From midori at ebi.ac.uk Tue Oct 5 12:42:07 2004 From: midori at ebi.ac.uk (Midori Harris) Date: Tue Oct 5 12:41:25 2004 Subject: [MOBY-l] Standards and Ontologies for Functional Genomics Message-ID: Dear Colleague, This is a final reminder that registration is still open for the second conference on Standards and Ontologies for Functional Genomics (SOFG) Meeting, which will be held on October 23-26, 2004 in Philadelphia, PA USA. (You may disregard the Sept. 23 deadline mentioned in the original announcement, which appears below.) http://www.jax.org/courses/events/coursedetails.do?id=44 We apologize if you receive multiple copies of this mail via different lists. ---------- Original SOFG 2 Announcement ---------- Dear Colleague, Registration Is Open for the 2nd Standards and Ontologies for Functional Genomics Meeting to be held at the University of Pennsylvania, Philadelphia, PA October 23-26, 2004 The 2nd Standards and Ontologies for Functional Genomics (SOFG) Meeting will be held on October 23-26, 2004 in Philadelphia, PA USA. Information about the SOFG meeting can be found at the SOFG site http://www.sofg.org/ or at http://www.jax.org/courses/events/coursedetails.do?id=44 . Registrations and abstracts will be accepted until Sept. 23, 2004 or until the event has filled. Student support to attend is available. Downloadable pdf registration form URL: http://www.jax.org/courses/2004/sfog_reg.pdf Abstracts submitted by Sept. 10 will be considered for oral presentation by Organizers and Session Chairs. Abstracts submitted after Sept 10 will be considered for poster session only. Abstract submissions will be reproduced and included with the conference notebook material. If you wish to submit, please follow the http://www.jax.org/courses/2004/functional_genomics_abstract_guidelines.html . The conference will focus on advances in the development of standards and ontologies to facilitate the exchange of biological information by computers and computation analysis applications. A particular emphasis will be on developments in ontological annotation systems for the genomics and bioinformatics communities. Toward this end, students and established investigators from different areas of computer science, experimental biology, and bioinformatics will have an opportunity to share new ideas, demonstrate new tools and applications, and identify potential collaborations. Topics include: * Ontological Systems: Theory and Development * Ontologies for Biology Systems * Ontology Systems Development: Electronic Demonstrations * Thesauri, Nomenclatures and the Biomedical Literature * Standards and Protocols * Functional Genomics Applications * From Resource to Application Plenary Speaker Carole Goble, University of Manchester Conference Organizers and Session Chairs: Judith Blake, The Jackson Laboratory Midori Harris, EBI-Hinxton Win Hide, SANBI Lynette Hirschman, MITRE Suzanna Lewis, UC Berkeley Helen Parkinson, EBI-Hinxton Martin Ringwald, The Jackson Laboratory Susanna-Assunta Sansone, EBI-Hinxton Chris Stoeckert, UPenn Please contact me with any questions about this meeting. Judi Alexander Medlin Lead Coordinator, Courses and Conferences The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6326 Fax: 207-288-6080 Please check out our web site http://www.jax.org/courses/events/current.do for the current listing of courses and conferences at The Jackson Laboratory. ----------------------------------------- ============================ Midori A. Harris, Ph.D. GO Editor EMBL - EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 (0) 1223 494667 Fax: +44 (0) 1223 494468 Email: midori@ebi.ac.uk From gss at ncgr.org Wed Oct 6 16:14:26 2004 From: gss at ncgr.org (Gary Schiltz) Date: Wed Oct 6 16:17:35 2004 Subject: [MOBY-l] Re: MOBY Meeting: 20-21 November in Santa Fe In-Reply-To: <415440E3.2070000@ncgr.org> References: <415440E3.2070000@ncgr.org> Message-ID: <41645222.1060907@ncgr.org> I've put information about the MOBY meeting on the Semantic MOBY web site - the URL is www.semanticmoby.org/meeting. It is currently missing a registration form, which I'll add by the end of the day. // Gary Gary Schiltz wrote: > Hello MOBY'ers! > > The next MOBY meeting will be held at NCGR (www.ncgr.org) in Santa Fe, > New Mexico, the weekend of 20-21 November, 2004. We'll finish by about > 3:00 MST on Sunday, so you could catch a flight as early as about > 5:30. Also, Mark Wilkinson will be giving a talk on MOBY Services at > NCGR on November 19 (some time in the afternoon, I believe); everyone > is welcome to attend, so consider coming a day early. I'll soon put > together a page of information with an agenda, links to accommodations > covering a range of prices, and other details. There will be a small > registration fee to cover breakfast and lunch for Saturday and Sunday. > > In the interim, please post suggestions for topics to cover at the > meeting. > > ---- > > Gary Schiltz > Principal Software Engineer > National Center for Genome Resources > Santa Fe, New Mexico > > gss@ncgr.org > 505-995-4414 (Work) > 505-670-5983 (Cell) > From tmo at ebi.ac.uk Thu Oct 7 03:40:15 2004 From: tmo at ebi.ac.uk (Tom Oinn) Date: Thu Oct 7 03:39:24 2004 Subject: [MOBY-l] Moby in workflows Message-ID: <4164F2DF.5050700@ebi.ac.uk> Hi all, I run the Taverna project (http://taverna.sf.net), a workflow design and enactment system which supports BioMoby and I figured it was time I de-lurked and started to pester you with questions, I hope you'll forgive me! I'd really just like to get a feel for whether people are using Taverna; if so for what and how could we improve it, and if not then why and how can we persuade you. I'm aware of a couple of shortcomings in our Moby support, there's an issue with empty results and we don't pick up annotations at all at the moment - it's the second of those that I'm curious about (we can sort the first out, it's mostly a technical issue). If you were chaining multiple service together how would the annotation information manifest in this flow? Cheers, Tom Oinn (EMBL-EBI) From markw at illuminae.com Thu Oct 7 04:25:25 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu Oct 7 04:24:42 2004 Subject: [MOBY-l] Moby in workflows In-Reply-To: <4164F2DF.5050700@ebi.ac.uk> References: <4164F2DF.5050700@ebi.ac.uk> Message-ID: <4164FD75.6000106@illuminae.com> Hi Tom, I know I'm going to see you next week anyway, but since I am sitting here in the myGrid lab and mapping out the next 12 months of myGrid/MOBY-S merging, I'd like to jump on this and express my pleasure that you have built MOBY-S support into Taverna. In addition, there has been considerable discussion that we (the Genome Canada bioinformatics platform grant) should spotlight Taverna as the "recommended" tool for interacting with web services for all genome centres nationwide - the advantage to us, of course, is that we then have a uniform landscape through which we can provide bioinformatics end-user service. An upcoming edition of our GC bioinformatics newsletter will do exactly that :-) Phil has indicated that additional MOBY-S support is being added to Taverna, so hopefully next week we can sit down over a pint and resolve the issues that remain foggy. Cheers! Mark Tom Oinn wrote: > Hi all, > > I run the Taverna project (http://taverna.sf.net), a workflow design > and enactment system which supports BioMoby and I figured it was time > I de-lurked and started to pester you with questions, I hope you'll > forgive me! > > I'd really just like to get a feel for whether people are using > Taverna; if so for what and how could we improve it, and if not then > why and how can we persuade you. I'm aware of a couple of shortcomings > in our Moby support, there's an issue with empty results and we don't > pick up annotations at all at the moment - it's the second of those > that I'm curious about (we can sort the first out, it's mostly a > technical issue). If you were chaining multiple service together how > would the annotation information manifest in this flow? > > Cheers, > > Tom Oinn (EMBL-EBI) > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From rebecca.ernst at gsf.de Thu Oct 7 07:01:41 2004 From: rebecca.ernst at gsf.de (Rebecca Ernst) Date: Thu Oct 7 07:01:08 2004 Subject: [MOBY-l] Moby in workflows In-Reply-To: <4164F2DF.5050700@ebi.ac.uk> References: <4164F2DF.5050700@ebi.ac.uk> Message-ID: <41652215.9000500@gsf.de> Hi Tom! Within the PlaNet project which aims to integrate European plant databases we are using BioMoby as the integration technology. We recently played with Taverna (Martin Senger told me that Taverna is 'mobyfied' now) and found it an amazingly good tool for building workflows! Since then we are certainly promoting it heavily! ;-) For making use of Taverna within the PlaNet project it would be perfect if there would be a possiblility of a standalone/non-interactive application of Taverna. e.g. we are building a portal through which people can access all our PlaNet databases (featured by BioMoby). It would be great if we could offer them to run several workflows which we built already without having to install Taverna on their machines. This would involve saving the workflows from Taverna, and then executing those saved workflows through e.g. a command-line call to Taverna. I don't know if you ever thought of this possibility!? Another thing which I realized : at the moment you will have to guess from the name of the service to his function. If I want to build a workflow integrating other peoples services as well, I need to know what exactly a service does. In BioMoby this is described on one hand in the human readable description and on the other hand by the input/output objects in Moby Central. Is this what you mean with annotation information? Or are you talking about the service notes? Cheers, Rebecca. Tom Oinn wrote: > Hi all, > > I run the Taverna project (http://taverna.sf.net), a workflow design > and enactment system which supports BioMoby and I figured it was time > I de-lurked and started to pester you with questions, I hope you'll > forgive me! > > I'd really just like to get a feel for whether people are using > Taverna; if so for what and how could we improve it, and if not then > why and how can we persuade you. I'm aware of a couple of shortcomings > in our Moby support, there's an issue with empty results and we don't > pick up annotations at all at the moment - it's the second of those > that I'm curious about (we can sort the first out, it's mostly a > technical issue). If you were chaining multiple service together how > would the annotation information manifest in this flow? > > Cheers, > > Tom Oinn (EMBL-EBI) > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > -- Rebecca Ernst MIPS, Inst. for Bioinformatics GSF Research Center for Environment and Health Ingolstaedter Landstr. 1 85764 Neuherberg fon: +49 89 3187 3583 email: Rebecca.Ernst@gsf.de From markw at illuminae.com Thu Oct 7 07:05:55 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu Oct 7 07:05:12 2004 Subject: [MOBY-l] Moby in workflows In-Reply-To: <41652215.9000500@gsf.de> References: <4164F2DF.5050700@ebi.ac.uk> <41652215.9000500@gsf.de> Message-ID: <41652313.1020800@illuminae.com> > Another thing which I realized : at the moment you will have to guess > from the name of the service to his function. If I want to build a > workflow integrating other peoples services as well, I need to know > what exactly a service does. In BioMoby this is described on one hand > in the human readable description and on the other hand by the > input/output objects in Moby Central. Is this what you mean with > annotation information? Or are you talking about the service notes? Phillip, Pinar and I are going to look very closely today at a way to more "richly" query for services using a tool that Pinar has been developing that (I believe) is a plug-in to Taverna. If this happens, the problem you discuss above will have been solved :-) M From gss at ncgr.org Thu Oct 7 16:18:18 2004 From: gss at ncgr.org (Gary Schiltz) Date: Thu Oct 7 16:21:20 2004 Subject: [MOBY-l] MOBY Meeting Registration Message-ID: <4165A48A.5010804@ncgr.org> The online registration form for the MOBY meeting is now available at www.semanticmoby.org/meeting/registration-form.html. Even if you have already sent an email letting me know that you're planning to attend, I'd appreciate it if you would fill out the form anyway; it will help me keep track a bit better. // Gary From simont at mcw.edu Thu Oct 7 18:09:02 2004 From: simont at mcw.edu (Simon Twigger) Date: Thu Oct 7 18:08:26 2004 Subject: [MOBY-l] Moby in workflows In-Reply-To: <4164F2DF.5050700@ebi.ac.uk> References: <4164F2DF.5050700@ebi.ac.uk> Message-ID: <7F2AC122-18AD-11D9-AA84-000A959D1D82@mcw.edu> Hi Tom, I havent used Taverna but have heard about it on the list and from Martin. We arent using Taverna at this point but I think this type of workflow tool is wonderful and will be a great help to people trying to chain services together. I gave Taverna a try for the first time this afternoon and had some issues on Mac OSX, I submitted a bug report on sourceforge. Consequently, I havent had a chance to really play with it so my thoughts so far are limited to rather superficial observations. I agree with Rebecca's point that a non-gui implementation would be great so that we can design workflows in Taverna but then pipe things into them behind the scenes. I'd love to be able to create a custom workflow in Taverna and then wrap it up as a 'component' or other black box and then be able to pipe input data to it from Java (perl?) and have the output come back such that I could use it appropriately. This would be a great way to quickly create code to solve complex problems. Thinking about giving this to average lab end users, is there any chance we can create workflows by dragging connections around on the Workflow diagram? The Model explorer no doubt gives more flexibility but it would be so intuitive if people could drag connections between objects rather than building in the explorer. I wonder if a drag and drop approach would work for running workflows - drag your input file onto a workflow icon to send it on its way, results being returned to the desktop (or similar). I'll try again on OS X and XP and explore some more and try some MOBY services and see what happens. Simon. On Oct 7, 2004, at 2:40 AM, Tom Oinn wrote: > Hi all, > > I run the Taverna project (http://taverna.sf.net), a workflow design > and enactment system which supports BioMoby and I figured it was time > I de-lurked and started to pester you with questions, I hope you'll > forgive me! > > I'd really just like to get a feel for whether people are using > Taverna; if so for what and how could we improve it, and if not then > why and how can we persuade you. I'm aware of a couple of shortcomings > in our Moby support, there's an issue with empty results and we don't > pick up annotations at all at the moment - it's the second of those > that I'm curious about (we can sort the first out, it's mostly a > technical issue). If you were chaining multiple service together how > would the annotation information manifest in this flow? > > Cheers, > > Tom Oinn (EMBL-EBI) > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > > -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw From tmo at ebi.ac.uk Fri Oct 8 05:24:43 2004 From: tmo at ebi.ac.uk (Tom Oinn) Date: Fri Oct 8 05:24:01 2004 Subject: [MOBY-l] Moby in workflows In-Reply-To: <7F2AC122-18AD-11D9-AA84-000A959D1D82@mcw.edu> References: <4164F2DF.5050700@ebi.ac.uk> <7F2AC122-18AD-11D9-AA84-000A959D1D82@mcw.edu> Message-ID: <41665CDB.5020406@ebi.ac.uk> Simon Twigger wrote: > Hi Tom, > > I havent used Taverna but have heard about it on the list and from > Martin. We arent using Taverna at this point but I think this type of > workflow tool is wonderful and will be a great help to people trying to > chain services together. I gave Taverna a try for the first time this > afternoon and had some issues on Mac OSX, I submitted a bug report on > sourceforge. Consequently, I havent had a chance to really play with it > so my thoughts so far are limited to rather superficial observations. > > I agree with Rebecca's point that a non-gui implementation would be > great so that we can design workflows in Taverna but then pipe things > into them behind the scenes. I'd love to be able to create a custom > workflow in Taverna and then wrap it up as a 'component' or other black > box and then be able to pipe input data to it from Java (perl?) and have > the output come back such that I could use it appropriately. This would > be a great way to quickly create code to solve complex problems. Hi Simon, Rebecca et al, We always intended Taverna to be heavily modular in structure - there's a clean seperation between the ui, the underlying data models and the enactor itself so although we don't currently have a command line version it would be trivial to write. To call the enactor from Java is probably about five to ten lines of code - PERL would be slightly harder as we wrap the data objects up in an XML format which you'd then have to deserialize (the Java API does this for you) but it's all documented; obviously anyone writing a PERL API for Taverna would have our full support :) We're currently working on a much more sophisticated drag and drop style workflow diagram, but it's a surprisingly hard thing to get right. We're in the planning stages at the moment but it will exist in the future. The idea of an interface which you could just drop files into is a good one, and should be relatively easy to do. I guess something which showed a panel with the description of the workflow and a 'drop here' for each input? The user could then drag files from the file system (or URLs from the browser) onto the targets and hit the 'go' button, presumably we could also then have drag sources corresponding to the outputs which the user could drag out to get the results. Could be a neat 'mini interface', I'll see if anyone wants to code it. The explorer bug is OSX only, so might take us some time to fix (we don't have any apple machines) but we'll investigate and see, often this means shouting at apple :) All these suggestions have been great, I'm cc'ing this mail to the taverna-users list but is there any chance you guys could join? You've obviously got some excellent ideas and I'm sure others would like to hear them. Cheers, Tom From p.lord at cs.man.ac.uk Mon Oct 11 07:15:59 2004 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: Mon Oct 11 10:14:44 2004 Subject: [MOBY-l] Moby in workflows In-Reply-To: <41652215.9000500@gsf.de> References: <4164F2DF.5050700@ebi.ac.uk> <41652215.9000500@gsf.de> Message-ID: >>>>> "Rebecca" == Rebecca Ernst writes: Rebecca> e.g. we are building a portal through which people can Rebecca> access all our PlaNet databases (featured by BioMoby). It Rebecca> would be great if we could offer them to run several Rebecca> workflows which we built already without having to install Rebecca> Taverna on their machines. This would involve saving the Rebecca> workflows from Taverna, and then executing those saved Rebecca> workflows through e.g. a command-line call to Taverna. This is a requirement that many of the users of the mygrid technologies have expressed. Indeed, as you might expect, the general requirement is for an easy web delivered access to both the workflow, and the end products of the workflow. We are working on general portal technologies. Others on the mygrid developers list can give a better status report than I. The second issue this raises is that of data integration. Like moby-s, we don't put a lot of requirements onto the service providers, so you get back a large pile of flat files, which you then need to wade through. So we are also working on some general approaches for helping to visualise the data. Rebecca> I don't know if you ever thought of this possibility!? Rebecca> Another thing which I realized : at the moment you will Rebecca> have to guess from the name of the service to his Rebecca> function. If I want to build a workflow integrating other Rebecca> peoples services as well, I need to know what exactly a Rebecca> service does. In BioMoby this is described on one hand in Rebecca> the human readable description and on the other hand by the Rebecca> input/output objects in Moby Central. Is this what you mean Rebecca> with annotation information? Or are you talking about the Rebecca> service notes? We also have this sort of semantic service discovery, but its not available in the main download at the moment. We will try to get this released soon, as quite a few people need this at the moment. As Mark says, we have been discussing this in some detail! Cheers Phil From michael at acutrans.net Mon Oct 11 10:15:59 2004 From: michael at acutrans.net (Michael Jensen) Date: Mon Oct 11 10:15:08 2004 Subject: [MOBY-l] Moby in workflows In-Reply-To: <4164FD75.6000106@illuminae.com> References: <4164F2DF.5050700@ebi.ac.uk> <4164FD75.6000106@illuminae.com> Message-ID: <12ED5510-1B90-11D9-B794-000393B6201C@acutrans.net> Mark: Not sure if I am just out of the loop or not, but you mentioned myGrid/MOBY-S merging. Can you expound on that or point me somewhere? Latest news on Biomoby.org is November 2003. -Michael On Oct 7, 2004, at 3:25 AM, Mark Wilkinson wrote: > Hi Tom, > > I know I'm going to see you next week anyway, but since I am sitting > here in the myGrid lab and mapping out the next 12 months of > myGrid/MOBY-S merging, I'd like to jump on this and express my > pleasure that you have built MOBY-S support into Taverna. In > addition, there has been considerable discussion that we (the Genome > Canada bioinformatics platform grant) should spotlight Taverna as the > "recommended" tool for interacting with web services for all genome > centres nationwide - the advantage to us, of course, is that we then > have a uniform landscape through which we can provide bioinformatics > end-user service. An upcoming edition of our GC bioinformatics > newsletter will do exactly that :-) > > Phil has indicated that additional MOBY-S support is being added to > Taverna, so hopefully next week we can sit down over a pint and > resolve the issues that remain foggy. > > Cheers! > > Mark > > > > Tom Oinn wrote: > >> Hi all, >> >> I run the Taverna project (http://taverna.sf.net), a workflow design >> and enactment system which supports BioMoby and I figured it was time >> I de-lurked and started to pester you with questions, I hope you'll >> forgive me! >> >> I'd really just like to get a feel for whether people are using >> Taverna; if so for what and how could we improve it, and if not then >> why and how can we persuade you. I'm aware of a couple of >> shortcomings in our Moby support, there's an issue with empty results >> and we don't pick up annotations at all at the moment - it's the >> second of those that I'm curious about (we can sort the first out, >> it's mostly a technical issue). If you were chaining multiple service >> together how would the annotation information manifest in this flow? >> >> Cheers, >> >> Tom Oinn (EMBL-EBI) >> _______________________________________________ >> moby-l mailing list >> moby-l@biomoby.org >> http://biomoby.org/mailman/listinfo/moby-l >> > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From markw at illuminae.com Mon Oct 11 12:11:48 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Mon Oct 11 12:11:13 2004 Subject: [MOBY-l] Moby in workflows In-Reply-To: <12ED5510-1B90-11D9-B794-000393B6201C@acutrans.net> References: <4164F2DF.5050700@ebi.ac.uk> <4164FD75.6000106@illuminae.com> <12ED5510-1B90-11D9-B794-000393B6201C@acutrans.net> Message-ID: <416AB0C4.8030701@illuminae.com> I'm not sure that I mentioned that publicly, but something along those lines is certainly in the pipe :-) Phil, Carole and I will make a more public announcement once the details are worked out. This should , as far as we can tell, have ZERO effect on existing MOBY service providers, so there are no worries there. There are a lot of strong reasons for MOBY-S and myGrid to join forces, and since I've been here in Manchester this week it has become apparent what a perfect fit this union would be! On first blush, nearly effortless! More details once we have hammered them out... M Michael Jensen wrote: > Mark: > > Not sure if I am just out of the loop or not, but you mentioned > myGrid/MOBY-S merging. Can you expound on that or point me somewhere? > Latest news on Biomoby.org is November 2003. > > -Michael > > > On Oct 7, 2004, at 3:25 AM, Mark Wilkinson wrote: > >> Hi Tom, >> >> I know I'm going to see you next week anyway, but since I am sitting >> here in the myGrid lab and mapping out the next 12 months of >> myGrid/MOBY-S merging, I'd like to jump on this and express my >> pleasure that you have built MOBY-S support into Taverna. In >> addition, there has been considerable discussion that we (the Genome >> Canada bioinformatics platform grant) should spotlight Taverna as the >> "recommended" tool for interacting with web services for all genome >> centres nationwide - the advantage to us, of course, is that we then >> have a uniform landscape through which we can provide bioinformatics >> end-user service. An upcoming edition of our GC bioinformatics >> newsletter will do exactly that :-) >> >> Phil has indicated that additional MOBY-S support is being added to >> Taverna, so hopefully next week we can sit down over a pint and >> resolve the issues that remain foggy. >> >> Cheers! >> >> Mark >> >> >> >> Tom Oinn wrote: >> >>> Hi all, >>> >>> I run the Taverna project (http://taverna.sf.net), a workflow design >>> and enactment system which supports BioMoby and I figured it was >>> time I de-lurked and started to pester you with questions, I hope >>> you'll forgive me! >>> >>> I'd really just like to get a feel for whether people are using >>> Taverna; if so for what and how could we improve it, and if not then >>> why and how can we persuade you. I'm aware of a couple of >>> shortcomings in our Moby support, there's an issue with empty >>> results and we don't pick up annotations at all at the moment - it's >>> the second of those that I'm curious about (we can sort the first >>> out, it's mostly a technical issue). If you were chaining multiple >>> service together how would the annotation information manifest in >>> this flow? >>> >>> Cheers, >>> >>> Tom Oinn (EMBL-EBI) >>> _______________________________________________ >>> moby-l mailing list >>> moby-l@biomoby.org >>> http://biomoby.org/mailman/listinfo/moby-l >>> >> _______________________________________________ >> moby-l mailing list >> moby-l@biomoby.org >> http://biomoby.org/mailman/listinfo/moby-l >> > > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From senger at ebi.ac.uk Mon Oct 11 12:32:24 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Mon Oct 11 12:31:40 2004 Subject: [MOBY-l] Re: [MOBY-dev] Re: MOBY Meeting: 20-21 November in Santa Fe In-Reply-To: <41645222.1060907@ncgr.org> Message-ID: Gary, You recommended SanteFe hotel. I thought that you had some sort of arrangement with them - such as a spacial and reasonable price for BioMoby meeting participants. Because without such arrangement it does not seem (at least for us from academia) to be a choice. The cheapest hotel room they offered us today was for 263 US dollars plus tax ! Is there a second choice that you can recommend perhaps? As you said, to stay in the same hotel may help us to socialize and so on. Thanks for your advise and with regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From gss at ncgr.org Mon Oct 11 15:55:56 2004 From: gss at ncgr.org (Gary Schiltz) Date: Mon Oct 11 15:58:59 2004 Subject: [MOBY-l] Re: [MOBY-dev] Re: MOBY Meeting: 20-21 November in Santa Fe In-Reply-To: References: Message-ID: <416AE54C.9030805@ncgr.org> Martin, I hope it's alright for me to post this to the lists, as it should be of interest to everyone thinking of coming to the MOBY meeting. I found a $99 per night rate through Hotel Santa Fe's web site. Go to http://www.hotelsantafe.com/home.html, click on "Rates & Reservations" on the left side of the window, and in the pop-up window that opens, enter 2004-November 19 for Arrival, 2004-November 21 for Departure, click "Check Availability", and scroll down to the "Hot Internet Rates" section - there should be a "Hotel Santa Fe-Traditional King" rate of $99 per night. That is very good for a nice hotel in Santa Fe. There are, however, cheaper alternatives; I found hotels for under $50 per night on Travelocity. If anyone needs less expensive places to stay, we can arrange for transportation (the cheaper places are a bit further away). Just use MapQuest to check the distance from a given hotel to the Santa Fe Hotel. Looking forward to seeing everyone in November! // Gary Martin Senger wrote: > Gary, > You recommended SanteFe hotel. I thought that you had some sort of > arrangement with them - such as a spacial and reasonable price for BioMoby > meeting participants. Because without such arrangement it does not seem > (at least for us from academia) to be a choice. The cheapest hotel room > they offered us today was for 263 US dollars plus tax ! > Is there a second choice that you can recommend perhaps? As you said, > to stay in the same hotel may help us to socialize and so on. > > Thanks for your advise and with regards, > Martin > From senger at ebi.ac.uk Mon Oct 11 16:11:31 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Mon Oct 11 16:11:46 2004 Subject: [MOBY-l] Re: [MOBY-dev] Re: MOBY Meeting: 20-21 November in Santa Fe In-Reply-To: <416AE54C.9030805@ncgr.org> Message-ID: > I hope it's alright for me to post this to the lists > Of course. > $99 per night rate through Hotel Santa Fe's web site > Indeed, it is true. The price 263, I mentioned in my email, was the one given to our admin when she asked by phone. Inded a difference. Thanks, and see you there. Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Mon Oct 18 10:20:34 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Mon Oct 18 10:19:28 2004 Subject: [MOBY-l] Urgent request for reminders Message-ID: <4173D132.7020606@illuminae.com> Hi all, I had a hard drive failure just before my trip to the UK. I have managed to recover almost everything from backups, but the one thing that I am unable to reload from backup is my Evolution Calendar. As such, I don't know when all of my meetings, conferences, teleconferences, presentations, etc. are, nor the contact details and such for these meetings. Could anyone who is expecting me to be somewhere at some time over the next four months please make contact with me ASAP with the details so that I can rebuild my "life"? Also, if you know of someone who is expecting me to be somewhere who is not on this list please let them know. Thanks! And sorry for the trouble! Mark From senger at ebi.ac.uk Mon Oct 18 11:53:38 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Mon Oct 18 11:52:40 2004 Subject: [MOBY-l] moby grapgs updated In-Reply-To: <4165A48A.5010804@ncgr.org> Message-ID: Hi all, I have updated moby graphs (and also few other things in jMoby - see docs/ChangeLog if you wish). The main change is that now there is a possibility to draw a path between two selected data types, and that the result can be expressed as a workflow definition that can be consequently loaded to Taverna and hopefully run. I expect (at least) two things to happen soon: * You will/may find that the caching in graph servlet is not yet perfect. I need some time to make it more robust, but I will be travelling now - so if you find problems, just try the same again, and blame me... * Having now generated workflow definitions, more people will try it in Taverna. This is perfect, it's an ultimate goal. But I again need more time to improve moby stuf in Taverna, again make it more robust. And I will - so again try to send your comments, suggestion and bug reports, and blame me... Also I hope that I fixed few things that Frank was reporting: > 1. MOBY allows multiple whitespace-separated words in the object > ontology, but when they are graphed, they show up as separate nodes. > This is probably just a matter of enclosing the node names in double > quotes for GraphViz. > 2. The first time I try to draw the object ontology, after reloading the > registry, I get an error from Tomcat like this: Finally, here is the URL of the new moby graphs (actually it is the same as before, you can still get there from the main BioMoby page): http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs With regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From midori at ebi.ac.uk Tue Oct 5 12:42:07 2004 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 5 Oct 2004 17:42:07 +0100 (BST) Subject: [MOBY-l] Standards and Ontologies for Functional Genomics Message-ID: Dear Colleague, This is a final reminder that registration is still open for the second conference on Standards and Ontologies for Functional Genomics (SOFG) Meeting, which will be held on October 23-26, 2004 in Philadelphia, PA USA. (You may disregard the Sept. 23 deadline mentioned in the original announcement, which appears below.) http://www.jax.org/courses/events/coursedetails.do?id=44 We apologize if you receive multiple copies of this mail via different lists. ---------- Original SOFG 2 Announcement ---------- Dear Colleague, Registration Is Open for the 2nd Standards and Ontologies for Functional Genomics Meeting to be held at the University of Pennsylvania, Philadelphia, PA October 23-26, 2004 The 2nd Standards and Ontologies for Functional Genomics (SOFG) Meeting will be held on October 23-26, 2004 in Philadelphia, PA USA. Information about the SOFG meeting can be found at the SOFG site http://www.sofg.org/ or at http://www.jax.org/courses/events/coursedetails.do?id=44 . Registrations and abstracts will be accepted until Sept. 23, 2004 or until the event has filled. Student support to attend is available. Downloadable pdf registration form URL: http://www.jax.org/courses/2004/sfog_reg.pdf Abstracts submitted by Sept. 10 will be considered for oral presentation by Organizers and Session Chairs. Abstracts submitted after Sept 10 will be considered for poster session only. Abstract submissions will be reproduced and included with the conference notebook material. If you wish to submit, please follow the http://www.jax.org/courses/2004/functional_genomics_abstract_guidelines.html . The conference will focus on advances in the development of standards and ontologies to facilitate the exchange of biological information by computers and computation analysis applications. A particular emphasis will be on developments in ontological annotation systems for the genomics and bioinformatics communities. Toward this end, students and established investigators from different areas of computer science, experimental biology, and bioinformatics will have an opportunity to share new ideas, demonstrate new tools and applications, and identify potential collaborations. Topics include: * Ontological Systems: Theory and Development * Ontologies for Biology Systems * Ontology Systems Development: Electronic Demonstrations * Thesauri, Nomenclatures and the Biomedical Literature * Standards and Protocols * Functional Genomics Applications * From Resource to Application Plenary Speaker Carole Goble, University of Manchester Conference Organizers and Session Chairs: Judith Blake, The Jackson Laboratory Midori Harris, EBI-Hinxton Win Hide, SANBI Lynette Hirschman, MITRE Suzanna Lewis, UC Berkeley Helen Parkinson, EBI-Hinxton Martin Ringwald, The Jackson Laboratory Susanna-Assunta Sansone, EBI-Hinxton Chris Stoeckert, UPenn Please contact me with any questions about this meeting. Judi Alexander Medlin Lead Coordinator, Courses and Conferences The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6326 Fax: 207-288-6080 Please check out our web site http://www.jax.org/courses/events/current.do for the current listing of courses and conferences at The Jackson Laboratory. ----------------------------------------- ============================ Midori A. Harris, Ph.D. GO Editor EMBL - EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 (0) 1223 494667 Fax: +44 (0) 1223 494468 Email: midori at ebi.ac.uk From gss at ncgr.org Wed Oct 6 16:14:26 2004 From: gss at ncgr.org (Gary Schiltz) Date: Wed, 06 Oct 2004 14:14:26 -0600 Subject: [MOBY-l] Re: MOBY Meeting: 20-21 November in Santa Fe In-Reply-To: <415440E3.2070000@ncgr.org> References: <415440E3.2070000@ncgr.org> Message-ID: <41645222.1060907@ncgr.org> I've put information about the MOBY meeting on the Semantic MOBY web site - the URL is www.semanticmoby.org/meeting. It is currently missing a registration form, which I'll add by the end of the day. // Gary Gary Schiltz wrote: > Hello MOBY'ers! > > The next MOBY meeting will be held at NCGR (www.ncgr.org) in Santa Fe, > New Mexico, the weekend of 20-21 November, 2004. We'll finish by about > 3:00 MST on Sunday, so you could catch a flight as early as about > 5:30. Also, Mark Wilkinson will be giving a talk on MOBY Services at > NCGR on November 19 (some time in the afternoon, I believe); everyone > is welcome to attend, so consider coming a day early. I'll soon put > together a page of information with an agenda, links to accommodations > covering a range of prices, and other details. There will be a small > registration fee to cover breakfast and lunch for Saturday and Sunday. > > In the interim, please post suggestions for topics to cover at the > meeting. > > ---- > > Gary Schiltz > Principal Software Engineer > National Center for Genome Resources > Santa Fe, New Mexico > > gss at ncgr.org > 505-995-4414 (Work) > 505-670-5983 (Cell) > From tmo at ebi.ac.uk Thu Oct 7 03:40:15 2004 From: tmo at ebi.ac.uk (Tom Oinn) Date: Thu, 07 Oct 2004 08:40:15 +0100 Subject: [MOBY-l] Moby in workflows Message-ID: <4164F2DF.5050700@ebi.ac.uk> Hi all, I run the Taverna project (http://taverna.sf.net), a workflow design and enactment system which supports BioMoby and I figured it was time I de-lurked and started to pester you with questions, I hope you'll forgive me! I'd really just like to get a feel for whether people are using Taverna; if so for what and how could we improve it, and if not then why and how can we persuade you. I'm aware of a couple of shortcomings in our Moby support, there's an issue with empty results and we don't pick up annotations at all at the moment - it's the second of those that I'm curious about (we can sort the first out, it's mostly a technical issue). If you were chaining multiple service together how would the annotation information manifest in this flow? Cheers, Tom Oinn (EMBL-EBI) From markw at illuminae.com Thu Oct 7 04:25:25 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 07 Oct 2004 01:25:25 -0700 Subject: [MOBY-l] Moby in workflows In-Reply-To: <4164F2DF.5050700@ebi.ac.uk> References: <4164F2DF.5050700@ebi.ac.uk> Message-ID: <4164FD75.6000106@illuminae.com> Hi Tom, I know I'm going to see you next week anyway, but since I am sitting here in the myGrid lab and mapping out the next 12 months of myGrid/MOBY-S merging, I'd like to jump on this and express my pleasure that you have built MOBY-S support into Taverna. In addition, there has been considerable discussion that we (the Genome Canada bioinformatics platform grant) should spotlight Taverna as the "recommended" tool for interacting with web services for all genome centres nationwide - the advantage to us, of course, is that we then have a uniform landscape through which we can provide bioinformatics end-user service. An upcoming edition of our GC bioinformatics newsletter will do exactly that :-) Phil has indicated that additional MOBY-S support is being added to Taverna, so hopefully next week we can sit down over a pint and resolve the issues that remain foggy. Cheers! Mark Tom Oinn wrote: > Hi all, > > I run the Taverna project (http://taverna.sf.net), a workflow design > and enactment system which supports BioMoby and I figured it was time > I de-lurked and started to pester you with questions, I hope you'll > forgive me! > > I'd really just like to get a feel for whether people are using > Taverna; if so for what and how could we improve it, and if not then > why and how can we persuade you. I'm aware of a couple of shortcomings > in our Moby support, there's an issue with empty results and we don't > pick up annotations at all at the moment - it's the second of those > that I'm curious about (we can sort the first out, it's mostly a > technical issue). If you were chaining multiple service together how > would the annotation information manifest in this flow? > > Cheers, > > Tom Oinn (EMBL-EBI) > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From rebecca.ernst at gsf.de Thu Oct 7 07:01:41 2004 From: rebecca.ernst at gsf.de (Rebecca Ernst) Date: Thu, 07 Oct 2004 13:01:41 +0200 Subject: [MOBY-l] Moby in workflows In-Reply-To: <4164F2DF.5050700@ebi.ac.uk> References: <4164F2DF.5050700@ebi.ac.uk> Message-ID: <41652215.9000500@gsf.de> Hi Tom! Within the PlaNet project which aims to integrate European plant databases we are using BioMoby as the integration technology. We recently played with Taverna (Martin Senger told me that Taverna is 'mobyfied' now) and found it an amazingly good tool for building workflows! Since then we are certainly promoting it heavily! ;-) For making use of Taverna within the PlaNet project it would be perfect if there would be a possiblility of a standalone/non-interactive application of Taverna. e.g. we are building a portal through which people can access all our PlaNet databases (featured by BioMoby). It would be great if we could offer them to run several workflows which we built already without having to install Taverna on their machines. This would involve saving the workflows from Taverna, and then executing those saved workflows through e.g. a command-line call to Taverna. I don't know if you ever thought of this possibility!? Another thing which I realized : at the moment you will have to guess from the name of the service to his function. If I want to build a workflow integrating other peoples services as well, I need to know what exactly a service does. In BioMoby this is described on one hand in the human readable description and on the other hand by the input/output objects in Moby Central. Is this what you mean with annotation information? Or are you talking about the service notes? Cheers, Rebecca. Tom Oinn wrote: > Hi all, > > I run the Taverna project (http://taverna.sf.net), a workflow design > and enactment system which supports BioMoby and I figured it was time > I de-lurked and started to pester you with questions, I hope you'll > forgive me! > > I'd really just like to get a feel for whether people are using > Taverna; if so for what and how could we improve it, and if not then > why and how can we persuade you. I'm aware of a couple of shortcomings > in our Moby support, there's an issue with empty results and we don't > pick up annotations at all at the moment - it's the second of those > that I'm curious about (we can sort the first out, it's mostly a > technical issue). If you were chaining multiple service together how > would the annotation information manifest in this flow? > > Cheers, > > Tom Oinn (EMBL-EBI) > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > -- Rebecca Ernst MIPS, Inst. for Bioinformatics GSF Research Center for Environment and Health Ingolstaedter Landstr. 1 85764 Neuherberg fon: +49 89 3187 3583 email: Rebecca.Ernst at gsf.de From markw at illuminae.com Thu Oct 7 07:05:55 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 07 Oct 2004 04:05:55 -0700 Subject: [MOBY-l] Moby in workflows In-Reply-To: <41652215.9000500@gsf.de> References: <4164F2DF.5050700@ebi.ac.uk> <41652215.9000500@gsf.de> Message-ID: <41652313.1020800@illuminae.com> > Another thing which I realized : at the moment you will have to guess > from the name of the service to his function. If I want to build a > workflow integrating other peoples services as well, I need to know > what exactly a service does. In BioMoby this is described on one hand > in the human readable description and on the other hand by the > input/output objects in Moby Central. Is this what you mean with > annotation information? Or are you talking about the service notes? Phillip, Pinar and I are going to look very closely today at a way to more "richly" query for services using a tool that Pinar has been developing that (I believe) is a plug-in to Taverna. If this happens, the problem you discuss above will have been solved :-) M From gss at ncgr.org Thu Oct 7 16:18:18 2004 From: gss at ncgr.org (Gary Schiltz) Date: Thu, 07 Oct 2004 14:18:18 -0600 Subject: [MOBY-l] MOBY Meeting Registration Message-ID: <4165A48A.5010804@ncgr.org> The online registration form for the MOBY meeting is now available at www.semanticmoby.org/meeting/registration-form.html. Even if you have already sent an email letting me know that you're planning to attend, I'd appreciate it if you would fill out the form anyway; it will help me keep track a bit better. // Gary From simont at mcw.edu Thu Oct 7 18:09:02 2004 From: simont at mcw.edu (Simon Twigger) Date: Thu, 7 Oct 2004 17:09:02 -0500 Subject: [MOBY-l] Moby in workflows In-Reply-To: <4164F2DF.5050700@ebi.ac.uk> References: <4164F2DF.5050700@ebi.ac.uk> Message-ID: <7F2AC122-18AD-11D9-AA84-000A959D1D82@mcw.edu> Hi Tom, I havent used Taverna but have heard about it on the list and from Martin. We arent using Taverna at this point but I think this type of workflow tool is wonderful and will be a great help to people trying to chain services together. I gave Taverna a try for the first time this afternoon and had some issues on Mac OSX, I submitted a bug report on sourceforge. Consequently, I havent had a chance to really play with it so my thoughts so far are limited to rather superficial observations. I agree with Rebecca's point that a non-gui implementation would be great so that we can design workflows in Taverna but then pipe things into them behind the scenes. I'd love to be able to create a custom workflow in Taverna and then wrap it up as a 'component' or other black box and then be able to pipe input data to it from Java (perl?) and have the output come back such that I could use it appropriately. This would be a great way to quickly create code to solve complex problems. Thinking about giving this to average lab end users, is there any chance we can create workflows by dragging connections around on the Workflow diagram? The Model explorer no doubt gives more flexibility but it would be so intuitive if people could drag connections between objects rather than building in the explorer. I wonder if a drag and drop approach would work for running workflows - drag your input file onto a workflow icon to send it on its way, results being returned to the desktop (or similar). I'll try again on OS X and XP and explore some more and try some MOBY services and see what happens. Simon. On Oct 7, 2004, at 2:40 AM, Tom Oinn wrote: > Hi all, > > I run the Taverna project (http://taverna.sf.net), a workflow design > and enactment system which supports BioMoby and I figured it was time > I de-lurked and started to pester you with questions, I hope you'll > forgive me! > > I'd really just like to get a feel for whether people are using > Taverna; if so for what and how could we improve it, and if not then > why and how can we persuade you. I'm aware of a couple of shortcomings > in our Moby support, there's an issue with empty results and we don't > pick up annotations at all at the moment - it's the second of those > that I'm curious about (we can sort the first out, it's mostly a > technical issue). If you were chaining multiple service together how > would the annotation information manifest in this flow? > > Cheers, > > Tom Oinn (EMBL-EBI) > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > > -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw From tmo at ebi.ac.uk Fri Oct 8 05:24:43 2004 From: tmo at ebi.ac.uk (Tom Oinn) Date: Fri, 08 Oct 2004 10:24:43 +0100 Subject: [MOBY-l] Moby in workflows In-Reply-To: <7F2AC122-18AD-11D9-AA84-000A959D1D82@mcw.edu> References: <4164F2DF.5050700@ebi.ac.uk> <7F2AC122-18AD-11D9-AA84-000A959D1D82@mcw.edu> Message-ID: <41665CDB.5020406@ebi.ac.uk> Simon Twigger wrote: > Hi Tom, > > I havent used Taverna but have heard about it on the list and from > Martin. We arent using Taverna at this point but I think this type of > workflow tool is wonderful and will be a great help to people trying to > chain services together. I gave Taverna a try for the first time this > afternoon and had some issues on Mac OSX, I submitted a bug report on > sourceforge. Consequently, I havent had a chance to really play with it > so my thoughts so far are limited to rather superficial observations. > > I agree with Rebecca's point that a non-gui implementation would be > great so that we can design workflows in Taverna but then pipe things > into them behind the scenes. I'd love to be able to create a custom > workflow in Taverna and then wrap it up as a 'component' or other black > box and then be able to pipe input data to it from Java (perl?) and have > the output come back such that I could use it appropriately. This would > be a great way to quickly create code to solve complex problems. Hi Simon, Rebecca et al, We always intended Taverna to be heavily modular in structure - there's a clean seperation between the ui, the underlying data models and the enactor itself so although we don't currently have a command line version it would be trivial to write. To call the enactor from Java is probably about five to ten lines of code - PERL would be slightly harder as we wrap the data objects up in an XML format which you'd then have to deserialize (the Java API does this for you) but it's all documented; obviously anyone writing a PERL API for Taverna would have our full support :) We're currently working on a much more sophisticated drag and drop style workflow diagram, but it's a surprisingly hard thing to get right. We're in the planning stages at the moment but it will exist in the future. The idea of an interface which you could just drop files into is a good one, and should be relatively easy to do. I guess something which showed a panel with the description of the workflow and a 'drop here' for each input? The user could then drag files from the file system (or URLs from the browser) onto the targets and hit the 'go' button, presumably we could also then have drag sources corresponding to the outputs which the user could drag out to get the results. Could be a neat 'mini interface', I'll see if anyone wants to code it. The explorer bug is OSX only, so might take us some time to fix (we don't have any apple machines) but we'll investigate and see, often this means shouting at apple :) All these suggestions have been great, I'm cc'ing this mail to the taverna-users list but is there any chance you guys could join? You've obviously got some excellent ideas and I'm sure others would like to hear them. Cheers, Tom From p.lord at cs.man.ac.uk Mon Oct 11 07:15:59 2004 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: 11 Oct 2004 12:15:59 +0100 Subject: [MOBY-l] Moby in workflows In-Reply-To: <41652215.9000500@gsf.de> References: <4164F2DF.5050700@ebi.ac.uk> <41652215.9000500@gsf.de> Message-ID: >>>>> "Rebecca" == Rebecca Ernst writes: Rebecca> e.g. we are building a portal through which people can Rebecca> access all our PlaNet databases (featured by BioMoby). It Rebecca> would be great if we could offer them to run several Rebecca> workflows which we built already without having to install Rebecca> Taverna on their machines. This would involve saving the Rebecca> workflows from Taverna, and then executing those saved Rebecca> workflows through e.g. a command-line call to Taverna. This is a requirement that many of the users of the mygrid technologies have expressed. Indeed, as you might expect, the general requirement is for an easy web delivered access to both the workflow, and the end products of the workflow. We are working on general portal technologies. Others on the mygrid developers list can give a better status report than I. The second issue this raises is that of data integration. Like moby-s, we don't put a lot of requirements onto the service providers, so you get back a large pile of flat files, which you then need to wade through. So we are also working on some general approaches for helping to visualise the data. Rebecca> I don't know if you ever thought of this possibility!? Rebecca> Another thing which I realized : at the moment you will Rebecca> have to guess from the name of the service to his Rebecca> function. If I want to build a workflow integrating other Rebecca> peoples services as well, I need to know what exactly a Rebecca> service does. In BioMoby this is described on one hand in Rebecca> the human readable description and on the other hand by the Rebecca> input/output objects in Moby Central. Is this what you mean Rebecca> with annotation information? Or are you talking about the Rebecca> service notes? We also have this sort of semantic service discovery, but its not available in the main download at the moment. We will try to get this released soon, as quite a few people need this at the moment. As Mark says, we have been discussing this in some detail! Cheers Phil From michael at acutrans.net Mon Oct 11 10:15:59 2004 From: michael at acutrans.net (Michael Jensen) Date: Mon, 11 Oct 2004 09:15:59 -0500 Subject: [MOBY-l] Moby in workflows In-Reply-To: <4164FD75.6000106@illuminae.com> References: <4164F2DF.5050700@ebi.ac.uk> <4164FD75.6000106@illuminae.com> Message-ID: <12ED5510-1B90-11D9-B794-000393B6201C@acutrans.net> Mark: Not sure if I am just out of the loop or not, but you mentioned myGrid/MOBY-S merging. Can you expound on that or point me somewhere? Latest news on Biomoby.org is November 2003. -Michael On Oct 7, 2004, at 3:25 AM, Mark Wilkinson wrote: > Hi Tom, > > I know I'm going to see you next week anyway, but since I am sitting > here in the myGrid lab and mapping out the next 12 months of > myGrid/MOBY-S merging, I'd like to jump on this and express my > pleasure that you have built MOBY-S support into Taverna. In > addition, there has been considerable discussion that we (the Genome > Canada bioinformatics platform grant) should spotlight Taverna as the > "recommended" tool for interacting with web services for all genome > centres nationwide - the advantage to us, of course, is that we then > have a uniform landscape through which we can provide bioinformatics > end-user service. An upcoming edition of our GC bioinformatics > newsletter will do exactly that :-) > > Phil has indicated that additional MOBY-S support is being added to > Taverna, so hopefully next week we can sit down over a pint and > resolve the issues that remain foggy. > > Cheers! > > Mark > > > > Tom Oinn wrote: > >> Hi all, >> >> I run the Taverna project (http://taverna.sf.net), a workflow design >> and enactment system which supports BioMoby and I figured it was time >> I de-lurked and started to pester you with questions, I hope you'll >> forgive me! >> >> I'd really just like to get a feel for whether people are using >> Taverna; if so for what and how could we improve it, and if not then >> why and how can we persuade you. I'm aware of a couple of >> shortcomings in our Moby support, there's an issue with empty results >> and we don't pick up annotations at all at the moment - it's the >> second of those that I'm curious about (we can sort the first out, >> it's mostly a technical issue). If you were chaining multiple service >> together how would the annotation information manifest in this flow? >> >> Cheers, >> >> Tom Oinn (EMBL-EBI) >> _______________________________________________ >> moby-l mailing list >> moby-l at biomoby.org >> http://biomoby.org/mailman/listinfo/moby-l >> > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From markw at illuminae.com Mon Oct 11 12:11:48 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 11 Oct 2004 09:11:48 -0700 Subject: [MOBY-l] Moby in workflows In-Reply-To: <12ED5510-1B90-11D9-B794-000393B6201C@acutrans.net> References: <4164F2DF.5050700@ebi.ac.uk> <4164FD75.6000106@illuminae.com> <12ED5510-1B90-11D9-B794-000393B6201C@acutrans.net> Message-ID: <416AB0C4.8030701@illuminae.com> I'm not sure that I mentioned that publicly, but something along those lines is certainly in the pipe :-) Phil, Carole and I will make a more public announcement once the details are worked out. This should , as far as we can tell, have ZERO effect on existing MOBY service providers, so there are no worries there. There are a lot of strong reasons for MOBY-S and myGrid to join forces, and since I've been here in Manchester this week it has become apparent what a perfect fit this union would be! On first blush, nearly effortless! More details once we have hammered them out... M Michael Jensen wrote: > Mark: > > Not sure if I am just out of the loop or not, but you mentioned > myGrid/MOBY-S merging. Can you expound on that or point me somewhere? > Latest news on Biomoby.org is November 2003. > > -Michael > > > On Oct 7, 2004, at 3:25 AM, Mark Wilkinson wrote: > >> Hi Tom, >> >> I know I'm going to see you next week anyway, but since I am sitting >> here in the myGrid lab and mapping out the next 12 months of >> myGrid/MOBY-S merging, I'd like to jump on this and express my >> pleasure that you have built MOBY-S support into Taverna. In >> addition, there has been considerable discussion that we (the Genome >> Canada bioinformatics platform grant) should spotlight Taverna as the >> "recommended" tool for interacting with web services for all genome >> centres nationwide - the advantage to us, of course, is that we then >> have a uniform landscape through which we can provide bioinformatics >> end-user service. An upcoming edition of our GC bioinformatics >> newsletter will do exactly that :-) >> >> Phil has indicated that additional MOBY-S support is being added to >> Taverna, so hopefully next week we can sit down over a pint and >> resolve the issues that remain foggy. >> >> Cheers! >> >> Mark >> >> >> >> Tom Oinn wrote: >> >>> Hi all, >>> >>> I run the Taverna project (http://taverna.sf.net), a workflow design >>> and enactment system which supports BioMoby and I figured it was >>> time I de-lurked and started to pester you with questions, I hope >>> you'll forgive me! >>> >>> I'd really just like to get a feel for whether people are using >>> Taverna; if so for what and how could we improve it, and if not then >>> why and how can we persuade you. I'm aware of a couple of >>> shortcomings in our Moby support, there's an issue with empty >>> results and we don't pick up annotations at all at the moment - it's >>> the second of those that I'm curious about (we can sort the first >>> out, it's mostly a technical issue). If you were chaining multiple >>> service together how would the annotation information manifest in >>> this flow? >>> >>> Cheers, >>> >>> Tom Oinn (EMBL-EBI) >>> _______________________________________________ >>> moby-l mailing list >>> moby-l at biomoby.org >>> http://biomoby.org/mailman/listinfo/moby-l >>> >> _______________________________________________ >> moby-l mailing list >> moby-l at biomoby.org >> http://biomoby.org/mailman/listinfo/moby-l >> > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From senger at ebi.ac.uk Mon Oct 11 12:32:24 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 11 Oct 2004 17:32:24 +0100 (BST) Subject: [MOBY-l] Re: [MOBY-dev] Re: MOBY Meeting: 20-21 November in Santa Fe In-Reply-To: <41645222.1060907@ncgr.org> Message-ID: Gary, You recommended SanteFe hotel. I thought that you had some sort of arrangement with them - such as a spacial and reasonable price for BioMoby meeting participants. Because without such arrangement it does not seem (at least for us from academia) to be a choice. The cheapest hotel room they offered us today was for 263 US dollars plus tax ! Is there a second choice that you can recommend perhaps? As you said, to stay in the same hotel may help us to socialize and so on. Thanks for your advise and with regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From gss at ncgr.org Mon Oct 11 15:55:56 2004 From: gss at ncgr.org (Gary Schiltz) Date: Mon, 11 Oct 2004 13:55:56 -0600 Subject: [MOBY-l] Re: [MOBY-dev] Re: MOBY Meeting: 20-21 November in Santa Fe In-Reply-To: References: Message-ID: <416AE54C.9030805@ncgr.org> Martin, I hope it's alright for me to post this to the lists, as it should be of interest to everyone thinking of coming to the MOBY meeting. I found a $99 per night rate through Hotel Santa Fe's web site. Go to http://www.hotelsantafe.com/home.html, click on "Rates & Reservations" on the left side of the window, and in the pop-up window that opens, enter 2004-November 19 for Arrival, 2004-November 21 for Departure, click "Check Availability", and scroll down to the "Hot Internet Rates" section - there should be a "Hotel Santa Fe-Traditional King" rate of $99 per night. That is very good for a nice hotel in Santa Fe. There are, however, cheaper alternatives; I found hotels for under $50 per night on Travelocity. If anyone needs less expensive places to stay, we can arrange for transportation (the cheaper places are a bit further away). Just use MapQuest to check the distance from a given hotel to the Santa Fe Hotel. Looking forward to seeing everyone in November! // Gary Martin Senger wrote: > Gary, > You recommended SanteFe hotel. I thought that you had some sort of > arrangement with them - such as a spacial and reasonable price for BioMoby > meeting participants. Because without such arrangement it does not seem > (at least for us from academia) to be a choice. The cheapest hotel room > they offered us today was for 263 US dollars plus tax ! > Is there a second choice that you can recommend perhaps? As you said, > to stay in the same hotel may help us to socialize and so on. > > Thanks for your advise and with regards, > Martin > From senger at ebi.ac.uk Mon Oct 11 16:11:31 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 11 Oct 2004 21:11:31 +0100 (BST) Subject: [MOBY-l] Re: [MOBY-dev] Re: MOBY Meeting: 20-21 November in Santa Fe In-Reply-To: <416AE54C.9030805@ncgr.org> Message-ID: > I hope it's alright for me to post this to the lists > Of course. > $99 per night rate through Hotel Santa Fe's web site > Indeed, it is true. The price 263, I mentioned in my email, was the one given to our admin when she asked by phone. Inded a difference. Thanks, and see you there. Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Mon Oct 18 10:20:34 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 18 Oct 2004 07:20:34 -0700 Subject: [MOBY-l] Urgent request for reminders Message-ID: <4173D132.7020606@illuminae.com> Hi all, I had a hard drive failure just before my trip to the UK. I have managed to recover almost everything from backups, but the one thing that I am unable to reload from backup is my Evolution Calendar. As such, I don't know when all of my meetings, conferences, teleconferences, presentations, etc. are, nor the contact details and such for these meetings. Could anyone who is expecting me to be somewhere at some time over the next four months please make contact with me ASAP with the details so that I can rebuild my "life"? Also, if you know of someone who is expecting me to be somewhere who is not on this list please let them know. Thanks! And sorry for the trouble! Mark From senger at ebi.ac.uk Mon Oct 18 11:53:38 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 18 Oct 2004 16:53:38 +0100 (BST) Subject: [MOBY-l] moby grapgs updated In-Reply-To: <4165A48A.5010804@ncgr.org> Message-ID: Hi all, I have updated moby graphs (and also few other things in jMoby - see docs/ChangeLog if you wish). The main change is that now there is a possibility to draw a path between two selected data types, and that the result can be expressed as a workflow definition that can be consequently loaded to Taverna and hopefully run. I expect (at least) two things to happen soon: * You will/may find that the caching in graph servlet is not yet perfect. I need some time to make it more robust, but I will be travelling now - so if you find problems, just try the same again, and blame me... * Having now generated workflow definitions, more people will try it in Taverna. This is perfect, it's an ultimate goal. But I again need more time to improve moby stuf in Taverna, again make it more robust. And I will - so again try to send your comments, suggestion and bug reports, and blame me... Also I hope that I fixed few things that Frank was reporting: > 1. MOBY allows multiple whitespace-separated words in the object > ontology, but when they are graphed, they show up as separate nodes. > This is probably just a matter of enclosing the node names in double > quotes for GraphViz. > 2. The first time I try to draw the object ontology, after reloading the > registry, I get an error from Tomcat like this: Finally, here is the URL of the new moby graphs (actually it is the same as before, you can still get there from the main BioMoby page): http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs With regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger