From c.lloyd at auckland.ac.nz Wed Dec 2 12:07:59 2009 From: c.lloyd at auckland.ac.nz (Catherine Lloyd) Date: Wed, 2 Dec 2009 12:07:59 +1300 Subject: [cellml-discussion] Terms of use for CellML models and associated content hosted on models.cellml.org Message-ID: <537F0659-1D93-4CA6-AAD3-5E078385CE82@auckland.ac.nz> Dear All We are looking towards using the MIRIAM Standard for the basic set of CellML model curation flags. In order to do this we need to consider how we are going to address the following point: "Is the model linked to a precise statement about the terms of distribution?" This issue has been raised at an Auckland CellML team meeting: http://www.cellml.org/community/meeting/minutes/2009/11.25 And it has also been discussed (briefly) on the Physiome tracker: https://tracker.physiomeproject.org/show_bug.cgi?id=2056 Before we come up with a definite solution to this problem we would like to open up the discussion further and invite the community to add any comments they might have to this tracker item. Thank you in advance for your thoughts and ideas! Best wishes Catherine From a.l.lister at newcastle.ac.uk Wed Dec 2 23:32:34 2009 From: a.l.lister at newcastle.ac.uk (Allyson Lister) Date: Wed, 2 Dec 2009 10:32:34 +0000 Subject: [cellml-discussion] Terms of use for CellML models and associated content hosted on models.cellml.org In-Reply-To: <537F0659-1D93-4CA6-AAD3-5E078385CE82@auckland.ac.nz> References: <537F0659-1D93-4CA6-AAD3-5E078385CE82@auckland.ac.nz> Message-ID: <841ae00912020232k2e025ab8sf0b05362e582b4b@mail.gmail.com> Hi all, This is an interesting point - thanks for bringing it to the community, Catherine! Though I am not a developer of CellML models, but rather a user of them (in the bioinformatics, data integration sense), I have a few points to make that might help this discussion. I have spent a lot of time thinking about licensing with respect to ontologies, which are similar beasts in terms of licensing, IMHO. Firstly: the distinction between *attribution* and *citation*. At the risk of tooting my own horn, me and a colleague Frank Gibson have written about this in the context of the life sciences here: http://themindwobbles.wordpress.com/2009/07/10/attribution-vs-citation-do-you-know-the-difference/. Basically, what I would like people to get from this point is that you need to carefully define what the goal is that you want to achieve with the terms of model distribution. Secondly: licensing (which guarantees attribution, but not necessarily citation). The most common requirement mentioned in the links below is attribution. Some have suggested GPL, others the CC-BY license. I would like to suggest that you do NOT use GPL. Although the name "viral" may be misleading, it is true that if a 3rd party wants to use your GPL-licensed models, that if you create a software program that *is a derived work of another software program, then that combined work must be distributed under these terms*. This means that you are restricting everyone down the line to using GPL. I would suggest a variant of the Creative Commons license, such as CC-BY. However, Creative Commons is explictly NOT designed for software. Here, you run into the same problem I had with figuring out a license for ontologies: are ontologies - and models - software or documents? It is my impression (and one that seems to be backed up by the Science Commons folks) that these are indeed documents, and would be suitable for CC. CC allows you to choose a license that isn't defined by any particular country. CC-BY forces attribution (http://creativecommons.org/licenses/by/3.0/) while CC-BY-SA (http://creativecommons.org/licenses/by-sa/3.0/) enforces attribution and for people to use similar, compatible (but not identical) licensing. (btw, it seems the BioModels terms of use are here, and might be worth a read: http://www.ebi.ac.uk/biomodels-main/termsofuse) Thirdly: attribution stacking. While it is a good idea (it's what I do) to require attribution in your license, because CellML models may be incorporated one into another into another into another etc, you may get the situation very quickly where it becomes rather unwieldy to ensure everything has been attributed properly. Conversely, if each model gets the attribution right each time, it may not be such a high wall to climb after all. The Science Commons people have something to say about this in general: http://themindwobbles.wordpress.com/2009/11/12/science-commons-provide-a-list-of-considerations-for-researchers-looking-to-license-their-ontology/. The link I provide here is about ontologies, but the broad points remain important. Finally, do you want links to the other model URIs, or to the DOIs of the papers they're described in? I'm guessing the former, as perhaps the latter will be included in the model's metadata anyway? However, model authors may be more keen, in terms of # of citations being an important metric, to see a DOI put in instead. Not sure, would have to ask the modellers themselves. Hope this helps, and sorry for the length - I didn't intend it to be so long when I started! :) allyson 2009/12/1 Catherine Lloyd > Dear All > > We are looking towards using the MIRIAM Standard for the basic set of > CellML model curation flags. In order to do this we need to consider how we > are going to address the following point: > > "Is the model linked to a precise statement about the terms of > distribution?" > > This issue has been raised at an Auckland CellML team meeting: > > http://www.cellml.org/community/meeting/minutes/2009/11.25 > > And it has also been discussed (briefly) on the Physiome tracker: > > https://tracker.physiomeproject.org/show_bug.cgi?id=2056 > > Before we come up with a definite solution to this problem we would like to > open up the discussion further and invite the community to add any comments > they might have to this tracker item. > > Thank you in advance for your thoughts and ideas! > > Best wishes > Catherine > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > -- Allyson Lister http://themindwobbles.wordpress.com CISBAN, http://www.cisban.ac.uk Newcastle University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hans.ekkehard.plesser at umb.no Thu Dec 3 00:54:05 2009 From: hans.ekkehard.plesser at umb.no (Dr. Hans Ekkehard Plesser) Date: Wed, 2 Dec 2009 12:54:05 +0100 Subject: [cellml-discussion] Terms of use for CellML models and associated content hosted on models.cellml.org In-Reply-To: <841ae00912020232k2e025ab8sf0b05362e582b4b@mail.gmail.com> References: <537F0659-1D93-4CA6-AAD3-5E078385CE82@auckland.ac.nz> <841ae00912020232k2e025ab8sf0b05362e582b4b@mail.gmail.com> Message-ID: <4B16555D.3080509@umb.no> Hi! You may want to look at work in licensing by Victoria Stodden, see http://www.stanford.edu/~vcs/ Best, Hans Allyson Lister wrote: > Hi all, > > This is an interesting point - thanks for bringing it to the community, > Catherine! > > Though I am not a developer of CellML models, but rather a user of them > (in the bioinformatics, data integration sense), I have a few points to > make that might help this discussion. I have spent a lot of time > thinking about licensing with respect to ontologies, which are similar > beasts in terms of licensing, IMHO. > > Firstly: the distinction between /attribution/ and /citation/. At the > risk of tooting my own horn, me and a colleague Frank Gibson have > written about this in the context of the life sciences here: > http://themindwobbles.wordpress.com/2009/07/10/attribution-vs-citation-do-you-know-the-difference/ > . Basically, what I would like people to get from this point is that you > need to carefully define what the goal is that you want to achieve with > the terms of model distribution. > > Secondly: licensing (which guarantees attribution, but not necessarily > citation). The most common requirement mentioned in the links below is > attribution. Some have suggested GPL, others the CC-BY license. I would > like to suggest that you do NOT use GPL. Although the name "viral" may > be misleading, it is true that if a 3rd party wants to use your > GPL-licensed models, that if you create a software program that /is a > derived work of another software program, then that combined work must > be distributed under these terms/. This means that you are restricting > everyone down the line to using GPL. I would suggest a variant of the > Creative Commons license, such as CC-BY. However, Creative Commons is > explictly NOT designed for software. Here, you run into the same problem > I had with figuring out a license for ontologies: are ontologies - and > models - software or documents? It is my impression (and one that seems > to be backed up by the Science Commons folks) that these are indeed > documents, and would be suitable for CC. CC allows you to choose a > license that isn't defined by any particular country. CC-BY forces > attribution (http://creativecommons.org/licenses/by/3.0/) while CC-BY-SA > (http://creativecommons.org/licenses/by-sa/3.0/) enforces attribution > and for people to use similar, compatible (but not identical) licensing. > (btw, it seems the BioModels terms of use are here, and might be worth a > read: http://www.ebi.ac.uk/biomodels-main/termsofuse) > > Thirdly: attribution stacking. While it is a good idea (it's what I do) > to require attribution in your license, because CellML models may be > incorporated one into another into another into another etc, you may get > the situation very quickly where it becomes rather unwieldy to ensure > everything has been attributed properly. Conversely, if each model gets > the attribution right each time, it may not be such a high wall to climb > after all. The Science Commons people have something to say about this > in general: > http://themindwobbles.wordpress.com/2009/11/12/science-commons-provide-a-list-of-considerations-for-researchers-looking-to-license-their-ontology/ > . The link I provide here is about ontologies, but the broad points > remain important. > > Finally, do you want links to the other model URIs, or to the DOIs of > the papers they're described in? I'm guessing the former, as perhaps the > latter will be included in the model's metadata anyway? However, model > authors may be more keen, in terms of # of citations being an important > metric, to see a DOI put in instead. Not sure, would have to ask the > modellers themselves. > > Hope this helps, and sorry for the length - I didn't intend it to be so > long when I started! > > :) allyson > > 2009/12/1 Catherine Lloyd > > > Dear All > > We are looking towards using the MIRIAM Standard for the basic set > of CellML model curation flags. In order to do this we need to > consider how we are going to address the following point: > > "Is the model linked to a precise statement about the terms of > distribution?" > > This issue has been raised at an Auckland CellML team meeting: > > http://www.cellml.org/community/meeting/minutes/2009/11.25 > > And it has also been discussed (briefly) on the Physiome tracker: > > https://tracker.physiomeproject.org/show_bug.cgi?id=2056 > > Before we come up with a definite solution to this problem we would > like to open up the discussion further and invite the community to > add any comments they might have to this tracker item. > > Thank you in advance for your thoughts and ideas! > > Best wishes > Catherine > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > > > > > -- > Allyson Lister > http://themindwobbles.wordpress.com > > CISBAN, http://www.cisban.ac.uk > Newcastle University > -- Dr. Hans Ekkehard Plesser Associate Professor Dept. of Mathematical Sciences and Technology Norwegian University of Life Sciences Phone +47 6496 5467 Fax +47 6496 5401 Email hans.ekkehard.plesser at umb.no Home http://arken.umb.no/~plesser From c.lloyd at auckland.ac.nz Thu Dec 3 08:57:49 2009 From: c.lloyd at auckland.ac.nz (Catherine Lloyd) Date: Thu, 3 Dec 2009 08:57:49 +1300 Subject: [cellml-discussion] Terms of use for CellML models and associated content hosted on models.cellml.org In-Reply-To: <4B16555D.3080509@umb.no> References: <537F0659-1D93-4CA6-AAD3-5E078385CE82@auckland.ac.nz> <841ae00912020232k2e025ab8sf0b05362e582b4b@mail.gmail.com> <4B16555D.3080509@umb.no> Message-ID: Dear Allyson and Hans Thank you for your thoughts on this topic... I'll add your comments to the tracker item to keep all the information in one place, and I will raise this issue again at next week's CellML meeting to keep the momentum going and hopefully come to a solution in the not too distant future! Best wishes Catherine On 3/12/2009, at 12:54 AM, Dr. Hans Ekkehard Plesser wrote: > > Hi! > > You may want to look at work in licensing by Victoria Stodden, see > > http://www.stanford.edu/~vcs/ > > Best, > Hans > > Allyson Lister wrote: >> Hi all, >> >> This is an interesting point - thanks for bringing it to the >> community, >> Catherine! >> >> Though I am not a developer of CellML models, but rather a user of >> them >> (in the bioinformatics, data integration sense), I have a few >> points to >> make that might help this discussion. I have spent a lot of time >> thinking about licensing with respect to ontologies, which are >> similar >> beasts in terms of licensing, IMHO. >> >> Firstly: the distinction between /attribution/ and /citation/. At the >> risk of tooting my own horn, me and a colleague Frank Gibson have >> written about this in the context of the life sciences here: >> http://themindwobbles.wordpress.com/2009/07/10/attribution-vs-citation-do-you-know-the-difference/ >> . Basically, what I would like people to get from this point is >> that you >> need to carefully define what the goal is that you want to achieve >> with >> the terms of model distribution. >> >> Secondly: licensing (which guarantees attribution, but not >> necessarily >> citation). The most common requirement mentioned in the links below >> is >> attribution. Some have suggested GPL, others the CC-BY license. I >> would >> like to suggest that you do NOT use GPL. Although the name "viral" >> may >> be misleading, it is true that if a 3rd party wants to use your >> GPL-licensed models, that if you create a software program that /is a >> derived work of another software program, then that combined work >> must >> be distributed under these terms/. This means that you are >> restricting >> everyone down the line to using GPL. I would suggest a variant of the >> Creative Commons license, such as CC-BY. However, Creative Commons is >> explictly NOT designed for software. Here, you run into the same >> problem >> I had with figuring out a license for ontologies: are ontologies - >> and >> models - software or documents? It is my impression (and one that >> seems >> to be backed up by the Science Commons folks) that these are indeed >> documents, and would be suitable for CC. CC allows you to choose a >> license that isn't defined by any particular country. CC-BY forces >> attribution (http://creativecommons.org/licenses/by/3.0/) while CC- >> BY-SA >> (http://creativecommons.org/licenses/by-sa/3.0/) enforces attribution >> and for people to use similar, compatible (but not identical) >> licensing. >> (btw, it seems the BioModels terms of use are here, and might be >> worth a >> read: http://www.ebi.ac.uk/biomodels-main/termsofuse) >> >> Thirdly: attribution stacking. While it is a good idea (it's what I >> do) >> to require attribution in your license, because CellML models may be >> incorporated one into another into another into another etc, you >> may get >> the situation very quickly where it becomes rather unwieldy to ensure >> everything has been attributed properly. Conversely, if each model >> gets >> the attribution right each time, it may not be such a high wall to >> climb >> after all. The Science Commons people have something to say about >> this >> in general: >> http://themindwobbles.wordpress.com/2009/11/12/science-commons-provide-a-list-of-considerations-for-researchers-looking-to-license-their-ontology/ >> . The link I provide here is about ontologies, but the broad points >> remain important. >> >> Finally, do you want links to the other model URIs, or to the DOIs of >> the papers they're described in? I'm guessing the former, as >> perhaps the >> latter will be included in the model's metadata anyway? However, >> model >> authors may be more keen, in terms of # of citations being an >> important >> metric, to see a DOI put in instead. Not sure, would have to ask the >> modellers themselves. >> >> Hope this helps, and sorry for the length - I didn't intend it to >> be so >> long when I started! >> >> :) allyson >> >> 2009/12/1 Catherine Lloyd > > >> >> Dear All >> >> We are looking towards using the MIRIAM Standard for the basic set >> of CellML model curation flags. In order to do this we need to >> consider how we are going to address the following point: >> >> "Is the model linked to a precise statement about the terms of >> distribution?" >> >> This issue has been raised at an Auckland CellML team meeting: >> >> http://www.cellml.org/community/meeting/minutes/2009/11.25 >> >> And it has also been discussed (briefly) on the Physiome tracker: >> >> https://tracker.physiomeproject.org/show_bug.cgi?id=2056 >> >> Before we come up with a definite solution to this problem we >> would >> like to open up the discussion further and invite the community to >> add any comments they might have to this tracker item. >> >> Thank you in advance for your thoughts and ideas! >> >> Best wishes >> Catherine >> >> _______________________________________________ >> cellml-discussion mailing list >> cellml-discussion at cellml.org >> http://www.cellml.org/mailman/listinfo/cellml-discussion >> >> >> >> >> -- >> Allyson Lister >> http://themindwobbles.wordpress.com >> >> CISBAN, http://www.cisban.ac.uk >> Newcastle University >> > > -- > Dr. Hans Ekkehard Plesser > Associate Professor > > Dept. of Mathematical Sciences and Technology > Norwegian University of Life Sciences > > Phone +47 6496 5467 > Fax +47 6496 5401 > Email hans.ekkehard.plesser at umb.no > Home http://arken.umb.no/~plesser > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From dj.cowan at auckland.ac.nz Fri Dec 4 08:27:34 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 04 Dec 2009 08:27:34 +1300 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-12-02 Message-ID: <4B181126.5030309@auckland.ac.nz> I have put the minutes from this week's meeting up at: http://www.cellml.org/community/meeting/minutes/2009/12.02 Dougal From alan.garny at dpag.ox.ac.uk Fri Dec 4 21:53:45 2009 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Fri, 4 Dec 2009 08:53:45 -0000 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-12-02 In-Reply-To: <4B181126.5030309@auckland.ac.nz> References: <4B181126.5030309@auckland.ac.nz> Message-ID: <000401ca74bf$49f99770$ddecc650$@dpag.ox.ac.uk> Hi guys, Just a couple of things regarding the minutes: - It might be useful, whenever referring to a particular tracker item (as is the case in the "Last week's action items" section) to have a link to the tracker item itself. Not only would it make it more convenient for those of us who use the tracker, but (most importantly) it might also get non tracker users to realise of the usefulness of the tracker (since they could 'quickly' check it out) and get them involved. - Item 6.3: tracker item 1716 is not a feature, it's purely and simply a bug. I wouldn't, however, want that tracker item to delay the next release, and would therefore be happy for it to be addressed in the next release. Alan > -----Original Message----- > From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- > bounces at cellml.org] On Behalf Of Dougal Cowan > Sent: 03 December 2009 19:28 > To: cellml-discussion at cellml.org > Subject: [cellml-discussion] ABI CellML meeting minutes 2009-12-02 > > I have put the minutes from this week's meeting up at: > > http://www.cellml.org/community/meeting/minutes/2009/12.02 > > > Dougal > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From ak.miller at auckland.ac.nz Wed Dec 9 12:29:32 2009 From: ak.miller at auckland.ac.nz (Andrew Miller) Date: Wed, 09 Dec 2009 12:29:32 +1300 Subject: [cellml-discussion] Description of CellML groupings In-Reply-To: <4B1ED9A7.70709@gmail.com> References: <4B1ED9A7.70709@gmail.com> Message-ID: <4B1EE15C.3080205@auckland.ac.nz> Dominick Layfield wrote: > Hi Catherine, > > Thanks for raising these issues. I would be more than happy to read and > comment on any material in the 1.2 spec or any revisions to the > tutorial. I appreciate that this is being looked into. Hi Dominick, Catherine has told me that you have found the part of the CellML 1.1 specification relating to the interpretation of grouping to be ambiguous. I'm CCing this to the cellml-discussion mailing list, which is a good place to discuss the CellML discussions (you need to subscribe at http://www.cellml.org/mailman/listinfo/cellml-discussion before you can post to the list). The plan going forward is to have two descriptions of CellML: - a normative description. This description uses precise technical language, and will be the official description of CellML which should be referred to in the case of any conflict between the documents, or ambiguity in the other documents. It won't contain any information which is unnecessary to achieve this purpose (so as to avoid accidentally contradicting itself). - an informative tutorial on CellML. This document will include examples, and will be based on the normative description. It can be updated to improve clarity and ensure that it properly reflects the normative description. Because everything depends on the normative description, we are working on completing that first. Due to the draft nature of the work, there is no one 'official' draft - but I will refer you to one draft which has been modified from the base to simply the connection element: http://www.cellml.org/Members/miller/draft-normative-spec-simplify-connections/toplevel.xhtml http://www.cellml.org/Members/miller/draft-normative-spec/toplevel.xhtml is more similar to CellML 1.1. The section "Interpretation of grouping" provides precise rules, in terms of graph theory, about which elements can legitimately be connected. Best wishes, Andrew > > -- Dominick > > > On 12/08/2009 03:47 PM, Catherine Lloyd wrote: >> Dear Dominick >> >> I raised your two comments about needing a better description of CellML >> groupings and also a CellML 1.1 model building tutorial at today's team >> meeting. >> >> Regarding the first comment, Andrew Miller has been working on the >> CellML 1.2 specification (currently a draft) and he will send you a link >> to it - asking if the description is any clearer in the new spec (there >> is a normative and an informative version of the 1.2 spec - hopefully >> Andrew will send you both. >> >> Regarding the second point (on the 1.1 tutorial) - the agenda item will >> be raised again at next week's meeting when 3 other key people will be >> present, and we will think about the best approach. >> >> Thanks again for your interest in CellML. >> >> Best wishes >> Catherine >> >> > From r.britten at auckland.ac.nz Wed Dec 9 16:36:01 2009 From: r.britten at auckland.ac.nz (Randall Britten) Date: Wed, 9 Dec 2009 16:36:01 +1300 Subject: [cellml-discussion] Brief outage of CellML SVN server Message-ID: <00c601ca7880$ba8cd820$2fa68860$@britten@auckland.ac.nz> Hi Due to system maintenance, there will be a 15 minute outage of the physiomeproject.org SVN server, tonight (9 December) 19:35 NZDT. This should have minimal impact, it affects the server that hosts the OpenCell "snapshot" builds, and the PMR2 codebase. We apologise for any inconvenience this may cause. Regards, Randall Britten ___________________________ Leader of the Bioengineering Software Development Group Auckland Bioengineering Institute Auckland University Auckland, New Zealand -------------- next part -------------- An HTML attachment was scrubbed... URL: From dj.cowan at auckland.ac.nz Thu Dec 10 19:04:09 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Thu, 10 Dec 2009 19:04:09 +1300 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-12-09 Message-ID: <4B208F59.2030007@auckland.ac.nz> I have put the minutes from this week's meeting up at: http://www.cellml.org/community/meeting/minutes/2009/12.09 Dougal From j.lawson at auckland.ac.nz Wed Dec 16 16:38:31 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Wed, 16 Dec 2009 16:38:31 +1300 Subject: [cellml-discussion] I am leaving the ABI Message-ID: <4B285637.4060600@auckland.ac.nz> Hi all, This is just a note to say that I will be leaving the Auckland Bioengineering Institute on January 14th 2010, after which point I will no longer be a regular contributor to the CellML project. I do plan to stay up to date with developments in the project and to keep in touch with the community after my departure. I'd like to say what a fantastic few years I've had on the project, and that I have very much enjoyed working with everyone who works tirelessly to make CellML the revolutionary technology that it is. Kind regards, James Lawson -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From dj.cowan at auckland.ac.nz Thu Dec 17 14:55:26 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Thu, 17 Dec 2009 14:55:26 +1300 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-12-16 Message-ID: <4B298F8E.4060800@auckland.ac.nz> I have put the minutes from this week's meeting up at: http://www.cellml.org/community/meeting/minutes/2009/12.16 Dougal From ak.miller at auckland.ac.nz Thu Dec 17 18:22:28 2009 From: ak.miller at auckland.ac.nz (Andrew Miller) Date: Thu, 17 Dec 2009 18:22:28 +1300 Subject: [cellml-discussion] Tracker / subversion outage tonight 9:30 PM to 11:30 PM Message-ID: <4B29C014.2020008@auckland.ac.nz> Hi all, The Physiome tracker and Subversion repositories containing software snapshots will be unavailable tonight from 9:30 PM until 11:30 PM NZDT (8:30 AM - 10:30 AM GMT) when power will be switched from the generator to mains power, following the power failure last night affecting the building housing the Auckland Bioengineering Institute. Hopefully everything should come back up after this, although there were some technical problems with the tracker following the power outage last night. I apologise for any inconvenience this may cause people. Best wishes, Andrew From alan.garny at dpag.ox.ac.uk Fri Dec 18 01:25:39 2009 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Thu, 17 Dec 2009 12:25:39 -0000 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-12-16 In-Reply-To: <4B298F8E.4060800@auckland.ac.nz> References: <4B298F8E.4060800@auckland.ac.nz> Message-ID: <001901ca7f14$0b95ca80$22c15f80$@dpag.ox.ac.uk> > From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- > bounces at cellml.org] On Behalf Of Dougal Cowan > Sent: 17 December 2009 01:55 > To: cellml-discussion at cellml.org > Subject: [cellml-discussion] ABI CellML meeting minutes 2009-12-16 > > I have put the minutes from this week's meeting up at: > > http://www.cellml.org/community/meeting/minutes/2009/12.16 Just a quick comment about the minutes: - "Randall said we will need a good way to indicate which license applies to each model - possibly in metadata." -- Metadata seems like an obvious place indeed. One thing to keep in mind (and I am sure you guys did, but I didn't see any mention of it) is that the license under which a particular model comes should be very obvious to anyone using PMR2. In other words, someone shouldn't have to, say, download a model and then check its metadata so that he knows about its license. Alan From j.lawson at auckland.ac.nz Fri Dec 18 09:25:01 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Fri, 18 Dec 2009 09:25:01 +1300 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-12-16 In-Reply-To: <001901ca7f14$0b95ca80$22c15f80$@dpag.ox.ac.uk> References: <4B298F8E.4060800@auckland.ac.nz> <001901ca7f14$0b95ca80$22c15f80$@dpag.ox.ac.uk> Message-ID: We (Catherine, Poul and I) were thinking that there are basically three places where you'd want to display / store this information within PMR2: in the metadata itself (thereby allowing it to be rendered by software, indexed and searched etc.), on the exposure somewhere (perhaps a rendering of the metadata,) and in the proposed blanket, site-wide 'terms of use' page. As Catherine has mentioned in the relevant tracker item (don't have the number on hand,) one of the issues which we must now decide on is whether to require that all models in the repository abide by CC attrib 3 or whether users can specify special cases. Cheers, James On 18/12/2009, at 1:25 AM, Alan Garny wrote: >> From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- >> bounces at cellml.org] On Behalf Of Dougal Cowan >> Sent: 17 December 2009 01:55 >> To: cellml-discussion at cellml.org >> Subject: [cellml-discussion] ABI CellML meeting minutes 2009-12-16 >> >> I have put the minutes from this week's meeting up at: >> >> http://www.cellml.org/community/meeting/minutes/2009/12.16 > > Just a quick comment about the minutes: > > - "Randall said we will need a good way to indicate which license > applies > to each model - possibly in metadata." -- Metadata seems like an > obvious > place indeed. One thing to keep in mind (and I am sure you guys did, > but I > didn't see any mention of it) is that the license under which a > particular > model comes should be very obvious to anyone using PMR2. In other > words, > someone shouldn't have to, say, download a model and then check its > metadata > so that he knows about its license. > > Alan > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From alan.garny at dpag.ox.ac.uk Sat Dec 19 00:35:54 2009 From: alan.garny at dpag.ox.ac.uk (alan.garny at dpag.ox.ac.uk) Date: Fri, 18 Dec 2009 11:35:54 -0000 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-12-16 In-Reply-To: References: <4B298F8E.4060800@auckland.ac.nz> <001901ca7f14$0b95ca80$22c15f80$@dpag.ox.ac.uk> Message-ID: <7deb8b8bda660e58fb549ca59690fcf2.squirrel@mail.physiol.ox.ac.uk> James Lawson wrote: > We (Catherine, Poul and I) were thinking that there are basically > three places where you'd want to display / store this information > within PMR2: in the metadata itself (thereby allowing it to be > rendered by software, indexed and searched etc.), on the exposure > somewhere (perhaps a rendering of the metadata,) and in the proposed > blanket, site-wide 'terms of use' page. > > As Catherine has mentioned in the relevant tracker item (don't have > the number on hand,) one of the issues which we must now decide on is > whether to require that all models in the repository abide by CC > attrib 3 or whether users can specify special cases. We should be open and therefore allow people to go for whatever license they want. However, they should be made aware that by doing so, they take the risk of their model not being used, etc. This being said, some authors might still prefer that outcome to not having their model on the CellML repository? Alan From ak.miller at auckland.ac.nz Sat Dec 19 00:48:13 2009 From: ak.miller at auckland.ac.nz (Andrew Miller) Date: Sat, 19 Dec 2009 00:48:13 +1300 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-12-16 In-Reply-To: <7deb8b8bda660e58fb549ca59690fcf2.squirrel@mail.physiol.ox.ac.uk> References: <4B298F8E.4060800@auckland.ac.nz> <001901ca7f14$0b95ca80$22c15f80$@dpag.ox.ac.uk> <7deb8b8bda660e58fb549ca59690fcf2.squirrel@mail.physiol.ox.ac.uk> Message-ID: <4B2B6BFD.6050602@auckland.ac.nz> alan.garny at dpag.ox.ac.uk wrote: > James Lawson wrote: >> We (Catherine, Poul and I) were thinking that there are basically >> three places where you'd want to display / store this information >> within PMR2: in the metadata itself (thereby allowing it to be >> rendered by software, indexed and searched etc.), on the exposure >> somewhere (perhaps a rendering of the metadata,) and in the proposed >> blanket, site-wide 'terms of use' page. >> >> As Catherine has mentioned in the relevant tracker item (don't have >> the number on hand,) one of the issues which we must now decide on is >> whether to require that all models in the repository abide by CC >> attrib 3 or whether users can specify special cases. > > We should be open and therefore allow people to go for whatever license > they want. However, they should be made aware that by doing so, they take > the risk of their model not being used, etc. This being said, some authors > might still prefer that outcome to not having their model on the CellML > repository? Hi Alan, Allowing people the ability to choose other licenses is something that I think can go into later releases of the repository; however, until then, the simplest thing to do is just to require that people need to license the model under the Creative Commons Attribution License. If we do allow other licenses, we do need to make sure that the license allows us to distribute the model to everyone who asks for it through the model repository - so a manual process of review of any new licenses would probably be required (but we could let users choose from several licenses we had pre-approved). I don't think that requiring people to license their contributions under a particular license is contrary to the principle of being open - the copyright holder of the model can freely license it under the terms and submit the model, and this ensures that everyone can download and adapt models from the repository - which is more open than it would be if some parts of the repository were more restricted. Best wishes, Andrew > > Alan > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From alan.garny at dpag.ox.ac.uk Sat Dec 19 07:09:17 2009 From: alan.garny at dpag.ox.ac.uk (alan.garny at dpag.ox.ac.uk) Date: Fri, 18 Dec 2009 18:09:17 -0000 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-12-16 In-Reply-To: <4B2B6BFD.6050602@auckland.ac.nz> References: <4B298F8E.4060800@auckland.ac.nz> <001901ca7f14$0b95ca80$22c15f80$@dpag.ox.ac.uk> <7deb8b8bda660e58fb549ca59690fcf2.squirrel@mail.physiol.ox.ac.uk> <4B2B6BFD.6050602@auckland.ac.nz> Message-ID: <2ea0e619e694c23bdcda523f9cd4c2c7.squirrel@mail.physiol.ox.ac.uk> Andrew Miller wrote: > alan.garny at dpag.ox.ac.uk wrote: >> We should be open and therefore allow people to go for whatever license >> they want. However, they should be made aware that by doing so, they >> take >> the risk of their model not being used, etc. This being said, some >> authors >> might still prefer that outcome to not having their model on the CellML >> repository? > > Allowing people the ability to choose other licenses is something that I > think can go into later releases of the repository; however, until then, > the simplest thing to do is just to require that people need to license > the model under the Creative Commons Attribution License. Indeed, but what if they don't want or can't (whatever the reason)? Does it mean that the model can't be made available on PMR2? Hopefully not. Alan