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MDhewei
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bioinformatics_big_papers_weekly_report

Retrieve recent bioinformatics papers and generate ranked TSV and PDF reports.

64|12|Updated Apr 7, 2026
Search Tags:#pdf#bioinformatics#report#ranking#literature#tsv#week
One-click install
npx skills add https://github.com/MDhewei/bioinfor-claw --skill bioinformatics-big-papers-weekly-report
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bioinformatics_big_papers_weekly_report
Source: https://github.com/MDhewei/bioinfor-claw/tree/main/paper-search-and-digest/big-papers-weekly-report
Command: npx skills add https://github.com/MDhewei/bioinfor-claw --skill bioinformatics-big-papers-weekly-report

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pandas, requests, reportlab, and includes scripts (resource) components.

What problem does it solve?

This skill automates weekly surveillance of high-impact bioinformatics papers, ranking them by journal prestige and relevance to user interests, and delivering a polished PDF report along with a TSV of results.

Core Features & Use Cases

  • Retrieve recent papers from a curated set of high-profile journals.
  • Rank papers using a transparent scoring mechanism that combines journal prestige, generic bioinformatics relevance, and user-specified keywords; generate a concise summary per paper and a structured TSV and a PDF report.
  • Suitable for PI group weekly digests, literature scouting for new grants, or keeping teams current on computational biology trends.

Quick Start

Run the weekly report script to generate the PDF and TSV outputs, e.g., python scripts/big_papers_weekly_report.py --output-prefix results/bioinfo_weekly_report

Frequently Asked Questions about bioinformatics_big_papers_weekly_report

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate weekly bioinformatics literature surveillance and generate a ranked PDF report?▼

Automate weekly bioinformatics literature surveillance by retrieving recent papers, applying a relevance scoring model, and outputting a structured TSV and polished PDF report. Configure the journal scope, date window, and user-interest keywords to produce ranked results.

How does the paper ranking mechanism work for bioinformatics literature reports?▼

The ranking mechanism scores papers by combining journal prestige, generic bioinformatics relevance, and user-specified keywords. It provides transparency into scoring components and generates a concise summary per paper within the TSV and PDF outputs.

Do I need Crossref and PubMed access to retrieve bioinformatics paper metadata and abstracts?▼

Crossref access is required for retrieving paper metadata, while PubMed enrichment for abstracts is optional. Both sources feed into the deterministic scoring model to produce the ranked weekly literature report.

Can I customize the journal scope and date window for high-impact bioinformatics paper retrieval?▼

The journal scope and date window are fully configurable for high-impact bioinformatics paper retrieval. Users specify these parameters alongside interest keywords to tailor the ranked TSV and PDF report outputs.

What's the best way to generate a PI group weekly digest of computational biology trends?▼

Generate a PI group weekly digest by running the report script with a configured journal set and interest keywords. The script produces a structured TSV and polished PDF suitable for sharing computational biology trends with the team.

Why does the weekly bioinformatics report use a deterministic output format with explicit input/output contracts?▼

The deterministic output format with explicit input/output contracts ensures consistent TSV and PDF report generation. This design guarantees reproducible weekly literature surveillance results across different runs and environments.

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