Continuous Tools for Scientific Publishing
Bibliographic record
Abstract
Advances in technology for data workflows have increased the speed and scope of scientific discovery, however, scientific dialogue still uses outdated technology for communicating and sharing knowledge. The widespread reliance on static PDF formats for research papers starkly contrasts with the complex, data-driven and increasingly computational nature of modern science. This gap, which is especially evident in the computational sciences, impedes the speed of research dissemination, reuse, and uptake. We require new mediums to compose ideas and ways to share research findings iteratively, as early as possible and connected directly to software and data. In this paper we discuss two tools for scientific authoring and publishing, MyST Markdown and Curvenote, and illustrate examples of improving metadata, reimagining the reading experience, including computational content, and transforming publishing practices for individuals and societies through automation and continuous practices. We focus on the unique aspects of the tools, which enable computational and interactive content, publishing and sharing continuously through automated checking and typesetting, and provide case studies from individuals to societies who have adopted these tools.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.089 | 0.294 |
| Meta-epidemiology (narrow) | 0.002 | 0.002 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.016 | 0.016 |
| Science and technology studies | 0.008 | 0.013 |
| Scholarly communication | 0.043 | 0.050 |
| Open science | 0.008 | 0.033 |
| Research integrity | 0.007 | 0.010 |
| Insufficient payload (model declined to judge) | 0.042 | 0.033 |
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 source (direct Gemma or distilled Codex), 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".