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_tex/index.tex

@@ -269,7 +269,7 @@ \section{Introduction}\label{sec-intro}
 can help this mode of standards development thrive and reach its full
 potential.
 
-\section{Use cases}\label{use-cases}
+\section{Use cases}\label{sec-use-cases}
 
 To understand how OSS development practices affect the development of
 data and metadata standards, it is informative to demonstrate this
@@ -364,12 +364,12 @@ \subsection{Community science}\label{community-science}
 the science.
 
 \section{Opportunities and risks for open-source
-standards}\label{sec-opportunities}
+standards}\label{sec-challenges}
 
 At the same time, these tools and practices are associated with risks
 that need to be mitigated.
 
-\subsection{Flexibility vs.~stability}\label{flexibility-vs.-stability}
+\subsection{Flexibility vs.~Stability}\label{flexibility-vs.-stability}
 
 One of the defining characteristics of OSS is its dynamism and its rapid
 evolution. Because OSS can be used by anyone and, in most cases,
@@ -433,33 +433,68 @@ \subsection{Cross-domain funding gaps}\label{cross-domain-funding-gaps}
 Data standardization investment is justified if the standard is
 generalizable beyond any specific science domain. However while the use
 cases are domain sciences based, data standardization is seen as a data
-infrastructure and not a science investment. Moreover due to how science
-research funding works, scientists lack incentives to work across
-domains, or work on infrastructure problems.
+infrastructure and not a science investment. Moreover, due to how
+science research funding works, scientists lack incentives to work
+across domains or to work on infrastructure problems.
 
 \subsection{Data instrumentation
 issues}\label{data-instrumentation-issues}
 
 Data for scientific observations are often generated by proprietary
-instrumentation due to commercialization or other profit driven
-incentives. There islack of regulatory oversight to adhere to available
-standards or evolve Significant data transformation is required to get
-data to a state that is amenable to standards, if available. If not
-available, there is lack of incentive to set aside investment or
-resources to invest in establishing data standards.
+instrumentation due to commercialization or other profit-driven
+incentives. There is a lack of regulatory oversight to adhere to
+available standards or evolve Significant data transformation is
+required to get data to a state that is amenable to standards, if
+available. If not available, there is a lack of incentive to set aside
+investment or resources to invest in establishing data standards.
+
+\subsubsection{Harnessing new computing paradigms and
+technologies}\label{harnessing-new-computing-paradigms-and-technologies}
+
+Open-source standards development faces the challenges of adapting to
+new computing paradigms and technologies. Cloud computing provides a
+particularly stark set of opportunities and challenges. On the one hand,
+cloud computing offers practical solutions for many challenges of
+contemporary data-driven research. For example, the scalability of cloud
+resources addresses some of the challenges of the scale of data that is
+produced by instruments in many fields. The cloud also makes data access
+relatively straightforward, because of the ability to determine data
+access permissions in a granular fashion. On the other hand, cloud
+computing requires reinstrumenting many data formats. This is because
+cloud data access patterns are fundamentally different from the ones
+that are used in local posix-style file-systems. Suspicion of cloud
+computing comes in two different flavors: the first by researchers and
+administrators who may be wary of costs associated with cloud computing,
+and especially with the difficulty of predicting these costs. Projects
+such as NSF's Cloud Bank seek to mitigate some of these concerns, by
+providing an additional layer of transparency into cloud costs (Norman
+et al. 2021). The other type of objection relates to the fact that cloud
+computing services, by their very nature, are closed ecosystems that
+resist portability and interoperability. Some aspects of the services
+are always going to remain hidden and privy only to the cloud computing
+service provider. In this respect, cloud computing runs afoul of some of
+the appealing aspects of OSS. That said, the development of ``cloud
+native'' standards can provide significant benefits in terms of the
+research that can be conducted. For example, NOAA plans to use cloud
+computing for integration across the multiple disparate datasets that it
+collects to build knowledge graphs that can be queried by researchers to
+answer questions that can only be answered through this integration.
+Putting all the data ``in one place'' should help with that. Adaptation
+to the cloud in terms of data standards has driven development of new
+file formats. A salient example is the ZARR format (Miles et al. 2024),
+which supports random access into array-based datasets stored in cloud
+object storage, facilitating scalable and parallelized computing on
+these data. Indeed, data standards such as NWB (neuroscience) and OME
+(microscopy) now use ZARR as a backend for cloud-based storage. In other
+cases, file formats that were once not straightforward to use in the
+cloud, such as HDF5 and TIFF have been adapted to cloud use (e.g.,
+through the cloud-optimized geoTIFF format).
 
 \subsection{Sustainability}\label{sustainability}
 
 \subsection{The importance of automated
 validation}\label{the-importance-of-automated-validation}
 
-\subsection{Harnessing new computing paradigms and
-technologies}\label{harnessing-new-computing-paradigms-and-technologies}
-
-Open-source standards development faces the challenges of adapting to
-new technologies The development of standards that are well-Cloud
-computing provides
-
 \section{Cross-sector interactions}\label{sec-cross-sector}
 
 The importance of standards stems not only from discussions within
@@ -569,12 +604,12 @@ \subsection{Industry}\label{industry}
 device vendors and researchers.
 
 \section{Recommendations for open-source data and metadata
-standards}\label{recommendations-for-open-source-data-and-metadata-standards}
+standards}\label{sec-recommendations}
 
 In conclusion of this report, we propose the following recommendations:
 
-\subsection{Funding or Grantmaking
-entities:}\label{funding-or-grantmaking-entities}
+\subsection{Policy-making and Funding
+entities:}\label{policy-making-and-funding-entities}
 
 \subsubsection{Fund Data Standards
 Development}\label{fund-data-standards-development}
@@ -588,20 +623,33 @@ \subsubsection{Fund Data Standards
 The OSS model is seen as a particularly promising avenue for an
 investment of resources, because it builds on previously-developed
 procedures and technical infrastructure and because it provides avenues
-for community input along the way. The clarity offered by procedures for
-enhancement proposals and semantic versioning schemes adopted in
-standards development offer avenues for a range of stakeholders to
-propose to funding bodies well-defined contributions to large and
-field-wide standards efforts.
-
-\subsubsection{Invest in Data Stewards Recognize data stewards as a
-distinct role
-in}\label{invest-in-data-stewards-recognize-data-stewards-as-a-distinct-role-in}
-
-research and science investment. Set up programs for training for data
-stewards and invest in career paths that encourage this role. Initial
-proposals for the curriculum and scope of the role have already been
-proposed (e.g., in (Mons 2018))
+for democratization of development processes and for community input
+along the way. The clarity offered by procedures for enhancement
+proposals and semantic versioning schemes adopted in standards
+development offer avenues for a range of stakeholders to propose to
+funding bodies well-defined contributions to large and field-wide
+standards efforts (e.g., (Pestilli et al. 2021)).
+
+\subsubsection{Invest in Data Stewards}\label{invest-in-data-stewards}
+
+Advancing the development and adoption of open-source standards requires
+the dissemination of knowledge to researchers in a variety of fields,
+but this dissemination itself may not be enough without the fostering of
+specialized expertise. Therefore, it is important to recognize
+\emph{data stewards} as a distinct role in research. To truly support
+experts whose role will be to develop, maintain, and facilitate the
+adoption and use of open-source standards, it will be necessary to set
+up programs for training for data stewards and invest in career paths
+that encourage this role. Initial proposals for the curriculum and scope
+of the role have already been proposed (e.g., in (Mons 2018)). In
+addition, in order for these individuals to be able to make the best use
+of open-source standards, it will be important for these individuals to
+be facile in the methodology of OSS. This does not mean that they need
+to become software engineers -- though there may be some overlap with
+the role of research software engineers (Connolly et al. 2023) -- but
+rather that they need to become familiar with those parts of the OSS
+development life-cycle that are useful for development of open-source
+standards.
 
 \subsubsection{Review Data Standards
 Pathways}\label{review-data-standards-pathways}
@@ -629,14 +677,14 @@ \subsubsection{Establish Governance}\label{establish-governance}
 \subsubsection{Program Manage Cross Sector
 alliances}\label{program-manage-cross-sector-alliances}
 
-Encourage cross sector and cross domain alliances that can impact
+Encourage cross-sector and cross-domain alliances that can impact
 successful standards creation. Invest in robust program management of
 these alliances to align pace and create incentives (for instance via
 Open Source Program Office / OSPO efforts). Similar to program officers
 at funding agencies, standards evolution need sustained PM efforts.
 Multi company partnerships should include strategic initiatives for
-standard establishment
-e.g.~\href{https://www.pistoiaalliance.org/news/press-release-pistoia-alliance-launches-idmp-1-0/}{Pistoiaalliance}.
+standard establishment e.g.
+\href{https://www.pistoiaalliance.org/news/press-release-pistoia-alliance-launches-idmp-1-0/}{Pistoiaalliance}.
 
 \subsubsection{Curriculum Development}\label{curriculum-development}
 
@@ -646,7 +694,7 @@ \subsubsection{Curriculum Development}\label{curriculum-development}
 \subsection{Science and Technology
 Communities:}\label{science-and-technology-communities}
 
-\subsubsection{User Driven Development}\label{user-driven-development}
+\subsubsection{User-Driven Development}\label{user-driven-development}
 
 Standards should be needs-driven and developed in close collaboration
 with users. Changes and enhancements should be in response to community
@@ -718,6 +766,13 @@ \section*{References}\label{references}
 et al. 2023. {``Data Preservation in High Energy Physics.''} \emph{The
 European Physical Journal C} 83 (9): 795.
 
+\bibitem[\citeproctext]{ref-Connolly2023Software}
+Connolly, Andrew, Joseph Hellerstein, Naomi Alterman, David Beck, Rob
+Fatland, Ed Lazowska, Vani Mandava, and Sarah Stone. 2023. {``{Software}
+{Engineering} {Practices} in {Academia}: Promoting the
+3Rs---{Readability}, {Resilience}, and {Reuse}.''} \emph{Harvard Data
+Science Review} 5 (2).
+
 \bibitem[\citeproctext]{ref-Gorgolewski2016BIDS}
 Gorgolewski, Krzysztof J, Tibor Auer, Vince D Calhoun, R Cameron
 Craddock, Samir Das, Eugene P Duff, Guillaume Flandin, et al. 2016.
@@ -729,6 +784,12 @@ \section*{References}\label{references}
 Koch, Christof, and R Clay Reid. 2012. {``Observatories of the Mind.''}
 \url{http://dx.doi.org/10.1038/483397a}.
 
+\bibitem[\citeproctext]{ref-zarr}
+Miles, Alistair, jakirkham, M Bussonnier, Josh Moore, Dimitri
+Papadopoulos Orfanos, Davis Bennett, David Stansby, et al. 2024.
+{``Zarr-Developers/Zarr-Python: V3.0.0-Alpha.''} Zenodo.
+\url{https://doi.org/10.5281/zenodo.11592827}.
+
 \bibitem[\citeproctext]{ref-Mons2018DataStewardshipBook}
 Mons, Barend. 2018. \emph{Data Stewardship for Open Science:
 Implementing FAIR Principles}. 1st ed. Vol. 1. Milton: CRC Press.
@@ -739,10 +800,25 @@ \section*{References}\label{references}
 {LEADERSHIP} {IN} {AI}: A Plan for Federal Engagement in Developing
 Technical Standards and Related Tools.''}
 
+\bibitem[\citeproctext]{ref-Norman2021CloudBank}
+Norman, Michael, Vince Kellen, Shava Smallen, Brian DeMeulle, Shawn
+Strande, Ed Lazowska, Naomi Alterman, et al. 2021. {``{CloudBank:
+Managed Services to Simplify Cloud Access for Computer Science Research
+and Education}.''} In \emph{Practice and Experience in Advanced Research
+Computing}. PEARC '21. New York, NY, USA: Association for Computing
+Machinery. \url{https://doi.org/10.1145/3437359.3465586}.
+
 \bibitem[\citeproctext]{ref-Nosek2019CultureChange}
 Nosek, Brian. n.d. {``Strategy for Culture Change.''}
 \url{https://www.cos.io/blog/strategy-for-culture-change}.
 
+\bibitem[\citeproctext]{ref-pestilli2021community}
+Pestilli, Franco, Russ Poldrack, Ariel Rokem, Theodore Satterthwaite,
+Franklin Feingold, Eugene Duff, Cyril Pernet, Robert Smith, Oscar
+Esteban, and Matt Cieslak. 2021. {``A Community-Driven Development of
+the Brain Imaging Data Standard (BIDS) to Describe Macroscopic Brain
+Connections.''} \emph{OSF}.
+
 \bibitem[\citeproctext]{ref-Poldrack2024BIDS}
 Poldrack, Russell A, Christopher J Markiewicz, Stefan Appelhoff, Yoni K
 Ashar, Tibor Auer, Sylvain Baillet, Shashank Bansal, et al. 2024. {``The

_tex/references.bib

@@ -1,3 +1,80 @@
+@software{zarr,
+  author       = {Alistair Miles and
+                  jakirkham and
+                  M Bussonnier and
+                  Josh Moore and
+                  Dimitri Papadopoulos Orfanos and
+                  Davis Bennett and
+                  David Stansby and
+                  Joe Hamman and
+                  James Bourbeau and
+                  Andrew Fulton and
+                  Gregory Lee and
+                  Ryan Abernathey and
+                  Norman Rzepka and
+                  Zain Patel and
+                  Mads R. B. Kristensen and
+                  Sanket Verma and
+                  Saransh Chopra and
+                  Matthew Rocklin and
+                  AWA BRANDON AWA and
+                  Max Jones and
+                  Martin Durant and
+                  Elliott Sales de Andrade and
+                  Vincent Schut and
+                  raphael dussin and
+                  Shivank Chaudhary and
+                  Chris Barnes and
+                  Juan Nunez-Iglesias and
+                  shikharsg},
+  title        = {zarr-developers/zarr-python: v3.0.0-alpha},
+  month        = jun,
+  year         = 2024,
+  publisher    = {Zenodo},
+  version      = {v3.0.0-alpha},
+  doi          = {10.5281/zenodo.11592827},
+  url          = {https://doi.org/10.5281/zenodo.11592827}
+}
+
+@inproceedings{Norman2021CloudBank,
+author = {Norman, Michael and Kellen, Vince and Smallen, Shava and DeMeulle, Brian and Strande, Shawn and Lazowska, Ed and Alterman, Naomi and Fatland, Rob and Stone, Sarah and Tan, Amanda and Yelick, Katherine and Van Dusen, Eric and Mitchell, James},
+title = {{CloudBank: Managed Services to Simplify Cloud Access for Computer Science Research and Education}},
+year = {2021},
+isbn = {9781450382922},
+publisher = {Association for Computing Machinery},
+address = {New York, NY, USA},
+url = {https://doi.org/10.1145/3437359.3465586},
+doi = {10.1145/3437359.3465586},
+abstract = {CloudBank is a cloud access entity founded to enable the computer science research and education communities to harness the profound computational potential of public clouds. By delivering a set of managed services designed to alleviate common points of friction associated with cloud adoption, Cloudbank serves as an integrated service provider to the research and education community. These services include front-line help desk support, cloud solution consulting, training, account management, cost monitoring and optimization support, and automated billing. CloudBank has a multi-cloud pay-per-use billing model and aims to serve the spectrum of cloud users from novice to advanced.},
+booktitle = {Practice and Experience in Advanced Research Computing},
+articleno = {45},
+numpages = {4},
+keywords = {Cloud Computing},
+location = {Boston, MA, USA},
+series = {PEARC '21}
+}
+
+@article{Connolly2023Software,
+	author = {Connolly, Andrew and Hellerstein, Joseph and Alterman, Naomi and Beck, David and Fatland, Rob and Lazowska, Ed and Mandava, Vani and Stone, Sarah},
+	journal = {Harvard Data Science Review},
+	number = {2},
+	year = {2023},
+	month = {apr 27},
+	note = {https://hdsr.mitpress.mit.edu/pub/f0f7h5cu},
+	publisher = {},
+	title = {
+
+{Software} {Engineering} {Practices} in {Academia}: Promoting the 3Rs---{Readability}, {Resilience}, and {Reuse}},
+	volume = {5},
+}
+
+@article{pestilli2021community,
+  title={A community-driven development of the Brain Imaging Data Standard (BIDS) to describe macroscopic brain connections},
+  author={Pestilli, Franco and Poldrack, Russ and Rokem, Ariel and Satterthwaite, Theodore and Feingold, Franklin and Duff, Eugene and Pernet, Cyril and Smith, Robert and Esteban, Oscar and Cieslak, Matt},
+  journal={OSF},
+  year={2021}
+}
+
 @MISC{Nosek2019CultureChange,
   title        = "Strategy for Culture Change",
   author       = "Nosek, Brian",