bioinfo-skills

Plugin bioinfo-skills from marketplace basm-claude-skills in brunoasm/my_claude_skills. Commands read from the repo's manifest — 24 days ago.

Skills (10)

• emu-bulk-upload

  Help museum insect curators bulk upload specimen data to the Emu database. Maps any input format to Emu's template, matches localities to existing records, finds parent sites, creates bulk upload tables, and walks users through the upload process.

• accounting

  Process receipts, track expenses in Google Sheets, reconcile records, and generate entertainment supplement tables for Field Museum procurement card accounting

• biogeobears

  Set up and execute phylogenetic biogeographic analyses using BioGeoBEARS in R. Use when users request biogeographic reconstruction, ancestral range estimation, or want to analyze species distributions on phylogenies. Handles input file validation, data reformatting, RMarkdown workflow generation, an

• document-ocr

  Convert scanned PDFs and document images into clean Markdown using docling for layout (figures, tables, reading order) plus a vision-language OCR model. Use when a user needs high-quality OCR of scanned documents, historical literature, or photographed pages — preserving multi-column reading order,

• extract-from-pdfs

  This skill should be used when extracting structured data from scientific PDFs for systematic reviews, meta-analyses, or database creation. Use when working with collections of research papers that need to be converted into analyzable datasets with validation metrics.

• grant-proposal-workflow

  Plan, write, edit, and review a multi-document grant application or resubmission (NSF, NIH, foundations, internal awards, and any program with its own solicitation): requirements, drafting, budgets and justifications, letters, citation and figure checks, cross-document consistency, mock panel review

• lab-ordering

  Place lab supply orders from member requests — route by request header to Amazon Business, the Pritzker Lab Google Form, or a direct vendor; stage the cart/form and stop for human review before any purchase. Use when the user pastes an order request or asks to order supplies, place an order, or fill

• nirc-badge-request

  Prepare Field Museum NIRC ID badge requests (Scientific Affiliate, Visitor, Contractor) and prefill the NIRC Badge Request Google Form for human review. Use this skill whenever the user mentions a badge, badge renewal, expiring badge, building access, door access, room access, West Lot parking for a

• busco-phylogeny

  Generate phylogenies from genome assemblies using BUSCO/compleasm-based single-copy orthologs with scheduler-aware workflow generation

• secure-raw-data-backup

  Archive irreplaceable raw data (sequencing runs, imaging, field data) to write-once cloud cold storage — generate checksums, verify before upload, stream a tarball to S3 Deep Archive under Object Lock, and prove the pipeline with a restore test before trusting it at scale. Use when the user asks to