From r.britten at auckland.ac.nz Mon Sep 1 10:15:30 2008 From: r.britten at auckland.ac.nz (Randall Britten) Date: Mon, 1 Sep 2008 10:15:30 +1200 Subject: [cellml-discussion] Trial of Litmus for software testing record keeping Message-ID: <015a01c90bb7$1474f620$3d5ee260$@britten@auckland.ac.nz> Hi While this will mostly be relevant to developers, there may be others interested in helping developers improve the software by providing feedback, so please feel free to read on or opt out. We would like to have a system that allows us to collaboratively record information about manual testing of software. Currently, Litmus is being used for PCEnv (Physiome CellML Environment), albeit on an instance that is only available from the ABI LAN. We would like to make this available more widely in the future, but would first like some feedback on its suitability. A test instance has been set up, for various developers and anyone else who is interested to try out. If we decide Litmus is sufficient, we will aim to deploy it at the ABI, or hosted elsewhere, for use by any of the Physiome projects. Discussions on this topic should be recorded on this tracker item: https://tracker.physiomeproject.org/show_bug.cgi?id=1313 The test instance is available at http://67.223.228.57/. You will need to create a login for yourself. It is already populated with test scripts and test results data duplicated from the instance running internally at the ABI. Feel free to add more testing result data, and more tests, or to update existing test scripts. Please e-mail me if you need different access levels etc. Note however that after the trial, all data will be discarded. Currently, the hosting will be available until 16 September 2008. Also note that some customisation has been done to Litmus, and minor adjustments might also be possible during the trial. Regards, Randall Britten ___________________________ Software Development Leader Bioengineering Institute Auckland University From j.lawson at auckland.ac.nz Mon Sep 1 13:28:16 2008 From: j.lawson at auckland.ac.nz (James Lawson) Date: Mon, 01 Sep 2008 13:28:16 +1200 Subject: [cellml-discussion] ABI CellML team meeting minutes for 2008-08-27 Message-ID: <48BB4530.10004@auckland.ac.nz> Dear CellML community, Last Wednesday's ABI CellML team meeting minutes are now available at: *http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-08-27/ *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 tommy.yu at auckland.ac.nz Wed Sep 3 11:57:38 2008 From: tommy.yu at auckland.ac.nz (Tommy Yu) Date: Wed, 03 Sep 2008 11:57:38 +1200 Subject: [cellml-discussion] Summary of PMR2 Prototype Discussions Message-ID: <48BDD2F2.3050005@auckland.ac.nz> Greetings everyone, Following up on the discussions made regarding the PMR2 prototype exercise, found at: https://tracker.physiomeproject.org/show_bug.cgi?id=248 I have summarized all the major issues and points to be addressed as we develop the final PMR2. The document can be found at: https://svn.physiomeproject.org/svn/physiome/plone_products/pmr2.hgpmr/trunk/SUMMARY.txt Cheers, Tommy. From sarala.dissanayake at auckland.ac.nz Thu Sep 4 20:32:33 2008 From: sarala.dissanayake at auckland.ac.nz (Sarala Dissanayake) Date: Thu, 04 Sep 2008 20:32:33 +1200 Subject: [cellml-discussion] CellML OWL work in progress Message-ID: <20080904203233.ui1ruzjkoc4oc00s@webmail.bioeng.auckland.ac.nz> Hi Randy and Ely, I'm developing a framework for annotating and visualizing CellML models. A solution has been developed that involves: - an ontology for storing CellML models in OWL format (CellMLOWL) and a set of rules for binding these CellMLOWL instances to CellML models. - an ontology which represents biophysical and biological concepts that are covered in CellML models (CellMLBio) and a set of rules for binding these concepts to CellMLOWL models; - a specification for building visual templates that support a visual language that can be used to represent all biophysical and biological processes covered in CellMLBio ontology and the rules for binding the visual language to concepts within the CellMLBio ontology; - a visual editing tool, that combines the visual language and ontologies to visualize CellML models. I'm currently writing up my thesis and 3 papers. I should be able to make these available to you in draft form soon. Cheers, Sarala ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From ely.matos at ufjf.edu.br Fri Sep 5 14:17:42 2008 From: ely.matos at ufjf.edu.br (Ely Edison Matos) Date: Thu, 4 Sep 2008 23:17:42 -0300 Subject: [cellml-discussion] CellML OWL work in progress References: <20080904203233.ui1ruzjkoc4oc00s@webmail.bioeng.auckland.ac.nz> Message-ID: <625D18130D3748298639EF33C978C64D@illusions> Hi Sarala, Thanks for the answer and news :-) CelO has a similar goal, except the "visual" subject (not covered on my work). And it is possible to use SWRL to "infer" some knowledge from the CellML Model. I'll wait with expectation for the drafts :-) []'s Ely ----- Original Message ----- From: "Sarala Dissanayake" To: "CellML Discussion List" Sent: Thursday, September 04, 2008 5:32 AM Subject: [cellml-discussion] CellML OWL work in progress > Hi Randy and Ely, > > I'm developing a framework for annotating and visualizing CellML models. > A solution has been developed that involves: > - an ontology for storing CellML models in OWL format (CellMLOWL) and a > set of rules for binding these CellMLOWL instances to CellML models. > - an ontology which represents biophysical and biological concepts that > are covered in CellML models (CellMLBio) and a set of rules for binding > these concepts to CellMLOWL models; > - a specification for building visual templates that support a visual > language that can be used to represent all biophysical and biological > processes covered in CellMLBio ontology and the rules for binding the > visual language to concepts within the CellMLBio ontology; > - a visual editing tool, that combines the visual language and ontologies > to visualize CellML models. > > I'm currently writing up my thesis and 3 papers. I should be able to make > these available to you in draft form soon. > > Cheers, > Sarala > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From r.britten at auckland.ac.nz Fri Sep 5 15:23:45 2008 From: r.britten at auckland.ac.nz (Randall Britten) Date: Fri, 5 Sep 2008 15:23:45 +1200 Subject: [cellml-discussion] Server Outages due to building power outage Saturday 6 Sept (NZ time). Message-ID: <011401c90f06$ce31f250$6a95d6f0$@britten@auckland.ac.nz> > -----Original Message----- > Hi all, > ... > > All IT servers will be unavailable from about 0730 to 1230. > > > This will mean that all the following services will be unavailable for 5 > hours. > ... > > * websites - www.cellml.org > - www.physiome.org.nz > - tracker.physiomeproject.org ... > > > It is possible the electrical work being undertaken will take longer > than scheduled, and hence the return to service of servers will depend > on this. But hopefully things should be back functioning by about 1230. > > > Sorry for the disruption that this will cause. > > Many Thanks > > Andrew Cantell > From heiland at indiana.edu Sat Sep 6 23:50:11 2008 From: heiland at indiana.edu (Randy Heiland) Date: Sat, 6 Sep 2008 07:50:11 -0400 Subject: [cellml-discussion] CellML OWL work in progress References: Message-ID: <8DDDAA42-0C3C-4B4D-AFC5-DAEF007DFEAB@indiana.edu> Thanks for the reply, Sarala. I/we look forward to your drafts. best, Randy Begin forwarded message: > From: cellml-discussion-request at cellml.org > Date: September 4, 2008 8:00:01 PM EDT > To: cellml-discussion at cellml.org > Subject: cellml-discussion Digest, Vol 50, Issue 4 > Reply-To: cellml-discussion at cellml.org > > Send cellml-discussion mailing list submissions to > cellml-discussion at cellml.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cellml.org/mailman/listinfo/cellml-discussion > or, via email, send a message with subject or body 'help' to > cellml-discussion-request at cellml.org > > You can reach the person managing the list at > cellml-discussion-owner at cellml.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of cellml-discussion digest..." > > > Today's Topics: > > 1. CellML OWL work in progress (Sarala Dissanayake) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 04 Sep 2008 20:32:33 +1200 > From: Sarala Dissanayake > Subject: [cellml-discussion] CellML OWL work in progress > To: CellML Discussion List > Message-ID: > <20080904203233.ui1ruzjkoc4oc00s at webmail.bioeng.auckland.ac.nz> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hi Randy and Ely, > > I'm developing a framework for annotating and visualizing CellML > models. A solution has been developed that involves: > - an ontology for storing CellML models in OWL format (CellMLOWL) and > a set of rules for binding these CellMLOWL instances to CellML models. > - an ontology which represents biophysical and biological concepts > that are covered in CellML models (CellMLBio) and a set of rules for > binding these concepts to CellMLOWL models; > - a specification for building visual templates that support a visual > language that can be used to represent all biophysical and biological > processes covered in CellMLBio ontology and the rules for binding the > visual language to concepts within the CellMLBio ontology; > - a visual editing tool, that combines the visual language and > ontologies to visualize CellML models. > > I'm currently writing up my thesis and 3 papers. I should be able to > make these available to you in draft form soon. > > Cheers, > Sarala > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > ------------------------------ > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > > > End of cellml-discussion Digest, Vol 50, Issue 4 > ************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.lawson at auckland.ac.nz Mon Sep 8 11:52:10 2008 From: j.lawson at auckland.ac.nz (James Lawson) Date: Mon, 08 Sep 2008 11:52:10 +1200 Subject: [cellml-discussion] ABI CellML team meeting minutes 2008-09-03 Message-ID: <48C4692A.7020906@auckland.ac.nz> Dear CellML community, The ABI CellML team meeting minutes are now available at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-09-03/ 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 r.britten at auckland.ac.nz Tue Sep 9 17:31:26 2008 From: r.britten at auckland.ac.nz (Randall Britten) Date: Tue, 9 Sep 2008 17:31:26 +1200 Subject: [cellml-discussion] Proposal to make a change to the tracker item page layout Message-ID: <001f01c9123d$4df86800$e9e93800$@britten@auckland.ac.nz> Hi We are considering making an alteration to the page view used per tracker item. The tracker item for this is https://tracker.physiomeproject.org/show_bug.cgi?id=1343. Please CC yourself to it and make comments there. Regards, Randall -------------- next part -------------- An HTML attachment was scrubbed... URL: From tommy.yu at auckland.ac.nz Mon Sep 15 16:58:14 2008 From: tommy.yu at auckland.ac.nz (Tommy Yu) Date: Mon, 15 Sep 2008 16:58:14 +1200 Subject: [cellml-discussion] Adding an information page for each model category Message-ID: <48CDEB66.7030203@auckland.ac.nz> Hi all, In the CellML meeting of 2008-09-10, a suggestion was raised, saying there should be a description page written for each of the categories. It will be nice to include this in PMR2, but it may be possible to implement this in the current PMR. PMR might be able to accommodate this feature. If an extensive editing interface is not required, it can piggyback onto the hack that enabled these categories. However the interface to present this descriptive page is still pending, I would like feedback on this feature if it is to be included in PMR. (such as where to display it, how to present the interface, etc.) Tracker item has been created, discussions can go into: https://tracker.physiomeproject.org/show_bug.cgi?id=1350 Cheers, Tommy. From dj.cowan at auckland.ac.nz Mon Sep 22 13:14:19 2008 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Mon, 22 Sep 2008 13:14:19 +1200 Subject: [cellml-discussion] Meeting minutes 2008-09-17 Message-ID: <48D6F16B.10003@auckland.ac.nz> Dear CellML community, The minutes for this week's ABI CellML team meeting are now available at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-09-17/ Dougal From c.lloyd at auckland.ac.nz Tue Sep 30 12:57:15 2008 From: c.lloyd at auckland.ac.nz (Catherine Lloyd) Date: Tue, 30 Sep 2008 12:57:15 +1300 Subject: [cellml-discussion] Announcing the CellML, SBGN, SBO, BioPAX, and MIASE 2009 Workshop Message-ID: <973689E4-DF47-4F12-8E77-B9ADD056811B@auckland.ac.nz> Dear All Following on from the success of the CellML Workshops in 2007 and 2008 we will be hosting another workshop in 2009 - this time with a slight difference. Discussions with various groups have lead to the idea of making this event a "super-workshop" combining the themes of: CellML, SBGN, SBO, BioPAX, and MIASE We believe this will be an excellent opportunity to bring together the various growing communities to discuss recent developments and future plans. This meeting will be held over 5 days, 5th-9th April 2009, on Waiheke Island - just a 40 minute ferry ride from downtown Auckland. Registration for this event is free and accommodation costs will be covered. If you would like to register for this event please do so at: http://www.cellml.org/workshop/workshop2009/register-cellml2009 The programme has yet to be confirmed, but we anticipate there will be a series of short presentations, with plenty of time reserved for group discussions. We will also be encouraging everyone to stay at the same centre (Waiheke Island Resort) to allow further opportunities for discussion. More information will be posted on the CellML website shortly (http://www.cellml.org/workshop/workshop2009/ ), but we would like to take the opportunity now to alert you to the event to allow you to incorporate it into your busy schedules. We look forward to seeing many of you again and also hope to welcome many new faces. Best wishes Poul Nielsen, Peter Hunter, Mike Hucka, and Catherine Lloyd -------------- next part -------------- An HTML attachment was scrubbed... URL: