Recent SDO/COMBINE legal entity issues

[Keating, Sarah M.]

Dear SBML Community

The issues of a) SBML joining SISO and b) COMBINE becoming a legal
entity were raised prior to the COMBINE meeting. These issues have been
discussed, both during COMBINE 2018 and on various mailing lists. The
conclusion of the SBML Editors is that the community does not see
joining SISO as a direction we wish to pursue at the present time, but
that SBML would fully support and participate in any effort to create a
COMBINE legal entity.

We appreciate the efforts of Jacob Barhak and Katherine Morse in
presenting SISO and inviting SBML to join. The main points raised as a
rationale for not joining SISO at this time are:
1. Joining a formal organization that requires people to pay a
membership fee to have voting privileges is not consistent with the very
inclusive principles that SBML has striven to adopt.
2. The name 'Simulation' as part of the SISO acronym may signal an
inaccurate impression regarding the scope of SBML, which is today used
as a standard for encoding models/aspects of models that are more than
simulations.
3. The community organization of SBML is already effectively an SDO,
with many procedures etc already in place, e.g., election procedures,
community decisions, implementation requirements.

The rationale for joining efforts for establishing COMBINE as a legal
entity is the prospect of this leading to funding opportunities for
meetings, infrastructure and additional outreach opportunities.

If anyone has any strong feelings about either of these topics that they
feel have not been considered we would appreciate your feedback.


SBML Editors

[Jacob Barhak]

Hi Sarah,

Can you please release some more information on this discussion such as:

1. Who attended?

2. If this was conducted through email, are there transcripts? I did not see any communication when I posted questions - so I assume this was private discussion. 

3. If there was voting, what are the votes?

4. Were all the details we were asked to add to the spreadsheets online considered and discussed? 

You see, those are very relevant elements that should be made public. This is also a difference between a formal SDO and an organization such as SBML.

Clearly there is some opposition to the SISO idea presented, yet was there a formal mechanism that was followed here when you posted this?

I am curious since this is at the heart of the discussion -  a formal SDO will have procedures in place to conduct this discussion. However, I did not see any discussion for quite a while in any of the channels that were opened and now I see this post.

Hopefully we can continue the discussion here publicly. and open the issues again. 

               Jacob

[Pnar Pir]

Dear Jacob,

As a subscriber of this mailing list and a long-term user of SBML, I have been following the discussions on SMBL joining SISO with great interest. 

I can see that you are a strong supporter of joining SISO, but I am not clear how your work will benefit from SBML being part of SISO? Hence I wonder the extend of your legal relationship with SISO. For example, are you paid by SISO or is any of your work funded by SISO? If so, I believe the SBML community should be informed about any such "conflict of interest" for the sake of transparency and to put this discussion into perspective.

I am sorry if I am being rude, but I am curious since I feel this may be at the heart of the discussion.

Kind regards,

Pnar 

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[Jacob Barhak]

Thanks Pnar,

Those are very good questions and I am very happy to answer them publicly.  Hopefully you find the text below sufficient to assess my motives and possible conflict. 

You have more than reasonable question regarding conflict. 

Actually , I am very new to SISO - I just went there once and presented a few months ago. Interestingly enough, I was presenting SBML to the SISO members and was accepted very well - in fact it may open future opportunities - see below. You may recall my question about if SBML is an SDO last year- this was way before I went to SISO. At this point I was curious since I did some work with SBML and the concept of an SDO was introduced to me and I wanted to explore this with the SBML community that I was working with.  

Here is when I started getting interested in this:

https://groups.google.com/forum/#!msg/sbml-discuss/3v0pKKMdFBE/7rZSs7ehAwAJ

And the answer then was that SBML is not an SDO. At this point I only heard about SISO. I actually visited SISO only a few months later to present SBML work.

What I saw in SISO made a lot of sense and I heard many stories. I participated in one working group discussion on enumeration and saw several other meetings - none of which were related to my work so I mostly listened and asked a few questions to better understand what is going on. Yet I saw the work of this society and was impressed for the good. I also heard about negative aspects that Katherine later shared at Combine and figured that this is something that the SBML community should know about - hence the discussion in Combine. 

As for conflict of interest  - I fund myself these days - you can see some more disclosures I got on my web page in a separate tab if you are curious on past payments: https://sites.google.com/site/jacobbarhak/disclosures. So there are no conflicts of interest I see from direct payment perspective. 

I do hold a patent on modeling technology and I am actively pushing technologies that may help it - SBML seems like a good technology to support it on the long run - although it is not a direct component.  

To be very explicit  I do tend to go to conferences that SBML folk do not go to - for example, I try to send a MODSIM paper once a year and sent a paper to I/ITSEC and regular in SummerSim and SpringSim conferences. I ran a track in SummerSim for a few years on biomedical and population modeling . And I can attest that many of the people in those conferences  have defense background and there is overlap with SISO members. I made several friends in those conferences beyond formal work like relationship. 

I do know one former Chair of the SISO Executive Committee for a few years from meetings in conferences . Yet until a few days ago when I asked him to join a proposal I plan to submit, we had no formal engagement - I am still waiting for formal paperwork. You see, I was looking for a standardization expert that reviewers asked for in a returned proposal and SISO seemed to have all elements in place while SBML is still starting in this path. I would have been glad to include an SBML expert if SBML was an actual formal standard since what I discuss in that proposal is standardization of data relevant to medical modeling.

Do note that after my meeting in SISO I started working on a proposal for standardization of Units due to engagement with folk I met in SISO. In fact, in the last combine meeting, I was looking for collaborators from the SBML community without success. This proposal is not yet approved. You can verify with multiple organizers that I was seeking support for this proposal in Combine - it was no secret. 

Also note that I have several proposals in different stages that have not yet been funded that are related to modeling and standardization - one with members of the SBML community. If those proposal are approved, the funds would constitute a conflict of interest. One of these proposals is highly SBML related and one will be submitted soon that will mention SISO and I plan to include a standardization expert - see above, although SISO is not the focus there. If you want me to go into further details there - it is possible if someone is really interested, yet I think I gave sufficient information to assess my level of conflict of interest. Let me know if this is enough for you or if more information is required to satisfy your concern about conflict of interest. 

And if I am describing my involvement with SISO, I should also explain my involvement with SBML, I am in the SBML discuss list after I met Herbert Sauro and Michael Hucka a few years ago at the NIH and they advertised SBML - I decided to test it as a possible way for disease modeling. Since then we did some work and published two papers in this path - this is related to my patent. After we worked together I started advocating for SBML use in multiple venues, including in SISO a few months ago. So I am advocating SBML as well without conflict of interest other than possible future pay if proposals get approved or my patent produces revenue. 

I think that merging both societies will bring a lot of benefit and in the long run more users to the SBML community. However, I see reluctance on the SBML/COMBINE part and I want the real reasons for this reluctance to appear publicly on the mailing list - it is only proper for a society described as open.

I tried to urge several members of this society to join this discussion by private email - hopefully I will see this discussion open up and discuss these important issues. 

--

Jacob Barhak Ph.D.

http://sites.google.com/site/jacobbarhak/

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[Brett Olivier]

Dear SBML editors

Thank you for taking the time to look into this situation and presenting them for feedback. I completely support your proposed course of action in this regard.

Brett (SBML community member)

[Nicolas Rodriguez]

On 14/12/2018 08:37, Brett Olivier wrote:

Dear SBML editors

Thank you for taking the time to look into this situation and presenting them for feedback. I completely support your proposed course of action in this regard.

I also support this plan of action.

And as an additional point for Jacob, most of the discussions happened during COMBINE. And the following discussions about it will be at Harmony. That's about the speed of things.

Nico

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[Jacob Barhak]

Thanks Nicolas, Thanks Brett,

Your public response is very welcome. So far I see no other support in joining SISO, so unless someone else writes differently, I can assume that the SBML community does not want to join an established SDO at this point in time.

However, Nicolas, the decision in COMBINE was that discussions will continue online on the COMBINE mailing list. I did not see any related activity for a while and therefore my posts to both lists. My suggestion for someone to present SBML in SISO was because I thought it is a good opportunity for someone else from the community to see what I saw and contribute to the discussion. In COMBINE I got no indication that this is out of the question - in fact, the documents still list it as a viable option to take. Therefore my call for discussion on the details. 

You see, even if you do not take the SISO route, there are important details that need attention to avoid all sorts of problematic issues. I noted some in the meeting and also added notes to the shared documents, yet saw no response for two months. 

Perhaps this is a sign for a low priority issue for the community. Yet I do think its important. Perhaps I am biased, yet I want to be able to claim that my models are using an established standard with a strong legal foundation - preferably an SDO, and I do want to be one of the first ones to be able to claim it. In my case, it will constitute a significant advantage. 

I do not think this is different than many in this community - I think our goals are quite similar.

I still hope someone from this community will see what I see.

                Jacob

To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/2dfb3000-8a45-4bed-2c2a-2705a3103fec%40ebi.ac.uk.

[Brett Olivier]

Dear Jacob

On Friday, December 14, 2018 at 4:03:43 PM UTC+1, Jacob Barhak wrote:

You see, even if you do not take the SISO route, there are important details that need attention to avoid all sorts of problematic issues. I noted some in the meeting and also added notes to the shared documents, yet saw no response for two months. 

Just a practical point, perhaps not everyone on this list is aware of, or has access to, these "shared documents". Could you please post links to the documents you refer to?

Regards
Brett

[Jacob Barhak]

Thanks Brett,

These links exist in the agenda of the combine meeting. Yet since you asked, I figured I will pull them out and place them on this list:

The word document with ideas we raised during the discussion: 

https://tinyurl.com/COMBINE-legal-entity

A spreadsheet discussing pros and cons of alternatives discussed:

https://tinyurl.com/yczj4wkz

Slides Katherine sent about SISO:

http://co.mbine.org/system/files/SISO_Overview.pdf

As you can see, there was little progress since COMBINE and therefore my repeated emails to the discussion list - we were supposed to discuss those.

Hopefully this communication will result in enhancing those documents to reach an informed decision.

               Jacob

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[Pnar Pir]

Dear Jacob,

Thanks for the reply, I know the debate is now mostly over, but I would like share my opinion anyway (I was suffering from flu since Friday)

In my opinion, applying for grants together with both communities is not a conflict of interest, but then I am not an expert on these matters.  But pushing a community to change towards your interests, and then blaming them to be an un-open society when your proposal is refused, is unethical to say the least (again, IMHO). I asked you about your conflict of interest because I had the impression that you promised someone that you will convince the community, but started to write aggressively when your initial proposal was not taken as seriously as you wanted.

Some other information you provided indicated that perhaps you would like to adapt SBML such that it allows your SBML-based product to be commercialized without any legal issues.  I am not sure if this change is really needed for your work. For example SimBiology of MATLAB is a commercial product and it can read/write SBML without any legal issues. And SBMLToolbox has always been freely available to MATLAB users, again with no legal issues. I wish MATLAB paid SBML community for these tools, but I don`t think they pay anything.

On commercializing tools: Building custom bioinformatics pipelines has a lot of commercial value, but the tools being used in these pipelines are free tools, actually bioinformatics companies avoid using a commercial tool in their pipeline, that would only complicate the things. Hence, what they commercialize is their expertise, not a software. In my experience in life sciences, only pharma industry is happy to pay for biochemical modelling software tools. But the new generation is well trained on programming and loves the flexibility of free and open software, so the future modelling teams of pharma will perhaps prefer free tools, too. 

What if the current decision is a terribly wrong and will destroy the community? Well, if COMBINE team declares that they will stop improving SBML as of tomorrow, I am sure SBML still will be the backbone of all SysBio tools for the decades to come. Same goes for Python, if Python community declares that Python can not be improved any further because of leadership issues, people will keep on developing tools based on Python. So please do not worry, SBML and Python will stand as long as we use them. 

Finally, my personal experience: Using COBRA Toolbox + SBML Toolbox was one my first systems biology experiences about two decades ago, I was amazed with what can be done with them. Many many years later, I was very excited to meet Nicolas Le Novere and other editors/developers who made them available to us. And every time I am invited to vote for election of an editor or express my opinion on any matter, I feel that I am part of an inclusive community. I encourage my students to join, too. I have no funding for memberships, nor do my students. We can be part of this community only as long as it remains free for us.

Best regards,

Pnar

To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3T25uHMU%2BjbgGAJzX9469OBNVy4K7F%3DrhGbTvWDk9HndA%40mail.gmail.com.

[Jacob Barhak]

Well Pnar,

A few things. You find me not feeling well as well, so I sympathize and I hope we both get better soon. 

As for conflict of interest, there are actually formal definitions. Once you mention the issue, I had to disclose information to be compliant. When I disclosed things that I had to disclose, I also disclosed intentions for the future so you will better understand my motives. I actually want SBML to grow so I am on your side. 

You mentioned a few things that require attention. You mention a possibility of a decision destroying a community. If a community, is taking moves without being informed of consequences, then I guess its a possibility. However, if you look at my arguments, they were aimed at the fact that there was lack of public discussion to explain consequences. Some arguments that were made in private did not reach this forum and therefore my requests to open the discussion. 

And it seems that people were not aware of the details, so now we can discuss those and make an informed decision. Hopefully I will see progress. I think the real discussion is actually ahead of us if the community wants to make an informed decision.  

As for voting that you mentioned. I will ask the same question I asked at COMBINE.  What prevents someone from a big company to recruit their employees to drive development of SBML in a certain direction? At COMBINE Lucian mentioned that there are some safeguards, I would like to learn the details as part of the legal entity discussion - this is highly relevant. 

It seems that you would like things to remain free. Well, what to you want to remain free? The products? The conferences? The discussion list? The web site? The Libraries? Membership? 

You see, even now things are not really free, professors with students are paid by their institutions and many times students are paid, or pay tuition. So if you look closely, you will find out that nothing is really free.

SBML has a nice welcoming structure - I admit it, yet I am not sure its enough to face pressures. If my arguments are seen as aggressive, when I am trying to ask for an open discussion, how will this community face real pressures from multiple entities trying to pull a standard their way? 

Fortunately this is not the case right now and people in the community are very nice. 

         Jacob

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[Keating, Sarah M.]

> legal issues. I wish MATLAB paid SBML community for these tools, but I
> don`t think they pay anything.
>

To be fair to MathWorks. They do support SBML import/export and yes,
they use/have used libSBML for free but they have also sponsored SBML
meetings in the past.

Sarah

[Chris Myers]

Hi Jacob,

You mentioned a few things that require attention. You mention a possibility of a decision destroying a community. If a community, is taking moves without being informed of consequences, then I guess its a possibility. However, if you look at my arguments, they were aimed at the fact that there was lack of public discussion to explain consequences. Some arguments that were made in private did not reach this forum and therefore my requests to open the discussion. 

I think you don’t completely understand how our community operates.  We have elected editorial boards for each of our standards, and it is their responsibility to manage the development of the standard with the consent of the community members.  In this case, the SBML editors considered the options presented at COMBINE, and decided that it was their opinion that joining SISO was not a direction the community wants to take, but joining a COMBINE legal entity was.  They reported back their findings and reasons for these findings. There is nothing improper with the editorial board conducting their discussions first.  This is what we elected them to do, since we don’t all have time to discuss every issue that comes up to the level of detail necessary to make an informed decision.  

Of course, the community can decide at this point that they do not agree with these findings, and indeed as a community member, you are within your rights to question these findings on the mailing list as you have been doing.  However, for the community to reject the editorial boards decision, there will need to be a motion and a vote to decide differently.  You are free to make the motion, but so far, I’ve only heard support of the editors conclusions and I’ve not heard any support for joining SISO except from you.  Therefore, it is not clear if your motion would even receive a second.  At this time, we should probably take a pause and see if anyone else supports reconsideration of this decision other than you.

And it seems that people were not aware of the details, so now we can discuss those and make an informed decision. Hopefully I will see progress. I think the real discussion is actually ahead of us if the community wants to make an informed decision.  

Again, this is not a fair characterization.  These were discussed at COMBINE, amongst the editors, and now on this list.  So far, the details that have been discussed have not swayed anyone.

As for voting that you mentioned. I will ask the same question I asked at COMBINE.  What prevents someone from a big company to recruit their employees to drive development of SBML in a certain direction? At COMBINE Lucian mentioned that there are some safeguards, I would like to learn the details as part of the legal entity discussion - this is highly relevant. 

SBML has been developed for about 20 years, and this has not been an issue.  Could it be an issue?  Maybe.  However, so far the companies that have used SBML and our other COMBINE standards have preferred to work with the community and not hijack it.  I would like to point out that SBOL has had industrial members of our editorial board and steering committee from the beginning.  They have been excellent and valuable community members.

It seems that you would like things to remain free. Well, what to you want to remain free? The products? The conferences? The discussion list? The web site? The Libraries? Membership? 

The ability to participate in these and other discussions about its development, as well as the software infrastructure that the community develops.  Note their are sometimes registration fees for the meetings, but they only support the food we eat, so we can save time.  There is no profit taken from these.  Indeed, we have been very fortunate at getting sponsorship to cover students registration and travel during most COMBINE events.

You see, even now things are not really free, professors with students are paid by their institutions and many times students are paid, or pay tuition. So if you look closely, you will find out that nothing is really free.

Yes, we are paid by our institutions, but NOT to do this.  We work on standards largely as a volunteer activity.  We have had some grants to support development, SBML in particular has been well funded by the NIH in the past due to their understanding that it is a critical community resource, but several of the other standards are not funded directly.  

If there is something that does require more discussion is how do we maintain development and pursue funding to do so.  This is where the COMBINE as a legal entity comes in, as it potentially provides such a means.

SBML has a nice welcoming structure - I admit it, yet I am not sure its enough to face pressures. If my arguments are seen as aggressive, when I am trying to ask for an open discussion, how will this community face real pressures from multiple entities trying to pull a standard their way? 

SBML is indeed a very welcoming community that does allow for open discussions.  We are indeed discussing this with you.  However, the “aggressive” part comes from the fact that most discussions we have are between groups with different opinions.  The minor opinion group can be quite small, but it is usual not one individual, as it appears to be in this case.  

While I respect your right to keep this discussion going, I think that unless some people are soon swayed to your side, we have other discussions that should take some of our limited energies, such has how to go about forming the COMBINE legal entity, or how we strengthen the community involvement at HARMONY and COMBINE Forums.

Cheers,

Chris

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[Jacob Barhak]

Hi Chris,

If you follow the discussion that develops now, you will see that people are now asking for information they were not aware of with regards to standardization bodies. So I see that the process of exploration is still ongoing. This was my point. After the COMBINE meeting I expected to see some discussion or comments on the documents that were left open. I saw no real discussion, yet I saw a decision. Perhaps I misunderstood, but from what I understood, the discussion was promised - and I am happy we are having it now since it has value. 

And if I am the only one in the group that sees value in joining an established SDO, then perhaps it because I actually went to the SISO meeting and saw how SISO operates. This is what I was suggesting to this group that someone else sees the same before making a decision. A good decision should be informed.

Only yesterday questions have been raised asking for input on what Katherine asked for in another thread on this mailing list:

https://groups.google.com/forum/#!topic/sbml-discuss/cc_wOW7uYUA

I ask that this exploration finish before you make statements about the direction that the community is taking - you should make an informed decision - not rush into one without exploring possibilities. Multiple people have been suggesting that a majority of the community is leaning a certain way before detailed were discussed fully. 

And Chris, there was one point that I saw in the discussion in Boston that was important that seems to be a key point that perhaps shows a critical components than needs discussion to plot a path.

In Boston, Lucian mentioned in the discussion the need to maintain the sbml libraries as part of the legal entity. The short conversation the followed seems to show an important point and I am rewriting it from recollection, so someone please correct me if I miss anything that happened. Yet this is what I recall:

Katherine then asked why would the SBML community develop the libraries. From my own understanding those libraries can be outsourced to multiple competing implementations . I can give an example of the python community where there are different implementations of the python library - e.g. cpython, jython . You seen there is value for competition for the consumer...

Lucian then explained that one of the activities to the SBML community is providing the SBML libraries in different languages to help the community and this is an activity that you want to maintain. 

To my understanding this a key point that will have to deal with when becoming a legal entity - I am not a lawyer, yet if the implementation of the libraries and the standards specifications are handled by the same entity, I am not sure it will be proper since it gives to much control to one entity. 

However, it seems that this kind of the current situation and the group wants it to remain like this. And believe me, I know the value of those libraries since I used them.

I myself want to see more discussion on this point and similar others we mentioned on the shared documents we compiled in COMBINE.  So I urge people to start annotating those files with comments. 

Once the community better defines itself, it would be better for everyone. 

And I really look forward to see Katherine's  response to Paul's question a this seems to be related to my example here.

                  Jacob

To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/29F22A25-2962-4825-BD68-1945CBF1D7AE%40ece.utah.edu.

[Pnar Pir]

Dear Jacob,

I wish you a quick recovery, too.

Yes, I prefer things to be kept free when they can be kept free, the reason is very simple: I have limited resources. Recently I invested in few MATLAB + toolboxes licences. I also invested in training courses by a local bioinformatics company as I desperately needed to speed up my team on our data analysis. I wouldn`t invest in MATLAB if COBRApy was more user friendly, and I wouldn`t pay for training if I could hire trained people. Still, paid memberships wouldn`t be on my list, any student will prefer to attend a local conference rather than paying a company for a membership that grants them the right to be on the SBML mailing list. 

Sarah has just mentioned that MathWorks sponsored some SBML meetings. I buy MATLAB just to be able to run COBRA/SBMLtoolbox on it, nice to know that they appreciate contributions of editors/developers and perhaps the money spent by users such as me... 

There were few new messages about "entities putting pressure on SBML to change it towards their own goals". It just occurred to me that MathWorks could have done that, for example, could have hired people to force SBML to be represented by matrices. That would be very interesting.

My best wishes for the festive season!

Pnar

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[Jacob Barhak]

So Pnar,

In your last sentence you start realizing what I am taking about.  MathWorks  is a nice organization - they make good tools I used int he past and it seems to behave well and are supportive, perhaps because there is currently no strong financial intensive. However, if SBML or one of the other COMBINE specifications becomes part of a very profitable endeavor, you will most probably experience pressures. 

As for things you want to remain free like the mailing lists. SISO is not that different than SBML from this perspective.

SISO standards are free to use - those are open standards.

The mailing lists are public and non members can use those and offer opinions and suggestions.

The only difference I see is when it comes to a vote to change things.

Only SISO members can vote on a SISO standard and those members need to pay a membership fee that is individual - if I understand correctly, this mechanism provides some protection from a company of over influencing the standard and part of the protection against things mentioned in the discussions. 

If you look at my questions about the decision the editors posted, I was asking who voted - according to Chris, this decision did not necessarily follow an open discussion.

So which of those governance structures would you prefer? Which one can be influenced more easily by an external entity? 

Again Pnar, if SBML is to remain an academic endeavor at the size it is now, then there is no need for any changes and this discussion is perhaps not efficient use of our time. Yet I see much potential in SBML - and I saw other modeling tools in the last few years so I have a reference point. I also see a movement within the SBML community towards legal formalization. So it seems the community does want to grow towards the next level. So its better we all be informed of possibilities. 

Many thanks for declaring your preferences in this discussion, those points should remain for reference in the discussion as well as the alternatives.

                Jacob

 

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[Matthias König]

@Jacob Barhak

Only SISO members can vote on a SISO standard and those members need to pay a membership fee that is individual - if I understand correctly, this mechanism provides some protection from a company of over influencing the standard and part of the protection against things mentioned in the discussions.

This is basically the opposite from protection from companies. Because companies are the only once who can afford 10s or 100s of memberships whereas academics are not. So having to pay for something makes companies more influential in this respect.

To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3TAjCeW4TkZ0Hyo3CsWxjgPurRu21FceuqpYW_MGdT3Mg%40mail.gmail.com.

For more options, visit https://groups.google.com/d/optout.

--

Matthias König, PhD.
Junior Group Leader LiSyM - Systems Medicine of the Liver
Humboldt Universität zu Berlin, Institute of Biology, Institute for Theoretical Biology
  https://livermetabolism.com
koni...@googlemail.com

https://twitter.com/konigmatt

https://github.com/matthiaskoenig
Tel: +49 30 2093 98435

[Pnar Pir]

Dear Jacob,

In my last sentence, I was joking about MATLAB overtaking SBML by converting it into matrices, so I am not really worried about SBML being hijacked.

I don't think that MathWorks is particularly nice, they are just clever... If SBML is getting very popular, they just make their relevant software compatible with it rather than attacking it. Then they proudly announce that their matrix-based software has this new amazing feature: Compatibility with SBML. 

It takes at most a week of a developer's time to write a converter between SBML and matrices, no other effort is made, no other money is spent, no legal issues whatsoever. When SBML gets updated, the developer spends another half day to implement the changes, and the life goes on. 

I suppose profitable endeavours are established by clever and efficient people. Rather than approaching SMBL to change it for their own goals, spending money and time on that sneaky plan, perhaps they will come up with this amazing format that beats SBML. Initially we will write a converter between the two, and then switch to it altogether. So they will win. But not via sneaky voting games, just by producing something better! 

All in all, I am not convinced that there may be a case where SBML community will be forced to make decisions against their will and against their needs. Although I am happy to vote when I am invited to, I am not horrified when some executive decisions are made by the editors, after all they are the ones who devote their time to SBML and they are the ones who has the most experience. I never doubt that they pick the best choice out of the possibilities (may it be a technical issue or a legal one). 

Best,

Pnar

To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3TAjCeW4TkZ0Hyo3CsWxjgPurRu21FceuqpYW_MGdT3Mg%40mail.gmail.com.

[Jacob Barhak]

Well Pnar,

To help keep this discussion fruitful, I suggest we move this discussion to the other thread that is developing the discussion nicely. 

https://groups.google.com/forum/#!topic/sbml-discuss/cc_wOW7uYUA

Matthias will find my response to his comment there.

Hopefully it will help us focus on the important issues.

                  Jacob

To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAPGcd8V_MchyOOknpab6aH6MkuH5MKk0xRuiFJQJpZQN-RcBzg%40mail.gmail.com.

[Pnar Pir]

Dear Jacob,

I guess you should check the group rules to see if marketing is allowed or not. If it is not allowed, you may get banned. I will not take part in any further discussion.

Best,

Pnar

To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3QY6QQ2MV5nOEYokDzVmSiMTEqkk2_iwKMnG7X5hbOKQw%40mail.gmail.com.

[Jacob Barhak]

Well Pnar,

There was no real commercialization here. In fact, you asked me to disclose conflict of interest. 

SBML related code I developed is public and free as far as I know and SISO is a non profit - I think it covers this discussion. It is kind of similar to presenting SBML in SISO - there is no problem in that. 

However, to keep discussion focused, let us please consolidate to the discussion in the other thread:

https://groups.google.com/forum/#!topic/sbml-discuss/cc_wOW7uYUA  

I hope it develops well.

             Jacob

To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAPGcd8V4pHqR0HBwVk2Y9_%2Bf-eO4GznoXDV2cvRvRmKh6QnN6A%40mail.gmail.com.

[Pnar Pir]

I replied after reading your message to Paul. That message aims marketing (from my point of view).

To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3SfGpSbARDmgx5Pr9MiX9D6Mga-7XHGVhN1wa1bn%3Di7DA%40mail.gmail.com.

[Jacob Barhak]

Well Pnar,

There is nothing sold here. And you can consider it part of my conflict of interest disclosure. I am a sole proprietor and I do develop multiple tools. The SBML related work I developed was published with members of this community. You can find the development efforts on this discussion list in the past. There was no issue with it in the past. 

The issue with SISO is highly relevant to this community and you can see acceptance of ideas raised in the other thread. 

I hope this clears it and we can move on to the discussion on the other thread.

https://groups.google.com/forum/#!topic/sbml-discuss/cc_wOW7uYUA   

             Jacob 

To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAPGcd8VWrhWK3_WJW1WhFQ%3DQAmRnU53uVa2DTLZQsm6t36ZbFw%40mail.gmail.com.

[Chris Myers]

Hi Jacob,

The issue with SISO is highly relevant to this community and you can see acceptance of ideas raised in the other thread. 

To be clear, there is acceptance that we can learn from the experiences of SISO, and we appreciate these being shared with us.  However, there is still no one besides yourself expressing the opinion that we should join SISO.  It is not even clear there is support to become an SDO.  The support so far has been limited to COMBINE becoming a legal entity.  

I hope this discussion can soon move to focus on what that will take.  

Cheers,

Chris

To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3TToqHhSN9297Lgo2CWOqE6ZY-8iuOQPOyh8mxRe4LPJg%40mail.gmail.com.

[Jacob Barhak]

So Chris,

Please move to the other thread and you can see how it develops.

https://groups.google.com/forum/#!topic/sbml-discuss/cc_wOW7uYUA  

It explains what is going on. There is no conflict here. and the support that you are mentioning is premature since the group has not defined what it wants. From legal perspective, you will not pass very simple tests. Look at the comments I made on the share document to understand how premature the situation is

https://tinyurl.com/COMBINE-legal-entity

First define what the group wants and make sure it complies with the laws. 

Currently the discussion is about supporting this or that path where there is no real conflict, the discussion should be on what the group wants. After defining those points we can proceed towards the legal path. Otherwise, when you come to the lawyer, they will charge you a lot of money to to those exact things.

Its better we do it now and be prepared. 

And let us please join the other thread to consolidate discussion.

              Jacob

To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/4231E65A-636E-427E-8CAC-7F0DD4F6DF95%40ece.utah.edu.