CommunityDevelopmentProcess

= This Page is an Archive of an old discussion - June 11th 2010 =

BioPAX Community Process
Our goal is to build a pathway exchange format in an inclusive, community consensus driven manner.

Community Exchange Format Development Process
Participation is encouraged and open to all interested. Active participation implies a commitment to attend workshops and conference calls, review ontology proposals and to disseminate the project.

Exchange format decisions are made by consensus at meetings by participants or their proxies and are recorded on the wiki. Consensus is essentially unanimity, but implies a commitment by those involved to respond to issues and iterate until agreement is reached. Decision making can be delegated.

Meetings are regularly scheduled or announced on biopax-discuss mailing list at least one week in advance. Meeting agendas should list issues at least one week in advance.

Subgroups can be formed by group consensus if enough participants are interested in an exchange format development topic not of general group interest. Subgroups are managed by their participants according to this process. Subgroup membership does not require commitment to attend all group meetings.

Wiki content speaks for the author unless indicated by a group endorsement message on the page.

Dissemination guidelines encourage use of BioPAX and participant attribution. Reference journal articles describing the data exchange format are the prime BioPAX citation. The article will be drafted by the active PI and will include an inclusive author list and contribution section. The draft will undergo a time-limited review process to get general agreement on content by authors and will assume tacit approval of non-responders. Other publications such as news articles, lecture presentations, posters, web pages, etc. that describe BioPAX are encouraged and should list the writers or presenters as authors and clearly acknowledge the work of the BioPAX workgroup. Technical documentation describing BioPAX should list all contributors as authors and separately list the main editors.

Open source licenses that are academic and corporate friendly are used for all work created by the group. We currently use the Creative Commons attribution license for documents or LGPL for code.

Administrative Support
Administrative support is required to avoid duplication of effort and to encourage timely delivery of the exchange format. Because the project was initiated by academic groups and all funding has come from government agencies, the principal investigator (PI) of an academic group is currently the administrative point of contact and is responsible for administrative support.

PI-community relationship. The PI is responsible to and is supported by the community. This volunteer role implies commitment to collaborate with stakeholders (i.e. data and tool providers and users), to make and openly report administrative decisions, to be responsive, to gather new funding to support workshops and project administration and to support the grant proposals of others for BioPAX exchange format, data and tool development. Participants are responsible for communicating their needs to the PI. This relationship depends on mutual trust among all participants.

Administrative duties include technical administration of websites and mailing lists, setup of group meetings and conference calls, editing of the specification, maintaining the exchange format, applying for workshop grants and making decisions about workshop funding. Duties can be delegated.

Meeting funding. Active community members, academics and those in greatest need will have priority of travel expense reimbursement from workshop grants. These decisions will be made by the grant PI. Speakers will be determined by active BioPAX participants, many of whom will be expected to speak about their work. Sessions will be chaired by the conference organizers. Participant diversity will be encouraged, all facilities will be accessible to the disabled and workshop registration materials will allow participants with disabilities to voluntarily identify any special needs (required by NIH funded workshops).

Grant history:
 * US DOE workshop grant for 2003-2004. PI: Chris Sander
 * US DOE workshop grant for 2004-2005. PI: Chris Sander
 * US DOE renewal grant for Japan 2005 meeting. PI: Chris Sander
 * Japan JST grant for Japan 2005 meeting. PI: Ken Fukuda
 * Japan MEXT grant for Japan 2005 meeting. PI: Ken Fukuda
 * Japan JSBi grant for Japan 2005 meeting. PI: Ken Fukuda
 * US NIH workshop grant for 2006-2009. PI: Chris Sander

Current admin contact: Sander lab, at the Computational Biology Center at Memorial Sloan-Kettering Cancer Center in New York. biopax-info@biopax.org