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the following parts of the repository are *NOT* open-source:
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(to be clear, the things in this list are not embargoed, the issue is just that
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they are not formally open-source)
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**WARNING**: this might not be an exhaustive list
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currently visible:
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-----
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Barbara Dobrin:
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schemas/VegBIEN/planning/growth_forms/Barbara_Dobrin.parsing.scripts/ScriptsAnnot.zip
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schemas/VegBIEN/planning/growth_forms/Barbara_Dobrin.parsing.scripts/ScriptsAnnot/File1.sql
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schemas/VegBIEN/planning/growth_forms/Barbara_Dobrin.parsing.scripts/ScriptsAnnot/File2.sql
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schemas/VegBIEN/planning/growth_forms/Barbara_Dobrin.parsing.scripts/ScriptsAnnot/File3.sql
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schemas/VegBIEN/planning/growth_forms/Barbara_Dobrin.parsing.scripts/ScriptsAnnot/File4.sql
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schemas/VegBIEN/planning/growth_forms/Barbara_Dobrin.parsing.scripts/ScriptsAnnot/File5.sql
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schemas/VegBIEN/planning/growth_forms/Barbara_Dobrin.parsing.scripts/ScriptsAnnot/File6.sql
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schemas/VegBIEN/planning/growth_forms/Barbara_Dobrin.parsing.scripts/ScriptsAnnot/File7.sql
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schemas/VegBIEN/planning/growth_forms/Barbara_Dobrin.parsing.scripts/ScriptsAnnot/KEY.docx
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schemas/VegBIEN/planning/growth_forms/Barbara_Dobrin.parsing.scripts/stage2Ed.sql
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Bob:
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schemas/VegBank/VegBank_Data_Model.with_Collections_intro.ppt
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schemas/VegBIEN/planning/BIEN_OctWG-Whtbrd1.jpg
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schemas/VegBIEN/planning/BIEN_OctWG-Whtbrd2.jpg
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schemas/VegBIEN/planning/BIEN_OctWG-Whtbrd3.jpg
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schemas/VegBIEN/planning/BIEN_OctWG-Whtbrd4.jpg
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schemas/VegBIEN/planning/methodAttributeExamples.xlsx
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schemas/VegBIEN/planning/New-DD.xlsx
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Bob+Mike Lee:
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schemas/VegBIEN/planning/methodAttributeExamples_MTL.xlsx
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Brad (some are open-source, but we need to figure out which):
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anything he created while not working for iPlant, from 2013-7-1..10-31 (4 mos)
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see wiki.vegpath.org/2013-06-13_conference_call?&he's+full-time+iPlant+until+end+of+June#Availability,
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wiki.vegpath.org/2013-10-31_conference_call?&Brad+is+getting+set+up+with+iPlant+again#Availability
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derived/TNRS/Modifications to procedure to scrubbing names using TNRS.docx
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derived/TNRS/Morphospecies and scope.eml
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inputs/BIEN2.datasources.xlsx
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inputs/FIA/_src/FIA tables and columns to import to BIEN.docx
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inputs/FIA/_src/Recommended FIA filter criteria for BIEN.docx
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inputs/NY/verify/specimens.ref.sql
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inputs/SALVIAS/verify/plots.ref.sql
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planning/goals/_archive/BIEN3_derived_data_products.docx
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planning/goals/BIEN_3_derived_data_products_NormalizedDB_only.docx
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planning/resources/taxonomy/Nomenclature_excerpt.ppt
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planning/workflow/bien3_architecture.pptx
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planning/workflow/bien3_architecture/stage_I.png
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planning/workflow/bien3_architecture/stage_II.png
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planning/workflow/bien3_architecture/stage_III.png
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planning/workflow/bien3_architecture/stage_IV.png
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planning/workflow/bien3_architecture/stages.png
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planning/workflow/normalized_vs_denormalized/bien3_architecture_denormalized.pptx
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planning/workflow/normalized_vs_denormalized/bien3_architecture_normalized.pptx
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planning/workflow/normalized_vs_denormalized/denormalized_import.png
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planning/workflow/normalized_vs_denormalized/denormalized.generic_standardizations.png
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planning/workflow/normalized_vs_denormalized/normalized_import.png
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planning/workflow/validation/_archive/BIEN2 GeoValidation Workflow.docx
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planning/workflow/validation/_archive/BIEN2 Validation Workflow.docx
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planning/workflow/validation/_archive/BIEN2_Analytical_DB_overview.docx
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planning/workflow/validation/CreateViews.UnixShellScript
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planning/workflow/validation/GeoDistKM.sql.txt
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schemas/BIEN_logo.png
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schemas/BIEN_logo.small.png
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schemas/BIEN2/datasource_schema/bien_web_datasource_schema.mwb
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schemas/BIEN2/datasource_schema/bien_web_datasource_schema.sql
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schemas/BIEN2/datasource_schema/BIEN2_datasource_schema.png
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schemas/DwC/DwC_bien.xlsx
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schemas/VegBIEN/planning/attribution/BIEN 3 data use and attribution.docx
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schemas/VegBIEN/planning/taxonomy/higherPlantGroup.xlsx
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schemas/VegCore/Brad_Boyle/BIEN 3 data use and attribution.docx
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schemas/VegCore/Brad_Boyle/BIEN database entities related to data provenance and ownership.docx
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schemas/VegCore/Brad_Boyle/vegbien_identifier_examples.xlsx
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schemas/VegCore/Brad_Boyle/vegbien_identifiers.xlsx
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Brad+Bob:
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planning/meetings/2010-12-08.working_group/BIEN3-plan.docx
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UArizona? (some are open-source, but we need to figure out which):
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BIEN2/traits_observation_counts.xls
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planning/goals/BIEN deliverables.png
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planning/goals/BIEN3_derived_data_products.docx
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planning/goals/iPlant_BIEN_Proposal_Final.pdf
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planning/goals/use_cases/BIEN_data_use_cases.doc
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planning/goals/use_cases/rare_species.png
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planning/goals/use_cases/Trait_BIEN_data_use_case.docx
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planning/meetings/2011-10-24~28.working_group/BIEN 3 database summary notes from brad_v3.docx
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planning/meetings/2011-10-24~28.working_group/BIEN3 database breakaway session.docx
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planning/meetings/2011-12-01.conf_call/BIEN_db_meeting_20111201.docx
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planning/meetings/2011-12-08.conf_call/BIEN_db_meeting_20111208.docx
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planning/meetings/2011-12-15.conf_call/BIEN_db_meeting_20111215.docx
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planning/meetings/2012-01-05.conf_call/BIEN_db_meeting_20120105.docx
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planning/meetings/2012-01-12.conf_call/BIEN_db_meeting_20120112.docx
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planning/meetings/2012-01-12.conf_call/BIEN_db_proposed_agenda_20120112.docx
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planning/meetings/2012-02-03.conf_call/BIEN_db_meeting_20120203.docx
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planning/meetings/2012-02-24.conf_call/12-02-24 BIEN db.docx
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planning/meetings/2012-03-02.conf_call/12-03-02 BIEN db.docx
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planning/meetings/2012-03-16.conf_call/12-03-16_BIEN_db.docx
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planning/meetings/2012-11-26~30.working_group/Potential validations on BIEN data 1 Dec.docx
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planning/meetings/2012-11-26~30.working_group/Potential validations on BIEN data.docx
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planning/timeline/milestones/_archive/BIEN3 Milestones and Development Timeline_MLN2.docx
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planning/timeline/milestones/_archive/BIEN3 Milestones and Development Timeline_MLN2.pdf
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planning/timeline/milestones/_archive/BIEN3_milestones.2011-12-13.doc
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planning/timeline/milestones/BIEN Milestone – feedback.docx
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planning/timeline/milestones/BIEN3 - Progress since the 2011 working group.docx
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planning/workflow/2010.working_group.white_board/Bien 3 dia.jpg
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planning/workflow/2010.working_group.white_board/Dia 2.jpg
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planning/workflow/2010.working_group.white_board/Diagram nceas.jpg
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planning/workflow/BIEN-modArch-Dec2010 NS-SBD 1.4.ppt
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schemas/BIEN2/bien2_core_schema.png
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schemas/BIEN2/ERD/BIEN2_ERD.mwb
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schemas/BIEN2/ERD/BIEN2_ERD.pdf
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schemas/BIEN2/ERD/BIEN2_ERD.png
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schemas/BIEN2/ERD/BIEN2_ERD.sql
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schemas/BIEN2/ERD/BIEN2_ERD.svg
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schemas/BIEN2/ERD/bien2.sql
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schemas/BIEN2/ERD/bien2.with_foreign_keys.sql
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schemas/BIEN2/Guide_to_the_BIEN2_database.pdf
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VegX:
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schemas/VegX/Veg-X_elements_relationships.png
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schemas/VegX/VegX_Schema_1.5.1.tables.svg
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-----
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deleted:
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anything deleted with a commit message containing "copyright scrub"
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129
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potentially some things deleted for reasons other than copyright scrubbing,
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which would be missing the "copyright scrub" tag. this applies especially to:
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131
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- things deleted before r12121 (2014-02-07), when this problem became apparent
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- things deleted before r11705 (2013-11-21), when we started copyright scrubbing
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