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From: Kjell P. <Kje...@bc...> - 2006-09-12 00:34:49
|
Summary day 2 of Seattle Jam. Here is todays summary of work in the group working on developing a standard DB schema for the MO as part of the MAGEstk. Cheers, K. |
From: Steve C. <Ste...@af...> - 2006-09-11 19:31:32
|
For the record, the answer is yes, as confirmed by discussion amongst folks here at the jamboree. To check the code out, go the the 'Subversion' link right next to the 'CVS' link at the top of the SF project page. It takes you here: http://sourceforge.net/svn/?group_id=16076 To check something out, say MAGE-Perl, execute this command: svn co https://svn.sourceforge.net/svnroot/mged/MAGE-Perl MAGE-Perl The last thing on the command line is the name of the local directory where you want the check out to go. Authentication uses https rather than ssh-keys (I think), so if you first login to your account on SF, the check out will proceed without trouble. A project admin needs to grant other developers SVN write acces. I did this for a few folks I deemed as still current. Anyone else who wants it can send a message to any admin requesting it. Cheers, Steve > From: Steve Chervitz <Ste...@af...> > Date: Mon, 11 Sep 2006 11:19:50 -0700 > To: Jason Stewart <jas...@gm...>, Adam Witney > <aw...@sg...> > Cc: <mge...@li...> > Conversation: [Mged-Jamboree] [Mged-mage] SVN on SF now active > Subject: Re: [Mged-Jamboree] [Mged-mage] SVN on SF now active > > So is the CVS repository now considered closed, at least for MAGE-Perl and > www? > > Seems best to go with one or the other but not try to keep both in sync. > > Cheers, > Steve > > >> From: Jason Stewart <jas...@gm...> >> Date: Mon, 11 Sep 2006 10:58:02 +0530 >> To: Adam Witney <aw...@sg...> >> Cc: <mge...@li...> >> Subject: Re: [Mged-Jamboree] [Mged-mage] SVN on SF now active >> >> Hey Adam, >> >> On 9/11/06, Adam Witney <aw...@sg...> wrote: >>> >>> Hi Jason, >>> >>> I am at the MGED Jamboree in seattle, and have just been trying to check >>> out the www module from SVN however the software directory >>> (www/software) seems to be missing. did this get missed in the import or >>> has it been moved elsewhere? >>> >> >> Hmmmm..... >> >> If it isn't there, it is because it didn't get imported. >> >> I haven't moved anything around yet except the MAGE-Perl stuff. >> >> I have a bit of a problem because of my slow india connection. The >> www/ directory was *really* big, and so I imported everything from an >> offsite machine in the US. Somehow my tarball must have excluded the >> www/software/ dir. >> >> Can you commit it? To do so I have to activate you for commit on SVN. >> >> You've got to go to the members admin page: >> >> https://sourceforge.net/project/admin/userperms.php?group_id=16076 >> >> and give any developer SVN commit privelege. I just activated you, but >> you will have to grant it to others (you are an admin, after all ;-). >> >> Cheers, jas. >> >> ------------------------------------------------------------------------- >> Using Tomcat but need to do more? Need to support web services, security? >> Get stuff done quickly with pre-integrated technology to make your job easier >> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >> _______________________________________________ >> Mged-jamboree mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-jamboree > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Mged-jamboree mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-jamboree |
From: Steve C. <Ste...@af...> - 2006-09-11 18:20:07
|
So is the CVS repository now considered closed, at least for MAGE-Perl and www? Seems best to go with one or the other but not try to keep both in sync. Cheers, Steve > From: Jason Stewart <jas...@gm...> > Date: Mon, 11 Sep 2006 10:58:02 +0530 > To: Adam Witney <aw...@sg...> > Cc: <mge...@li...> > Subject: Re: [Mged-Jamboree] [Mged-mage] SVN on SF now active > > Hey Adam, > > On 9/11/06, Adam Witney <aw...@sg...> wrote: >> >> Hi Jason, >> >> I am at the MGED Jamboree in seattle, and have just been trying to check >> out the www module from SVN however the software directory >> (www/software) seems to be missing. did this get missed in the import or >> has it been moved elsewhere? >> > > Hmmmm..... > > If it isn't there, it is because it didn't get imported. > > I haven't moved anything around yet except the MAGE-Perl stuff. > > I have a bit of a problem because of my slow india connection. The > www/ directory was *really* big, and so I imported everything from an > offsite machine in the US. Somehow my tarball must have excluded the > www/software/ dir. > > Can you commit it? To do so I have to activate you for commit on SVN. > > You've got to go to the members admin page: > > https://sourceforge.net/project/admin/userperms.php?group_id=16076 > > and give any developer SVN commit privelege. I just activated you, but > you will have to grant it to others (you are an admin, after all ;-). > > Cheers, jas. > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Mged-jamboree mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-jamboree |
From: Jason S. <jas...@gm...> - 2006-09-11 05:34:52
|
Hey Adam, On 9/11/06, Adam Witney <aw...@sg...> wrote: > > Hi Jason, > > I am at the MGED Jamboree in seattle, and have just been trying to check > out the www module from SVN however the software directory > (www/software) seems to be missing. did this get missed in the import or > has it been moved elsewhere? > Hmmmm..... If it isn't there, it is because it didn't get imported. I haven't moved anything around yet except the MAGE-Perl stuff. I have a bit of a problem because of my slow india connection. The www/ directory was *really* big, and so I imported everything from an offsite machine in the US. Somehow my tarball must have excluded the www/software/ dir. Can you commit it? To do so I have to activate you for commit on SVN. You've got to go to the members admin page: https://sourceforge.net/project/admin/userperms.php?group_id=16076 and give any developer SVN commit privelege. I just activated you, but you will have to grant it to others (you are an admin, after all ;-). Cheers, jas. |
From: Allen D. <all...@uc...> - 2005-09-11 12:07:12
|
Hi, I just realized I wasn't subscribed to the Jamboree list anymore. Well, I've resubscribed. How are we going to organize tasks; are we going to use the SF tracker again? I've thought of a few items to address in the OM and/or Perl SDK, and thought I'd make tickets on SF... if that's what we're doing. Kjell or Cathy? -Allen |
From: Stathis S. <si...@bi...> - 2005-09-11 09:52:31
|
ARG, horrific typo: should be "de facto". sorry about that |
From: Stathis S. <si...@bi...> - 2005-09-11 09:48:34
|
Hello all, In one of the previous jams I tried to expand OntologyHelper to include OWL support, but this was left unfinished. I have checked out the JavaGenerator module for the CVS but it seems that it does not contain anything OWL-related. I think the first step would be to sit down and merge the OWL-related code that I have to the current version of JavaGenerator (I'm a bit behind). Another thing: is Jena the defactor standard for OWL parsing? Thanks, Stathis |
From: Kjell P. <Kje...@bc...> - 2005-09-06 17:34:07
|
Hi all, I thought I should just drop a note to the list in case anyone subscribing can't make it this year :) If you have input on - needed functionality - other suggestions - etc for discussions / design / implementation at the jamboree, it will be much appreciated. Cheers, Kjell |
From: Angel P. <an...@ma...> - 2005-03-24 22:10:59
|
In short, we accomplished quite a bit in terms of the FuGE model. The mantra was more or less, if it's too hard to explain, then it isn't a good model. For some things such as n-dimensional data, a hard explaination is un-avoidable, in which case we opted for the easier solution, if sometimes not as elegant. In a lot of cases, classes that would tempt developers with forbidden fruit have been deleted from the model. Andy Jones is currently going through the model for a first round of fine-grained evaluation of cardinalities and inheritence. A WG report will be coming out shortly to put FuGE in a context that readily explains the relationships between modules, with furhter in-depth discussion on those modules that are critical to interepret the biologists use cases. Currently, all of the files are hosted on my delagoya.com/fuge site, which is not optimal. We will be mmoving to a SF.net site soon. Many thanks for all your hard work. I am very excitied about our progress and expect a full release (if provisional) of FuGE within the next few months. I think as it stands, it has an excellent chance of being accepted by the Func Gen community at large. -angel |
From: Angel P. <an...@ma...> - 2005-03-23 23:50:38
|
Uh, there are about three of us sitting in the big room being very silent, so if one of the other groups is cramped, please come keep us company -angel |
From: Catherine B. <ba...@ge...> - 2005-03-23 20:08:52
|
The dude is setting up right now. Salad today. |
From: Angel P. <an...@ma...> - 2005-03-22 23:13:03
|
coffe man brought some just now for those that need it. -angel |
From: Catherine B. <ba...@ge...> - 2005-03-21 20:01:15
|
Hi Jamboree'ers, If you got this message but are not participating in the Jamboree, read no further -- you'll only feel sad and left out. The wine tasting tonight (Monday night) will commence at approximately 6 pm in the Community Building of Stanford West Apartments (700 Clark Way, Palo Alto). Stanford West is an easy 10-15 minute walk from CCSR (but please be careful jaywalking across Sand Hill Road). I have made an ugly web page with three maps: a MapQuest map, a Stanford Map, and an anal-retentive zoomed view of the Stanford map. On the MapQuest picture, the Community Building is indicated by the star. On the Stanford map, the building where we're having the jamboree (Center for Clinical Science Research or CCSR) is located at coordinates E-5 and the Stanford West Community Building is located at coordinates right at the boundary of A-4 and B-4. The anal-retentive map shows you the approximate walking path (follow the tracks) from CCSR (marked with a blue star) to the Stanford West Community Building (marked with a yellow rubber ducky). There is parking available in the parking lot near the Community Building. I'll print out a few copies of the map if anyone wants one. The URL is: http://genetics.stanford.edu/~ball/wine.html The important part of the evening is the wine -- we will be tasting barrel samples made from single grape varieties (red and white) and then comparing them to the blended wine that the winery sells. All wines are from Tablas Creek Vineyard, an organic vineyard and winery in Paso Robles, California. For the curious, you can learn more about Tablas Creek by visiting their URL: http://www.tablascreek.com/ Hope to see you there (and if you haven't chipped in your $20US, please feel free to do so soon)! Cheers, Cathy |
From: Tina B. <bou...@ge...> - 2005-01-28 20:47:08
|
Hi All, I am going to close the registration for the jamboree, as we are already at 24 people registered, and the is our maximum capacity for the room. I have went off the descriptions of what everyone has said they would like to work on at the jamboree and I have made 4 "working groups" and assigned a prospective group leader for each group, whom I hope can set a tentative agenda for what they feel should be accomplished during the jamboree, sorry guys, but you really wouldn't want me to make the agenda for MAGE2 :). Being in one group does not prohibit one from participating in other groups. The groups are as follows: MAGE2: leaders => Spellman and Miller Ugis Sarkans Juergen Lorenz Angel Pizarro John Moy Jeremy Gollub MAGEstk: leader => Kjell Peterson Joe White Ihad Awad Robert Byrnes Mohammad Shojatalab Niran Abeygunawardena Integration of ontologies into the MO: leaders => Joe White and Helen Parkinson Trish Whetzel Joe White Susanna Sansone Andrew Jones Cathy Ball Sumeet Muju Norman Morrison Web Services: leader => Derek Fowler Farrell Wymore Tina Boussard It would also be great if each group "leader" prepared a 15 minute presentation to start the jamboree off, with information on the "State of the Group" and what they want to get accomplished during the jamboree. If I have put you in the wrong group, please let me know. The following people did not say on their registration what they would like to do, so please let me know which group you would like to work with: Philippe Rocca-Serra John Moy Here is the schedule for the jamboree, although we can stay in the room until midnight if we like: Monday, March 21, 2005 from 8:00 am - 5:00 pm Tuesday, March 22, 2005 from 12:00 pm - 5:00 pm Wednesday, March 23, 2005 from 10:30 am - 5:00 pm Thursday, March 24, 2005 from 8:00 am - 5:00 pm On a happier note, we are trying to get some wine tasting set up for Wednesday evening and lunch and snacks will be provided! Looking forward to working with all of you, Tina Boussard |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2005-01-04 18:19:51
|
Hi Tina, Thanks for your work in setting this up. For those who might be interested, Ugis and I are working on the Query Service submission to the OMG and there should be a good working draft by the time the jamboree comes around. The plan is that there will be an abstract model for the query service and an implementation as a web service. Although MAGE is based on a dtd, since it will only be used as an input and output parameter in the query service api, that won't be a hindrance. I'd also like to see the ADF discussion be broadened to take in more areas--the current tools for BioAssays and Experiments are difficult to install unless you are a perl programmer and for BioAssays not really stand alone. cheers, Michael Michael Miller Lead Software Developer Rosetta Biosoftware mic...@ro... www.rosettabio.com > -----Original Message----- > From: own...@eb... > [mailto:own...@eb...] On Behalf Of Tina Boussard > Sent: Monday, January 03, 2005 10:03 AM > To: mge...@li...; > <mge...@li...>; 'mge...@eb...' > Subject: MGED programming jamboree > > > Hi Everyone, > > This is a reminder that The Stanford Microarray Database will > host the next > MGED Programming Jamboree at Stanford University from March > 21 through > March 24, 2005. > > I have set up a web page with a registration form here: > http://genome-www5.stanford.edu/mged/ As space is limited, please register so that we know how many people to expect. Registration deadline is March 1, 2005 and there will be no charge for attendance. So far, the proposed agenda items are listed below. Depending on attendance, we will try and prioritize the items that will most benefit the entire group. +Summary of conclusions reached in Toronto. +MAGE version 2 discussions +MAGE-ML ADFs +Integration of MAGE version 2 with the proposals from the Proteomics Standards Initiative (PSI-OM). +Integration of MGED Ontology and MAGEstk +MAGEstk Java discussions List of current registered participants: Joseph White Kjell Petersen Trish Whetzel Susanna Sansone Philippe Rocca-Serra Andrew Jones Jeremy Gollub Ihab Awad Please send any additional items that you want to be addressed at the jamboree to this mailing list. Also, please note we have not scheduled a tutorial for this jamboree, but a few have requested to give short presentations. Cheers, Tina Boussard =============================================== Tina Hernandez-Boussard, PhD Sr. Computational Biologist Stanford Microarray Database Stanford University School of Medicine CCSR 2255a Stanford, CA 94305 TEL: (650) 736-0077 FAX: (650) 724-3701 |
From: Tina B. <bou...@ge...> - 2005-01-03 18:02:50
|
Hi Everyone, This is a reminder that The Stanford Microarray Database will host the next MGED Programming Jamboree at Stanford University from March 21 through March 24, 2005. I have set up a web page with a registration form here: http://genome-www5.stanford.edu/mged/ As space is limited, please register so that we know how many people to expect. Registration deadline is March 1, 2005 and there will be no charge for attendance. So far, the proposed agenda items are listed below. Depending on attendance, we will try and prioritize the items that will most benefit the entire group. +Summary of conclusions reached in Toronto. +MAGE version 2 discussions +MAGE-ML ADFs +Integration of MAGE version 2 with the proposals from the Proteomics Standards Initiative (PSI-OM). +Integration of MGED Ontology and MAGEstk +MAGEstk Java discussions List of current registered participants: Joseph White Kjell Petersen Trish Whetzel Susanna Sansone Philippe Rocca-Serra Andrew Jones Jeremy Gollub Ihab Awad Please send any additional items that you want to be addressed at the jamboree to this mailing list. Also, please note we have not scheduled a tutorial for this jamboree, but a few have requested to give short presentations. Cheers, Tina Boussard =============================================== Tina Hernandez-Boussard, PhD Sr. Computational Biologist Stanford Microarray Database Stanford University School of Medicine CCSR 2255a Stanford, CA 94305 TEL: (650) 736-0077 FAX: (650) 724-3701 |
From: Gavin S. <she...@ge...> - 2005-01-03 16:25:53
|
Hi all, Here is a slightly amended version of the Toronto Jamboree report, with a URL for more information regarding the ADF format, that Steve Chervitz sent me, Cheers, Gavin |
From: Gavin S. <she...@ge...> - 2004-12-01 22:31:10
|
Hi all, Here is a report on what happened at the jamboree in Toronto - thanks to everyone who sent me their write-ups. Hopefully this will be useful in planning the next jamboree at Stanford. If you have any corrections, I'm happy to amend the document, Cheers, Gavin |
From: Gavin S. <she...@ge...> - 2004-06-08 15:06:08
|
Dear Jammers, Apologies if you get this twice (or more). I have volunteered (or been volunteered) to organize the MGED programming jamboree that will immediately follow MGED7 in Toronto this September (http://www.microarrays.ca/MGED7.html). From what I have heard of the recently finished jamboree at TIGR, I understand it was the most productive and well organized one thus far - hence I want to emulate Joe's success for the Toronto jamboree. Based on the outcome of the last jamboree (Joe's email below in case anyone didn't get a copy) could people send me their suggestions for what software should be the focus of the next jamboree. Also, if you are planning on being at the next jamboree, can you let me know what you want to volunteer for in terms of programming projects and duties, Many thanks, Gavin ________________________________________________________ Gavin Sherlock Dept. of Genetics Center for Clinical Sciences Research 269 Campus Drive, Room 2255b, Stanford, CA 94305-5120 Tel: 650 498 6012 Fax: 650 724 3701 > From: JW...@ti... > Subject: Summary of MAGE workshop at TIGR > Date: June 7, 2004 7:29:12 AM PDT > To: mge...@eb... > Cc: mge...@li... > > Hi Everyone, > > Attached is a summary of the work done at the recent jamboree at TIGR. > The meeting was successful in that we were able to produce several > tools that will--I think--be useful to users of MAGE-ML and the > MGEDOntology. These include: > > 1. MGEDOntologyHelper: perl modules and java classes that produce > MAGE-ML for OntologyEntry using policies set forth by the Ontology > Working Group. These classes are currently functional prototypes. > 2. MGEDOntology_parser.pl: this perl script will parse both OWL and > DAML files. The script is based on the Redland RDF reader. > 3. BioMoby Web service: initial plans for a BioMoby MGEDOntology web > service were made. > 4. MO Term Tracker: will be set up at CBIL to manage term submissions > to MGEDOntology > 5. Standalone ADF converter: simplified ArrayDesign format. > > In addition, progress was made in MAGE v2 model discussions (details > in attachment). > > The software produced for the Perl and Java APIs is now in cvs.sf.net. > (See attachment for locations.) > > If you have questions, please let me know. > > Joe White > TIGR > |
From: Joseph X. <jx...@bm...> - 2004-06-04 01:07:26
|
From: <jul...@la...> - 2003-09-12 12:51:20
|
Hi there,=0D=0ADoes someone have the Howto for installing MAGE-java on wi= ndows?=0D=0AI'd like to work on it this week, so good time for testing th= e=0D=0Ahowto by installing MAGE-stk on my computer.=0D=0AThanks,=0D=0A=0D= =0A--------------------------------------------------=0D=0AJulien Bauer=0D= =0ABioinformatics Research Assistant =0D=0AHuman Molecular Genetics Group= =0D=0ADepartment of Pathology=0D=0AUniversity of Cambridge, Tennis Court = Road=0D=0ACambridge CB2 1QP UK=0D=0Amailto: jb...@ca...=0D=0A--------= ------------------------------------------=0A=0AAcc=E9dez au courrier =E9= lectronique de La Poste : www.laposte.net ; =0A3615 LAPOSTENET (0,34=80/m= n) ; t=E9l : 08 92 68 13 50 (0,34=80/mn)=0A=0A |
From: Steve C. <ste...@af...> - 2003-09-09 01:35:20
|
[I sent this message earlier today, but it bounced due to a 'Temporary local problem' at mail.sourceforge.net. Trying again...] Here's a message from Jason relevant for all. -Steve From: ja...@op... (Jason E. Stewart) Date: Mon Sep 8, 2003 07:16:02 Europe/Paris To: Steve Chervitz <ste...@af...> Cc: ja...@op... (Jason E. Stewart) Subject: Re: XML::Xerces on OSX... Update Steve Chervitz <ste...@af...> writes: > On Sunday, Sep 7, 2003, at 17:53 Europe/Paris, Jason E. Stewart wrote: > >> Steve Chervitz <ste...@af...> writes: >> >>> I noticed that your DOMParse module that is in the XML::Xerces-1.7.0 >>> isn't included in XML::Xerces-2.3.0. Was this intentional? >> >> Yes. 2.0 introduced the XML::Xerces::DOMWriter that does all this. The >> one drawback is that pretty printing doesn't seem to be working, >> still. >> >> There's a lot of XML pretty printers out there though, so it's not a >> big deal. >> >> see t/DOMWriter.t for instructions > > The reason I ask is that utils/XMI.pm in MAGE-Perl still depends on > the old DOMParse: > > > $self->{parser} = XML::Xerces::DOMParser->new(); > > Also, the DOM examples at http://xml.apache.org/xerces-p/samples.html > don't work. Yes, I know - thanks. Xerces and MAGEstk are two projects that are severely suffering because I don't have any funding to work on them. If I could gather even a minor amount of funding to polish them up, they'd both be top-notch pieces of software - but, I can't convince myself to work on them because when I have hacking time I need to spend it doing things that help pay the bills... > FYI: Folks are pretty much calling it quits for the day > today. Tomorrow is the last day of the jamboree. I'm heading out in > the AM, so I won't be there. Angel is also taking off. But some other > perl folks will be here tomorrow. Two days was a very short agenda, but I'm grateful so many people turned up to help - it would be great if people could stay active and organized *after* the jamboree. That way MAGEstk could still progress forward outside the jamboree's. jas. |
From: Mohammad s. <sh...@eb...> - 2003-09-07 12:42:47
|
Hi All, I've sent a simple patch for Perl API (Writer.pm) but it might be applicable for Java API as well. This is what I've been using at EBI and its useful for generating the 'dataFormat' attribute in MAGE-ML file. Mohammad |
From: Kjell P. <kj...@ii...> - 2003-09-07 10:14:08
|
Heres my updated build.xml file. K. -- Kjell Petersen Researcher Computational Biology Unit Bioinformatics group Bergen Center for Computational Science Department of Informatics Unifob A/S University of Bergen |
From: SourceForge.net <no...@so...> - 2003-09-07 09:16:37
|
Feature Requests item #801906, was opened at 2003-09-07 02:04 Message generated for change (Comment added) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=366076&aid=801906&group_id=16076 Category: None Group: None Status: Open Priority: 5 Submitted By: Allen Day (allenday) Assigned to: Nobody/Anonymous (nobody) Summary: bioperl / mage bridges Initial Comment: write adaptors for MAGE->bioperl (SAX event handlers for reader) and bioperl->MAGE (easier) ---------------------------------------------------------------------- >Comment By: Jason E. Stewart (jason_e_stewart) Date: 2003-09-07 02:44 Message: Logged In: YES user_id=85550 Hey Allen, What are the relevant parts of BioPerl that overlap with MAGE. Not that I'm skeptical, I'd just like to know where the main focus lies. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=366076&aid=801906&group_id=16076 |