Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking
Bibliographic record
Abstract
BACKGROUND: The Bluejay genome browser has been developed over several years to address the challenges posed by the ever increasing number of data types as well as the increasing volume of data in genome research. Beginning with a browser capable of rendering views of XML-based genomic information and providing scalable vector graphics output, we have now completed version 1.0 of the system with many additional features. Our development efforts were guided by our observation that biologists who use both gene expression profiling and comparative genomics gain functional insights above and beyond those provided by traditional per-gene analyses. RESULTS: Bluejay 1.0 is a genome viewer integrating genome annotation with: (i) gene expression information; and (ii) comparative analysis with an unlimited number of other genomes in the same view. This allows the biologist to see a gene not just in the context of its genome, but also its regulation and its evolution. Bluejay now has rich provision for personalization by users: (i) numerous display customization features; (ii) the availability of waypoints for marking multiple points of interest on a genome and subsequently utilizing them; and (iii) the ability to take user relevance feedback of annotated genes or textual items to offer personalized recommendations. Bluejay 1.0 also embeds the Seahawk browser for the Moby protocol, enabling users to seamlessly invoke hundreds of Web Services on genomic data of interest without any hard-coding. CONCLUSION: Bluejay offers a unique set of customizable genome-browsing features, with the goal of allowing biologists to quickly focus on, analyze, compare, and retrieve related information on the parts of the genomic data they are most interested in. We expect these capabilities of Bluejay to benefit the many biologists who want to answer complex questions using the information available from completely sequenced genomes.
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 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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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".