Meeting Minutes 4th September 2006
Meeting Minutes 21th August 2006
Present: Poul Nielsen, Tommy Yu, Shane Blackett, Karl Tomlinson, Andrew Miller
Poul: Attended a conference in Seoul on Engineering & Medicine. Met with Richard Kidney's PhD students, who are involved in synthetic biology. They have been taking part in MIT's competitions to design functions to incorporate into E. coli (which must be measurable). They said that CellML was ideal for assisting them in modelling (due to the import functionality, which SBML doesn't have). They have been creating functional blocks to assemble together into larger network models. While these blocks don't correspond to published papers, Poul, is keen to put them into the repository. Poul will get back to the students about this, and will also post a URL about their research to the CellML list.
Poul also noted that Edmund, Peter, and Poul have been looking at the modularity associated with signalling pathways, with a view towards separating out standalone recurring modules.
Karl is keen to use CellML from within CMISS. After correspondence with Andre, it turns out that he currently wants to start entirely new runs (for now) for each change in constant value (which we currently support without a recompile) rather than to stream results into the integrator each time it needs to know a value. There was consensus that we need a way to support this latter use case, however. Andrew was keen for this to be treated in the same way as imports into CellML models, but through the CellML API, and Poul agreed that they were conceptually similar. Shane was concerned, however, that for this to work, you had to have a model with specified exactly the initial values you don't plan to change, and so you would need to change a large number of models (so he favoured an approach which allowed parts of models to be overriden). However, Poul was more keen on producing a partly specified model, and then providing a fully specified model through the import functionality. The group agreed to think about it more and revisit it at the meeting next week.
Andrew noted that there was a simulation metadata meeting, and that we agreed to use most of the specification in PCEnv, but to defer the integrator choice for later.
He also noted that he has been working on an automated build system in order to constantly test CellML_DOM_API and produce binaries on Linux, Win32, and OSX. He also asked if presentation metadata (such as which graphs to draw) was a high priority for the first release of PCEnv. The group agreed that it was. Andrew will produce a presentation metadata specification, but will concurrently continue working on getting a working PCEnv build.
Andrew noted that he had received an e-mail forwarded through Peter from one of Dan Beard's students, who wanted support with the Java CellML editor, and asked what the process should be to deal with such requests. Poul suggested that this be passed on to Matt, and the group agreed. Andrew will forward the e-mail on to Matt, and reply to Peter and the student.
Poul: Attended a conference in Seoul on Engineering & Medicine. Met with Richard Kidney's PhD students, who are involved in synthetic biology. They have been taking part in MIT's competitions to design functions to incorporate into E. coli (which must be measurable). They said that CellML was ideal for assisting them in modelling (due to the import functionality, which SBML doesn't have). They have been creating functional blocks to assemble together into larger network models. While these blocks don't correspond to published papers, Poul, is keen to put them into the repository. Poul will get back to the students about this, and will also post a URL about their research to the CellML list.
Poul also noted that Edmund, Peter, and Poul have been looking at the modularity associated with signalling pathways, with a view towards separating out standalone recurring modules.
Karl is keen to use CellML from within CMISS. After correspondence with Andre, it turns out that he currently wants to start entirely new runs (for now) for each change in constant value (which we currently support without a recompile) rather than to stream results into the integrator each time it needs to know a value. There was consensus that we need a way to support this latter use case, however. Andrew was keen for this to be treated in the same way as imports into CellML models, but through the CellML API, and Poul agreed that they were conceptually similar. Shane was concerned, however, that for this to work, you had to have a model with specified exactly the initial values you don't plan to change, and so you would need to change a large number of models (so he favoured an approach which allowed parts of models to be overriden). However, Poul was more keen on producing a partly specified model, and then providing a fully specified model through the import functionality. The group agreed to think about it more and revisit it at the meeting next week.
Andrew noted that there was a simulation metadata meeting, and that we agreed to use most of the specification in PCEnv, but to defer the integrator choice for later.
He also noted that he has been working on an automated build system in order to constantly test CellML_DOM_API and produce binaries on Linux, Win32, and OSX. He also asked if presentation metadata (such as which graphs to draw) was a high priority for the first release of PCEnv. The group agreed that it was. Andrew will produce a presentation metadata specification, but will concurrently continue working on getting a working PCEnv build.
Andrew noted that he had received an e-mail forwarded through Peter from one of Dan Beard's students, who wanted support with the Java CellML editor, and asked what the process should be to deal with such requests. Poul suggested that this be passed on to Matt, and the group agreed. Andrew will forward the e-mail on to Matt, and reply to Peter and the student.