SeqMonitor: Influenza Analysis Pipeline and Visualization
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Bibliographic record
Abstract
Unprecedented sequencing effort has led to daily submissions of influenza genomes to public repositories such as the NCBI GenBank. With the decreasing cost of genome sequencing, it is expected that rapidly evolving viruses such as influenza will be sampled in even greater depth in the future. Keeping analyses up to date and managing this data is a prime concern for researchers and public-health officials alike. We have developed an influenza sequence pipeline, polymorphism data warehouse, and an interactive web-based analysis program to assist in managing the flow of sequence data. The system provides a framework for studying polymorphic associations with various metadata, for downloading subsets based on metadata criteria, as well as for tracking polymorphisms geographically and temporally. SeqMonitor is accessible at http://ratite.cs.dal.ca/SeqMonitor. Systems recently developed and under development are allowing the quick identification of important, novel mutations using 3-d protein structures [5] , as well as H3N2 antigenic-site-based vaccine prediction systems ( http://influenza.nhri.org.tw/ATIVS/index.jsp ) [6] . This type of automated detection and monitoring of novel mutations affecting antigenicity, convergent evolution, and inter/intra-host reassortment needs to be performed on a continual basis on the everincreasing dataset to keep abreast of new influenza threats. To this end, we have created an automated pipeline that can download the latest sequences from NCBI GenBank and add them to existing alignments of homologous sequences, as well as extract metadata such as antiviral resistance, collection date and location name. Each sequence can then be geotagged by an automated, user-verified extraction and querying engine which uses the GeoNames web service ( http://www.geonames.org ). The data are made available through our data warehouse and web application, SeqMonitor. The current version of SeqMonitor allows users to submit H1N1 protein sequences of the hemagglutinin or neuraminidase genes to a BLAST query, with the top matches being plotted on a geographic map. Novel and rare mutations of the query sequence can then be analyzed versus any subset of the data, defined for instance by oseltamivir resistance or country of collection. The geographic and related metadata files, along with the precomputed amino acid alignments constructed with the pipeline can be downloaded by users and processed by geographic and sequence data analysis packages such as GenGIS ( http://kiwi.cs.dal.ca/GenGIS ) [7][8] . SeqMonitor can be accessed at http://ratite.cs.dal.ca/SeqMonitor .
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.
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 | 0.001 |
| 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 it