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Re: [ddlm-group] Stakeholders
- To: Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org>
- Subject: Re: [ddlm-group] Stakeholders
- From: Joe Krahn <krahn@niehs.nih.gov>
- Date: Tue, 01 Dec 2009 19:46:46 -0500
- In-Reply-To: <566795.18643.qm@web87004.mail.ird.yahoo.com>
- References: <C7398588.126B6%nick@csse.uwa.edu.au> <275884.79342.qm@web87006.mail.ird.yahoo.com> <alpine.BSF.2.00.0911300636400.56763@epsilon.pair.com> <4B13CFB6.5000405@pdb-mail.rutgers.edu> <alpine.BSF.2.00.0911300927480.56763@epsilon.pair.com> <279aad2a0911301456g4f6a36c3o9493fdc2f330637f@mail.gmail.com> <4B150794.1030106@pdb-mail.rutgers.edu> <alpine.BSF.2.00.0912010736110.27482@epsilon.pair.com><566795.18643.qm@web87004.mail.ird.yahoo.com>
SIMON WESTRIP wrote: > At whatever stage CIF2 is presented to 'end users' I think its success > or otherwise > will depend on how well we 'sell it'. For example, when I simply > described some of the > possible changes to a colleague recently, one 'gut reaction' was 'why?', > followed by > 'why not just convert to xml...!' That is, I had to sell the idea that > DDLm would > make life easier for the end user by e.g. deriving missing data, and > that CIF2 > would enable us to include far richer content in our CIFs... I am essentially an end-user here. My answers: Why not XML? XML is an ugly, overly-verbose mess. It is particularly inefficient for tables/arrays of data. It's only value is standardization. Why DDLm? I have no idea; I'm just here to discuss CIF2. Why CIF2? I suppose the main reason is that lists are useful. It should be possible to use nested loops defined by STAR, but excluded by CIF, but a list syntax is more efficient. There are also some situations that are not well defined in CIF, such as how to enclose a large string with all three types of close-quotes. Unfortunately (in my opinion), the current set of changes seems to go beyond addressing the CIF1 shortcomings. I think it would be easier to sell a conversion of value lists to CSV syntax, rather than an increasingly complex and non-standard quoting system. > > I would have no idea of how to sell this to the macromolecular community - > especially without a working implementation that could demonstrate some > benefit? Apparently, Herbert's group is already doing some CIF2 (or CIF1.5?) coding, which might give some good examples, but also is causing problems because it is a moving target. I would be in favor of presenting a tentative CIF2 format, with some alternatives, and get more feedback from developers. The number of subscribers here is too small. For example, maybe most developers want comma-delimited lists. Joe > ------------------------------------------------------------------------ > *From:* Herbert J. Bernstein <yaya@bernstein-plus-sons.com> > *To:* jwest@rcsb.rutgers.edu; Group finalising DDLm and associated > dictionaries <ddlm-group@iucr.org> > *Sent:* Tuesday, 1 December, 2009 12:45:41 > *Subject:* Re: [ddlm-group] Stakeholders > > Dear John, > > > Circulating a request for comment on community lists carries an > > implication impending change. For PDB users this will be viewed > > by many as adding confusion and complexity to a format that is > > already viewed as over complicated. > > Isn't the very intention of this effort that there be "impending change"? > Don't those same users have to see a specification of CIF 2 before it > comes into use? Will not the "maximally disruptive" approach adopted > by this group add "confusion and complexity to a format that is already > viewed as overly complicated" whenever they learn of this? > > Surely the sooner we start the necessary educational process and > the sooner we build support infrastructure for what has been made into > an intrinsicly difficult transition, the better. > > Regards, > Herbert > ===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 121 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu <mailto:yaya@dowling.edu> > ===================================================== > > On Tue, 1 Dec 2009, John Westbrook wrote: > > > Hi James and Herb, > > > > My comments are not directed at the style of organizing a software > > engineering effort, rather my concerns related to standardization > > and managing change from the perspective of an archive. > > > > Circulating a request for comment on community lists carries an > > implication impending change. For PDB users this will be viewed > > by many as adding confusion and complexity to a format that is > > already viewed as over complicated. > > > > I think that James' suggestion to post this on the cif-developers > > list is perhaps the best path forward. > > > > John > > > > James Hester wrote: > >> Dear all: > >> > >> Let's remember that we are only talking about the syntax specification > >> here, and as such our audience is almost completely restricted to > >> software authors. I would therefore have thought that the > >> cif-developers list would be a suitable forum to post a syntax draft. > >> > >> The process I had envisioned runs like this: > >> > >> 1. We finalise a syntax specification in this group - I remind you that > >> we only have one or two outstanding issues, both of which could be drawn > >> to a close with a vote fairly soon as we have had enough time to air our > >> opinions; > >> > >> 2. The draft syntax specification is posted on the IUCr website together > >> with an information page describing brief reasons for our choices, and > >> directing people to the archive of our discussions; > >> > >> 3. Feedback is requested from COMCIFS (who will have to approve it) and > >> the cif-developers list (where most of the people directly affected are > >> located), and any other appropriate list > >> > >> 4. We discuss and incorporate this feedback into our final draft, which > >> we submit to COMCIFS for approval. > >> > >> On Tue, Dec 1, 2009 at 1:49 AM, Herbert J. Bernstein > >> <yaya@bernstein-plus-sons.com <mailto:yaya@bernstein-plus-sons.com> > <mailto:yaya@bernstein-plus-sons.com > <mailto:yaya@bernstein-plus-sons.com>>> wrote: > >> > >> Dear John, > >> > >> I understand your point. You are espousing the classic > hierarchical > >> view of software engineering as seen in joint application design and > >> other > >> middle-manager-to-middle-manager design protocols. I am > espousing the > >> Scandinavian method, also called participatory design, in which > >> implementors deal directly with users. > >> > >> Both approaches have their passionate adherents. I suggest the > >> following compromise to allow us to benefit from the virtues of both > >> approaches: > >> > >> 1. Whatever the current state of the design of CIF2 and CIF > 1.5, the > >> essential user externals issues be summarized in a "one-pager" to be > >> reviewed and approved by this group, hopefully within the next week. > >> > >> 2. Then James, in the name of this group, forward that document > >> to the > >> appropriate managerial level contacts for the stakeholders, > asking them > >> for their thoughts and comments, say by the beginning of the new > year. > >> > >> 3. Then, in response to that feedback, that this group try to > have a > >> revised one-pager vetted both by this group and by any interested > >> managerial level contacts, say by the beginning of February. > >> > >> 4. Then, the revised one-pager be posted to the appropriate lists > >> for a > >> six-week comment period. > >> > >> That should then put us in good shape to have something to > discuss with > >> people at the ACA meeting in summer 2010. > >> > >> Regards, > >> Herbert > >> > >> ===================================================== > >> Herbert J. Bernstein, Professor of Computer Science > >> Dowling College, Kramer Science Center, KSC 121 > >> Idle Hour Blvd, Oakdale, NY, 11769 > >> > >> +1-631-244-3035 > >> yaya@dowling.edu <mailto:yaya@dowling.edu> > <mailto:yaya@dowling.edu <mailto:yaya@dowling.edu>> > >> ===================================================== > >> > >> On Mon, 30 Nov 2009, John Westbrook wrote: > >> > >> > The wwPDB will provide collective comment on issues of policy with > >> > respect to its use of CIF. wwPDB should include the BMRB as an > >> > organization as well. > >> > > >> > Comments to lists regarding changes to CIF or mmCIF need to be > vetted > >> > carefully by all of these groups prior to any public announcements. > >> > To give the impression that CIF is suddenly changing may be very > >> > detrimental to the entire CIF/mmCIF enterprise and could well > reverse > >> > the progress in adoption of this format. > >> > > >> > Regards, > >> > > >> > John > >> > > >> > > >> > Herbert J. Bernstein wrote: > >> >> Dear Colleagues, > >> >> > >> >> Before this discussion goes much further on any of its > threads, I > >> >> would suggest agreeing on a list of stakeholders and > consulting them > >> >> on what has been proposed and trying to come up with an external > >> >> user specification that they understand and agree to. Some of > >> >> the stakeholders that come to mind are: > >> >> > >> >> 1. The PDB in Rutgers > >> >> 2. The PDB in Europe > >> >> 3. The PDB in Japan > >> >> 4. People to speak for the Powder diffraction community > >> >> 5. People to speak for the NMR community > >> >> 6. The IUCr journal operation > >> >> 7. CCDC > >> >> 8. The writers of the various structure solution packages that > >> >> write (and in some cases read) CIF files > >> >> 9. The writers of visualization programs that read (and in > some > >> >> cases write) CIF files > >> >> 10. The synchrotron data collection community. > >> >> 11. Service crystallographers > >> >> 12. Diffraction equipment vendors > >> >> > >> >> I expect I have missed some and hope that others will add to > >> this list. > >> >> > >> >> I would suggest we prepare a summary of the current best > >> definition of > >> >> CIF 2 and, if this groups accepts the idea, CIF 1.5, and send > it out > >> >> the lists that cover these stakeholders, starting with the PDB > >> and CCP4 > >> >> lists, and see what feedback we get. > >> >> > >> >> Regards, > >> >> Herbert > >> >> > >> >> ===================================================== > >> >> Herbert J. Bernstein, Professor of Computer Science > >> >> Dowling College, Kramer Science Center, KSC 121 > >> >> Idle Hour Blvd, Oakdale, NY, 11769 _______________________________________________ ddlm-group mailing list ddlm-group@iucr.org http://scripts.iucr.org/mailman/listinfo/ddlm-group
Reply to: [list | sender only]
- References:
- Re: [ddlm-group] Space as a list item separator (Nick Spadaccini)
- Re: [ddlm-group] Space as a list item separator (SIMON WESTRIP)
- [ddlm-group] Stakeholders (Herbert J. Bernstein)
- Re: [ddlm-group] Stakeholders (John Westbrook)
- Re: [ddlm-group] Stakeholders (Herbert J. Bernstein)
- Re: [ddlm-group] Stakeholders (James Hester)
- Re: [ddlm-group] Stakeholders (John Westbrook)
- Re: [ddlm-group] Stakeholders (Herbert J. Bernstein)
- Re: [ddlm-group] Stakeholders (SIMON WESTRIP)
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