Digital Drosophila Archive
61 lines
7.0 KiB
JSON
61 lines
7.0 KiB
JSON
{
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"schema": "lfs-publication-plan-v1",
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"source_root": "/data/digital-drosophila",
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"groups": [
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{
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"id": "malecns-raw-core",
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"paths": ["datasets/male-cns-v1.0/raw/annotations", "datasets/male-cns-v1.0/raw/connectivity", "datasets/male-cns-v1.0/raw/_manifests"],
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"license": {"data": "CC-BY-4.0", "url": "https://creativecommons.org/licenses/by/4.0/", "local_manifests_scripts": "Project-authored provenance; no new blanket software license"},
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"provenance": {"version": "male-cns:v1.0", "source_page": "https://male-cns.janelia.org/download/", "source_prefix": "gs://flyem-male-cns/v1.0/connectome-data/flat-connectome/", "attribution": "Male CNS collaboration: FlyEM (HHMI Janelia), University of Cambridge Department of Zoology, MRC Laboratory of Molecular Biology, Google Research; retain original dataset author credits", "changes": "Data file bytes unchanged; archival compression and path manifest only. Download logs excluded."}
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},
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{
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"id": "malecns-swc",
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"paths": ["datasets/male-cns-v1.0/raw/skeletons"],
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"license": {"data": "CC-BY-4.0", "url": "https://creativecommons.org/licenses/by/4.0/"},
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"provenance": {"version": "male-cns:v1.0", "source_page": "https://male-cns.janelia.org/download/", "source_prefix": "gs://flyem-male-cns/v1.0/segmentation/skeletons-malecns/skeletons-swc/", "attribution": "Male CNS collaboration: FlyEM (HHMI Janelia), University of Cambridge Department of Zoology, MRC Laboratory of Molecular Biology, Google Research", "changes": "Unchanged downloaded SWC bytes; not restricted to the later neuron-only canonical set. No EM images."}
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},
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{
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"id": "malecns-processed",
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"paths": ["datasets/male-cns-v1.0/processed"],
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"license": {"derived_data": "CC-BY-4.0", "url": "https://creativecommons.org/licenses/by/4.0/", "local_scripts_reports": "Project-authored processing and provenance; no new blanket software license"},
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"provenance": {"dataset": "male-cns:v1.0", "source_page": "https://male-cns.janelia.org/download/", "attribution": "Original Male CNS collaboration; Digital Drosophila project for local processing", "changes": "Existing Phase 3 all-body and Phase 3B neuron-only tables, index mappings, CSR and audit reports, copied byte-for-byte. These were previously derived by filtering/reindexing official data, not new preprocessing. Phase 3 historical outputs are not the approved SNN input; use neuron-only for current runtime.", "canonical_neurons": 166700, "canonical_edges": 25582938, "canonical_synaptic_weight_sum": 124177617}
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},
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{
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"id": "malecns-synaptic-partners",
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"paths": ["experiments/phase4aa-apl-pn-scope/external-resources"],
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"license": {"data": "CC-BY-4.0", "url": "https://creativecommons.org/licenses/by/4.0/", "local_provenance": "Project-authored"},
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"provenance": {"source_page": "https://male-cns.janelia.org/download/", "source_url": "https://storage.googleapis.com/flyem-male-cns/v1.0/connectome-data/flat-connectome/syn-partners-male-cns-v1.0-minconf-0.5.feather?generation=1780494942562468", "registered_file_sha256": "959d8ef4173b35382a3e6acfaf5167c795b6d10b877572d146af04e1b487bc07", "attribution": "Male CNS collaboration: FlyEM (HHMI Janelia), University of Cambridge Department of Zoology, MRC Laboratory of Molecular Biology, Google Research", "changes": "Unchanged downloaded paired-synapse file and provenance; syn-points and EM were not downloaded."}
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},
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{
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"id": "celltype-explorer",
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"paths": ["experiments/phase4f-retinotopic-vision/external-resources/celltype-explorer"],
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"license": {"upstream": "CC-BY-4.0", "url": "https://creativecommons.org/licenses/by/4.0/", "evidence_file": "LICENSE", "evidence_sha256": "9ba9550ad48438d0836ddab3da480b3b69ffa0aac7b7878b5a0039e7ab429411"},
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"provenance": {"repository": "https://github.com/reiserlab/celltype-explorer-drosophila-male-cns", "commit": "789cc6c105798ce2fd70ba85dab394f90899616b", "attribution": "Reiser Lab and Male CNS Cell Type Explorer contributors; retain upstream notices", "changes": "Unchanged pinned working-tree file bytes; .git, environments, caches and credentials excluded. A source snapshot, not a full Git clone."}
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},
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{
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"id": "visualpathways",
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"paths": ["experiments/phase4f-retinotopic-vision/external-resources/visualpathways"],
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"license": {"upstream": "GPL-3.0 as supplied in upstream LICENSE; no assertion of only/or-later option", "evidence_file": "LICENSE", "evidence_sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986", "third_party_notices": "Retained; no relicensing of third-party components"},
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"provenance": {"repository": "https://github.com/reiserlab/visualpathways", "commit": "23f6ac131529b5f56894c6eeb9b88b17894fc00d", "attribution": "Reiser Lab and visualpathways contributors; original copyright notices and source retained", "changes": "Unchanged source/resource file bytes from pinned checkout; .git, credentials, environments and caches omitted; explicit exclusions recorded. No software execution or model alteration."}
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},
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{
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"id": "door-data",
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"paths": ["experiments/phase4l-olfactory-grounding/external-resources/DoOR.data"],
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"license": {"upstream": "CC-BY-SA-4.0", "url": "https://creativecommons.org/licenses/by-sa/4.0/", "evidence_file": "DESCRIPTION", "evidence_sha256": "27db2a92eb651d67969de94959990d51668a5857a33c4750a3b6ef49c5880504"},
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"provenance": {"repository": "https://github.com/ropensci/DoOR.data", "commit": "eea72d64b42a4e91dafe822cf0b5204de33f8d34", "version": "2.0.1", "attribution": "Daniel Münch, C. Giovanni Galizia, Shouwen Ma, Martin Strauch, Anja Nissler; see upstream DESCRIPTION and data-source references", "papers": ["https://doi.org/10.1038/srep21841", "https://doi.org/10.1093/chemse/bjq042"], "changes": "Unchanged pinned data package; .git omitted. ShareAlike terms remain attached to this package, not asserted over unrelated repository content."}
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},
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{
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"id": "shiu-author-model-source",
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"paths": ["experiments/phase4ac-lif-semantics/external-resources"],
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"license": {"upstream": "MIT", "evidence_file": "LICENSE", "evidence_sha256": "3621f6d6476189190e2960fa43f11b275ba4eca848fdac50a1ba2925de6223e8"},
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"provenance": {"repository": "https://github.com/philshiu/Drosophila_brain_model", "commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", "attribution": "Philip Shiu and Drosophila_brain_model contributors; original MIT copyright and permission notice retained", "paper": "https://www.nature.com/articles/s41586-024-07763-9", "changes": "The previously downloaded model.py, environment_full.yml, LICENSE and local provenance only. This is model source, not pretrained weights, and not a strict original-model reproduction claim."}
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}
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],
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"exclude_paths": [
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"datasets/male-cns-v1.0/processed/_staging",
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"experiments/phase4f-retinotopic-vision/external-resources/visualpathways/.env_sample",
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"experiments/phase4f-retinotopic-vision/external-resources/visualpathways/pdfversion",
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"experiments/phase4f-retinotopic-vision/external-resources/visualpathways/docs/column_coord.pdf"
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]
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}
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