> 10) Joe White (Dana-Farber/Harvard Cancer Center) >>> >>> >>> Agenda: >>> >>> 1) Tim - Final version of MAGE-TAB >>> >>> 2) Alvis/Ugis - MAGE-TAB object model: >>> >>> a) Possible move to FUGE-TAB >>> >>> b) Discussion of basic concepts (no formal proposal yet). >>> >>> 3) Don - The "one-parser" requirement and how to satisfy >> it for MAGE-TAB: >>> >>> a) There is thought to be a strong requirement to have >> exactly one >>> MAGE-TAB parser in one body of code in one language that >> can be used from >>> either a Java or a Perl programming environment. >> Satisfying this requirement >>> would ensure that MAGE-TAB never destroys itself on the >> shoals of disagreeing >>> acceptors. >>> >>> b) Proposal for how to satisfy this requirement. >> > > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2007-03-23 17:51:49
|
hi don, =20 as this is the real world, one cannot dictate that developers cannot go off on their own to do what ever they want. so my thought is that realistically we can not require something that is unlikely to be satisfied. =20 what we can do is release THE official validating parser which if there is a question as to whether a set of files that claims to be MAGE_TAB compliant is or isn't, it will definitively answer yea or nay. =20 if someone were to find this official parser wasn't efficient enough in the context of their application they would not be doing their job to develop one that did work fast enough for their application. but having this official validating parser would be wonderful to make sure the in-house application stayed compliant. =20 for instance, in-house, we have our own version of the java MAGEstk parser which is much more efficient and faster than the one in the official stk. (actually i'd like to put it in the official stk code but it got caught up in some unnecessary imports that prevent releasing it until those can be removed.) =20 cheers, michael =20 ________________________________ From: Don Maier [mailto:dM...@ge...]=20 Sent: Friday, March 23, 2007 10:31 AM To: Miller, Michael D (Rosetta) Cc: Junmin Liu; mged-mage2; MGED-mage Subject: Re: [Mged-mage] [Mged-mage2] MGED Jamboree next week - March 27-30! =09 =09 Hi Michael,=20 Thank you for your enthusiastic support for the "one-parser" requirement -- at least, in your initial statement about it. Two comments about your comments: i) There likely will be a performance tradeoff. In my view, any modest performance cost is utterly trivial compared to the gain in solving this problem once and for everyone. Of course, there were those who invoked the specter of performance to justify continuing continuing careers in assembly language programming. ii) The architecture of a push parser makes it possible to perform any set of "custom" actions that are conjoined with the parse. This includes performing operations on your favorite database and flagging constructs that an installation prefers not to support. There *is* a problem, a really big problem, with having more than one parser. Two is too many. I hope that I can clearly convey this to the group. Regards, Don M. On Mar 23, 2007, at 9:55 AM, Miller, Michael D (Rosetta) wrote: hi junmin, that's great work, if i could get a copy of the presentation when it's ready, that would be much appreciated. hi don, a) There is thought to be a strong requirement to have=20 exactly one=20 MAGE-TAB parser in one body of code in one language that=20 can be used from=20 either a Java or a Perl programming environment. =20 Satisfying this requirement=20 would ensure that MAGE-TAB never destroys itself on the=20 shoals of disagreeing=20 acceptors. i think this is a great requirement, similar to the OMG compliancy section, but i have one caveat with the wording. yes, we definitely should have as a goal a definitive MAGE-TAB parser that has a mode that verifies that a set of files is MAGE-TAB compliant (including resolving the references between the files). And it should have a mode that developers could certainly use as the basis of their import implementation. exactly one=20 MAGE-TAB parser in one body of code in one language that=20 can be used from=20 either a Java or a Perl programming environment. =20 my caveat is that there is no problem having more than one, often for efficiency reasons for an application there would be a parser tuned to specific database schema and additional application rules for standard, compliant MAGE-TAB files (for instance, the application rules might restrict MAGE-TAB to require certain columns for the application that in general aren't required). i would change the wording to: exactly one official validating MAGE-TAB parser in one body of code in one language that=20 can also be used from=20 either a Java or a Perl programming environment by any import application. note that if it is in one language there will be by necessity, i think, a bit of an impedance using it in a different language. cheers, michael -----Original Message----- From: mge...@li...=20 =09 [mailto:mge...@li...] On Behalf=20 Of Junmin Liu Sent: Friday, March 23, 2007 9:17 AM To: Don Maier Cc: mged-mage2; MGED-mage Subject: Re: [Mged-mage2] MGED Jamboree next week - March 27-30! Hi, Don and Jamboree attendees, Since last Oct., for one of the requirement of our in-house=20 data loading=20 pipeline, we developed an extendable framework MR_Ti and a set of=20 toolkits to help loading MIAMI-compliant documents in=20 different formats=20 into our GUS schema. Chris has suggested me to present this on the=20 Jamboree to get feedback and to see if it can be useful to the=20 communities. Note MAGE-Tab is part of our pipeline, we have started to=20 generate and=20 load MAGE-Tabs to GUS, we will also like to show public the files we=20 have and make sure they are exchangable and compliant with=20 MAGE-Tab spec.=20 1.0 release. Thanks, ---junmin On Wed, 21 Mar 2007, Don Maier wrote: Hi friends, We're looking forward to seeing and meeting with you in=20 next week in sunny=20 California. Current forecasts are for a cloudy Tuesday,=20 but a sunny=20 remainder of the week in the upper 60's. Here's my current list of attendees and agenda. Please=20 let me know if you=20 wish to contribute any more bodies or agenda items! Regards, Don Maier MAGE Jamboree: March 27 - 30 Stanford University: Clark Center, Rm. 362 Attendees: 1) Cathy Ball (SMD) 2) Cate Beauheim (Stanford) 3) Alvis Brazma (EBI) 4) Steve Chervitz (Affymetrix) 5) Junmin Liu (U. Penn) 6) Don Maier (SMD) 7) Tim Rayner (EBI) 8) Ugis Sarkans (EBI) 9) Paul Spellman (Lawrence Berkeley National Laboratory) 10) Joe White (Dana-Farber/Harvard Cancer Center) Agenda: 1) Tim - Final version of MAGE-TAB 2) Alvis/Ugis - MAGE-TAB object model: a) Possible move to FUGE-TAB b) Discussion of basic concepts (no formal proposal yet). 3) Don - The "one-parser" requirement and how to satisfy=20 it for MAGE-TAB: a) There is thought to be a strong requirement to have=20 exactly one=20 MAGE-TAB parser in one body of code in one language that=20 can be used from=20 either a Java or a Perl programming environment. =20 Satisfying this requirement=20 would ensure that MAGE-TAB never destroys itself on the=20 shoals of disagreeing=20 acceptors. b) Proposal for how to satisfy this requirement. =09 ------------------------------------------------------------------------ - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash =09 http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDE V _______________________________________________ Mged-mage mailing list Mge...@li... https://lists.sourceforge.net/lists/listinfo/mged-mage =09 =09 |
From: Don M. <dM...@ge...> - 2007-03-23 17:05:12
|
Hi Junmin, As I mentioned, it will be great for us to have a chance to review =20 your work with processing MIAME-compliant documents of various sorts. Your concern about MAGE-TAB compliance ties directly into the agenda =20 item under my name: If we have one and only one parser (accepter) =20 for MAGE-TAB, then every question of compliance is settled once and =20 for everyone. Regards, Don Maier On Mar 23, 2007, at 9:16 AM, Junmin Liu wrote: > Hi, Don and Jamboree attendees, > Since last Oct., for one of the requirement of our in-house data =20 > loading pipeline, we developed an extendable framework MR_Ti and a =20 > set of toolkits to help loading MIAMI-compliant documents in =20 > different formats into our GUS schema. Chris has suggested me to =20 > present this on the Jamboree to get feedback and to see if it can =20 > be useful to the communities. > > Note MAGE-Tab is part of our pipeline, we have started to generate =20 > and load MAGE-Tabs to GUS, we will also like to show public the =20 > files we have and make sure they are exchangable and compliant with =20= > MAGE-Tab spec. 1.0 release. > > Thanks, > ---junmin > > > > On Wed, 21 Mar 2007, Don Maier wrote: > >> Hi friends, >> >> We're looking forward to seeing and meeting with you in next week =20 >> in sunny California. Current forecasts are for a cloudy Tuesday, =20= >> but a sunny remainder of the week in the upper 60's. >> >> Here's my current list of attendees and agenda. Please let me =20 >> know if you wish to contribute any more bodies or agenda items! >> >> Regards, >> Don Maier >> >> >> MAGE Jamboree: March 27 - 30 >> Stanford University: Clark Center, Rm. 362 >> >> Attendees: >> >> 1) Cathy Ball (SMD) >> 2) Cate Beauheim (Stanford) >> 3) Alvis Brazma (EBI) >> 4) Steve Chervitz (Affymetrix) >> 5) Junmin Liu (U. Penn) >> 6) Don Maier (SMD) >> 7) Tim Rayner (EBI) >> 8) Ugis Sarkans (EBI) >> 9) Paul Spellman (Lawrence Berkeley National Laboratory) >> 10) Joe White (Dana-Farber/Harvard Cancer Center) >> >> >> Agenda: >> >> 1) Tim =96 Final version of MAGE-TAB >> >> 2) Alvis/Ugis =96 MAGE-TAB object model: >> >> a) Possible move to FUGE-TAB >> >> b) Discussion of basic concepts (no formal proposal yet). >> >> 3) Don =96 The =93one-parser=94 requirement and how to satisfy it = for =20 >> MAGE-TAB: >> >> a) There is thought to be a strong requirement to have exactly =20= >> one MAGE-TAB parser in one body of code in one language that can =20 >> be used from either a Java or a Perl programming environment. =20 >> Satisfying this requirement would ensure that MAGE-TAB never =20 >> destroys itself on the shoals of disagreeing acceptors. >> >> b) Proposal for how to satisfy this requirement. > ----------------------------------------------------------------------=20= > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to =20 > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?=20 > page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV____________________________= ____=20 > _______________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage Don Maier Sr. Software Designer/Research Dept. of Biochemistry Stanford University School of Medicine |
From: Helen P. <par...@eb...> - 2007-03-23 17:18:30
|
I suggest that we do some round tripping of MAGETAB. Don Maier wrote: > Hi Junmin, > > As I mentioned, it will be great for us to have a chance to review > your work with processing MIAME-compliant documents of various sorts. > > Your concern about MAGE-TAB compliance ties directly into the agenda > item under my name: If we have one and only one parser (accepter) for > MAGE-TAB, then every question of compliance is settled once and for > everyone. > > Regards, > Don Maier > > > On Mar 23, 2007, at 9:16 AM, Junmin Liu wrote: > >> Hi, Don and Jamboree attendees, >> Since last Oct., for one of the requirement of our in-house data >> loading pipeline, we developed an extendable framework MR_Ti and a >> set of toolkits to help loading MIAMI-compliant documents in >> different formats into our GUS schema. Chris has suggested me to >> present this on the Jamboree to get feedback and to see if it can be >> useful to the communities. >> >> Note MAGE-Tab is part of our pipeline, we have started to generate >> and load MAGE-Tabs to GUS, we will also like to show public the files >> we have and make sure they are exchangable and compliant with >> MAGE-Tab spec. 1.0 release. >> >> Thanks, >> ---junmin >> >> >> >> On Wed, 21 Mar 2007, Don Maier wrote: >> >>> Hi friends, >>> >>> We're looking forward to seeing and meeting with you in next week in >>> sunny California. Current forecasts are for a cloudy Tuesday, but a >>> sunny remainder of the week in the upper 60's. >>> >>> Here's my current list of attendees and agenda. Please let me know >>> if you wish to contribute any more bodies or agenda items! >>> >>> Regards, >>> Don Maier >>> >>> >>> MAGE Jamboree: March 27 - 30 >>> Stanford University: Clark Center, Rm. 362 >>> >>> Attendees: >>> >>> 1) Cathy Ball (SMD) >>> 2) Cate Beauheim (Stanford) >>> 3) Alvis Brazma (EBI) >>> 4) Steve Chervitz (Affymetrix) >>> 5) Junmin Liu (U. Penn) >>> 6) Don Maier (SMD) >>> 7) Tim Rayner (EBI) >>> 8) Ugis Sarkans (EBI) >>> 9) Paul Spellman (Lawrence Berkeley National Laboratory) >>> 10) Joe White (Dana-Farber/Harvard Cancer Center) >>> >>> >>> Agenda: >>> >>> 1) Tim – Final version of MAGE-TAB >>> >>> 2) Alvis/Ugis – MAGE-TAB object model: >>> >>> a) Possible move to FUGE-TAB >>> >>> b) Discussion of basic concepts (no formal proposal yet). >>> >>> 3) Don – The “one-parser” requirement and how to satisfy it for >>> MAGE-TAB: >>> >>> a) There is thought to be a strong requirement to have exactly one >>> MAGE-TAB parser in one body of code in one language that can be used >>> from either a Java or a Perl programming environment. Satisfying >>> this requirement would ensure that MAGE-TAB never destroys itself on >>> the shoals of disagreeing acceptors. >>> >>> b) Proposal for how to satisfy this requirement. >> ------------------------------------------------------------------------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys-and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV_______________________________________________ >> <http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV_______________________________________________> >> Mged-mage mailing list >> Mge...@li... <mailto:Mge...@li...> >> https://lists.sourceforge.net/lists/listinfo/mged-mage > > Don Maier > Sr. Software Designer/Research > Dept. of Biochemistry > Stanford University School of Medicine > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > ------------------------------------------------------------------------ > > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > -- Helen Parkinson, PhD Curation Coordinator Microarray Informatics Team, EBI EBI 01223 494672 Skype: helen.parkinson.ebi |
From: Chris S. <sto...@pc...> - 2007-03-23 17:57:02
|
Great idea. Chris On Mar 23, 2007, at 1:18 PM, Helen Parkinson wrote: > I suggest that we do some round tripping of MAGETAB. > > Don Maier wrote: >> Hi Junmin, >> >> As I mentioned, it will be great for us to have a chance to review >> your work with processing MIAME-compliant documents of various sorts. >> >> Your concern about MAGE-TAB compliance ties directly into the agenda >> item under my name: If we have one and only one parser (accepter) for >> MAGE-TAB, then every question of compliance is settled once and for >> everyone. >> >> Regards, >> Don Maier >> >> >> On Mar 23, 2007, at 9:16 AM, Junmin Liu wrote: >> >>> Hi, Don and Jamboree attendees, >>> Since last Oct., for one of the requirement of our in-house data >>> loading pipeline, we developed an extendable framework MR_Ti and a >>> set of toolkits to help loading MIAMI-compliant documents in >>> different formats into our GUS schema. Chris has suggested me to >>> present this on the Jamboree to get feedback and to see if it can be >>> useful to the communities. >>> >>> Note MAGE-Tab is part of our pipeline, we have started to generate >>> and load MAGE-Tabs to GUS, we will also like to show public the =20 >>> files >>> we have and make sure they are exchangable and compliant with >>> MAGE-Tab spec. 1.0 release. >>> >>> Thanks, >>> ---junmin >>> >>> >>> >>> On Wed, 21 Mar 2007, Don Maier wrote: >>> >>>> Hi friends, >>>> >>>> We're looking forward to seeing and meeting with you in next =20 >>>> week in >>>> sunny California. Current forecasts are for a cloudy Tuesday, but a >>>> sunny remainder of the week in the upper 60's. >>>> >>>> Here's my current list of attendees and agenda. Please let me know >>>> if you wish to contribute any more bodies or agenda items! >>>> >>>> Regards, >>>> Don Maier >>>> >>>> >>>> MAGE Jamboree: March 27 - 30 >>>> Stanford University: Clark Center, Rm. 362 >>>> >>>> Attendees: >>>> >>>> 1) Cathy Ball (SMD) >>>> 2) Cate Beauheim (Stanford) >>>> 3) Alvis Brazma (EBI) >>>> 4) Steve Chervitz (Affymetrix) >>>> 5) Junmin Liu (U. Penn) >>>> 6) Don Maier (SMD) >>>> 7) Tim Rayner (EBI) >>>> 8) Ugis Sarkans (EBI) >>>> 9) Paul Spellman (Lawrence Berkeley National Laboratory) >>>> 10) Joe White (Dana-Farber/Harvard Cancer Center) >>>> >>>> >>>> Agenda: >>>> >>>> 1) Tim =96 Final version of MAGE-TAB >>>> >>>> 2) Alvis/Ugis =96 MAGE-TAB object model: >>>> >>>> a) Possible move to FUGE-TAB >>>> >>>> b) Discussion of basic concepts (no formal proposal yet). >>>> >>>> 3) Don =96 The =93one-parser=94 requirement and how to satisfy it = for >>>> MAGE-TAB: >>>> >>>> a) There is thought to be a strong requirement to have exactly one >>>> MAGE-TAB parser in one body of code in one language that can be =20 >>>> used >>>> from either a Java or a Perl programming environment. Satisfying >>>> this requirement would ensure that MAGE-TAB never destroys =20 >>>> itself on >>>> the shoals of disagreeing acceptors. >>>> >>>> b) Proposal for how to satisfy this requirement. >>> --------------------------------------------------------------------=20= >>> ----- >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to >>> share your >>> opinions on IT & business topics through brief surveys-and earn cash >>> http://www.techsay.com/default.php?=20 >>> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV__________________________= ____=20 >>> _________________ >>> <http://www.techsay.com/default.php?=20 >>> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV__________________________= ____=20 >>> _________________> >>> Mged-mage mailing list >>> Mge...@li... <mailto:Mged-=20 >>> ma...@li...> >>> https://lists.sourceforge.net/lists/listinfo/mged-mage >> >> Don Maier >> Sr. Software Designer/Research >> Dept. of Biochemistry >> Stanford University School of Medicine >> >> >> ---------------------------------------------------------------------=20= >> --- >> >> ---------------------------------------------------------------------=20= >> ---- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to =20 >> share your >> opinions on IT & business topics through brief surveys-and earn cash >> http://www.techsay.com/default.php?=20 >> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV >> ---------------------------------------------------------------------=20= >> --- >> >> _______________________________________________ >> Mged-mage mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage >> > > --=20 > Helen Parkinson, PhD > Curation Coordinator > Microarray Informatics Team, > EBI > > EBI 01223 494672 > Skype: helen.parkinson.ebi > > > ----------------------------------------------------------------------=20= > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to =20 > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?=20 > page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Don M. <dM...@ge...> - 2007-03-23 23:46:41
|
Here's a revised list of bodies and topics for our meeting: =EF=BF=BC Also attached is a description (complete with working code!) of the =20 "One-Parser" proposal that generated a bit of animated (and perhaps =20 premature) discussion today: =EF=BF=BC Regards, Don M. P.S. A previous attempt to send this was clothelined by the 100 kb. =20 message limit. Hence the display html. On Mar 21, 2007, at 3:13 PM, Don Maier wrote: > Hi friends, > > We're looking forward to seeing and meeting with you in next week =20 > in sunny California. Current forecasts are for a cloudy Tuesday, =20 > but a sunny remainder of the week in the upper 60's. > > Here's my current list of attendees and agenda. Please let me =20 > know if you wish to contribute any more bodies or agenda items! > > Regards, > Don Maier > > > MAGE Jamboree: March 27 - 30 > Stanford University: Clark Center, Rm. 362 > > Attendees: > > 1) Cathy Ball (SMD) > 2) Cate Beauheim (Stanford) > 3) Alvis Brazma (EBI) > 4) Steve Chervitz (Affymetrix) > 5) Junmin Liu (U. Penn) > 6) Don Maier (SMD) > 7) Tim Rayner (EBI) > 8) Ugis Sarkans (EBI) > 9) Paul Spellman (Lawrence Berkeley National Laboratory) > 10) Joe White (Dana-Farber/Harvard Cancer Center) > > > Agenda: > > 1) Tim =E2=80=93 Final version of MAGE-TAB > > 2) Alvis/Ugis =E2=80=93 MAGE-TAB object model: > > a) Possible move to FUGE-TAB > > b) Discussion of basic concepts (no formal proposal yet). > > 3) Don =E2=80=93 The =E2=80=9Cone-parser=E2=80=9D requirement and = how to satisfy it =20 > for MAGE-TAB: > > a) There is thought to be a strong requirement to have exactly =20 > one MAGE-TAB parser in one body of code in one language that can be =20= > used from either a Java or a Perl programming environment. =20 > Satisfying this requirement would ensure that MAGE-TAB never =20 > destroys itself on the shoals of disagreeing acceptors. > > b) Proposal for how to satisfy this requirement. |
From: Tim R. <ra...@eb...> - 2007-03-23 11:56:16
|
Hi, I'm pleased to be able to announce the initial release of our MAGE-TAB parser on SourceForge. The parsing scripts, implemented in Perl, are currently rather alpha-grade (or beta if you're charitable). The code is available from the following web page: http://sourceforge.net/project/showfiles.php?group_id=120325&package_id=149795&release_id=495838 The scripts are included in the Tab2MAGE development package, version 1.9.7. Installation and usage instructions are included with the download (see also this link: http://tab2mage.sourceforge.net/#magetab). We have also made available an early release of a script, written by Faisal Rezwan in our group, which can be used to convert Tab2MAGE spreadsheets into MAGE-TAB IDF and SDRF documents: http://sourceforge.net/project/showfiles.php?group_id=120325&package_id=226041&release_id=495679 Cheers, Tim -- Tim Rayner ArrayExpress |
From: Junmin L. <ju...@pc...> - 2007-03-23 15:18:51
|
Hi, Tim and all, We, here in CBIL, also developed a suite of toolkit for MAGE-Tab, actually potentially for any kind of MIAMI-complianct mage doc including MAGE-ML, SOFT and MAGE-Tab. Included in the toolkit are parsers for mage-ml, mage-tab, soft (soon to completed), writers for mage-tab, mage-ml, soft (need to implemented), conversion,visualization and validation tool, GUI interface on top of those tools. Note we developed a simple object model for consuming the mage-tab, the mage-tab reader will deserialize the mage-tab into the objects. And I understand there are similar agenda items on stanford workshop for these.. The mage2tab we put on tab2mage sourceforge site is part of the toolkit. We already heavily use the toolkit as part of data loading pipeline. We will figure out how to release the toolkit very soon. ---junmin On Fri, 23 Mar 2007, Tim Rayner wrote: > Hi, > > I'm pleased to be able to announce the initial release of our MAGE-TAB > parser on SourceForge. The parsing scripts, implemented in Perl, are > currently rather alpha-grade (or beta if you're charitable). The code is > available from the following web page: > > http://sourceforge.net/project/showfiles.php?group_id=120325&package_id=149795&release_id=495838 > > The scripts are included in the Tab2MAGE development package, version > 1.9.7. Installation and usage instructions are included with the download > (see also this link: http://tab2mage.sourceforge.net/#magetab). > > We have also made available an early release of a script, written by > Faisal Rezwan in our group, which can be used to convert Tab2MAGE > spreadsheets into MAGE-TAB IDF and SDRF documents: > > http://sourceforge.net/project/showfiles.php?group_id=120325&package_id=226041&release_id=495679 > > Cheers, > > Tim > > -- > Tim Rayner > ArrayExpress > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > |
From: Tim R. <ra...@eb...> - 2007-03-23 15:32:41
|
Hi Junmin, Thanks for the email; just a quick question - is there an updated version of the mage2tab code you would like us to put on the SF page before the jamboree? I think the latest version we have is 0.6. Cheers, Tim On Fri, 23 Mar 2007, Junmin Liu wrote: > Hi, Tim and all, > We, here in CBIL, also developed a suite of toolkit for MAGE-Tab, actually > potentially for any kind of MIAMI-complianct mage doc including MAGE-ML, > SOFT and MAGE-Tab. > > Included in the toolkit are parsers for mage-ml, mage-tab, soft (soon to > completed), writers for mage-tab, mage-ml, soft (need to implemented), > conversion,visualization and validation tool, GUI interface on top of > those tools. > > Note we developed a simple object model for consuming the mage-tab, the > mage-tab reader will deserialize the mage-tab into the objects. And I > understand there are similar agenda items on stanford workshop for these.. > > The mage2tab we put on tab2mage sourceforge site is part of the toolkit. > We already heavily use the toolkit as part of data loading pipeline. We > will figure out how to release the toolkit very soon. > > ---junmin > > On Fri, 23 Mar 2007, Tim Rayner wrote: > >> Hi, >> >> I'm pleased to be able to announce the initial release of our MAGE-TAB >> parser on SourceForge. The parsing scripts, implemented in Perl, are >> currently rather alpha-grade (or beta if you're charitable). The code is >> available from the following web page: >> >> http://sourceforge.net/project/showfiles.php?group_id=120325&package_id=149795&release_id=495838 >> >> The scripts are included in the Tab2MAGE development package, version >> 1.9.7. Installation and usage instructions are included with the download >> (see also this link: http://tab2mage.sourceforge.net/#magetab). >> >> We have also made available an early release of a script, written by >> Faisal Rezwan in our group, which can be used to convert Tab2MAGE >> spreadsheets into MAGE-TAB IDF and SDRF documents: >> >> http://sourceforge.net/project/showfiles.php?group_id=120325&package_id=226041&release_id=495679 >> >> Cheers, >> >> Tim >> >> -- >> Tim Rayner >> ArrayExpress >> >> ------------------------------------------------------------------------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to share your >> opinions on IT & business topics through brief surveys-and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Mged-mage mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage >> > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > |
From: Junmin L. <ju...@pc...> - 2007-03-23 16:19:23
|
Hi, Tim, Upon we release MAGE-Tab 1.0 spec in Stanford, I will make sure the mage2tab converter will be upgraded and generate the right MAGE-Tab. Thanks, ---junmin On Fri, 23 Mar 2007, Tim Rayner wrote: > Hi Junmin, > > Thanks for the email; just a quick question - is there an updated version of > the mage2tab code you would like us to put on the SF page before the > jamboree? I think the latest version we have is 0.6. > > Cheers, > > Tim > > On Fri, 23 Mar 2007, Junmin Liu wrote: > >> Hi, Tim and all, >> We, here in CBIL, also developed a suite of toolkit for MAGE-Tab, actually >> potentially for any kind of MIAMI-complianct mage doc including MAGE-ML, >> SOFT and MAGE-Tab. >> >> Included in the toolkit are parsers for mage-ml, mage-tab, soft (soon to >> completed), writers for mage-tab, mage-ml, soft (need to implemented), >> conversion,visualization and validation tool, GUI interface on top of >> those tools. >> >> Note we developed a simple object model for consuming the mage-tab, the >> mage-tab reader will deserialize the mage-tab into the objects. And I >> understand there are similar agenda items on stanford workshop for these.. >> >> The mage2tab we put on tab2mage sourceforge site is part of the toolkit. >> We already heavily use the toolkit as part of data loading pipeline. We >> will figure out how to release the toolkit very soon. >> >> ---junmin >> >> On Fri, 23 Mar 2007, Tim Rayner wrote: >> >>> Hi, >>> >>> I'm pleased to be able to announce the initial release of our MAGE-TAB >>> parser on SourceForge. The parsing scripts, implemented in Perl, are >>> currently rather alpha-grade (or beta if you're charitable). The code is >>> available from the following web page: >>> >>> http://sourceforge.net/project/showfiles.php?group_id=120325&package_id=149795&release_id=495838 >>> >>> The scripts are included in the Tab2MAGE development package, version >>> 1.9.7. Installation and usage instructions are included with the download >>> (see also this link: http://tab2mage.sourceforge.net/#magetab). >>> >>> We have also made available an early release of a script, written by >>> Faisal Rezwan in our group, which can be used to convert Tab2MAGE >>> spreadsheets into MAGE-TAB IDF and SDRF documents: >>> >>> http://sourceforge.net/project/showfiles.php?group_id=120325&package_id=226041&release_id=495679 >>> >>> Cheers, >>> >>> Tim >>> >>> -- >>> Tim Rayner >>> ArrayExpress >>> >>> ------------------------------------------------------------------------- >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to share >>> your >>> opinions on IT & business topics through brief surveys-and earn cash >>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >>> _______________________________________________ >>> Mged-mage mailing list >>> Mge...@li... >>> https://lists.sourceforge.net/lists/listinfo/mged-mage >>> >> >> ------------------------------------------------------------------------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to share >> your >> opinions on IT & business topics through brief surveys-and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Mged-mage mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage >> > |