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Level 3 Package Proposal Voting Results: spatial

The call for votes for the 'spatial' package was issued on November 15 and closed on December 1, 2011. A total of 15 votes were cast. One individual was not a member of the sbml-discuss or sbml-spatial mailing lists; removing their responses left 14 valid votes.

The outcome of this vote is accept.

This outcome is based on the final question of the survey, which had four mutually-exclusive choices: Accept (proposal addresses a need that SBML should cover, and the approach clearly follows the stated principles), Reject (proposal does not address a need that SBML should cover), Revise (approach either does not follow the stated principles, or there is insufficient information to tell if it does), or Abstain, (I cannot fully assess the proposal as given, or do not wish to state an opinion). The following graph presents the results for this question:

The voting for this package proposal used an updated format that requested additional information from voters. The responses for each of these additional questions are reported separately below. The comments written by respondents for the overall assessment question are provided at the end of this page.

Question about UTILITY

The question was posed as follows: Utility: the package addresses a problem whose solution SBML users are likely to find useful. It had four possible answer choices: (a) Agree, (b) Disagree, (c) Insufficient info, and (d) Abstain.

The following graph shows the overall total responses:


The following are the individual comments written by respondents. The votes in particular are indicated in parentheses before the comments.

  • (Voted 'Agree') However, the package is overly broad and should be restricted to items (1) and (2) above.
    • Editorial comment: the reference to items in this respondent's comments is likely to have been in reference to the following paragraph in the text of the survey: Approach: The focus of the spatial processes effort is on extending SBML to support representing at least the following: (1) the size and shape of physical entities, whether compartments or reacting species; (2) the absolute or relative spatial location of reacting species in compartments, for instance in a volume, on membrane surfaces, or along microtubules; (3) the rates of diffusion of species through compartments; and (4) the definition of rate equations and algebraic constraints describing phenomena either at specific locations, or distributed across compartments.

Question about BIOLOGICAL ORIENTATION

The question was posed as follows: Biological orientation: the package's overall aim is to support the description of biological processes and phenomena. It had four possible answer choices: (a) Agree, (b) Disagree, (c) Insufficient info, and (d) Abstain.

The following graph shows the overall total responses:


There were no comments left in conjunction with this question.

Question about COHERENCE

The question was posed as follows: Coherence: the package extends SBML in a way that follows naturally from Level 3 Core and other packages. It had four possible answer choices: (a) Agree, (b) Disagree, (c) Insufficient info, and (d) Abstain.

The following graph shows the overall total responses:


The following are the individual comments written by respondents. The votes in particular are indicated in parentheses before the comments.

  • (Voted 'Agree') With the restriction to describing geometries, it would.
  • (Voted 'Agree') My only suggestion here is that you might consider *extending* the SId namespace instead of creating your own new spatialId namespace. I know you did this in response to a different earlier suggestion, but hey. You still couldn't use spatial IDs in core constructs, but you could then use your extended SId namespace in any mathml you yourself defined.

Question about ORTHOGONALITY

The question was posed as follows: Orthogonality: within reason, the package does not duplicate the purpose or data captured by other packages. It had four possible answer choices: (a) Agree, (b) Disagree, (c) Insufficient info, and (d) Abstain.

The following graph shows the overall total responses:


The following are the individual comments written by respondents. The votes in particular are indicated in parentheses before the comments.

  • (Voted 'Disagree') Process description (e.g., diffusion, transport) would appear to cross into other packages.

Question about overall assessment

In addition to asking for an overall assessment (the response to which is the first result on this page), the survey also provided space for respondents to include comments with their overall assessment. The following are the explanations that people provided, together with the way they voted on the overall assessment question.

  • (Voted 'Revise') A spatail description may need to include microscopic rate constnats at the reaction radius in order to be physcially consistent, see "David Fange, Otto G. Berg, Paul Sjöberg & Johan Elf (2010) Modeling of intracellular reaction-diffusion processes: Approaching the molecular limit PNAS 107:19820-5"
  • (Voted 'Accept') The proposal document as link on the webpage seems to have been last revised in april and it does not seem to be finished since many sections seem to be incomplete and many open question are still highlighted in red. There are also no examples linked on the webpage or included in the document which would help in making some of the principles more clear. Especially with respect to the "Parametric Geometry", I am a bit puzzled as to what this actually does. I guess it is supposed to define mesh based geometries, but an example would could easily clarify this. If I am wrong, mesh based geometries are missing from the proposal.
  • (Voted 'Revise') The concern is only with the name of the package and the third and fourth goals. There is a major difference between spatial geometries (a bit of a redundant phrase in itself) and spatial processes. The former seems to be the focus of work that has been done previously for this package. A different package (and approach) would be needed for describing spatial processes, working out overlaps with other parts of SBML.
  • (Voted 'Reject') From page 12: "The type attribute is of type string and indicates the type of boundary condition. The boundary condition can be one of two types: Flux (Neumann) or Value (Dirichlet)." The Robin boundary condition is not listed. A Robin boundary condition is a general form for advection–diffusion equations. At the boundary -u x C + D x dC/dx = 0, where u is the advective velocity and D is the diffusion coefficient. The advective and diffusive fluxes add to zero. Robin conditions are essential.


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