Re: [Miase-discuss] SBML/sedML Patent Issue

[<hen...@no...>]

Hi Nicholas,

are you sure it only applies to commercial companies using the software? 
In my opinion also non-profit organization are not allowed to 
develop and distribute software (and any other things) that violate topics 
covered by patents. And this certainly applies in this case to 
all SBML software simulating events ... if used and produced at 
universities or in companies (and all possible combinations).

/Henning





Nicolas Le novère <le...@eb...> 
04.03.2009 15:20
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Re: SBML/sedML Patent Issue






Henning,

Thanks a lot for the information. I think this does not affect us because 
it deals with running the sequence experiments and not describing the 
sequence. But we should keep an eye if we want SEDML to be used by 
companies (they already use simulators using SBML events ...)

hen...@no... wrote:
> 
> Hi Mike and Nicholas,
> 
> hope both of you are doing fine! Here in Basel everything is ok and the 
> rate of development on the toolbox has
> gotten even higher :) Just need to convince my bosses to make it 
> publicly available at some point in time.
> 
> During my work here something came up which might have an impact on SBML 

> and sedML in terms of "intellectual property".
> 
> Are you aware of the following patent by Entelos: 
> http://www.google.com/patents?vid=USPAT6983237
> 
> What they patented are "sequenced experiments". This means you run one 
> experiment on a model until a certain
> time, then based on the last statevector you update the states and 
> parameters (manually or automatically by a script / program / etc.)
> of the model and run this second experiment and so forth.
> 
> This procedure has been used for many years and is certainly not new. 
> Especially for very time consuming simulations
> one often simulates until a certain time, saves the statevector and can 
> then from there simulate different scenarios.
> I guess almost every modeler has used this idea at some point in time 
> (especiall in the older days with slower
> computers).
> 
> Anyway, initially I thought that this only covers single experiment 
> descriptions that then are run in a sequence.
> Now, I heard from Entelos that they think their patent also covers 
> changes of parameters or states DURING a
> simulation experiment, which are implemented using events.
> 
> Since SBML allows to change states and parameters using events during 
> simulations all users simulating such SBML
> models would in principle need to pay license fees to Entelos :) Same of 

> course for sedML users, since some of the
> experimental settings might be implemented using events.
> 
> One good thing: its only a US patent and similar things are not 
> patentable in Europe (afaik).
> 
> It would be great if you could check out the patent too and let me know 
> what you think. In my view a patent like this should
> not be around for too long, since it in principle subjects all SBML 
> tools to license fees to Entelos.
> 
> All the best,
> Henning
> 
> 


-- 
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho...
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/