Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024
Bibliographic record
Abstract
The “COmputational Modeling in BIology NEtwork” (COMBINE) initiative aims to harmonise the development of diverse community standards for computational models in biology [<a class="link link-bibr" title="1. Hucka, M, Nickerson, DP, Bader, GD, Bergmann, FT, Cooper, J, Demir, E, et al.. Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative. Front Bioeng Biotechnol 2015;3:1–6. https://doi.org/10.3389/fbioe.2015.00019.Search in Google Scholar PubMed PubMed Central " href="https://www.degruyterbrill.com/document/doi/10.1515/jib-2024-0015/html#j_jib-2024-0015_ref_001" data-bs-target="j_jib-2024-0015_ref_001" data-bs-toggle="tooltip">1</a>, <a class="link link-bibr" title="2. Waltemath, D, Golebiewski, M, Blinov, ML, Gleeson, P, Hermjakob, H, Hucka, M, et al.. The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). J Integr Bioinform 2020;17:20200005. https://doi.org/10.1515/jib-2020-0005.Search in Google Scholar PubMed PubMed Central " href="https://www.degruyterbrill.com/document/doi/10.1515/jib-2024-0015/html#j_jib-2024-0015_ref_002" data-bs-target="j_jib-2024-0015_ref_002" data-bs-toggle="tooltip">2</a>]. It coordinates standard development to support the associated projects towards establishing a suite of compatible, interoperable and comprehensive standards that address the full spectrum of modeling in systems and synthetic biology. <a class="link link-fig" href="https://www.degruyterbrill.com/document/doi/10.1515/jib-2024-0015/html#j_jib-2024-0015_fig_001" data-bs-target="j_jib-2024-0015_fig_001">Figure 1</a> provides a comprehensive view of the COMBINE standards along with related efforts. Special issues focusing on COMBINE standards have been released regularly since 2016, offering updates from 2015 through 2023 as documented in [<a class="link link-bibr" title="3. König, M, Gleeson, P, Golebiewski, M, Gorochowski, TE, Hucka, M, Keating, SM, et al.. Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. J Integr Bioinform 2023;20:20230004. https://doi.org/10.1515/jib-2023-0004.Search in Google Scholar PubMed PubMed Central " href="https://www.degruyterbrill.com/document/doi/10.1515/jib-2024-0015/html#j_jib-2024-0015_ref_003" data-bs-target="j_jib-2024-0015_ref_003" data-bs-toggle="tooltip">3</a>–<a class="link link-bibr" title="9. Schreiber, F, Gleeson, P, Golebiewski, M, Gorochowski, TE, Hucka, M, Keating, SM, et al.. Specifications of standards in systems and synthetic biology: status and developments in 2021. J Integr Bioinform 2021;18:20210026. https://doi.org/10.1515/jib-2021-0026.Search in Google Scholar PubMed PubMed Central " href="https://www.degruyterbrill.com/document/doi/10.1515/jib-2024-0015/html#j_jib-2024-0015_ref_009" data-bs-target="j_jib-2024-0015_ref_009" data-bs-toggle="tooltip">9</a>].
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.003 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.000 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".