Adding information collected in minutes #13
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this is a first draft for trying to summarise previous discussion and ease onboarding
jcolomb
commented
Apr 24, 2023
jcolomb
commented
Apr 24, 2023
add 04 link
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Hi @jcolomb Thanks for going ahead and compiling these infos. I added some change suggestions to the current proposal. @SylvainTakerkart Do you have more comments regarding the BEP032 or the general organization?
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| # Relation and tools | ||
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| - Openminds :links needed here: openminds for electrophysiology expansion. |
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Suggested change
| - Openminds :links needed here: openminds for electrophysiology expansion. | |
| - OpenMinds: [OpenMinds for electrophysiology](https://github.com/HumanBrainProject/openMINDS_ephys) expansion. |
| ## Files combinations | ||
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| - BIDS requires different data files for different modalities (electrophy data, behavior recording, ..., meaning different data collection equipment) , while nwb/nix combine them. | ||
| - Several sessions/run will be included in nix/nwb, BIDS should get session specific files |
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Suggested change
| - Several sessions/run will be included in nix/nwb, BIDS should get session specific files | |
| - BIDS should accept nwb and nix files that contain multi-part recordings (e.g. multiple stimulation & recording snippets). Metadata for these will be handled in the `events.tsv` file. Alternatively, these individual recording snippets can also be split into multiple nix/nwb files and described as different `runs`. |
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| ## Decisions | ||
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| - one set of metadata files for each run (redundant but simpler) |
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Suggested change
| - one set of metadata files for each run (redundant but simpler) | |
| - BEP032 proposes one set of metadata files for each run (redundant but simpler). Depending on the BIDS inheritance principle the number metadata files can be reduced for sessions with shared metadata. |
| I am a research engineer in the Neurophysiology of Repetitive Behaviors Lab (Head Eric Burguière). I have a background in robotics and IA and from my PhD I gained experience in computational neuroscience, in-vivo electrophysiology in freely moving rodents and real-time analysis of ephys data. I’m an enthusiast for new technologies in the neuroscience space and also support open-source tools and data sharing. | ||
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| Ida Aasebø (Dept of Medicine, University of Oslo, Norway). Curation team leader EBRAINS/the Human Brain Project with Lyuba Zehl. The work from my PhD focused primarily on rodent electrophysiology and behavior, analytics and experiments. Multimodal and heterogeneous data clearly makes data sharing problematic in EBRAINS and other repositories, interested in hearing about and discussing alternatives. | ||
| Tom Gillespie (Department of Neurosciences, University of California, San Diego). I wear a number of different hats. Maintainer of/ontologist for the Neuroscience Information Framework Standard Ontology (NIFSTD/NIF-Ontology) and InterLex (successor to NeuroLex). Co-maintainer of the Research Resource Identifier (RRID) system. Principal developer for the automated curation pipelines for SPARC data structure. I participate in the development of the data models for SPARC, BICCN, and HBP. I became interested in neuroinformatics while I was still an experimentalist working in an electrophysiology lab and wanted to build a system to completely automate the data and provenance collection for my experiments that would cover everything from mouse breeding to workflow automation for patching and recording cells. My PhD work focuses on representation and communication of scientific protocols. |
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Suggested change
| Tom Gillespie (Department of Neurosciences, University of California, San Diego). I wear a number of different hats. Maintainer of/ontologist for the Neuroscience Information Framework Standard Ontology (NIFSTD/NIF-Ontology) and InterLex (successor to NeuroLex). Co-maintainer of the Research Resource Identifier (RRID) system. Principal developer for the automated curation pipelines for SPARC data structure. I participate in the development of the data models for SPARC, BICCN, and HBP. I became interested in neuroinformatics while I was still an experimentalist working in an electrophysiology lab and wanted to build a system to completely automate the data and provenance collection for my experiments that would cover everything from mouse breeding to workflow automation for patching and recording cells. My PhD work focuses on representation and communication of scientific protocols. | |
| Tom Gillespie (Department of Neurosciences, University of California, San Diego). I wear a number of different hats. Maintainer of/ontologist for the Neuroscience Information Framework Standard Ontology (NIFSTD/NIF-Ontology) and InterLex (successor to NeuroLex). Co-maintainer of the Research Resource Identifier (RRID) system. Principal developer for the automated curation pipelines for SPARC data structure. I participate in the development of the data models for SPARC, BICCN, and HBP. I became interested in neuroinformatics while I was still an experimentalist working in an electrophysiology lab and wanted to build a system to completely automate the data and provenance collection for my experiments that would cover everything from mouse breeding to workflow automation for patching and recording cells. My PhD work focuses on representation and communication of scientific protocols. |
| I am a research engineer in the Neurophysiology of Repetitive Behaviors Lab (Head Eric Burguière). I have a background in robotics and IA and from my PhD I gained experience in computational neuroscience, in-vivo electrophysiology in freely moving rodents and real-time analysis of ephys data. I’m an enthusiast for new technologies in the neuroscience space and also support open-source tools and data sharing. | ||
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| Ida Aasebø (Dept of Medicine, University of Oslo, Norway). Curation team leader EBRAINS/the Human Brain Project with Lyuba Zehl. The work from my PhD focused primarily on rodent electrophysiology and behavior, analytics and experiments. Multimodal and heterogeneous data clearly makes data sharing problematic in EBRAINS and other repositories, interested in hearing about and discussing alternatives. | ||
| Tom Gillespie (Department of Neurosciences, University of California, San Diego). I wear a number of different hats. Maintainer of/ontologist for the Neuroscience Information Framework Standard Ontology (NIFSTD/NIF-Ontology) and InterLex (successor to NeuroLex). Co-maintainer of the Research Resource Identifier (RRID) system. Principal developer for the automated curation pipelines for SPARC data structure. I participate in the development of the data models for SPARC, BICCN, and HBP. I became interested in neuroinformatics while I was still an experimentalist working in an electrophysiology lab and wanted to build a system to completely automate the data and provenance collection for my experiments that would cover everything from mouse breeding to workflow automation for patching and recording cells. My PhD work focuses on representation and communication of scientific protocols. |
There was a problem hiding this comment.
Suggested change
| Tom Gillespie (Department of Neurosciences, University of California, San Diego). I wear a number of different hats. Maintainer of/ontologist for the Neuroscience Information Framework Standard Ontology (NIFSTD/NIF-Ontology) and InterLex (successor to NeuroLex). Co-maintainer of the Research Resource Identifier (RRID) system. Principal developer for the automated curation pipelines for SPARC data structure. I participate in the development of the data models for SPARC, BICCN, and HBP. I became interested in neuroinformatics while I was still an experimentalist working in an electrophysiology lab and wanted to build a system to completely automate the data and provenance collection for my experiments that would cover everything from mouse breeding to workflow automation for patching and recording cells. My PhD work focuses on representation and communication of scientific protocols. | |
| Tom Gillespie (Department of Neurosciences, University of California, San Diego). I wear a number of different hats. Maintainer of/ontologist for the Neuroscience Information Framework Standard Ontology (NIFSTD/NIF-Ontology) and InterLex (successor to NeuroLex). Co-maintainer of the Research Resource Identifier (RRID) system. Principal developer for the automated curation pipelines for SPARC data structure. I participate in the development of the data models for SPARC, BICCN, and HBP. I became interested in neuroinformatics while I was still an experimentalist working in an electrophysiology lab and wanted to build a system to completely automate the data and provenance collection for my experiments that would cover everything from mouse breeding to workflow automation for patching and recording cells. My PhD work focuses on representation and communication of scientific protocols. | |
| Julia Sprenger (Institut de Neurosciences de la Timone, Marseille, France). Research software engineer and main contributor to the BEP032 (so far). Background in physics, ephys data analysis, Python. Some experience in publishing datasets using Nix, odML and NWB. |
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