diff --git a/model/reproinventory_data.yaml b/model/reproinventory_data.yaml index 435baa1..1ae97a9 100644 --- a/model/reproinventory_data.yaml +++ b/model/reproinventory_data.yaml @@ -32,10 +32,12 @@ last_updated: '2023' functionality: null assessment: false - prerequisite: None - source: ReproNim; Johanna Bayer; Fellow-22 + prerequisite: null + source: + - ReproNim + - Johanna Bayer + - Fellow-22 review: null - exclude_from_reproinventory: false alias_links: null notes: null quadrants: @@ -43,7 +45,8 @@ - learning-oriented (tutorials) - id: 5 tag_team: - - CW/JB + - CW + - JB course_name: 'Data Science in Communication: Python and Reproducible Research' url: 'GitHub - yibeichan/COMM160DS: COMM 160DS: Data Science in Communication: Python and Reproducible Research (Spring 2023, University of California, Santa Barbara)' @@ -76,22 +79,27 @@ - NA imaging_modality: - NA - open_dataset: null + open_dataset: NA last_updated: '2023' functionality: null assessment: true - prerequisite: None - source: ReproNim; Yibei Chen; Fellow-22; UCSB + prerequisite: null + source: + - ReproNim + - Yibei Chen + - Fellow-22 + - UCSB review: JupyterHub no longer accessible. Need to link GitHubClassroom to GitHub (uclear if links work once you do that) - exclude_from_reproinventory: null alias_links: null notes: null quadrants: - learning-oriented (tutorials) - id: 7 tag_team: - - MH/CF/JB + - MH + - CF + - JB course_name: Reproducible Data Management with DataLad - University of Munster 18/11/22 url: https://onedrive.live.com/?authkey=%21AFsNiGzveqZ750s&id=86184EF59C004002%21416672&cid=86184EF59C004002&parId=root&parQt=sharedby&o=OneUp level: @@ -120,17 +128,21 @@ last_updated: '2022' functionality: null assessment: false - prerequisite: None - source: ReproNim; Julian Kosciessa; Fellow-22; Donders Institute + prerequisite: null + source: + - ReproNim + - Julian Kosciessa + - Fellow-22 + - Donders Institute review: Short slide deck, very clear - exclude_from_reproinventory: false alias_links: null notes: link does not work for me (JB) can someone double check quadrants: - understanding-oriented (explanation) - id: 8 tag_team: - - CW/CF + - CW + - CF course_name: Reproducible Data Management with DataLad - MEG/EEG Meeting DCCN 2022-11-28 url: https://onedrive.live.com/?authkey=%21AANsp4ZosaSOK2o&id=86184EF59C004002%21416988&cid=86184EF59C004002&parId=root&parQt=sharedby&o=OneUp level: @@ -160,11 +172,15 @@ last_updated: '2022' functionality: null assessment: false - prerequisite: Basic Git/None - source: ReproNim; Julian Kosciessa; Fellow-22; Donders Institute + prerequisite: + - Basic Git + source: + - ReproNim + - Julian Kosciessa + - Fellow-22 + - Donders Institute review: Relatively quick overview - more just what is DataLad vs detailed how to use - exclude_from_reproinventory: false alias_links: null notes: null quadrants: @@ -172,7 +188,9 @@ - understanding-oriented (explanation) - id: 9 tag_team: - - CW/CF/JB + - CW + - CF + - JB course_name: Reusable (big) data management with DataLad - Donders Nexus url: https://1drv.ms/b/s!AgJAAJz1ThiGms0Vdo-WifbI8FKPOA?e%3DourGa2&sa=D&source=editors&ust=1718948936539613&usg=AOvVaw0nBhMBkdri9NRmpgP0Wfu1 level: @@ -202,10 +220,13 @@ last_updated: '2022' functionality: null assessment: false - prerequisite: None - source: ReproNim; Julian Kosciessa; Fellow-22; Donders Institute + prerequisite: null + source: + - ReproNim + - Julian Kosciessa + - Fellow-22 + - Donders Institute review: Very short slide deck on GIT - exclude_from_reproinventory: false alias_links: null notes: null quadrants: @@ -213,7 +234,8 @@ - information-oriented (reference) - id: 10 tag_team: - - BH/CF + - BH + - CF course_name: Git Workshop url: https://1drv.ms/b/s!AgJAAJz1ThiGms0Z1FcP8964X7sAxw?e=ZpBDCi level: @@ -242,17 +264,22 @@ last_updated: '2023' functionality: null assessment: false - prerequisite: None - source: ReproNim; Julian Kosciessa; Fellow-22; Donders Institute + prerequisite: null + source: + - ReproNim + - Julian Kosciessa + - Fellow-22 + - Donders Institute review: Practical intro to bash and git - exclude_from_reproinventory: false alias_links: null notes: null quadrants: - understanding-oriented (explanation) - id: 11 tag_team: - - CW/CF/JB + - CW + - CF + - JB course_name: ISMRM QC 2022 url: https://www.nipreps.org/qc-book/welcome.html level: @@ -290,18 +317,24 @@ last_updated: '2022' functionality: null assessment: true - prerequisite: MRI preprocessing, R, Python - source: ReproNim; Celine Provins; Fellow-22 + prerequisite: + - MRI preprocessing + - R + - Python + source: + - ReproNim + - Celine Provins + - Fellow-22 review: Focuses on QC in reference to MRIQC; has lots of big picture info about QC/QA in general - exclude_from_reproinventory: false alias_links: null notes: null quadrants: - learning-oriented (tutorials) - id: 16 tag_team: - - CW/CF + - CW + - CF course_name: Reproducible Computation Environments url: https://uicapture.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=0640440b-c7ab-46c7-9bca-afdc00f914e6 level: @@ -330,17 +363,21 @@ last_updated: '2022' functionality: null assessment: false - prerequisite: Shell scripting - source: ReproNim; Avery Van De Water; Fellow-22 + prerequisite: + - Shell scripting + source: + - ReproNim + - Avery Van De Water + - Fellow-22 review: labeled as part 1 - unclear where part 2 is - exclude_from_reproinventory: null alias_links: null notes: null quadrants: - learning-oriented (tutorials) - id: 18 tag_team: - - BH/DNK + - BH + - DNK course_name: Guide to reproducible neuroimaging research url: https://github.com/compneuro-ncu/reproducible-neuroimaging level: @@ -370,10 +407,11 @@ last_updated: '2021' functionality: NA assessment: false - prerequisite: None - source: ReproNim; Karolina Finc + prerequisite: null + source: + - ReproNim + - Karolina Finc review: Some sections are under-developed - exclude_from_reproinventory: true alias_links: null notes: Reproducible Neuroimaging, tutorial guide, for cog sci students audience quadrants: null @@ -398,8 +436,7 @@ - Statistics course_length: 1 day instruction_medium: - - Hands-on tutorial - - notebooks + - Hands-on tutorial / notebooks delivery: - self-paced language: @@ -410,20 +447,25 @@ - NA imaging_modality: - MRI - open_dataset: true + open_dataset: 'True' last_updated: '2024' functionality: null assessment: true - prerequisite: Unix, Basic Python - source: ReproNim; MIchael Joseph; Fellow-20 + prerequisite: + - Unix + - Basic Python + source: + - ReproNim + - MIchael Joseph + - Fellow-20 review: Basic Imaging Overview. Focus on BIDS - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null - id: 22 tag_team: - - CW/JB + - CW + - JB course_name: Carpentries Incubator-SDC-BIDS-functional MRI url: https://carpentries-incubator.github.io/SDC-BIDS-fMRI/ level: @@ -453,14 +495,17 @@ - Python imaging_modality: - Functional - open_dataset: true + open_dataset: 'True' last_updated: '2024' functionality: null assessment: true - prerequisite: Python - source: ReproNim; MIchael Joseph; Fellow-20 + prerequisite: + - Python + source: + - ReproNim + - MIchael Joseph + - Fellow-20 review: Tutorial on functional neuroimaging in Python - exclude_from_reproinventory: false alias_links: null notes: null quadrants: @@ -483,8 +528,7 @@ - Statistics course_length: 1 day instruction_medium: - - Hands-on tutorial - - notebooks + - Hands-on tutorial / notebooks delivery: null language: - English @@ -494,14 +538,18 @@ - Python imaging_modality: - DWI - open_dataset: true + open_dataset: 'True' last_updated: '2024' functionality: null assessment: true - prerequisite: Unix, Basic Python - source: ReproNim; MIchael Joseph; Fellow-20 + prerequisite: + - Unix + - Basic Python + source: + - ReproNim + - MIchael Joseph + - Fellow-20 review: null - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null @@ -538,10 +586,14 @@ last_updated: '2020' functionality: null assessment: false - prerequisite: Unix, Basic Python - source: ReproNim; Jennifer Legault; Fellow-20 + prerequisite: + - Unix + - Basic Python + source: + - ReproNim + - Jennifer Legault + - Fellow-20 review: example syllabus for hackathon/course - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null @@ -573,10 +625,13 @@ last_updated: '2023' functionality: null assessment: false - prerequisite: NA - source: ReproNim; Sook-Lei Liew; Fellow-20; ReproRehab + prerequisite: null + source: + - ReproNim + - Sook-Lei Liew + - Fellow-20 + - ReproRehab review: Entire first year bootcamp videos online - exclude_from_reproinventory: false alias_links: null notes: null quadrants: null @@ -595,8 +650,7 @@ - multivariate analysis course_length: 1+ weeks instruction_medium: - - Hands-on tutorial - - notebooks + - Hands-on tutorial / notebooks delivery: null language: - English @@ -610,11 +664,15 @@ last_updated: '2020' functionality: null assessment: false - prerequisite: basic programming - source: ReproNim; Elizabeth McDevitt; Fellow-20; Princeton + prerequisite: + - basic programming + source: + - ReproNim + - Elizabeth McDevitt + - Fellow-20 + - Princeton review: Jupyter tutorials from the basics to advanced machine learning analyses on fMRI data - exclude_from_reproinventory: false alias_links: null notes: null quadrants: null @@ -646,10 +704,12 @@ last_updated: '2020' functionality: null assessment: true - prerequisite: None - source: ReproNim; Chris Rorden; Fellow-20 + prerequisite: null + source: + - ReproNim + - Chris Rorden + - Fellow-20 review: Syllabus for course on fMRI, including slides, from collection to inferencing - exclude_from_reproinventory: false alias_links: null notes: null quadrants: null @@ -681,10 +741,14 @@ last_updated: NA functionality: null assessment: true - prerequisite: moderate programming experience; must have bash/unix shell experience - source: ReproNim; Julie Schneider; Fellow-20 + prerequisite: + - moderate programming experience + - must have bash/unix shell experience + source: + - ReproNim + - Julie Schneider + - Fellow-20 review: Syllabus for reproducible neuroimaging multi-week course - exclude_from_reproinventory: false alias_links: null notes: null quadrants: null @@ -718,16 +782,19 @@ last_updated: '2020' functionality: null assessment: false - prerequisite: UNIX, Basic Python - source: ReproNim + prerequisite: + - UNIX + - Basic Python + source: + - ReproNim review: syllabus for tutorial; details unclear. Might be unfinished. - exclude_from_reproinventory: true alias_links: null notes: null quadrants: null - id: 32 tag_team: - - CW /JB + - CW + - JB course_name: DataLad Handbook url: https://handbook.datalad.org/en/latest/ level: @@ -756,10 +823,12 @@ last_updated: '2024' functionality: '2025' assessment: false - prerequisite: DataLad Handbook. Has Beginner and Advanced use cases - source: ReproNim; Adina Wagner + prerequisite: + - DataLad Handbook. Has Beginner and Advanced use cases + source: + - ReproNim + - Adina Wagner review: very good resource for data provenance - exclude_from_reproinventory: false alias_links: null notes: null quadrants: null @@ -794,10 +863,10 @@ last_updated: '2024' functionality: null assessment: false - prerequisite: NA - source: AI campus + prerequisite: null + source: + - AI campus review: Nice videos and course material on AI - exclude_from_reproinventory: false alias_links: null notes: null quadrants: null @@ -832,10 +901,12 @@ last_updated: '2021' functionality: null assessment: false - prerequisite: NA - source: ReproNim; Lennart Wittkuhn; Adina Wagner + prerequisite: null + source: + - ReproNim + - Lennart Wittkuhn + - Adina Wagner review: Good video - exclude_from_reproinventory: false alias_links: null notes: null quadrants: null @@ -872,7 +943,6 @@ prerequisite: null source: null review: Course outline for Data Lad Course - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null @@ -906,10 +976,11 @@ last_updated: '2024' functionality: null assessment: false - prerequisite: NA - source: ReproNim; Lennart Wittkuhn + prerequisite: null + source: + - ReproNim + - Lennart Wittkuhn review: null - exclude_from_reproinventory: false alias_links: null notes: null quadrants: null @@ -945,16 +1016,18 @@ last_updated: '2021' functionality: null assessment: false - prerequisite: NA - source: ReproNim; Xihe Xie + prerequisite: null + source: + - ReproNim + - Xihe Xie review: Review of previous materials, full course - exclude_from_reproinventory: false alias_links: null notes: null quadrants: null - id: 39 tag_team: - - CW/JB + - CW + - JB course_name: ReproNim Workshop Schedule url: https://github.com/mick-d/repronim-fcbg level: @@ -985,16 +1058,19 @@ last_updated: '2019' functionality: null assessment: false - prerequisite: NA - source: ReproNim; Michael Dayan; Fellow-19 + prerequisite: null + source: + - ReproNim + - Michael Dayan + - Fellow-19 review: Syllabus for ReproNim workshop - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null - id: 40 tag_team: - - CW/JB + - CW + - JB course_name: Syllabus - Research Imaging Informatics url: https://docs.google.com/document/d/1J-wCg62yIJNCdZd_bTDYkOWCXn0eqD1j7l17MQlE4qM/edit level: @@ -1021,11 +1097,15 @@ last_updated: '2019' functionality: null assessment: false - prerequisite: Computational Methods, Neuroimaging experience - source: ReproNim; Aaron Kemp; Fellow-19 + prerequisite: + - Computational Methods + - Neuroimaging experience + source: + - ReproNim + - Aaron Kemp + - Fellow-19 review: Syllabus for Research Imaging Informatics course. Overview of neuroimaging methods and basic processing - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null @@ -1046,8 +1126,7 @@ - Collect course_length: 1-3 days instruction_medium: - - Hands-on tutorial - - notebooks + - Hands-on tutorial / notebooks delivery: null language: - English @@ -1061,10 +1140,10 @@ last_updated: '2020' functionality: null assessment: true - prerequisite: NA - source: ReproNim + prerequisite: null + source: + - ReproNim review: Syllabus for workshop that has been given - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null @@ -1097,10 +1176,11 @@ last_updated: '2021' functionality: null assessment: false - prerequisite: NA - source: ReproNim; Princeton + prerequisite: null + source: + - ReproNim + - Princeton review: Very nice overview of different fMRI topics - exclude_from_reproinventory: false alias_links: null notes: null quadrants: @@ -1136,10 +1216,11 @@ last_updated: '2019' functionality: null assessment: false - prerequisite: NA - source: ReproNim; Etienne Roesch + prerequisite: null + source: + - ReproNim + - Etienne Roesch review: Pretty good if you want to teach fMRI analysis from scratch - exclude_from_reproinventory: false alias_links: null notes: null quadrants: @@ -1177,11 +1258,12 @@ last_updated: '2019' functionality: null assessment: false - prerequisite: NA - source: ReproNim; Sebastien Tourbier + prerequisite: null + source: + - ReproNim + - Sebastien Tourbier review: Single presentation, good for an intro class to data management and data version control - exclude_from_reproinventory: false alias_links: null notes: null quadrants: @@ -1202,8 +1284,7 @@ - Carpentry course_length: 1+ weeks instruction_medium: - - Hands-on tutorial - - notebooks + - Hands-on tutorial / notebooks delivery: null language: - English @@ -1216,11 +1297,11 @@ last_updated: '2024' functionality: null assessment: false - prerequisite: NA - source: Carpentries + prerequisite: null + source: + - Carpentries review: If you want to teach carpentries use this tool - not only shell scripting, but also intro to R, Python and HPC - exclude_from_reproinventory: false alias_links: https://github.com/jdkent/incf-fellow-jdkent/blob/gh-pages/index.md notes: null quadrants: @@ -1255,10 +1336,11 @@ last_updated: NA functionality: null assessment: false - prerequisite: NA - source: ReproNim; David Warren + prerequisite: null + source: + - ReproNim + - David Warren review: For internal usage - exclude_from_reproinventory: true alias_links: null notes: Link to Github Importer broken quadrants: null @@ -1294,14 +1376,13 @@ neuroimaging_software: - Python imaging_modality: null - open_dataset: null + open_dataset: NA last_updated: null functionality: null assessment: null prerequisite: null source: null review: null - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null @@ -1316,7 +1397,7 @@ platform: - Windows keywords: null - course_length: null + course_length: NA instruction_medium: null delivery: null language: null @@ -1324,14 +1405,13 @@ neuroimaging_software: null imaging_modality: - NA - open_dataset: null + open_dataset: NA last_updated: null functionality: null assessment: null prerequisite: null source: null review: null - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null @@ -1348,21 +1428,20 @@ - Windows - Linux keywords: null - course_length: null + course_length: NA instruction_medium: null delivery: null language: null programming_language: null neuroimaging_software: null imaging_modality: null - open_dataset: null + open_dataset: NA last_updated: null functionality: null assessment: null prerequisite: null source: null review: null - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null @@ -1374,29 +1453,30 @@ level: null platform: null keywords: null - course_length: null + course_length: NA instruction_medium: null delivery: null language: null programming_language: null neuroimaging_software: null imaging_modality: null - open_dataset: null + open_dataset: NA last_updated: null functionality: null assessment: null prerequisite: null source: null review: null - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null - id: 57 tag_team: - CF + - SS + - JB course_name: List of open neuroscience resources - url: https://github.com/asoplata/open-computational-neuroscience-resources + url: https://asoplata.github.io/open-computational-neuroscience-resources/ level: - Beginner - Intermediate @@ -1428,14 +1508,14 @@ - Behavioral - Resting-State - MRI - open_dataset: true + open_dataset: 'True' last_updated: '2024' functionality: '2024' assessment: false - prerequisite: NA - source: Github Repo added by Charlotte Fraze + prerequisite: null + source: + - Github Repo added by Charlotte Fraze review: Great resource - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null @@ -1447,21 +1527,20 @@ level: null platform: null keywords: null - course_length: null + course_length: NA instruction_medium: null delivery: null language: null programming_language: null neuroimaging_software: null imaging_modality: null - open_dataset: null + open_dataset: NA last_updated: null functionality: null assessment: null prerequisite: null source: null review: null - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null @@ -1473,21 +1552,20 @@ level: null platform: null keywords: null - course_length: null + course_length: NA instruction_medium: null delivery: null language: null programming_language: null neuroimaging_software: null imaging_modality: null - open_dataset: null + open_dataset: NA last_updated: null functionality: null assessment: null prerequisite: null source: null review: null - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null @@ -1499,21 +1577,20 @@ level: null platform: null keywords: null - course_length: null + course_length: NA instruction_medium: null delivery: null language: null programming_language: null neuroimaging_software: null imaging_modality: null - open_dataset: null + open_dataset: NA last_updated: null functionality: null assessment: null prerequisite: null source: null review: null - exclude_from_reproinventory: null alias_links: null notes: null quadrants: null @@ -1525,21 +1602,20 @@ level: null platform: null keywords: null - course_length: null + course_length: NA instruction_medium: null delivery: null language: null programming_language: null neuroimaging_software: null imaging_modality: null - open_dataset: null + open_dataset: NA last_updated: null functionality: null assessment: null prerequisite: null source: null review: null - exclude_from_reproinventory: null alias_links: null notes: null - quadrants: null + quadrants: null \ No newline at end of file diff --git a/model/reproinventory_schema.yaml b/model/reproinventory_schema.yaml index 964f79e..f82f17d 100644 --- a/model/reproinventory_schema.yaml +++ b/model/reproinventory_schema.yaml @@ -25,7 +25,7 @@ enums: NA: CourseLengthEnum: permissible_values: - "<1 hr": + "<1 hr": "1-4 hrs": "1 day": "1-3 days": @@ -77,40 +77,32 @@ enums: FSL: Freesurfer: Python: + Multiple: NA: ImagingModalityEnum: permissible_values: DWI: Structural: Functional: - Task-based: - Resting-State: + "Task-based": + "Resting-State": EEG: Behavioral: MEG: MRI: NA: - AssessmentEnum: - permissible_values: - Yes: - No: - NA: OpenDatasetEnum: permissible_values: Yes: No: NA: - ExcludeFromReproInventoryEnum: - permissible_values: - Yes: - No: - NA: QuadrantsEnum: permissible_values: "information-oriented (reference)": "understanding-oriented (explanation)": "learning-oriented (tutorials)": "problem-oriented (how to guides)": + NA: classes: ReproInventoryEntry: @@ -143,7 +135,6 @@ classes: slots: id: - range: integer identifier: true tag_team: range: string @@ -188,15 +179,17 @@ slots: functionality: range: string assessment: - range: AssessmentEnum + range: bool prerequisite: range: string + multivalued: true source: range: string + multivalued: true review: range: string exclude_from_repro_inventory: - range: ExcludeFromReproInventoryEnum + range: bool alias_links: range: string notes: