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MIxS Standards, Data Submission & Stewardship (MG-RAST/EBI) Training | SRA/ENA, Manifests, FAIR & DOIs

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Microbiome, Metagenomics & Environmental Bioinformatics >> MIxS Standards, Data Submission & Stewardship (MG-RAST/EBI) Training | SRA/ENA, Manifests, FAIR & DOIs

MIxS Standards, Data Submission & Stewardship (MG-RAST/EBI) — Hands-on

Turn microbiome outputs into shareable, citable, and regulation-ready datasets. This hands-on module covers MIxS standards and ENVO terms, building clean sample/experiment/run schemas, preparing manifests and checksums, and submitting to NCBI SRA/ENA/EBI as well as MG-RAST. You will practice validation, fix common metadata errors, apply FAIR principles, assign licenses/DOIs, and ship a reproducible archive bundle with SOPs and environment files.

MIxS Standards, Data Submission & Stewardship (MG-RAST/EBI)
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Session 1
Fee: Rs 8800
MIxS, ENVO & Metadata Modeling
  • MIxS overview & packages
  • MIxS-Core, MIMS, MIMARKS environmental packages (soil/water/host) required vs optional fields
  • ENVO & controlled terms
  • habitat/biome/feature terms units/URIs & term lookup NCBI Taxonomy & host terms
  • Schema design & mapping
  • Sample ⇄ BioSample ⇄ Run BioProject & study hierarchy templates & versioning
Session 2
Fee: Rs 11800
SRA/ENA & MG-RAST Submissions (Hands-on)
  • NCBI SRA / ENA pathways
  • BioProject/BioSample creation FASTQ packaging & md5 SRA Toolkit, Aspera/FTP
  • MG-RAST submissions
  • metadata sheets & projects processing options & QC retrieving IDs & sharing
  • Re-submissions & updates
  • embargoes & release timing corrections & replacements linking to publications
Session 3
Fee: Rs 14800
Validation, Manifests & Controlled Vocabularies
  • Checklists & validators
  • template checks & field types date/geo/unit sanity checks common error patterns
  • Manifests & linking
  • Sample ↔ Run ↔ File mapping paired-end conventions checksums & integrity
  • Vocabularies & harmonization
  • ENVO, CHEBI, UO units synonyms & mappings CSV/TSV curation tips
Session 4
Fee: Rs 18800
FAIR, Licenses, DOIs & Reproducible Archive Bundles
  • FAIR & stewardship
  • findable/indexed metadata access & reuse guidelines consent/ethics pointers
  • Licensing, DOIs & citations
  • CC-BY/CC0 choices ORCID & author IDs dataset citation formats
  • Archive & deliverables
  • README + SOPs + env files manifest/metadata JSON release notes & changelogs


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