Re: [cellml-discussion] Java error on Mac OSX10.8.2
Hi Mark, FYI, there is a new CellML simulation tool called OpenCOR being developed by Alan Garny that is becoming our primary platform for CellML-based modelling (see http://www.cellml.org/getting-started/tutorials/opencordemo for download instructions). This will shortly have CellML authoring capability and is a more robust environment than OpenCell, although I currently use both - OpenCell for authoring models and OpenCOR for running simulations. OpenCOR has facilities for annotating models against bio-ontologies such as GO, although access to the Ricordo webservices for providing the ontologies is a wee way off (hopefully achieved by the time of the CellML workshop in Auckland in a few weeks). Rgds, Peter On 26/02/2013 4:37 a.m., Mark Cannell wrote: Hi All I've been trying to test the new open cell 0.8 on a mac but all I get is a java runtime error and I have no idea how to get over it: [Exception... Component returned failure code: 0x80004005 (NS_ERROR_FAILURE) [cellml_servicesICellMLIntegrationService.compileModelODE] nsresult: 0x80004005 (NS_ERROR_FAILURE) location: JS frame :: chrome://opencell/content/util/Integration.js :: StartCollectingResults :: line 18 data: no] Has anyone run open cell on a mac? I used cor0.8 under a windows emulator and that worked Ok but trying to use an integrated platform/interface for student teaching is not working… Any ideas? Thanks Mark B. Cannell Ph.D. FRSNZ Professor of Cardiac Cell Biology School of Physiology Pharmacology Medical Sciences Building University of Bristol Bristol BS8 1TD UK mark.cann...@bristol.ac.uk ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Solicitation of feedback on CellML 1.2
Hi Andre, Support for models with parameter uncertainty is pretty urgent in relation to grants but I'm in your hands re optimal strategy for getting there. Cheers, Peter -- Sent using BlackBerry From: David Nickerson [mailto:david.nicker...@gmail.com] Sent: Monday, October 29, 2012 10:36 PM To: CellML Discussion List cellml-discussion@cellml.org Subject: [cellml-discussion] Solicitation of feedback on CellML 1.2 Dear all, At the 5th International CellML Workshophttp://www.cellml.org/community/events/workshop/2011/, we discussed the main list of features that were desirable to have in CellML 1.2. The CellML Editorial Board has been discussing the implementation of these features in regard to the next version of the CellML standard. Early on, we decided that the entire list of features arising from the workshop was too broad and far reaching to accommodate an easy transition from CellML 1.1 to CellML 1.2 in a timely manner. We have therefore selected a subset of these features which we feel address immediate shortcomings in the CellML 1.1 specification and introduce a minimal set of often requested new features. Tracker item 55https://tracker.physiomeproject.org/showdependencytree.cgi?id=55 shows a detailed overview of our current plans. This is by no means meant to be the final composition of CellML 1.2, but it reflects the current view of the editorial board as to the types of models users wish to encode in CellML and what is possible to implement in both the specification and software tools. Jonathan Cooper presented our thoughts on CellML 1.2 at the recent COMBINE 2012 meetinghttp://co.mbine.org/events/COMBINE_2012/agenda. Please see the slides and video of the presentation to get a more consumable view of the proposed changes. This email is to solicit specific feedback from the community regarding the subset of changes that we have selected for inclusion in CellML 1.2. The CellML 1.2 specification will mark a significant change in the way the CellML standard is specified, and we hope that this change will enable a more rapid process for standardising new features that modellers require in order to encode and share their models using CellML. From tracker item 55https://tracker.physiomeproject.org/show_bug.cgi?id=55, we would like to highlight the following main changes that we think should be in CellML 1.2: * Remove reaction element (tracker item 49https://tracker.physiomeproject.org/show_bug.cgi?id=49); * Remove the directional aspect of connections (tracker item 337https://tracker.physiomeproject.org/show_bug.cgi?id=337); * Replace grouping with a simplified encapsulation-only mechanism (tracker item 356https://tracker.physiomeproject.org/show_bug.cgi?id=356); * Delayed variables (introduction of the evaluatedAt operator with reduced functionality to allow infinitesimal delays and initial values) (tracker item 70https://tracker.physiomeproject.org/show_bug.cgi?id=70). In addition, we specifically ask for feedback on the issue of moving to MathML 3.0 (tracker item 67https://tracker.physiomeproject.org/show_bug.cgi?id=67) and the inclusion of stochastic variation in models (tracker item 2809https://tracker.physiomeproject.org/show_bug.cgi?id=2809). The editors generally agree that switching to MathML 3.0 at this time provides too little benefit (mathematical clarity) for the cost involved in making the change (tool support, interoperability with other exchange formats). While the proposal for stochastic variation is fairly mature, we feel that it requires further work to meet the requirements for inclusion in the CellML standard. We also think that given sufficient impetus from the community this could be one of the first proposals to pass through the new development process for CellML. The editorial board will shortly be releasing our proposed guidelines for the development of the CellML standard. As mentioned above, we hope this new process will allow new features (such as for stochastic variation in models) to move more quickly from feature requests through to changes in the standard specifications. Thanks, The CellML Editorial Board. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] ABI CellML Meeting Minutes, 25th May 2011
Thanks Lucian, my mistake I think, I got *Darren *Wilkinson mixed up with *Daryl *Shanley - both at Newcastle. Cheers, Peter On 27/05/2011 9:43 a.m., Lucian Smith wrote: For what it's worth, it's 'Darren', not 'Darryl' (the SBML 'distrib' package guy). -Lucian * Dougal Cowandj.co...@auckland.ac.nz [2011-05-26 22:32] writes: I have put the minutes from this week's meeting up at: http://www.cellml.org/community/meeting/minutes/2011/05.25 Cheers, Dougal ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Remote attendance at the CellML hackathon and workshop
Thanks Catherine! -- Sent using BlackBerry - Original Message - From: cellml-discussion-boun...@cellml.org cellml-discussion-boun...@cellml.org To: CellML Discussion List cellml-discussion@cellml.org Sent: Wed Feb 10 09:03:00 2010 Subject: [cellml-discussion] Remote attendance at the CellML hackathon and workshop Dear All We have received a number of requests for an audio-visual connection to the CellML hackathon and workshop allowing people to attend remotely. I have set up meeting rooms on Evo: http://evo.caltech.edu/evoGate/ If you would like to remotely attend the hackathon and/or the workshop you will need to pre-register (for free) in advance at Evo. The meetings are called CellML Hackathon (Feb 24th 8.30-16.00 NZ time), CellML Workshop (Feb 25th 8.30-17.30 NZ time) and CellML Workshop (day 2) (Feb 26th 8.30-18.00 NZ time). The meetings are password protected: for the hackathon - cellmlhack, and for the workshop (both days) cellmlwork. We intend to have both audio and visual connections set up. If the connection becomes unstable there are also phone numbers supplied by Evo which can be called (for free). Please trial the software in advance and let me know if you have any questions. Best wishes Catherine ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] ABI CellML meeting minutes 2009-09-30
Thanks Dagmar. We are committed to SED-ML! Your comments are very helpful. Peter
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Subject: Re: [cellml-discussion] ABI CellML meeting minutes 2009-09-30
Dear all,
I'd like to comment on the last meeting minutes, particularly on the
metadata specification comments made by Andre:
* Andre said that SED-ML does not yet support everything that we
need to do for simulation and graphing.
I agree that SED-ML still is at quite an early stage and might not cover
everything needed.
However, even if the structure of SED-ML does not offer particular
constructs for some of your needs, you are allowed (by definition of the
SED-ML schema) to attach annotations to *any* SED-ML element. Thus, you
could extend SED-ML towards supporting whatever additional needs you
might have for information to put in the simulation description file.
Do you think that would be sufficient? As Nicolas mentioned, that would
actually be a nice benchmark for us to see in what way SED-ML needs to
be extended (certainly by what you would put in the annotations often).
* Andrew said that we are still trying to convince the SED-ML group
to separate out graphing and simulation.
I can say that SED-ML is *not* about graphing at all - in the sense that
I understand graphing. SED-ML should provide the description of the data
that is used to create the output, and also how these data relate, e.g.
for a 2 dimensional plot you would have to specify what to plot against
what (x and y axes). Let me cite Nicolas again from an earlier mail:
E.g. we can create a report {time, var1, var2}, but some information
will only emerge if we plot var1 versus var2. In some sense the
relationship between var1 and var2 representation is part of the
post-processing.
* Andre said that you might want to change some of the graphing
metadata to get different graphs from the same simulation, or vice
versa.
If we are talking about running one simulation and creating a number of
different graphs (say, many 2D plots) from that simulation, this is
already possible in SED-ML right now. All you have to do is to define a
number of (what we call) data generators, referring to the
variables/parameters you want to use for your output. Then you can
define as many outputs as you want, referring to the same or different
data generators and to the same of different simulation setups.
If you look at the example given in the publication of CMSB 2008, on
page 9/10 (http://www.springerlink.com/content/n67n137071431xt7/), we
defined a data generator called time and we use it to create 2
different curves from one single simulation (only the x axis is varying
here, using 2 different models).
If we, however, are talking about producing the same graph one time with
a red line, one time with a green line - those things are not part of
SED-ML core information, and they should go to the above mentioned
annotations.
* Peter said that we want to encourage cooperation, and use accepted
standards if they exist.
I cannot tell you how much we would like to see CellML using SED-ML :-)
I know that we do progress pretty slowly, and I am very sorry for that.
* Andre said that the minimal information standard should be out soon.
Maybe a word on that: We are currently (and have been for a while...
slow again, I know) working on writing up the MIASE guidelines. In my
opinion, we do make good progress and I think that we have come to quite
a good consensus already. So, there is hope that soon won't take too long.
I am happy to answer all the questions you might have!
Many greetings from Rostock,
Dagmar
Dougal Cowan wrote:
I have put the minutes from this Wednesday's meeting up at:
http://www.cellml.org/community/meeting/minutes/2009/10.07
Dougal
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Re: [cellml-discussion] ABI CellML team meeting minutes 2009-07-22
Hi Justin, Some agenda items for the next CellML mtg: 1. I noticed a bug on the new website where the 'home page' reverts to the models top page instead of the CellML home page. 2. A plea from users for implementation of more session files. In particular the Iribe et al model needs to be setup for OpenCell. 3. Has the implementation of the SBML API been discussed for OpenCell? 4. A number of comments from people who attended the IUPS workshop about the great job you guys did. Cheers, Peter -- Sent using BlackBerry - Original Message - From: cellml-discussion-boun...@cellml.org cellml-discussion-boun...@cellml.org To: CellML Discussion List cellml-discussion@cellml.org Sent: Mon Aug 03 09:54:48 2009 Subject: [cellml-discussion] ABI CellML team meeting minutes 2009-07-22 Dear CellML community, The ABI CellML team meeting minutes for 2009-07-22 are belatedly available at: http://www.cellml.org/community/meeting/minutes/2009/07.22 Kind Regards, Justin Marsh. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] in case you haven't seen it | Why Are Computational Neuroscience and Systems Biology So Separate?
Hi James, Re your final question - the Physiome Project at the moment is largely about (i) the development of the markup languages CellML and FieldML ( maybe ModelML for the physics) and their associated model repositories and software tools, and (ii) strategies for bridging spatial and temporal scales. I see no reason at all not to include neuroscience in this picture - in fact there are a number of initiatives relating to a 'brain physiome' just getting underway. The essence of the Physiome is the recognition of the need to link models of structure and function across spatial scales from nm to m and temporal scales from brownian motion to human lifetime turnover of proteins. Easy to say ... While CellML and SBML are in some way competing standards, both communities are helping one another greatly by promoting the idea of modelling standards .. and provided we can convert between them, there's no particular disadvantage in having two standards. Cheers, Peter James Lawson wrote: Hi folks, Pretty interesting read. I actually came to what I do now through a heavy cellular neurosci background so this disconnect between systems biology and neurosci is something that has really bugged me. They mention in the paper that SBML doesn't provide the spatial support needed for it to be useful to computational neuroscientists. CellML with its emphasis on multiscalar integration and modularity along with FieldML to describe the geometric information could address these issues. Also, I'm always interested in how CellML is represented in these kinds of publications. It is usually seen (as in this paper,) by systems biologists as a competing language for describing systems biology, which is understandable but only partly true. I think we need to seriously market CellML as a Physiome language, a lot more than we do. This will be a topic in the upcoming paper about the CellML repository I'm starting to put together - that is: the name of the software is Physiome Model Repository 2 - what has it got to do with the Physiome Project then? Kind regards, James David Nickerson wrote: Why Are Computational Neuroscience and Systems Biology So Separate? http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.178 some interesting comments, although not totally accurate... ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:Peter Hunter FRS n:Hunter;Peter org:University of Auckland;Auckland Bioengineering Institute (ABI) adr:70 Symonds St;;Level 6;Auckland;;;New Zealand email;internet:[EMAIL PROTECTED] title:Director tel;work:+649 373 7599 x88395 tel;fax:+649 367 7157 tel;home:+649 307 6662 tel;cell:+6421 505033 url:http://www.bioeng.auckland.ac.nz/ version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] ABI CellML team meeting minutes 2008-05-32
Hi James, Excellent notes! Frank Sachse's name is misspelt near the end. Cheers, Peter James Lawson wrote: Apologies, that link should be http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-05-21/ James James Lawson wrote: Dear all, The ABI CellMl team meeting minutes are now up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-05-21/?portal_status_message=Changes%20saved. Kind regards, James Lawson ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:Peter Hunter FRS n:Hunter;Peter org:University of Auckland;Auckland Bioengineering Institute (ABI) adr:70 Symonds St;;Level 6;Auckland;;;New Zealand email;internet:[EMAIL PROTECTED] title:Director tel;work:+649 373 7599 x88395 tel;fax:+649 367 7157 tel;home:+649 307 6662 tel;cell:+6421 505033 url:http://www.bioeng.auckland.ac.nz/ version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Bug in Nygren model
Title: Bug in Nygren model Hi Daniel, Thanks for figuring that out. Would you mind sending the change (or corrected model) to James (CC'd) - he is our principal CellML curator at the moment. Cheers, Peter [EMAIL PROTECTED] wrote: Hi, I found a bug in the Nygren et al. model of the CellML repository. Mathematical Model of an Adult Human Atrial Cell: The Role of K+ Currents in Repolarization As given, it does not reproduce the findings in the original paper. After coordinating with the primary author, the problem was found and I would like to correct the mistake and submit the correct model. How can I do that? It seems one needs a membership login to edit models? Or would that be handled by a dedicated curator? Cheers, Daniel Mit freundlichen Gren / Best regards / Cordialement Dr. Daniel Ziemek Sanofi-Aventis Deutschland GmbH GS Bioinformatics Industriepark Hoechst Bldg. G879, Room 218 D-65926 Frankfurt am Main t: +49 69 305 22737 w: www.sanofi-aventis.de ** Sanofi-Aventis Deutschland GmbH Sitz der Gesellschaft: Frankfurt am Main Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschftsfhrer: Dr. Heinz-Werner Meier (Vorsitzender), Dr. Matthias Braun, Herv Gisserot, Dieter Kohl, Prof. Dr. Dr. Werner Kramer, Dr. Martin Siewert ** ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:Peter Hunter FRS n:Hunter;Peter org:University of Auckland;Auckland Bioengineering Institute (ABI) email;internet:[EMAIL PROTECTED] title:Director tel;work:+649 3737599 x88395 tel;fax:+649 367 7157 version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
Dear All, Poul and I have looked at the discussion on this thread and to best encompass the various suggestions we've decided to ask Tommy to do the following: 1. Include both a category field with predefined terms (Tommy has this in now) and an additional general 'key word' field. A model can be in multiple categories. 2. The sort facility on the repository will have three ways of sorting: The 1st is the above list of categories, the 2nd is a drop down list that provides more options (see next point), and the 3rd is the curation level. 3. The 2nd sort facility will present several options such as keyword search, species, cell type, etc, and access to more extensive boolean searches (author, year, etc). Cheers, Peter Matt wrote: On 6/8/07, James Lawson [EMAIL PROTECTED] wrote: So for example someone's trying to build a large model but the only components (or data to build components) available are from non-matching species? Yes. So the LFID (I looked it up but it went over my head) provides a way we can do that which is more precise and flexible than simply referring to NCBI taxonomy? Read the paper I referenced, it has a very simple breakdown of LSID and the taxonomy naming issue. The critical thing for us is that a single model will quite often contain elements that derive their mechanism or parameters from studies on different organisms, so we need to be quite rigorous in looking at all components in a model and identifying their origin. This is obviously one facet where imports should be helping us to put circles around species specific submodels. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:Peter Hunter FRS n:Hunter;Peter org:University of Auckland;Auckland Bioengineering Institute (ABI) email;internet:[EMAIL PROTECTED] title:Director tel;work:+649 3737599 x88395 tel;fax:+649 367 7157 version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] PMR categories
Dear All, The intention of this discussion was to decide on a list of items for a drop-down list of predefined terms that would be available when choosing 'key words' for a new model and which would be the list of terms used to display models on www.cellml.org/models (together with the default 'All models' item). The idea was that choosing one or more of these key words terms would be mandatory when defining model metadata but that one could also enter additional keywords for more advanced searching. It may be that the additional key words should adhere to terms from an ontology as Matt suggests and should use the predictive completion facility that Andre suggests. But I am keen to keep this first list of terms fairly short. My suggestion is the following list. I've checked through the repository and less than 10% of the models would end up solely under 'Other'. I am sure we will need to expand this list as the repository grows and I suggest we have a policy of keeping the number that end up solely in the 'Other' category to less than 10% of the total. We may also later need a policy to refine the classification when too many models are displayed under one term. Calcium dynamics Cell cycle Cell migration Circadian rhythms Electrophysiology Excitation-contraction coupling Gene regulation Mechanical constitutive laws Metabolism Myofilament mechanics Signal transduction Other (the default key word in the list of predefined terms) Let me know if you can think of other more appropriate terms or additional ones, then I'll ask Tommy to implement it. I'm happy to then go through and classify all current models in the repository into these categories. Cheers, Peter David Nickerson wrote: One thing I have found useful in other taxonomy/keyword type web interfaces (e.g., see drupal) is that when entering such keywords the interface dynamically completes the terms and/or presents alternatives based on what the user enters. I'd imagine such an interface would work well at pulling terms out of the ontologies Matt is talking about. David. Tommy Yu wrote: Just had a discussion with Peter, Randall and James about this. The keywords are in the metadata for the models, and there is no limit to what can go in there. The concern about that is the list could get too big (for minor categories), or variations in the name (electrophysiology vs electrophysiological), or just spelling in general. What was decided is to have the same category list, but it would act as a "blessed" list of keywords that will serve as a guide to what should be added to the model, and as a broad category filter for the main repository listing. Users would still be able to add or search by other keywords (from the advance search interface) if they wish. Tommy. Matt wrote: On 6/6/07, David Nickerson [EMAIL PROTECTED] wrote: James Lawson wrote: David Nickerson wrote: Would I be correct in assuming that these terms will be key words added to the model metadata and that the division into categories on the main repository page will be assembled from queries on each of these predefined key words? Well potentially, there could be many many different keywords, so Peter suggested that we might not necessarily want to base the categories on just the keywords. At the moment, Tommy's sorting function is based on keywords but he suggested that we could have both a keyword and a more general category selection system. not sure I like the idea of a separate category, seems to me adding some special piece of metadata to models just to make a repository dump look pretty isn't the way to go. It would be nicer to make use of the keywords (which are genuinely useful metadata to more than just the model repository), possibly with the addition of a guided part of the metadata editing workflow which prompts the user to choose at least one of the predefined "category" keywords and a filter smart enough to put models without one of the special keywords into an "other" category. This way the main repository page layout could be easily changed to add or remove keywords that get pulled out as categories without having to change the models. It would also be nice if we can analyse all the repository searching to keep track of the most popular keywords and adjust the categories on the main page accordingly :-) Well, I'm hoping to steal all the keywords and lay them out in the physiome ontology and then put them back in as bioentities (or math related) metadata pointing into this. So the long term relationship between keywords and this "ontology" metadata is where my thinking lies. I like the idea of reflecting this information into keywords, e.g. for 'cardiovascular' the bioentity would be some big long uri pointing into the instance of the term 'cardiovascular'
Re: [cellml-discussion] Interactions between SVG diagrams and PCEnv.
Hi Andre,
The plan is definitely to link up with Sarala's work - we'll
hand-create the svg diagrams only until the output of Sarala's work can
generate these directly from the CellML model.
Cheers,
Peter
David Nickerson wrote:
Hi Andrew,
I'm wondering how (if?) this fits in with the visualisation work that
Sarala is doing?
While I'm not sure how standard it is, I know inkscape allows you to add
links to any object in an SVG diagram where you can set xlink properties
like: href, type, role, arcrole, title, show, and actuate. I would
imagine that these are plenty to be able to link SVG objects to other
resources (assuming this is standard SVG, which it seems to be looking
at plain SVG diagrams exported from inkscape).
In the diagrams I have been creating with Sarala's help I have
envisioned that these links would be used to link to associated
graphs/math/etc provided in a "reference description" of the model. I
guess for an interactive tool like PCEnv you'd probably link to some
PCEnv specific resource telling the GUI what to do. Maybe you'd simply
link directly to a graph trace and PCEnv would be able to interpret such
a request and show the appropriate trace, but that might get a bit
restrictive.
Andre.
Andrew Miller wrote:
Hi all,
Peter Hunter has proposed that it be possible to create SVG diagrams
which interact with PCEnv so that you can click on parts of the SVG
diagram and have PCEnv update the styles of traces being displayed on a
graph.
For example, someone might click on a sodium channel in the SVG diagram,
and have a trace showing sodium concentrations come up on their graph.
There are several possible ways to implement this, and I am looking for
feedback from potential users on which way they would find the most useful:
1) Create a generic language which describes the relationship between
elements in an SVG diagram and trace resources in the graph metadata.
This relationship could describe what happens when the SVG diagram is
clicked. This would probably be the most useful for tools other than
PCEnv to process, although it is not clear whether this would actually
be useful to such tools.
2) Provide an API which _javascript_ in SVG diagrams can use to
manipulate PCEnv traces, perhaps by giving the resource URI.
If we choose to use this _javascript_ API, there are several choices as to
how we could construct the API:
a) Provide an API which allows trace properties to be directly changed, e.g.
var tc = new TraceController();
tc.setTraceStyle(graphURI, traceURI, "invisible");
tc.setTraceColour(graphURI, traceURI, "#ff00ff");
The problem with this approach is that _javascript_ code will often want
to highlight variables, but if this is done through hiding traces and/or
changing colours, code would have to keep track of what changes are
made, and store enough information to be able to reverse the changes.
b) Use the above API style, but provide additional API functions to save
all trace styles / colours on a graph and restore them again, by name.
The only problem here is that the use might have changed something, and
then their change will get reverted.
c) Make some sort of transactional system, where temporary changes can
be made in transactions, and the transaction can be rolled back. The
user will see changes, but if they modify the same variable, their
change will be committed so will not be rolled back.
The problem with option c is that it is very complex both to implement
and to learn how to use, which means it might end up never being used
anyway.
d) Create a highly specialised API allowing the 'highlighted variable'
to be set, such that only one highlighted variable can be set at a time.
If the user changes the variable, it gets unhighlighted automatically.
This is more similar to option 1.
Option 1 and 2d would probably the simplest to use, with there being a
realistic possibility that option 1 could one day be edited in something
other than a text editor. However, they do not give the same flexibility
as the other options would.
I welcome any opinions on what approach would be best.
Best regards,
Andrew Miller
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