About the Bioprotocols Working Group

The Bioprotocols Working Group is an open community organization developing a free and open standard for representation of biological protocols.

To join the Bioprotocols Working Group:

• Join the community mailing list at: https://groups.google.com/g/bioprotocols
• Join the #collab-bioprotocols channel on the Bits in Bio Slack.

Help fund development! Get in contact with community leadership about how to contribute.

Leadership

Elected Term: October 3rd, 2023 - October 3rd, 2024

Chair: Tim Fallon (UCSD)

Finance Committee:

• Bryan Bartley (BBN)
• Luiza Hesketh (State University of Campinas, Brazil)
• Dan Bryce (SIFT)

Former Elected Term: August 24th, 2022 - October 3rd, 2023

Chair: Dan Bryce (SIFT)

Finance Committee:

• Jeremy Cahill (Metamer Labs)
• Mark Doerr (University of Greifswald)
• Tim Fallon (UCSD)

Governance

Approved by community vote on August 16th, 2022

Mission:

The Bioprotocols Working Group is an open community organization developing free and open standards for representation of biological protocols. In support of that goal, the organization also develops tools and practices and works with other organizations to facilitate dissemination and adoption of these standards.

As an organization, the Bioprotocols Working Group holds the following values:

• The standards developed by the community should be available under permissive free and open licenses.
• Technical decisions of the community should be made following open and inclusive processes.
• The community is strengthened by fostering a culture of diversity and inclusion, in which all constructive participants feel comfortable making their voices heard.

Organization:

This organization has the following structure:

• Bioprotocols Working Group: all members of the bioprotocols@googlegroups.com mailing list, and the ultimate authority for the community.
• Chair: operational executive for the community, elected by the Bioprotocols Working Group
• Finance Committee: responsible for managing organizational funds, including fund-raising, budgeting, and approving expenditures, elected by the Bioprotocols Working Group.
• Steering Committee: major financial stakeholders in the organization, charged with overseeing and approving the work of the Finance Committee. Determined by financial contributions to the community.

Bioprotocols Working Group

Membership in the Bioprotocols Working Group is open to all interested parties. Individuals interested in joining the group should apply to join the mailing list.

The Bioprotocols Working Group as a whole is the ultimate authority and source of legitimacy for decisions on standards and on community governance. All elections, standards changes, and governance changes are voted on by the Bioprotocols Working Group according to the procedures below.

The primary means of communication for the Bioprotocols Working Group are currently:

• The bioprotocols@googlegroups.com mailing list: This is the formal and archival means of communication for the community. All significant decisions on governance and the evolution of the standard must be discussed via this mailing list.
• The #collab-bioprotocols channel on the Bits-in-Bio Slack: This is a higher-frequency instant-messaging location, intended for ad-hoc discussions and questions.
• Development calls: These are meetings held regularly (currently weekly) for technical coordination, planning, and discussion.

All of these are open to participation from any interested party.

In addition, the Bioprotocols Working Group holds workshops twice per year. These may be stand-alone workshops or in combination with another event (e.g., COMBINE meetings), but must provide ample time for attending members to hold focused discussions on the standards and tool development.

All members of the Bioprotocols Working Group are encouraged (but not required) to:

• Attend development calls and workshops
• Participate in discussions on the mailing list and Slack
• Cast votes for elections, standards changes, and governance changes
• Support the working group standards in any tools and systems they work on
• Provide constructive feedback for improving working group standards and tools

Only a small subset of the Bioprotocols Working Group are expected to be actively coordinating on the creation of standards and tools, whether supported by organization funds or by external funding. This subgroup has no formal organizational status, but coordinating and supporting these active developers is the primary responsibility of the Chair and Finance Committee.

Voting Procedures

In the following procedures, working days are defined as Monday through Friday.

Elections Process:

Before any election, there is a nomination period of at least 5 working days. All members of the Bioprotocols Working Group are eligible for all offices (except where this would conflict with requirements that offices be held by persons from different organizations). Any member can self-nominate or can nominate any other member. Voting runs for 5 working days, starting at the end of the nomination period. All members of the Bioprotocols Working Group are eligible to vote. Candidates are elected by plurality. Note that this may need to be changed to a more sophisticated tallying system if elections become strongly contested.

Standards/Governance Voting Process:

Any member of the Bioprotocols Working Group can submit a proposal on standards (creation or modification) or to modify this governance to the community at large. All changes should be made based on rough consensus, which is later confirmed by a vote. The Chair is expected to move a proposal for a vote once they deem that a rough consensus has been achieved; a vote may also be moved and seconded by any two members of the Bioprotocols Working Group.

• When a vote is initiated, the Chair posts a voting form (see below) before the vote begins for a final discussion period of 2 working days.
• Voting runs for 5 working days, starting at the end of the discussion period.
• All members of the Bioprotocols Working Group are eligible to vote, with one vote per person. Note that this may need to be changed to organization-based voting if any organization becomes problematically over-represented amongst active voters.
• The Chair may extend the voting period by up to an additional 5 working days when they feel that an insufficient number of votes have been obtained.
• The Chair tallies and calls the vote, with a ⅔ majority being judged sufficient to confirm rough consensus.

Voting forms should:

• Clearly summarize the proposal and provide a link to a stable document with its full details.
• State the eligibility criteria for voting, “All members of the Bioprotocols Working Group are eligible to vote.”
• Provide the following options for the vote:
  • accept — vote to accept the proposal
  • reject — vote to reject the proposal
  • abstain — no opinion, abstain votes will not be counted when determining majorities
  • defer / table for further discussion — keep the proposal as a draft so that it can be again put to a vote after further discussion and amendment (in contrast to “abstain” this vote will be counted when determining majorities).

Chair

The Bioprotocols Working Group designates a Chair to help coordinate the activities of the organization. The responsibilities of the Chair are:

• Organizing regular development calls
• Running community votes
• Working with the Finance Committee and Steering Committee to ensure fund-raising and transparent use of funds in the interest of the community.

The Chair can delegate execution to others as needed: the Chair’s responsibility is to see that work deemed necessary by the members of the Bioprotocols Working Group is done, whether by themselves or others.

The Chair is elected for a 1 year period, and may be re-elected.

To increase the perspectives represented and to reduce the potential for conflict of interest, the Chair must not be from the same organization as any of the members of the Finance Committee.

If the community raises sufficient resources, funds may be allocated to pay for part or all of the Chair’s labor. The organization budget, however, should reflect development as the primary goals of the organization.

Note: if the scale of standards and organizational work outgrows a reasonable scale for a single individual, the Chair role should be expanded to a group of elected Editors, similar to what is used by other COMBINE standards. At present, with work dominated by tools, the Chair will serve as a sole elected Editor.

Finance Committee:

The Finance Committee is responsible for managing the financial resources of the Bioprotocols Working Group. These responsibilities include fund-raising, budgeting, approving expenditures, and any other fiscal activities necessary for an equitable and transparent use of funds in the interest of the community.

The Finance Committee has three members. Members are elected for a 1 year period, and may be re-elected.

To increase the perspectives represented and to reduce the potential for conflict of interest, the members of the Finance Committee must be from different organizations, and also may not be from the same organization as the Chair.

Likewise, to reduce the potential for conflict of interest, Finance Committee Members must act as volunteers, and cannot be paid by the Bioprotocols Working Group.

Budget process

The budget for the Bioprotocols Working Group shall be prepared and approved as follows:

• The Finance Committee should provide financial reports and solicit input on priorities from the full Bioprotocols Working Group.
• Based on the priorities input from the Bioprotocols Working Group, the Finance Committee shall prepare a budget plan, at least once per year.
• The budget is approved by a vote of the Chair plus the Steering Committee.
• The Finance Committee then executes following the approved budget, with supervision from the Chair.
• Budget changes in response to changing circumstances may be approved by the same process.

Information regarding potential fund-raising and related communications shall be managed to appropriately preserve the privacy of personal information by the Chair and the Finance Committee.

The organization budget, minutes from budget-related meetings, and financial transactions shall all be made public for the sake of transparency.

Steering Committee

The Steering Committee is the only non-elected position in the Bioprotocols Working Group. This is because the purpose of the Steering Committee is to ensure that the major financial contributors to the Bioprotocols Working Group are comfortable with how their contributions are being spent.

The Steering Committee is composed of:

• Any person or organization who has contributed at least $25K/year
• One designated person or organization from a group of smaller contributors who join together with a sum of contributions of at least $25K/year

Tenure on the Steering Committee runs 1 year forward from the point where contributions hit the threshold (i.e., if a Steering Committee organization stops being able to contribute, they have a “grace period” of 1 year before leaving the committee).

Note that qualifying contributions are specifically only monetary: in-kind contributions (e.g., labor or supplies) are explicitly excluded.

The responsibilities of the steering committee are:

• Review and approve budget plans provided by the Finance Committee
• Provide advice to the Chair upon the chair’s request

Code of Conduct:

The Bioprotocols Working Group is dedicated to providing a harassment-free experience for everyone, regardless of gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race, ethnicity, religion (or lack thereof), or technology choices. We do not tolerate harassment of participants in our meetings, email lists, and other communication mechanisms in any form. Sexual language and imagery is not appropriate for any of these venues, including talks, workshops, parties, email lists, and other online media. Participants in our meetings and discussions violating these rules may be sanctioned or expelled from our mailing lists and our meetings at the discretion of the Chair.

Ground-rules for moderating community discussions

The following are suggested ground rules for discussions intended to promote constructive dialogue and inclusion of the greatest breadth of stakeholder perspectives:

• No interruptions; signal to the moderator that you wish to speak. If a person goes on too long, however, the moderator may ask them to give the next person a turn to speak.
• Moderator maintains a queue of speakers, calling on each in turn.
• Pause periodically for “step back” and explicitly invite comments by less-heard voices, possibly specifically inviting individual people. Spend at least 30 seconds waiting before continuing.
• Speaking about people or value judgements promotes conflict rather than constructive discussion. Instead, speak about ideas and facts in terms of specific concerns and consequences.
  • e.g., “You are wrong” is problematic for communication because it is about people (“you”) and value judgements (“wrong”). It will tend to promote rather than resolve conflict.
  • Instead: “I am concerned that proposal X will have negative consequence Y.”
• Heated conversation suppresses sharing of legitimate concerns. If discussion is getting heated, it should be paused, the emotional concern acknowledged, and restarted with a cooler tone.
• Side issues should be recorded to revisit later if they become a significant distraction.