NEP

Understanding the PDBx/mmCIF macromolecular structure file format (categories, items, loops, the underlying CIF/STAR syntax) and how to map its contents to netCDF dimensions, variables, and attributes for a read-only NEP UDF handler. Use together with the pdb-legacy skill when the legacy PDB format is also relevant.

Understanding the legacy Protein Data Bank (PDB) fixed-column text format for macromolecular structures, its record types, and how it relates to the modern PDBx/mmCIF format. Use this together with the mmcif skill when implementing a NEP reader for protein structure files.

Using libjpeg / libjpeg-turbo for 8-bit JPEG decompression from memory, with build-system detection and error handling suitable for NEP UDF readers.

Understanding DICOM (Digital Imaging and Communications in Medicine) file format, data elements, transfer syntaxes, pixel data encoding, and how to implement a read-only DICOM UDF handler for NEP.

Create a LibreOffice Writer concordance file (.sdi, semicolon-delimited) for use with the AutoMark feature to automatically generate a book index. Use when given text, a chapter, or a list of terms that need to be indexed.

Understanding the NetCDF-C library architecture including dispatch tables, format implementations (NetCDF-3, HDF5, Zarr, DAP), I/O layers, and metadata structures. Use when working on NetCDF-C codebase, debugging format issues, adding new features, or understanding how different storage backends interact.

Understanding OPeNDAP (Open-source Project for a Network Data Access Protocol) for accessing remote scientific data via HTTP, including DAP2/DAP4 protocols, constraint expressions, data models, and client integration. Use when working with OPeNDAP URLs, writing data access code, or integrating with NetCDF.