PEtab development process
Motivation for this document / general remarks
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, until recently, there was no broadly supported format for the specification of parameter estimation problems in systems biology. Therefore, we developed PEtab. Having released the specifications for PEtab version 1.0, we would like to keep development of PEtab active by attracting more users and tool developers. We acknowledge that it is important for any potential contributors to know how PEtab is managed and developed, which we will explain in the remainder of this document.
We are committed to diversity, open communication, transparent processes, democratic decision-making by the community and fostering a welcoming environment. While we want to have clear processes, we don’t want to overformalize things to avoid unnecessary slowdowns.
Roles within the PEtab community
The following subsections describe the different roles in the development of PEtab.
Anybody interested in PEtab
Input from every interested person is welcome.
propose changes to PEtab
The PEtab forum includes anybody who is interested in PEtab and is subscribed to the PEtab mailing list using their real name. (Although anybody is invited to subscribe to the mailing list with any name or email address, we require the use of real names for participation in any votes. This is to ensure that every person has only one vote.)
The PEtab forum …
votes for changes to PEtab
PEtab is meant to be a community effort. Decisions should therefore be made as far as possible by a broad community interested in the use and development of PEtab. Nevertheless, such a project cannot run fully autonomously, but requires a core team of editors to take care of certain management tasks. The PEtab editorial board is a team of 5 representatives nominated and elected by the PEtab forum.
The duties / privileges of the editors include the following:
organizing and announcing annual meetings / hackathons
deciding minor PEtab issues among themselves (“minor” as defined by the editors but reasons for the decision need to be communicated)
managing the PEtab mailing lists
managing the PEtab GitHub organization and respective repositories
delegating any of the above
Other roles may be created as required based on the decision of the editors by majority vote.
The main discussion channel should be the GitHub issues / discussion pages. Additionally, the mailing list is used for the announcement of new releases, polls, and the likes and can be used for discussions that seem unfit for GitHub. An archive of the mailing list shall be publicly accessible. The PEtab Editors can be contacted through https://groups.google.com/g/petab-editors, which is only readable by the current Editors. Regular, ideally non-virtual, PEtab hackathons are planned to happen at least annually, e.g., in combination with COMBINE events.
Election of Editors
Editors are elected for 3 years by the PEtab forum. Editors may serve multiple terms, but there needs to be a break of 1 year between subsequent terms. To maintain continuity, not all editors shall be replaced at the same time. Editors may resign any time before the end of their term.
Whenever an Editor position becomes vacant:
Editors announce upcoming elections and request nominations via the PEtab mailing list. The time given for nominations shall be no shorter than 10 days.
Interested parties submit nominations including a short statement on the reason for nomination before the deadline. Self-nominations are allowed.
Editors ask the nominees whether they accept the nomination (nominees are given 5 days to accept). This step may start already during the nomination phase.
Editors announce the nominees who accepted their nomination along with the submitted statements and open the poll via the PEtab mailing list. The editors choose a sensible medium and deadline for the poll.
The PEtab forum casts their votes secretly. (Votes may have to be open to the editors, as they need to verify that only qualified votes are counted. However, the editors are required to maintain confidentiality.) Every participant has 1 vote per vacant position.
After passing the deadline, the editors count the votes and ask the editor-elect to accept or decline the election. No acceptance before the end of the deadline set by the editors, which shall not be less than 3 days, is considered decline.
If an editor-elect declines, the position will be offered to the next candidate according to the number of votes. (If there is no candidate left with at least one vote, the election for the vacant position needs to be repeated.
If there is a tie between candidates of which only a subset can become an editor, run-off elections including only those candidates have to be organized by the PEtab editors as soon as possible. Voters will again have a number of votes equal to the number of vacant positions.
If the editor-elect accepts, the other editors announce the new editor on the PEtab mailing list. The editors shall furthermore announce the number of votes each nominee, elected or not, has received.
Special procedure for the first election (February, 2021):
The first election was held among the authors of the original PEtab publication. Nominees were not required to be among the authors. The election was managed by two persons who were not among the candidates and were coming from two different labs. To avoid a simultaneous replacement of all of the editors elected during the first election, the first election was subject to the following special rules: 2 persons were elected for 3 years, 2 persons for 2 years and one person for 1 year. The persons with more votes were elected for a longer period (if they accepted for the longer period). In case of an equal number of votes among any of the top 5 candidates, there would have been run-off elections between those candidates with equal numbers of votes. The editors-elect were given 3 working days to accept the election. If an editor would decide to hand over his editorial role before the end of their term, an editor elected for a shorter term period could decide to take over and extend their term to the end of the leaving editor’s original term.
PEtab format development process
We acknowledge that PEtab cannot accommodate everybody’s needs, but we are committed to addressing current and future requirements in upcoming versions of the PEtab format. Although we value backwards-compatibility, we don’t want to exclude breaking changes if justified by the benefits.
Anybody is welcomed to propose changes or additions to PEtab. Any proposals shall be made using GitHub issues. Benefits, problems, and potential alternatives shall be discussed in the respective thread.
A proposal is considered accepted for inclusion in the next version of PEtab if it’s endorsed by the majority of the PEtab editors and if distinct developers of at least 2 tools provide a prototype implementation. For any changes, respective test cases sufficiently covering the changes are to be added to the PEtab test suite prior to release.
Requirements for new releases:
Updated format specifications
Updated test suite
The PEtab editors jointly decide whether these requirements are met.
Upon a new release, the PEtab editors ensure that
a new release is created in the GitHub repository
the new version of the specifications is deposited at Zenodo
the new release is announced on the PEtab mailing list
Versioning of the PEtab format
The PEtab specifications follow semantic versioning. Any changes to the PEtab specifications require a new release. Any necessary clarifications or corrections shall be collected on an Errata page until a new version is released.
The time for a new PEtab release is left to the discretion of the editors. However, accepted changes should be released within 2 months after acceptance.
With any new PEtab version it shall be ensured that a converter between the new and the previous version(s) is available. Parallel maintenance of multiple versions is not intended.
Generally, any parameter estimation problem that could have been specified in an earlier version should be specifiable in a new version (potentially requiring different syntax). Any changes to the PEtab specifications that would remove certain features without adequate replacement require the support of at least 4 out of the 5 editors.
Changes to these processes
Changes to the processes specified above require a public vote with agreement of the majority of voters. Any other changes not directly affecting those processes, such as changes to structure, orthography, grammar, formatting, the preamble can be made by the editors any time.