From markw at illuminae.com Tue Nov 8 11:13:47 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Tue Nov 8 11:36:17 2005 Subject: [MOBY-l] The service map on the new homepage Message-ID: <1131466427.19554.24.camel@bioinfo.icapture.ubc.ca> Thanks to Mathieu Rouard, the map of MOBY Services on the new homepage is now almost-live (updated every few hours). Thanks Mathieu! Mark -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From bogus@does.not.exist.com Fri Nov 25 12:16:16 2005 From: bogus@does.not.exist.com () Date: Fri, 25 Nov 2005 17:16:16 -0000 Subject: No subject Message-ID: (though horrific) query, and we shouldn't prevent people from doing this. The disadvantages of sending one request at a time are numerous, not the least of which is the overhead of SOAP itself, which is painfully slow... I'd rather claw my eyes out than have to do 1000 identical SOAP queries one at a time! Another problem is that some services will *require* a list... e.g. sequence alignment services. I don't want to have to define special "list" objects on top of it all :-P Given that we are going to eventually have some sort of error object, the service provider can use this to choke if it thinks the query is unreasonable... of course, it would be nicer to know this before the query was submitted, especially when it comes to automating service transactions. M -- -------------------------------- "Speed is subsittute fo accurancy." ________________________________ Dr. Mark Wilkinson, RA Bioinformatics National Research Council, Plant Biotechnology Institute 110 Gymnasium Place, Saskatoon, SK, Canada phone : (306) 975 5279 pager : (306) 934 2322 mobile: markw_mobile at illuminae.com From bogus@does.not.exist.com Fri Nov 25 12:16:16 2005 From: bogus@does.not.exist.com () Date: Fri, 25 Nov 2005 17:16:16 -0000 Subject: No subject Message-ID: jas. From bogus@does.not.exist.com Fri Nov 25 12:16:16 2005 From: bogus@does.not.exist.com () Date: Fri, 25 Nov 2005 17:16:16 -0000 Subject: No subject Message-ID: reliability/interpretability of "semantic-free" cross-references, and lurking dangers of loose service definitions, it sounds as though you are beginning to lean toward the perspective that we can afford to be more prescriptive about the "right way" to structure one's data and present a "useful" interface to that data. While I don't want to push too hard at this stage in one direction or another, I do think it's important to respect the lurking danger of being so prescriptive that nobody wants to take the big leap from the way they're already doing things (presumably for some good reasons) to the way we've decided to look at things. At any rate, your point below about focus is well taken. Believe it or not, that is what I'm trying to do (in a vaguely academic, missive-oriented way). Defining the behavior of the system would be a nice thing to accomplish... Andrew > > I think it is more useful at this point to focus on: > > (1) the behaviour of the system we are trying to build - e.g. are tangential > relationships derived from cross-references going to produce interpretable results? > Are cross-references themselves going to be uniformly interpretable and reliable > since they are optional and server dependent? Is it "dangerous" to so loosely > define the relationship between the input and output of a service? > > (2) the level of data complexity required to achieve this behaviour - e.g. how many > ontologies do we need, how detailed do they need to be, how much data should we pass > in our objects, should they be hierarchical or loose collections... > > (3) the data formats - presumably XML, but how should we structure that data to > achieve the behaviour and complexity we need? > > I have a lot of ideas about the behaviour of the system, and have discussed them at > length both on and off the list... but certainly my conversations with Carole > (myGrid) a few weeks ago opened my eyes to the potential dangers lurking in my > approach. I am still hashing out these things, especially with the myGrid people, > though sadly much of this discussion is happening off the list. > > As I see it, we're in a bit of a holding pattern at the moment while we work out > what role ontologies will play in determining MOBY behaviour, and whether or not > these need to be built from scratch, or whether existing ontologies, such as those > generated by the myGrid project, will work in the somewhat looser (currently) MOBY > environment. Once we have these nailed down, we will be in a much better position > to decide what underlying technologies we need to achieve this... I think the > current discussion, though academically interesting, is likely a bit premature in > its intensity and that the best implementation choices will become much clearer when > we know for certain what exactly we need to achieve. > > I'm also convinced that there are some things that we will not be able to determine > through debate and academic missives... There are probably multiple equally valid > ways to achieve the goal, though they may or may not be equally difficult to > implement - I'm sure there will be times when we'll just have to set things up and > try them out! :-) > > M > > > > -- > -------------------------------- > "Speed is subsittute fo accurancy." > ________________________________ > > Dr. Mark Wilkinson, RA Bioinformatics > National Research Council, Plant Biotechnology Institute > 110 Gymnasium Place, Saskatoon, SK, Canada > > phone : (306) 975 5279 > pager : (306) 934 2322 > mobile: markw_mobile at illuminae.com > > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From markw at illuminae.com Tue Nov 8 11:13:47 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 08 Nov 2005 08:13:47 -0800 Subject: [MOBY-l] The service map on the new homepage Message-ID: <1131466427.19554.24.camel@bioinfo.icapture.ubc.ca> Thanks to Mathieu Rouard, the map of MOBY Services on the new homepage is now almost-live (updated every few hours). Thanks Mathieu! Mark -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From markw at illuminae.com Fri Nov 25 12:45:27 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 25 Nov 2005 09:45:27 -0800 Subject: [MOBY-l] biomoby.org moving to new server Message-ID: <1132940727.27789.48.camel@bioinfo.icapture.ubc.ca> Hi all, heads up that the DNS changes are about to start propagating through the net. By tomorrow we should be serving everything from the new server. LSID resolution should not be affected, since the lsid SRV records are held on a different machine entirely... but touch wood in any case. Please let me know ASAP if you notice any problems. M -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274