From 461af1d662786cac45541e8d3761f05b233352bc Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Thu, 23 Jan 2025 12:49:46 +0000 Subject: [PATCH 1/9] fix: fix URL with DataJoint domain --- mkdocs.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mkdocs.yaml b/mkdocs.yaml index d2d91b3..a0db789 100644 --- a/mkdocs.yaml +++ b/mkdocs.yaml @@ -1,7 +1,7 @@ # ---------------------- PROJECT SPECIFIC --------------------------- site_name: DataJoint Documentation -site_url: http://localhost/docs +site_url: https://datajoint.com/docs repo_name: datajoint/datajoint-docs repo_url: https://github.com/datajoint/datajoint-docs nav: @@ -127,7 +127,7 @@ extra: - icon: fontawesome/brands/python link: https://pypi.org/user/datajointbot name: PyPI - - icon: fontawesome/brands/stack-overflow +TODO: - icon: fontawesome/brands/stack-overflow link: https://stackoverflow.com/questions/tagged/datajoint name: StackOverflow - icon: fontawesome/brands/youtube From cde718b50dabb5f2196b7738408fb13c70a7ecdb Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Thu, 23 Jan 2025 12:50:43 +0000 Subject: [PATCH 2/9] fix: update citation.md --- src/about/citation.md | 70 +++++++++++++++++++++++++++++++++---------- 1 file changed, 54 insertions(+), 16 deletions(-) diff --git a/src/about/citation.md b/src/about/citation.md index 926ea85..54fa1e5 100644 --- a/src/about/citation.md +++ b/src/about/citation.md @@ -1,27 +1,65 @@ # Citation Guidelines -If your work uses the DataJoint Python, MATLAB, or Elements, please cite the -respective manuscripts and Research Resource Identifiers (RRIDs). +When your work uses the DataJoint Python, MATLAB, or Elements framework, please cite the +respective manuscripts and include their associated Research Resource Identifiers +(RRIDs). Proper citation helps credit the contributors and supports the broader +scientific community by highlighting the tools used in research. -## DataJoint Python and MATLAB +## Citing DataJoint Elements -- Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton - RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or - Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658 +If your work utilizes **DataJoint Elements**, please cite the following manuscript: -- [RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543) +- **Manuscript**: Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki + M, Sitonic D, Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for + Neurophysiology. bioRxiv. 2021 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358 -## DataJoint Relational Model +- **RRID**: [RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894) -- Yatsenko D, Walker EY, Tolias AS. DataJoint: a simpler relational data model. - arXiv:1807.11104. 2018 Jul 29. doi: https://doi.org/10.48550/arXiv.1807.11104 +You should also cite the **DataJoint Core manuscript** detailed below. -- [RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543) +## Citing the DataJoint Relational Model -## DataJoint Elements +For any work relying on the **DataJoint Relational Model**, include the following +citation: -- Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki M, Sitonic D, - Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for - Neurophysiology. bioRxiv. 2021 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358 +- **Manuscript**: Yatsenko D, Walker EY, Tolias AS. DataJoint: A simpler relational data + model. arXiv:1807.11104. 2018 Jul 29. doi: https://doi.org/10.48550/arXiv.1807.11104 + +- **RRID**: [RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543) + +## Citing DataJoint Python and MATLAB + +For work using **DataJoint Python** or **DataJoint MATLAB**, cite the following +manuscript: + +- **Manuscript**: Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, + Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: Managing big scientific data + using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: + https://doi.org/10.1101/031658 + +- **RRID**: [RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543) + +## Citing SciOps and Capability Maturity Model + +If your work references **SciOps** or the **Capability Maturity Model for Data-Intensive +Research**, please use the following citation: + +- Manuscript: Johnson EC, Nguyen TT, Dichter BK, Zappulla F, Kosma M, Gunalan K, + Halchenko YO, Neufeld SQ, Schirner M, Ritter P, Martone ME. SciOps: Achieving + Productivity and Reliability in Data-Intensive Research. arXiv preprint + arXiv:2401.00077v2. 2024 Nov 6. (Under review) + +- **RRID**: TBD + +# Why Cite DataJoint? + +By citing DataJoint and its associated resources: + +You give credit to the authors and contributors who developed these tools. + +You help other researchers identify and use these tools effectively. + +You strengthen the visibility and impact of open-source tools in scientific research. -- [RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894) +For further questions or assistance with citations, please reach out to the DataJoint +support team (support@datajoint.com). From 8e106a45a4990021dc356850d4caaca6c802b79a Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Thu, 23 Jan 2025 12:51:06 +0000 Subject: [PATCH 3/9] fix: update contribute.md --- src/about/contribute.md | 198 ++++++++++++++++------------------------ 1 file changed, 80 insertions(+), 118 deletions(-) diff --git a/src/about/contribute.md b/src/about/contribute.md index fdc701e..8a09850 100644 --- a/src/about/contribute.md +++ b/src/about/contribute.md @@ -1,114 +1,97 @@ # Contribution Guidelines -Thank you for your interest in contributing! 🤝 +Thank you for your interest in contributing to DataJoint Elements! -To help keep everyone in alignment and coordinated in the community effort, we’ve -created this document. It serves as the contribution guideline that outlines how -open-source software development is to be conducted. Any software development that makes -reference to this document can be assumed to adopt the policies outlined below. We’ve -structured the guideline in a FAQ (frequently asked questions) format to make it easier -to digest. Feel free to review the questions below to determine any specific policy. +These guidelines are designed to ensure smooth collaboration, high-quality +contributions, and a welcoming environment for all contributors. Please take a moment to +review this document in order to make the contribution process easy and effective for +everyone involved. The principal maintainer of DataJoint and associated tools is the DataJoint company. The pronouns “we” and “us” in this guideline refer to the principal maintainers. We invite reviews and contributions of the open-source software. We compiled these guidelines to make this work clear and efficient. -## Feedback +## How to Contribute -DataJoint APIs, DataJoint Web GUIs, and DataJoint Elements are supported by NIH grant -U24 NS116470 for disseminating open-source software for neuroscience research. Your -feedback is essential for continued funding. Your feedback also helps shape the -technology development roadmap for the DataJoint ecosystem. Please tell us about your -projects by filling out the [DataJoint Census](https://community.datajoint.io). +### Feedback and Communication -## 1) Which issue should I contribute towards? +Engage with the community through GitHub Issues and PR discussions. -There are three primary things to consider when looking to contribute. +Use inclusive and professional language. -**Availability:** An indication of whether anyone is currently working on a fix for the -given issue. Availability is indicated by who is `assigned`. Issues that are -`unassigned` mean that there is no one yet working on resolving the issue and the issue -is available for someone to work on. If an issue has been assigned, then any additional -work on that issue should be coordinated with the assignee. +For general questions or ideas, discussions and live debugging support, please join +[DataJoint Slack channel](https://join.slack.com/t/datajoint/shared_invite/enQtMjkwNjQxMjI5MDk0LTQ3ZjFiZmNmNGVkYWFkYjgwYjdhNTBlZTBmMWEyZDc2NzZlYTBjOTNmYzYwOWRmOGFmN2MyYzU0OWQ0MWZiYTE) +or [other community forums](https://stackoverflow.com/questions/tagged/datajoint), but +direct technical contributions should stay in GitHub. Response times may vary depending +on maintainer availability. -**Specification:** In order for issues to be properly addressed, the requirements of -satisfying and closing the issue should be clear. If it is not, a label will be added as -`unspecified`. This could be due to more debug info being necessary, more details on -intended behavior, or perhaps that further discussion is required to determine a good -solution. Feel free to help us arrive at a proper specification. +### Reporting Issues -**Priority:** As a community, we work on a concerted effort to bring about the -realization of the milestones. We utilize milestones as a planning tool to help focus a -group of changes around a release. To determine the priority of issues, simply have a -look at the next milestone that is expected to arrive. Therefore, each milestone -following this can be understood as lower in priority respectively. Bear in mind that -much like a hurricane forecast, the execution plan is much more likely to be accurate -the closer to today’s date as opposed to milestones further out. Extremely low priority -issues are assigned to the `Backburner` milestone. Since `Backburner` does not have a -target date, this indicates that its issues may be deferred indefinitely. Occasionally -the maintainers will move issues from `Backburner` as it makes sense to address them -within a release. Also, issues `unassigned` to a milestone can be understood as new -issues which have not been triaged. +Use `GitHub Issues` to report bugs or request features. Clearly describe the issue, +including: -After considering the above, you may comment on the issue you’d like to help fix and a maintainer will assign it to you. +- Steps to reproduce (if applicable). +- Expected and actual outcomes. +- Any relevant error messages, logs, or screenshots. +- Include environment details (e.g., OS, library versions) to speed up troubleshooting. -## 2) What is the proper etiquette for proposing changes as contribution? +Check existing issues to avoid duplicates. -What is generally expected from new contributions are the following: +### Proposing Features/Changes -Any proposed contributor changes should be introduced in the form of a pull request (PR) -from their fork. +Before significant contributions, open a `GitHub Issue` to discuss your proposal. Please +include: -Proper branch target specified. The following are the generally the available branches -that can be targeted: +- A clear problem statement. +- Proposed solution or feature details. +- Relevant examples or use cases. -- `main` or `master`: Represents the single source of truth and the latest in completed development. +### Submitting Pull Requests (PRs) -- `pre`: Represents the source at the point of the last stable release. +1. Fork the repository and clone it to your local machine. +2. Create a descriptive branch name, e.g., `fix/typo-docs` or `feature/add-logging`. +3. Follow [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/): Use + commit messages following the commit types for versioning: -For larger more involved changes, a maintainer may determine it best to create a -feature-specific branch and adjust the PR accordingly. +- `fix`: Bug fixes (PATCH in Semantic Versioning). +- `feat`: New features (MINOR in Semantic Versioning). +- `docs`: Documentation updates. +- `Breaking changes`: Use ! after the type or add BREAKING CHANGE in the commit footer. -A summary description that describes the overall intent behind the PR. +- `Example: fix(auth): resolve token expiration bug.` -Proper links to the issue(s) that the PR serves to resolve. +4. Reference related issue(s) in your PR description (e.g., Closes #123). +5. Cover new functionality or bug fixes with appropriate tests. Ensure all tests pass + before submission. Typically as it relates to tests, this means: + 1. No syntax errors + 2. No integration errors + 3. No style errors e.g. PEP8, etc. + 4. Similar or better code coverage +6. Additional documentation to reflect new feature or behavior introduced. +7. Provide a detailed PR description explaining the changes and their impact. +8. Submit the PR for review. Maintainers will also ensure that PR’s have the appropriate + assignment for reviewer. -Newly introduced changes must pass any required checks. Typically as it relates to tests, this means: - -1. No syntax errors -1. No integration errors -1. No style errors e.g. PEP8, etc. -1. Similar or better code coverage - -Additional documentation to reflect new feature or behavior introduced. - -Necessary updates to the changelog following [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) -convention. - -A contributor should not approve or merge their own PR. +A contributor should not approve or merge their own PR. A maintainer will review and +approve the PR. Reviewer suggestions or feedback should not be directly committed to a branch on a contributor’s fork. A less intrusive way to collaborate would be for the reviewer to PR to the contributor’s fork/branch that is associated with the main PR currently in review. -Maintainers will also ensure that PR’s have the appropriate assignment for reviewer, milestone, and project. +### Code Reviews -## 3) How can I track the progress of an issue that has been assigned? +Expect constructive feedback from maintainers. Maintainers will review your PR and +suggest changes or improvements. Be responsive to feedback and iterate as needed. +Reviews focus on code quality and adherence to standards, and documentation and test +coverage. Once approved, the PR will be merged. -Since milestones represent the development plan, projects represent the actual -execution. Projects are typically fixed-time sprints (1-2 weeks). A ‘workable’ number of -issues that have been assigned to developers and assigned to the next milestone are -selected and tracked in each project to provide greater granularity in the week-to-week -progress. Automation is included observing the `Automated kanban with reviews` template. -Maintainers will adjust the project assignment to reflect the order in which to resolve -the milestone issues. +## Releases -## 4) What is the release process? How do I know when my merged contribution will officially make it into a release? - -Releases follow the standard definition of [semantic versioning](https://semver.org/spec/v2.0.0.html). -Meaning: +Releases follow the standard definition of +[semantic versioning](https://semver.org/spec/v2.0.0.html). Meaning: `MAJOR` . `MINOR` . `PATCH` @@ -118,53 +101,32 @@ Meaning: - `PATCH` version when you make backwards compatible bug fixes. -Each release requires tagging the commit appropriately and is then issued in the normal -medium for release e.g. PyPi, NPM, YARN, GitHub Release, etc. - -Minor releases are triggered when all the issues assigned to a milestone are resolved -and closed. Patch releases are triggered periodically from `main` or `master` after a -reasonable number of PR merges have come in. - -## 5) I am not yet too comfortable contributing but would like to engage the community. What is the policy on community engagement? - -In order to follow the appropriate process and setting, please reference the following flow for your desired mode of engagement: - -### 5a) Generally, how do I perform __________? - -If the documentation does not provide clear enough instruction, please see StackOverflow -posts related to the [datajoint](https://stackoverflow.com/questions/tagged/datajoint) -tag or ask a new question tagging it appropriately. You may refer to our -[datajoint tag wiki](https://stackoverflow.com/tags/datajoint/info) -for more details on its proper use. - -### 5b) I just encountered this error, how can I resolve it? - -Please see StackOverflow posts related to the -[datajoint](https://stackoverflow.com/questions/tagged/datajoint) tag or ask a new -question tagging it appropriately. You may refer to our -[datajoint tag wiki](https://stackoverflow.com/tags/datajoint/info) for more details on -its proper use. - -### 5c) I just encountered this error and I am sure it is a bug, how do I report it? - -Please file it under the issue tracker associated with the open-source software. +Each release requires tagging the commit appropriately and is then issued following the +GitHub automated semantic release. The release and Changelog will be generated +automatically after the PR is merged. -### 5d) I have an idea or new feature request, how do I submit it? +## Community Engagement -Please file it under the issue tracker associated with the open-source software. +- For resolving bugs, errors, or debugging issues, please submit it through **GitHub + Issues**. +- For live debugging, urgent help, or broader discussions, join the + [DataJoint Slack](https://join.slack.com/t/datajoint/shared_invite/enQtMjkwNjQxMjI5MDk0LTQ3ZjFiZmNmNGVkYWFkYjgwYjdhNTBlZTBmMWEyZDc2NzZlYTBjOTNmYzYwOWRmOGFmN2MyYzU0OWQ0MWZiYTE). + Keep in mind maintainers’ availability may be limited. +- For feature requests, directly in the GitHub Issue Tracker of the respective + repository Provide sufficient details to facilitate discussion and prioritization. -### 5e) I am curious why the maintainers choose to __________? i.e. questions that are ‘opinionated’ in nature with answers that some might disagree. +## Prerequisites -Please join the community on the -[DataJoint Slack](https://join.slack.com/t/datajoint/shared_invite/enQtMjkwNjQxMjI5MDk0LTQ3ZjFiZmNmNGVkYWFkYjgwYjdhNTBlZTBmMWEyZDc2NzZlYTBjOTNmYzYwOWRmOGFmN2MyYzU0OWQ0MWZiYTE) -and ask on the most relevant channel. There, you may engage directly with the maintainers for proper discourse. +- Familiarize yourself with the project documentation and guidelines. +- Install necessary tools and dependencies listed in the repository's `README`. -### 5f) What is the timeline or roadmap for the release of certain supported features? +## Contribution Acknowledgment -Please refer to milestones and projects associated with the open-source software. +We deeply appreciate every contribution! By adhering to these guidelines, you help +maintain the quality, usability, and success of DataJoint Elements. -### 5g) I need urgent help best suited for live debugging, how can I reach out directly? +For any questions, feel free to reach out via GitHub Issues, our +[community Slack](https://join.slack.com/t/datajoint/shared_invite/enQtMjkwNjQxMjI5MDk0LTQ3ZjFiZmNmNGVkYWFkYjgwYjdhNTBlZTBmMWEyZDc2NzZlYTBjOTNmYzYwOWRmOGFmN2MyYzU0OWQ0MWZiYTE) +or contact `support@datajoint.com`. -Please join the community on the -[DataJoint Slack](https://join.slack.com/t/datajoint/shared_invite/enQtMjkwNjQxMjI5MDk0LTQ3ZjFiZmNmNGVkYWFkYjgwYjdhNTBlZTBmMWEyZDc2NzZlYTBjOTNmYzYwOWRmOGFmN2MyYzU0OWQ0MWZiYTE) -and ask on the most relevant channel. Please bear in mind that as open-source community software, availability of the maintainers might be limited. +Thank you for your contributions! From 32813fcd22e5a80474cbf695e45824df31f84e61 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Thu, 23 Jan 2025 12:51:40 +0000 Subject: [PATCH 4/9] fix: update datajoint-team.md --- src/about/datajoint-team.md | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/src/about/datajoint-team.md b/src/about/datajoint-team.md index 8567f26..545a509 100644 --- a/src/about/datajoint-team.md +++ b/src/about/datajoint-team.md @@ -5,10 +5,11 @@ as Principal Investigator. ## Scientists -- Dimitri Yatsenko - PI -- Thinh Nguyen - Data Scientist -- Kushal Bakshi - Data Scientist -- Milagros Marín - Data Scientist +- Dimitri Yatsenko, PhD - PI & Chief Science and Technology Officer + +- Thinh Nguyen, PhD - SciOps Engineer +- Kushal Bakshi, PhD - SciOps Engineer +- Milagros Marín, PhD - SciOps Engineer ## Engineers @@ -17,8 +18,8 @@ as Principal Investigator. ## Past contributors -- Edgar Y. Walker - System Architect, Data Scientist, Project Manager -(from project start to Jan, 2021) +- Edgar Y. Walker - System Architect, Data Scientist, Project Manager (from project + start to Jan, 2021) - Andreas S. Tolias - Grant proposal contributor - Jacob Reimer - Grant proposal contributor - Shan Shen - Data Scientist @@ -45,6 +46,6 @@ The first-person pronouns "we" and "our" in these documents refer to those liste ## External contributors The principal components of the Resource are developed and distributed as open-source -projects and external contributions are welcome. We have adopted a -[Contribution Guide](contribute.md) for DataJoint, DataJoint Elements, -and related open-source tools. +projects and external contributions are welcome. We have adopted a +[Contribution Guide](contribute.md) for DataJoint, DataJoint Elements, and related +open-source tools. From b50b7c57e4526b00c7a3f1ea6eb7b53317b90c3e Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Thu, 23 Jan 2025 12:52:35 +0000 Subject: [PATCH 5/9] fix: update adoption.md --- src/elements/management/adoption.md | 94 ++++++++++++++++++++++------- 1 file changed, 71 insertions(+), 23 deletions(-) diff --git a/src/elements/management/adoption.md b/src/elements/management/adoption.md index 32c3b43..ce789ac 100644 --- a/src/elements/management/adoption.md +++ b/src/elements/management/adoption.md @@ -1,33 +1,81 @@ # Guidelines for Adoption -You have several options for adopting DataJoint workflows for your own experiments. +DataJoint Elements offer flexible options for adoption, enabling researchers to +seamlessly integrate them into their workflows. Below are the available paths for +adoption based on your expertise and needs for your experiments. -## Adopt independently +## Independent Adoption -DataJoint Elements are designed for adoption by independent users with moderate software -development skills, good understanding of DataJoint principles, and adequate IT -expertise or support. +DataJoint Elements are designed for independent users who have: -If you have not yet used DataJoint, we recommend completing our online training -tutorials or attending a workshop either online or in person. Interactive tutorials -can be found on the [DataJoint -Tutorials](https://github.com/datajoint/datajoint-tutorials) repository. +- Moderate software development skills. +- A solid understanding of DataJoint principles. +- Adequate IT expertise or support. -## Support from DataJoint +If you are **new to DataJoint**, we recommend starting with these resources to build a +strong foundation: -Our team provides support to labs to adopt DataJoint workflows in their research. +### 1. Online Training Tutorials -This includes: +Learn to set up your DataJoint pipeline with interactive tutorials hosted on GitHub +Codespaces: -- User training -- Developer training -- Data and computation hosting - - on your premises - - using your own cloud accounts - - fully managed cloud hosting by DataJoint -- Workflow execution - - configuration and automation - - optional fully managed service by DataJoint -- Interfaces for data entry, export and publishing +- **[DataJoint Tutorials Repository](https://github.com/datajoint/datajoint-tutorials):** + A comprehensive set of tutorials to get started with DataJoint Python, organized in + Jupyter notebooks. -These services may be subsidized by grant funding for qualified research groups. +- **Element-Specific Interactive Tutorials:** Explore detailed guides for designing and + interacting with specific Element pipelines: + - [DataJoint Element Array Ephys](https://github.com/datajoint/element-array-ephys#interactive-tutorial) + - [DataJoint Element Calcium Imaging](https://github.com/datajoint/element-calcium-imaging#interactive-tutorial) + - [DataJoint Element DeepLabCut](https://github.com/datajoint/element-deeplabcut#interactive-tutorial) + - [DataJoint Element Facemap](https://github.com/datajoint/element-facemap#interactive-tutorial) + - [DataJoint Element MoSeq](https://github.com/datajoint/element-moseq#interactive-tutorial) + - [DataJoint Element Miniscope](https://github.com/datajoint/element-miniscope#interactive-tutorial) + - [DataJoint Element Optogenetics](https://github.com/datajoint/element-optogenetics#interactive-tutorial) + - [DataJoint Element Zstack](https://github.com/datajoint/element-zstack#interactive-tutorial) + - [DataJoint Element Electrode Localization](https://github.com/datajoint/element-electrode-localization#interactive-tutorial) + - [DataJoint Element Visual Stimulus](https://github.com/datajoint/element-visual-stimulus#interactive-tutorial) + +### 2. Workshops + +Participate in [workshops and events](../../support-events.md) (online or in person) to +gain hands-on experience and practical knowledge for implementing DataJoint workflows +effectively. + +## Adoption with Support from DataJoint + +For institutions and labs requiring additional assistance, the DataJoint team offers +tailored support services, including: + +### Training + +- **User Training:** Guidance for end-users to effectively utilize workflows. +- **Developer Training:** Support for developers implementing or extending workflows. + +### Hosting and Infrastructure + +- **Data and Computation Hosting:** + - On-premises setups for your institution or lab. + - Integration with your existing cloud accounts. + - Fully managed cloud hosting by DataJoint. + +### Workflow Execution + +- **Configuration and Automation:** Assistance with setting up and automating workflows. +- **Fully Managed Services:** Optional services to oversee workflow execution and + management entirely. + +### Interfaces + +- **Data Entry, Export, and Publishing:** Streamlined interfaces to efficiently manage + and share your research data. + +### Subsidized Support + +Qualified research groups may be eligible for subsidized services through grant funding. +Contact the DataJoint team to explore funding options and determine your eligibility. + +By choosing the adoption path that best suits your lab's expertise and requirements, you +can leverage DataJoint Elements to optimize your research workflows. For additional +information or assistance, please contact the DataJoint team at support@datajoint.com. From 33c4d7ff7493bbc8d8c8fc8d8f530eef3272cc25 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Thu, 23 Jan 2025 12:53:02 +0000 Subject: [PATCH 6/9] fix: update governance.md --- src/elements/management/governance.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/elements/management/governance.md b/src/elements/management/governance.md index 5214d14..22619cf 100644 --- a/src/elements/management/governance.md +++ b/src/elements/management/governance.md @@ -3,13 +3,14 @@ ## Funding This Resource is supported by the National Institute Of Neurological Disorders And -Stroke of the National Institutes of Health under Award Number U24NS116470. The content -is solely the responsibility of the authors and does not necessarily represent the -official views of the National Institutes of Health. +Stroke of the National Institutes of Health (NIH) under Award Number **U24NS116470**. +The content is solely the responsibility of the authors and does not necessarily +represent the official views of the National Institutes of Health. ## Scientific Steering Group -The project oversight and guidance is provided by the Scientific Steering Group comprising +The project oversight and guidance is provided by the Scientific Steering Group +comprising - [Mackenzie Mathis (EPFL)](http://www.mackenziemathislab.org/team) - [John Cunningham (Columbia U)](https://stat.columbia.edu/~cunningham/) From 37b79a24fba38bc9674f77514881bf6690a211de Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Thu, 23 Jan 2025 12:53:30 +0000 Subject: [PATCH 7/9] fix: update outreach.md --- src/elements/management/outreach.md | 57 ++++++++++++++++------------- 1 file changed, 32 insertions(+), 25 deletions(-) diff --git a/src/elements/management/outreach.md b/src/elements/management/outreach.md index aee116c..92b25da 100644 --- a/src/elements/management/outreach.md +++ b/src/elements/management/outreach.md @@ -1,33 +1,40 @@ # Outreach Plan -Broad engagement with the neuroscience community is necessary for the optimization, -integration, and adoption of the Resource components. - -We conduct five types of outreach activities that require different approaches: +Broad engagement with the neuroscience community is essential for the optimization, +integration, and adoption of the Resource components. To achieve this, we conduct five +types of outreach activities, each requiring a tailored approach: ## 1. Precursor Projects -Our [Selection Process](../selection) requires a "Precursor Project" for any new -experiment modality to be included in DataJoint Elements. A precursor project is a -project that develops a DataJoint pipeline for its own experiments either independently -or in collaboration with our team. We reach out to teams who develop DataJoint -pipelines for new experiment paradigms and modalities to identify essential design -motifs, analysis tools, and related tools and interfaces. We interview the core team to -learn about their collaborative culture, practices, and procedures. We jointly review -their open-source code and their plans for dissemination. In many cases, our team -already collaborates with such teams through our other projects and we have a good -understanding of their process. As we develop a new Element to support the new -modality, we remain in contact with the team to include their contribution, solicit -feedback, and evaluate design tradeoffs. When the new Element is released, a full -attribution is given to the Precursor Project. - -**Rationale:** The Resource does not aim to develop fundamentally new solutions for - neurophysiology data acquisition and analysis. Rather it aims to systematize and - disseminate existing open-source tools proven in leading research projects. +As part of our [Selection Process](../selection), a Precursor Project is required for +any new experimental modality to be incorporated into DataJoint Elements. + +A Precursor Project involves the development of a DataJoint pipeline for specific +experiments, either independently or in collaboration with our team. Our outreach +activities for Precursor Projects include: + +- Engaging Development Teams: Reaching out to teams developing DataJoint pipelines for + new experimental paradigms or modalities. +- Identifying Key Components: Collaborating with these teams to identify essential + design motifs, analysis tools, and related interfaces. +- Team Interviews: Conducting interviews the core team to understand their collaborative + culture, practices, and procedures. +- Code and Dissemination Review: Reviewing their open-source code and dissemination + plans to assess compatibility and adaptability. +- Continuous Collaboration: Staying in contact with the team throughout the Element + development process to incorporate their contributions, gather feedback, and evaluate + design tradeoffs. + +When the new Element is released, a full attribution is given to the Precursor Project, +ensuring their contributions are recognized. + +**Rationale:** The Resource does not aim to create fundamentally new solutions for +neurophysiology data acquisition and analysis. Instead, it systematizes and disseminates +existing open-source tools already proven in leading research projects. ## 2. Tool Developers -DataJoint pipelines rely on analysis tools, atlases, data standards, archives and -catalogs, and other neuroinformatics resources developed and maintained by the broader -scientific community. To ensure sustainability of the Resource, we reach out to the -tool developer to establish joint sustainability roadmaps. +DataJoint pipelines depend on a variety of analysis tools, atlases, data standards, +archives, catalogs, and other neuroinformatics resources created and maintained by the +broader scientific community. To ensure the long-term sustainability of the Resource, we +reach out to the tool developers to establish shared sustainability roadmaps. From d230ff5eb3793f49242a78610f80fc50bddcbe89 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Thu, 23 Jan 2025 12:53:46 +0000 Subject: [PATCH 8/9] fix: update plan.md --- src/elements/management/plan.md | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/src/elements/management/plan.md b/src/elements/management/plan.md index 3ec7455..e467a73 100644 --- a/src/elements/management/plan.md +++ b/src/elements/management/plan.md @@ -8,11 +8,10 @@ figure below: The following sections provide detailed information. -- [Team](../team) -- [Project Governance](../governance) -- [Project Selection Process](../selection) -- [Quality Assurance](../quality-assurance) -- [Contribution Guideline](../../../community/contribute) -- [Outreach Plan](../outreach) -- [Dissemination Plan](../dissemination) -- [Licenses and User Agreements](../../../community/licenses) +- [Team](../../about/datajoint-team.md) +- [Project Governance](./governance.md) +- [Project Selection Process](selection.md) +- [Quality Assurance](quality-assurance.md) +- [Contribution Guideline](../../about/contribute.md) +- [Outreach Plan](outreach.md) +- [Dissemination Plan](dissemination.md) From aaaac69ccc5fbec79f8ba7541723a68d99963ee5 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Thu, 23 Jan 2025 12:54:48 +0000 Subject: [PATCH 9/9] fix: update selection.md --- src/elements/management/selection.md | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/src/elements/management/selection.md b/src/elements/management/selection.md index cfd89a3..d1dfdac 100644 --- a/src/elements/management/selection.md +++ b/src/elements/management/selection.md @@ -1,7 +1,7 @@ # Project Selection Process The project milestones are set annually by the team under the stewardship of the NIH -programmatic staff and with the guidance of the project's +programmatic staff and with the guidance of the project's [Scientific Steering Group](../governance) We have adopted the following general criteria for selecting and accepting new projects @@ -9,18 +9,18 @@ to be included in the Resource. 1. **Open Precursor Projects** - At least one open-source DataJoint-based precursor project must exist for any new - experiment modality to be accepted for support as part of the Resource. The - precursor project team must be open to interviews to describe in detail their - process for the experiment workflow, tools, and interfaces. + At least one open-source DataJoint-based Precursor Project must exist for any new + experiment modality to be accepted for support as part of the Resource. The Precursor + Project team must be open to interviews to describe in detail their process for the + experiment workflow, tools, and interfaces. - The precursor projects must provide sample data for testing during development and - for tutorials. The precursor projects will be acknowledged in the development of the + The Precursor Projects must provide sample data for testing during development and + for tutorials. The Precursor Projects will be acknowledged in the development of the component. **Rationale:** This Resource does not aim to develop fundamentally new solutions for - neurophysiology data acquisition and analysis. Rather it seeks to systematize and - disseminate existing open-source tools proven in leading research projects. + neurophysiology data acquisition and analysis. Rather it seeks to systematize and + disseminate existing open-source tools proven in leading research projects. 1. **Impact** @@ -30,7 +30,7 @@ to be included in the Resource. 1. **Sustainability** For all third-party tools or resources included in the proposed component, their - long-term maintenance roadmap must be established. When possible, we will contact - the developer team and work with them to establish a sustainability roadmap. If no - such roadmap can be established, alternative tools and resources must be identified - as replacement. + long-term maintenance roadmap must be established. When possible, we will contact the + developer team and work with them to establish a sustainability roadmap. If no such + roadmap can be established, alternative tools and resources must be identified as + replacement.