Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-26 Thread Tommy Yu
David Nickerson wrote: Hi Tommy, That looks good - its all starting to make sense to me now. I'm just wondering how your system would handle a case where two authors independently encode the same published model. The first author to upload their encoding would get ownership of the

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-26 Thread Matt
I don't understand the purpose of this. It looks like you are inventing a versioning system to implement from scratch. I don't see how this system would work with someone working on a filesystem and not wanting to use a browser - you'd have to invent client software for this. Start by reviewing

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-26 Thread Tommy Yu
Matt wrote: I don't understand the purpose of this. It looks like you are inventing a versioning system to implement from scratch. That's what it looks like, but if you recall the software choices I have written down I have been considering them, and have been going through the features

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-26 Thread Matt
On 6/26/07, Tommy Yu [EMAIL PROTECTED] wrote: Matt wrote: I don't understand the purpose of this. It looks like you are inventing a versioning system to implement from scratch. That's what it looks like, but if you recall the software choices I have written down I have been

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-26 Thread Matt
This is my view of where things should be heading: The main impetus for this thread is moving the cellml.org site forward. In this sense I would like to see a description of what it currently does and what features have been informally slated. Then I'd like to see a document that re-writes these

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-25 Thread Tommy Yu
Hi, I thought Andrew's ideas here is worth expanding, and I wrote a page based on that. http://www.cellml.org/Members/tommy/BaseRepository Cheers, Tommy. Andrew Miller wrote: Matt wrote: - Version/Variant It already clogged up the system. There is no proper revision control mechanism,

Re: [cellml-discussion] Concerning the CellML Model Repository | version/variant metadata?

2007-06-24 Thread James Lawson
My $0.02 on this is (please forgive me if I get some of the technical stuff mixed up): The current naming scheme is as it translates to the web address is: author(s)_date_versionXX_variantXX I think it should be author(s)_date_variantXX_versionXX instead, since IMO, one should be thinking in

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-24 Thread Matt
On 6/25/07, James Lawson [EMAIL PROTECTED] wrote: What is 'agnositic' and what does it mean here? It's one of those english terms that is being hijacked in some IT circles. E.g. platform agnostic : http://www.e-consultancy.com/knowledge/glossary/20312/platform-agnostic.html I quite like it

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-22 Thread Matt
On 6/22/07, Tommy Yu [EMAIL PROTECTED] wrote: Matt wrote: Hi Tommy, Can you continue to update/fill out your document as well as begin associated proposals with information contained in the replies people are submitting. The goal of this process is a scoping document with associated

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-22 Thread David Nickerson
Do we really want to proxy remote repositories? Can we start smaller for now but keep that in mind? I think this will be an essential feature of the model repository as we move forward. We are trying to present model authors with a common platform for the distribution and archiving of their

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-22 Thread David Nickerson
It might also be worth looking into what the folks over at http://www.biomodels.net/ are up to. Given they seem to have curation built into their repository and maybe some other features worth looking into? And if we're going to be starting from scratch, there might be some value into seeing

[cellml-discussion] Concerning the CellML Model Repository

2007-06-21 Thread Tommy Yu
Hi, I have written down some of my thoughts on how the model repository could be put together. http://www.cellml.org/Members/tommy/repository_redesign.html It is still a pretty rough document. The usage example section gives a rough outline on what I see people might be doing with the

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-21 Thread David Nickerson
Hi Tommy, looks like a good starting point for some discussion. Just to help me think through some of the issues, is there any chance you could add a usage example illustrating how this system would deal with a model made from the combination of a bunch of papers (i.e., a single model where

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-21 Thread Matt
Hi Tommy, I found the document seemed to be too far ahead of itself. I also didn't find any of the pros and cons very compelling because they don't address specific problems and those problems are not described. 1) What are you actually trying to achieve? It would be useful to describe the parts

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-21 Thread Andrew Miller
Tommy Yu wrote: Hi, I have written down some of my thoughts on how the model repository could be put together. http://www.cellml.org/Members/tommy/repository_redesign.html It is still a pretty rough document. The usage example section gives a rough outline on what I see people might be

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-21 Thread Tommy Yu
Hi Andrew, A couple notes: I don't think it is a bad thing to have a one-way cache of metadata somewhere for technical / performance reasons (perhaps in a relational database), but I think that we should replicate data for each model (perhaps using a deep copy-on-write approach if this is

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-21 Thread Tommy Yu
David Nickerson wrote: Hi Tommy, looks like a good starting point for some discussion. Just to help me think through some of the issues, is there any chance you could add a usage example illustrating how this system would deal with a model made from the combination of a bunch of papers

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-21 Thread Matt
Hi Tommy, Can you continue to update/fill out your document as well as begin associated proposals with information contained in the replies people are submitting. The goal of this process is a scoping document with associated content. More comments below. On 6/22/07, Tommy Yu [EMAIL PROTECTED]

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-21 Thread Tommy Yu
Matt wrote: Hi Tommy, Can you continue to update/fill out your document as well as begin associated proposals with information contained in the replies people are submitting. The goal of this process is a scoping document with associated content. It will be done when I am done refining

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-21 Thread Andrew Miller
Matt wrote: - Version/Variant It already clogged up the system. There is no proper revision control mechanism, what we have now is an ad-hoc emulated system. I don't think it has clogged the system I just think it has been improperly used both by authors and by the user interface.