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IQSS / dataverse

Open source research data repository software
http://dataverse.org
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See: #9034. 3 | 1.3.2 | Research and discovery phase for biomedical workflows support | 5 #9139

Closed mreekie closed 1 year ago

mreekie commented 2 years ago

References:

Problem Statement

XXXX

Proposed Solution XXXX

Acceptance Criteria XXXX

Last updated: Thu Dec 15 2022 before I left for the holiday Report: Dec 2022 See 1.3.1

10%

mreekie commented 2 years ago

This issue represents a deliverable funded by the NIH This deliverable supports the NIH Initiative to Improve Access to NIH-funded Data

Aim 3: Support standards for sharing code, workflows, and containers

The Harvard Dataverse currently supports depositing any type of file, including code/software and documentation files that accompany data, or files within a research replication package. In this project, we plan to facilitate researchers’ efforts to share and publish their entire workflows or containers that describe the main transformations and analysis of the data, following the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. As a result, the research findings will be portable and reproducible (ideally) with a single command.

Though the services will be available to any researcher, special attention will be given to the NIH-funded work. The Dataverse project has already undertaken the development of Codemeta metadata (based on the standard schema.org) within the software. The project will assess the use of Codemeta for research software code and incorporate RO-Crate (for research objects metadata), which allows high flexibility in replication package content.

Further, we will explore container metadata and the use of standardized container images for research. Containerization services, including software security scanning, exist for the Harvard Medical School (HMS) O2 high performance computing cluster, are in use by a number of laboratories, and are being developed by BioGrids, a HMS partner that specializes in creating replicable biomedical software packages and containers. As part of this project, we will explore the integration of these containerization services with the Harvard Dataverse repository to support sharing, discovery, and archival of replicable biomedical research.

This issue represents a deliverable funded by the NIH This deliverable supports the NIH Initiative to Improve Access to NIH-funded Data

1.3.1 | 3 | Support software metadata | 5 1.3.2 | 3 | Research and discovery phase for biomedical workflows support | 5 2.3.1 | 3 | Support biomedical workflows | 5 2.3.2 | 3 | Research and discovery phase for containers and research objects support | 5 3.3.1 | 3 | Support containers and research objects  | 10 4.3.1 | 3 | Apply container, RO, workflows support to a few NIH-funded projects | 10

mreekie commented 1 year ago

Last Updated: Mon Dec 5 2022 (No changes)

See 1.3.1

mreekie commented 1 year ago

Last updated: Thu Dec 15 2022 before I left for the holiday Report: Dec 2022 See 1.3.1

mreekie commented 1 year ago

Next steps:

mreekie commented 1 year ago

Scheduled a meeting: See https://github.com/IQSS/dataverse-pm/issues/11

mreekie commented 1 year ago

The workflow has been release in 5.12. What is needed is to needed is to add support for additional use cases specific to the biomedical fields.

The terms for the MVP were chosen.

The container work is also open.

pdurbin commented 1 year ago

Next step here is to touch base with the person from the community who is working on this already (@pdurbin) mentioned the connection today.

That would be @carlsonp and @poikilotherm who met today and plan to meet again on Thursday.

mreekie commented 1 year ago

monthly update:

Next Steps:

mreekie commented 1 year ago

Monthly January: see 1.3.2

mreekie commented 1 year ago

deprecating this deliverable placeholder to reflect how we've been reporting on it, which is both 1.3.1 and 1.3.2 together. Alone this issue does not add value