CommunityProcessDiscussion/Discussion page

= This Page is an Archive of an old discussion - June 11th 2010 = Add discussion items below. Please include your name.

Joanne Luciano

"Early decisions were made by the founding members (Peter Karp, Chris Sander and Chris Hogue) and by initial participants in the project as a group." The BioPathways Consortium was involved in the founding of BioPAX and in decision making, community liaison and financial (as well as in-kind) support for BioPAX. The grant from the DOE, which was agreed to be put in the name of Chris Sander as a courtsey, was obtained by the BioPathways Consortium for the devlopment of BioPAX and for other BioPathways Consortium activities.

Some history. BioPAX emerged from the community and those involved in the founding intended to keep it a community project with decisions made by the community, not by the PI as in a research project. Having a PI was the easiest mechanism whereby US funds could be obtained for consulting/community development and workshops. The role of PI was (and in my persoanl opinion, should remain) titular. The agendas and determination of how funds would be distributed should be made by the community according to rules of governance. The biopax workgroup (then called the core group) made the administrative decisions. While supporting the community, participation in the BioPAX core group was by invitation only. The people that administrated BioPAX initially and got it off the ground were Joanne Luciano and Mike Cary. Later Gary Bader joined and these three formed the core of the core, so to speak. As BioPAX developed the workgroup would need to change to reflect the different expertise needed as the ontology moved from metabolic pathway representation to biomolecular interactions to signal transduction and gene retulatory. Growing pains, in particular in the administration and governance have been severe and persistent dispite the good intentions of many of the participants. Nasty and rude behavior has occurred and double standards been applied and there have been cases where some members have undermined the efforts of others. People have put their interests ahead of the communities. It would be good if this stopped. It hasn't yet. It undermines the community for which it claims to serve and seeing this upsets me deeply.

AlanRuttenberg

"Active participation implies a commitment to attend workshops and conference calls, review ontology proposals and to disseminate the project." - What does disseminate the project mean? Does participant mean one has to do all of these? I think something more along the lines of "Active participation implies a commitment to doing something of use for the project". This encourages there to be members with diverse interests, talents, and contributions. For example, many open source projects have people who volunteer to write documentation, even if they are not actively developing the code for the project. We need some of those ourselves.

"Decision making can be delegated." - How?

"Subgroups can be formed by group consensus if enough participants are interested in an exchange format development topic not of general group interest" - This hasn't been the definition of subgroups thus far, rather subgroups have formed to work on issues of general group interest. And how do we know whether something is of "general group interest"? For example, would the DX group be considered a subgroup by your definition. Why or why not?

"Wiki content speaks for the author unless indicated by a group endorsement message on the page". How does such an endorsement come into being?

"PI". Can anyone be a PI? BioPAX is in need of additional funding, can anyone submit a grant for BioPAX support? Personally I don't like the mention of a PI in this context because it creates two classes of members.

"This relationship depends on mutual trust among all participants". Regretably, it is not the case that such trust currently exists. While we should strive for it, I don't think it would be accurate to assume it at the moment.

"Administrative duties". Many items you list are not administrative in nature. While arrangements for venue, once decided up, might be considered administrative, agendas for technical meeting and decisions on which which participants to support with funding, for example invited experts, is something that influences the technical work, and should therefore remain in the hands of the working group. I have previously said that we need more funding for BioPAX activities, as evidenced by the lack of funds to support the Manchester meeting. We should be encouraging others to apply for grants, rather than saying it is limited to current PIs. Editing of the specification is another issue that should be the province of the working group. For one thing, this eliminates a potential "broken telephone" sitation. In addition, documentation is difficult work and we should be looking for additional volunteers to help in the editing task, as I have done in the last version.

"Sessions will be chaired by the conference organizers". I see no reason to include this. In fact some of the best chairing at Japan was done by people other than the organizers, as the organizers had proposals on the table.

Summary: I don't see much advance in this document compared to the previous governance discussion, and few of the real issues that have been the source of problems are addressed by it.

Jonathan Rees

We seem to be dancing around the real issues. I don't know if I can clarify this muddle, but let me try.

When I came to the group I had no preconceptions about how it was run; I was simply invited to a meeting (January 2005) whose nature was unknown to me. I think this was shortly after the original core group decided to open some or all of the exchange format development process up to broader participation.

Some time passed, and I observed some conflicts and confusion, and I tried to figure out how decisions were made - not technical decisions (what Gary calls "Community Process"), but those relating to how the group is run (what I call "Governance") - who's in charge, what the charter is, how are grants applied for and administered, who decides location and timing of meetings, who gets to make public statements on behalf of the project, and so on.

In Detroit I heard Chris Sander say that the effort was a "do-ocracy": if you did something you had control. I also heard, I think from Gary, that it was run by group consensus; this is a very different idea. I also heard the idea that there was or ought to be an "executive committee" that could make governance decisions (also from Gary but seconded by Peter). I also observed that most important decisions were made behind closed doors by people who did not feel it was important or desirable to report on what they were doing. Whether they had good reasons for being shy I couldn't tell.

I really wanted to find out where things stood, so that conflicts could be resolved fairly and so that if any changes in governance were to be made we'd at least have a documented starting point. I thought it would be enough to get a dialog about governance started in the wiki; I would write something incorrect, then others with more knowledge than me, and more of a stake than me, would correct it. But so far this approach has failed, and we are no closer to governance transparency than we were 12 months ago.

It appears that Chris is very interested in having control over the important issues. He cares about the outcome and he has something at stake. He and those in or recently in his research group have practiced "do-ocracy" and are not too concerned about transparency. They apply for grants in the name of BioPAX without talking to the group about it, and set meeting places, times, and agenda without much discussion. The effect is that BioPAX is effectively a project of the Sander group. Everyone else is a sort of volunteer helper with the ability to affect fine-grained technical decisions but no other influence.

There has been a funny rhetorical war going on. Some of us outside the inner circle try to talk about governance and transparency of non-technical aspects, and others inside the circle respond that the process is open and consensus-based. But they're really talking only about technical decisions (and even then not the important ones, such as goals). The important stuff - what Gary calls "administrative" (connotation: uncontroversial) and I call "executive" (connotation: critical to project success) remains out of sight.

It's the discord between what's asserted (consensus, etc.) and what's actually practiced (secrecy, etc.) that is so infuriating. Using something like the W3C process for all decisions would be great. But if there is clarity that we will have two kinds of decision-making, one closed and one open, and that the Sander group or some other "executive committee" gets to make all governance decisions, that's fine with me, although it might lead me to leave the group completely. To get people to stay, the sponsoring body would have to treat its volunteers with respect, and respect means (among other things) some degree of transparency.

Maybe it is time to formalize our process and create a corporation. Then at least the governance process would be written down. It would not guarantee that the process was followed, of course. In any case, one would hope that there would be less heavyhanded ways to achieve some clarity.