Dockstore 2.0: Enhancing a community platform for sharing cloud-agnostic research tools
Bibliographic record
Abstract
Dockstore is a platform that was created in response to the many challenges faced during the PCAWG study (Pan-Cancer Analysis of Whole Genomes). It is a repository of scientific workflows described using popular workflow languages with their dependencies distributed in Docker images. This powerful combination of technologies allows for improved sharing and portability of scientific workflows. Docker is used to describe the environment that the workflow will run in along with all of the dependencies required. Workflow languages are used to describe the steps involved in running a workflow and how they are dependent on each other, including all inputs and outputs. We currently support CWL, WDL and Nextflow. These descriptor documents can be stored on GitHub, Bitbucket, GitLab, or directly on dockstore.org.
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 | 0.013 | 0.021 |
| Meta-epidemiology (narrow) | 0.001 | 0.002 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.005 | 0.003 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.005 | 0.009 |
| Open science | 0.007 | 0.020 |
| Research integrity | 0.003 | 0.004 |
| Insufficient payload (model declined to judge) | 0.012 | 0.008 |
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".