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\title{Response to ASAPbio RFA : Center for Open Science}



\author[1]{Josh Nicholson}%
\author[1]{Deyan Ginev}%
\affil[1]{Authorea}%


\vspace{-1em}



  
  \date{April 25, 2026}


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This following document is the HTML version
of~\url{https://dx.doi.org/10.17605/OSF.IO/V6M2T}

\emph{Brian Nosek, Melanie Benjamin, Sara Bowman, Michael Haselton,
David Litherland, Natalie Meyers, Nicole Pfeiffer, Andrew Sallans, Rusty
Speidel, Jeffrey Spies, Matthew Spitzer}

\section*{Summary (up to 1000 words)}

{\label{660623}}

\emph{Provide a summary of your strategy for implementing and managing
the CS.}

Scholarship advances by open exchange of ideas and evidence. A
substantial portion of this exchange occurs via publication of journal
articles following peer review. Preprints provide a means of
accelerating scholarly communication by sharing manuscripts prior to
formal peer review. Preprints are well established in some fields such
as physics and economics, and just emerging in other fields such as
biology and chemistry. Effective expansion of preprints requires modern,
open infrastructure to operate preprint services and facilitate deposit
and discovery, and community-based governance to test innovations, share
good practices, and establish norms and standards across scholarly
domains.

We will create a life science preprints commons (hereafter ``The
Commons'') that meets and exceeds the requirements of ASAPbio RFA for a
central service. This open infrastructure will make preprints from any
service easy to discover, access, and deposit through a single
interface. The Commons will be governed by ASAPbio's Governing Board;
the service providers will be the technical partner to that governing
board.

\par\null

COS established \href{http://osf.io/preprints/}{OSF Preprints} as an
interface to the \href{http://osf.io/}{OSF}--an open scholarly commons
for data and workflow management archiving and sharing. OSF Preprints
aggregates search across existing preprint services (11 preprint
services 2M preprints as of April 2017) using
\href{http://share.osf.io/}{SHARE} another COS-led consortium project.
Groups can operate branded interfaces and aggregators for their own
communities. Five are in production and seven will launch soon including
partnerships with funding organizations (e.g. Mind \& Life Institute)
and consortia (e.g. \href{http://www.nellco.org}{NELLCO Law Library
Consortium}).

\par\null

A collaborative team from \href{http://manuscriptsapp.com/}{Manuscripts}
\href{http://authorea.com/}{Authorea} and others are prepared to
contribute as a technical partner for document conversion. Existing
services interoperate with DOCX HTML Markdown and JATS XML amongst other
formats. The team will offer and extend open structured document editing
and conversion technologies.

\par\null

The Commons will connect preprint services in a community-based model.
For the typical user discovery interface The Commons will facilitate
discovery of preprints and guide users to engage with the preprint on
that service. For preservation and data mining research applications The
Commons will store full-text of preprints that qualify for storage. This
community-centered model is illustrated with 12 attached letters of
support from preprint services: \href{http://arxiv.org/}{arXiv},
\href{http://biorxiv.org/}{bioRxiv},
\href{http://agrixiv.org/}{AgriXiv},
\href{https://www.maregroup.org/}{MarXiv},
\href{https://www.mindandlife.org/}{MindrXiv},
\href{https://twitter.com/paleorxiv?lang=en}{PaleorXiv},
\href{https://osf.io/preprints/bitss}{BITSS},
\href{http://socarxiv.org/}{SocArXiv},
\href{http://scielo.org/}{SciELO},
\href{http://psyarxiv.org/}{PsyArXiv},
\href{http://engrxiv.org/}{engrXiv},\href{http://engrxiv.org/}{}and\href{http://engrxiv.org/}{}\href{https://www.fusfoundation.org/}{FocUS
Archive}.

\par\null

Our approach achieves the benefits of interoperability, programmatic
access, preservation, and discoverability via centralization and the
benefits of innovation, independence, and sharing of best practices via
decentralization. Standards and best practices are identified most
efficiently by facilitating an open marketplace for innovation.
Standards and best practices are adopted most effectively by
facilitating collaboration among the community of stakeholders.

\par\null

The Commons will be built on the OSF scholarly commons--modern
extensible scalable public goods infrastructure that archives papers
data protocols registrations and connects the research lifecycle. The
commons is modular such that the underlying tools and services are
independent of the interfaces. This fosters economy of scale and mutual
benefits across stakeholder communities. Feature enhancements to The
Commons will extend to the other services built on OSF (e.g. preprint
services registries repositories research management). Simultaneously
OSF's rich services provide substantial added value to The Commons. For
example the RFA requests integration between preprints and a data
repository to encourage open data. OSF is a data archiving service but
it is also a commons of repositories. Authors will be able to connect
their preprints with data in general and domain-specific biomedical
repositories. To illustrate we attach 15 letters of support from
biomedical-relevant repositories: \href{http://datadryad.org/}{Dryad},
\href{http://www.rcsb.org/pdb/home/home.do}{Protein Data Bank},
\href{http://childes.talkbank.org/}{TalkBank},
\href{https://www.niagads.org/}{NIAGADS},
\href{http://neuromorpho.org/}{NeuroMorpho},
\href{http://www.icpsr.umich.edu/icpsrweb/content/NAHDAP/staff.html}{NAHDAP},
\href{https://www.icpsr.umich.edu/icpsrweb/}{ICPSR},
\href{http://figshare.com}{Figshare},
\href{http://flybase.org/}{flybase},
\href{http://phenome.jax.org/}{Mouse Phenome Database},
\href{https://dataverse.harvard.edu/}{Dataverse},
\href{http://protocols.io/}{Protocols},
\href{https://www.synapse.org/}{Sage Bionetworks (Synapse)},
\href{http://dip.doe-mbi.ucla.edu/dip/Main.cgi}{DIP}, and
\href{https://www.vectorbase.org/}{Vector Base}. We will also work with
\href{https://www.nlm.nih.gov/NIHbmic/nih_data_sharing_repositories.html}{NIH-hosted
repositories} (NIH staff cannot write letters of support).

\par\null

The RFA priorities for open, free infrastructure are highly aligned with
COS's mission and approach. COS builds entirely free, open
infrastructure to support the research lifecycle. COS services are built
to scale, and already support preprints. We can deliver an initial
version of The Commons immediately. Our highly skilled team will deliver
rapid, incremental advancement of The Commons during the grant period.

\par\null

The proposed budget anticipates consistent interest by the Governing
Body (GB) in expanding features. As a 501(c)3 non-profit organization,
we welcome regular budget negotiation and transparent accounting of the
actual costs to run the service. We also propose a substantial marketing
campaign to support adoption of preprints. This portion of the budget
can be adjusted depending on delegation of responsibilities with
ASAPbio.

\par\null

The RFA goals for sustainability are perfectly aligned with
\href{https://osf.io/x2w9h/}{COS's model}. The Commons infrastructure
and content are public goods. COS is developing a sustainability model
for the scholarly commons that will be elaborated and implemented during
the grant period. The plan will ensure that the user public will always
have free deposit and access to preprints. The long-term costs for The
Commons will be substantially lower than other approaches because the
scholarly commons aligns the interests of many stakeholder communities
with shared tools.

\emph{If you represent a consortium of organizations, please indicate
why these partnerships were formed and how they will best serve the
execution of the project and the interests of the scientific community.}

\emph{}

Public goods infrastructure is most effective with a distributed,
coordinated model of contributorship to draw on multiple sources of
expertise and to promote inclusivity. There are five key components of
The Commons:

\begin{enumerate}
\tightlist
\item
  Preprints Repository: COS's \href{http://share.osf.io/}{SHARE} service
  already meets most of the requirements for the repository of preprints
  for aggregated indexing, search, and discovery.
\item
  Submission Service: COS's \href{http://osf.io/preprints/}{OSF
  Preprints} already meets most of the requirements for the submission
  service for preprints.
\item
  Conversion Tools: Manuscripts.app and Authorea have developed
  conversion libraries, renderers, and editors that can be extended to
  meet functionality requirements. Additional contributions by a
  community of experts (e.g., CoKo Foundation, Pandoc, CiteSeerx) will
  chart a meta-roadmap for an open suite of services.
\item
  Automated Screening Tools:
  \href{https://www.crossref.org/services/similarity-check/}{Crossref
  offers services} for automated screening for plagiarism that offer
  immediate value for a fee. COS and the community experts will advance
  open solutions.
\item
  Service Administration: COS's community team already provides user and
  administrative support for the operation of the OSF. This team will
  add personnel dedicated to efficient service administration of The
  Commons.
\end{enumerate}

\section*{Technical capability (2000
words)}

{\label{627532}}

Explain why your organization or consortia of organizations are
well-qualified to undertake the development and management of the CS.
Please address the questions below:

\emph{What previous data archive solutions have you hosted, managed or
developed? Please describe size and complexity. Has your organization
undertaken projects of the scope of developing the CS?}

\emph{}

COS maintains a free, open source infrastructure composed of a set of
backend services (e.g., file storage, file rendering,
authentication/authorization) and interfaces built on top of those
services (e.g., OSF.io, OSF Preprints). The OSF is a scholarly commons
of composable services and data archiving. The scope and complexity of
the OSF significantly exceeds the requirements for The Commons. The OSF
was designed from the start for enterprise-level quality for
scalability, efficient extensibility via modular design, and reliable
security, access, and preservation via modern solutions. Collectively,
the \href{https://github.com/CenterForOpenScience}{OSF's entirely
open-source, composable suite of services} consist of
\textasciitilde{}330,000 lines of code produced via 53,491 commits
maintained by an expert infrastructure team of product, engineering,
labs, and QA of about 40 full-time employees. OSF hosts
\textasciitilde{}14,400 gB of research data across more than 76,000
projects, 7,500 registrations, and with dozens of partners. SHARE
contains more than 25 million research events harvested from
\textasciitilde{}150 providers.

COS's modular development approach enables developers to make real
contributions to the codebase right away and scale developers quickly
with their motivation, ability, and accelerated learning. Many of the
ASAPbio requirements for The Commons are already met with the OSF,
SHARE, and OSF Preprints services. This is illustrated with established
partnerships with 12 groups and consortia already for hosting their
preprint services, five of which are \href{http://osf.io/preprints}{in
production} as of April 2017.

\emph{Has your organization(s) undertaken software development projects?
If so, please describe the project, how it was executed, and the current
state of this software.}

\emph{}

The\href{https://github.com/CenterForOpenScience}{OSF is a suite of
modular, open software tools and services} to support scholarly
investigation, communication, and preservation--similar to what NIH has
described as the data commons. OSF includes (1) a set of services such
as authentication, file storage, file rendering, databases for metadata,
search, analytics, commenting, moderation, and documentation, (2) an
add-on ecosystem of third-party services created by abstracting their
APIs to a common API for the purpose of linking researcher tools/storage
services already widely adopted to those core OSF services, and (3) an
open dataset of metadata called \href{http://share-research.org/}{SHARE}
containing research events from many sources in the scholarly community.

OSF is a platform-as-a-service for scholarly research and communication,
much like Salesforce or Amazon Web Services are for their purposes.
Interfaces can be built on these open, modular tools to provide service
for a variety of functions around the research lifecycle and serving the
needs of specific communities. COS develops interfaces and workflows for
different stages of the research lifecycle including registries,
preprints, meetings, institutions, journals, and repositories. These
interfaces are built on top of the OSF services, add-on ecosystem, and
SHARE data.

\par\null

Each interface can be customized and branded for groups to administer
themselves in serving their communities. With community interfaces,
groups gain access to technologies to increase openness and
reproducibility, and simultaneously retain control for governance, norm
setting, and experimentation. Establishing branded services also
facilitates integration with other services. For example, with OSF
Institutions, a university can enable single sign-on so that researchers
can login to the OSF using their university credentials. Universities
can connect services such as institutional repositories or computational
platforms to the OSF to connect them more closely with researchers'
workflows and the rest of the research lifecycle. The Commons gains
features such as university single sign-on and integration with
institutional repositories ``for free'' by being an interface on OSF.
Community interfaces dramatically lower the technical and resource
barriers for groups to provide enterprise-quality services for their
community.

\par\null

Examples of interfaces to the OSF scholarly commons include:

\begin{itemize}
\tightlist
\item
  \url{http://osf.io/} : Primary interface for individual researchers to
  interact with the OSF and its suite of project management, archiving,
  and registration services.
\item
  \url{http://osf.io/preprints/} : General interface for preprints that
  aggregates search across preprint services and has a simple,
  user-friendly interface for depositing preprints.
\item
  \url{http://socarxiv.org/} : Community-branded version of the OSF
  Preprints interface operated by that community (others accessible via
  \url{http://osf.io/preprints/}).
\item
  \url{http://osf.io/registries/} : Another general interface on OSF,
  but this one for aggregating search across registries.
\item
  \url{https://osf.io/institutions/nyu/} : Illustration of an
  institution-branded interface on OSF.
\end{itemize}

Continual iteration and development can be followed on the
\href{https://docs.google.com/spreadsheets/d/1SocElbBjc_Nhme4-SJv2_zytBd1ys8R5aZDb3POe94c/edit\#gid=1340026270}{Public
Requirements and Roadmap} and all code is open source at
\url{https://github.com/CenterForOpenScience}.

\emph{Has your organization(s) undertaken open source software
development projects? If so, please describe the project, how it was
executed, and the current state of this software as well as any
experience with managing community contributions.}

COS develops exclusively
\href{https://github.com/CenterForOpenScience}{open public goods tools
and services}. All existing and future COS-developed software is openly
licensed for permissive use. Across projects approximately 200
developers have contributed code. For example \url{http://osf.io/} has
had \href{https://github.com/CenterForOpenScience/osf.io}{123
contributors} and
\href{https://github.com/CenterForOpenScience/SHARE}{SHARE has had 31
contributors}. COS facilitates community contributions with hack-a-thons
informal development sessions on-site visits and small grants to
developer teams to connect services to the framework.

\emph{Describe any experience/capacity you have in managing the
conversion of files to structured XML and highlight any experience you
have in validating documents converted to an XML standard.}

\emph{}

\href{http://manuscriptsapp.com/}{Manuscripts} is a scholarly word
processing environment that uniquely offers a fully offline,
desktop-based experience in addition to online editing and annotating.
The product is follow-up to the award winning Papers reference manager
from a team with a track record of building high-end scholarly software
for millions of academics. They offer a deep understanding of authoring
and publishing workflows and relevant technologies for both web and
offline uses. Manuscripts interoperates with DOCX, HTML, Markdown and
JATS XML amongst 10+ other formats, and is prepared to offer its
structured document editing and conversion technologies under an open
source license.

\href{http://authorea.com/}{Authorea} focuses on research document
conversion and creation. Authorea has experience with every mainstream
format for academic writing and supports many combinations of
import-to-export flows. This includes converting and exporting directly
into a JATS-compliant XML. The conversion process is automated upon
importing or submitting a document, while the core service allows edits
to be made easily by editors, typesetters, and authors. Authorea has
deep experience with relevant technologies (JATS/HTML5/ePub/Pandoc).

Other organizations named in this proposal to support conversion tools
likewise have substantial relevant experience. We will convene a yearly
meeting with expert groups, and others with relevant interests, to
identify a meta-roadmap of shared interests in open tools for conversion
services. Also, we included budget to support community developers for
tasks that will support the GB's requirements. The following community
partners will play key roles:

\begin{itemize}
\tightlist
\item
  Collaborative Knowledge Foundation builds open source solutions for
  improving how knowledge is created, produced, and reported. For
  example, INK Framework converts content and data across formats such
  as Word, HTML5, XML, and ePub. The team has extensive experience in
  publishing and open tools.
\item
  Pandoc is a universal document converter across many formats, and is
  the most mature open library in this space. The project is maintained
  by John MacFarlane.
\item
  Lee Giles's lab at Penn State has very successful projects such as
  CiteSeerx and can support both conversion and screening efforts.
\end{itemize}

\emph{Describe what experience/capacity you have in taking data from a
variety of sources to create a single database.}

\href{https://share.osf.io/}{SHARE} is an open dataset of metadata about
all research events. Research events include publications preprints
trial registrations data deposits grant awards and researcher profiles.
SHARE facilitates curation of research outputs and activities to be
identified as elements of a single research activity. The curated SHARE
data enhances search and discovery of research objects across the
research lifecycle. The SHARE dataset can power search for any scholarly
service. SHARE provides opportunity for innovation---by anyone---on
communication visualization and dissemination of information about
research events. As of April 2017 there were \textgreater{}25 million
events in SHARE aggregated from \textasciitilde{}150 sources. The SHARE
database powers OSF's aggregated \href{http://osf.io/preprints}{preprint
search} and aggregated \href{http://osf.io/registries/}{registry
search}. In partnership with the Association of Research Libraries
curation associates are connecting related research events such as a
preprint stored on bioRxiv with a dataset stored on Dryad with a
publication appearing in an Elsevier journal with a grant award from
NIH. With maturation of those curation tools The Commons will facilitate
discovery of other activities related to the preprint wherever it is
stored.

\emph{Describe what experience you have in running user-login and
submission systems.}

OSF uses Central Authentication Service (CAS) software to provide users
secure, single sign-on (SSO) to access multiple research applications
(preprints, branded preprints, registries, meetings, institutions) while
providing login and password credentials only once. Because CAS supports
multiple authentication protocols including SAML, OSF provides
institutions (e.g., University of Notre Dame) and other services (e.g.,
ORCID) the ability for their users to use their institutional
credentials to access OSF services. Additionally, OSF offers two-factor
authentication for added account security.

\par\null

OSF offers easy mechanisms for deposit of research content of any kind
an email submission service for \href{http://osf.io/meetings/}{meetings}
and a structured workflow for \href{http://cos.io/prereg/}{submission of
preregistrations}. Most relevant for The Commons COS developed a simple
guided \href{http://osf.io/preprints/}{workflow for submitting
preprints} that extends to all the branded preprint services it hosts.
The preprint submission workflow is easily followed by authors wishing
to submit directly from authoring services such as Overleaf Authorea or
Manuscripts.

\emph{Describe your experience with building and working with APIs.}

With its \href{http://api.osf.io/v2/}{HTTP API}, COS is facilitating an
interoperable services ecosystem. Once a service is connected to the
ecosystem, it is also connected to all the other services in the
ecosystem. As of April 2017, there were 10 add-ons: ownCloud, GitHub,
Dropbox, figshare, Box.com, Dataverse, Google Drive, Amazon S3,
Mendeley, and Zotero. There are also third-party products that connect
to the add-on ecosystem including: Open Sesame, JASP Stats, and
Overleaf. Six others are scheduled to be in production by July 2017
including Dryad, bitbucket, Gitlab, OneDrive, Fedora, DMPTool, and Rmap.

\par\null

The modular approach minimizes user lock-in to any service. Connecting
services makes it easy for end users to integrate the services they use.
For example, if a user deposits a preprint on OSF Preprints, they can
add datasets to the preprint by storing it on OSF, figshare, Dataverse,
Dryad, or any other connected storage solution.

\par\null

\href{http://developer.osf.io/}{Substantial API documentation}
facilitates use by others in the developer community. The add-on
ecosystem provides a substantial efficiency gain for the community of
open science service developers. For example, the University of Notre
Dame Center for Research Computing integrated their computational
platform with OSF. By creating a single connection to OSF, they maintain
a single connection and have access to 10+ storage solutions. As more
repositories or other services are connected to ecosystem, they become
available to Notre Dame users immediately and automatically. This also
presents an opportunity that preprints at The Commons could eventually
become highly reproducible with attached data and code, and cloud-based
execution to reproduce findings and figures on the fly.

\emph{Describe what experience/capacity you have in providing a
staffed-helpdesk facility.}

COS has adopted industry standard tools to facilitate user support and
service administration for its growing user base of 50000+. Helpdesk
staff uses tools such as desk.com Zoom Slack Google Groups and
ScreenSteps to respond to user questions and feedback submitted via
email and social media. Support staff maintains a detailed
knowledge-base for FAQs and \href{http://help.osf.io}{step-by-step
documentation} to help new users become power users. COS maintains
extensive tracking of bug reports and feature requests using JIRA and
Github. Helpdesk staff is currently US-based and English-speaking with
escalated calls and debugging handled by senior product management.
Support staff responds to all initial inquiries within 1 business day
averaging more than 250 per month and historically 40\% are resolved on
the first reply.

\section*{}

{\label{858966}}

\section*{Organization and management considerations (up to 750
words)}

{\label{858966}}

\emph{Please insert a diagram of your organization/consortium's planned
structure relevant to this project (e.g. Organization Chart)}

See COS and The Commons Organizational Charts in the Appendix.

\emph{Briefly describe the staff that would be responsible for
developing and maintaining the CS. State the numbers and qualifications
of staff who could work directly on such a project. Name existing
individuals and their credentials if known. Indicate key personnel that
would need to be hired.}

Brian Nosek (Executive Director, co-founder). Product vision, strategic
direction, executive management, community engagement.

Nici Pfeiffer (Product Manager/Lead). Product management; Product
requirements, UI specification development and maintenance of the
product roadmap. Supported by Sara Bowman, product manager.

Jeffrey Spies (CTO, co-founder; SHARE co-director). Product/technical
vision, strategic direction, technical architecture; management of COS
Labs (R\&D)

\par\null

David Litherland (Senior Project Manager). Technical management.
Previously at ScholarOne and Silverchair Information Systems.

Michael Haselton (Technical Lead). Technical leadership of developer
team.

Developers. Core for delivering on the technical requirements for The
Commons. Staffing will draw from COS's outstanding team with some
rotation depending on matching expertise with product development tasks
for the 7 FT devs split among OSF Preprints interface, OSF supporting
tools, SHARE, add-on ecosystem, and supporting conversion/screening
services and 1 FT UI/UX designer.

Amanda Liscouski (QA Lead). Quality assurance management. Supported by
QA associates: Todd Sacco, Allison Schiller.

TBN (Technical Evangelist). Support and collaborative management with
domain data repositories and other services connecting via API to The
Commons (e.g., scholarly publishing platforms, authoring services, data
repositories).

Rebecca Rosenblatt (User Support). Service administrator, product
documentation, help desk support, and service administration. Supported
by TBN service administrator/user support. Additional service
administration personnel added as The Commons scales.

Melanie Benjamin (Funding Lead). Sustainability plan. Supported by TBN
grants specialist and TBN sustainability account manager.

Rusty Speidel (Marketing Manager). Direction of COS marketing.
Previously at major online retailers, scholarly publishers and digital
design, technology and PR firms. Speidel supported by a TBN marketing
specialist.

Matt Spitzer (Community Manager). Community engagement. Supported by
Jolene Esposito (Community Programs Lead).

\emph{Describe what project management methodology you would use, and
what experience you have with this methodology. Also, describe other
projects you have managed on behalf of a consortium and how you kept the
consortium up-to-date with progress etc.}

\textbf{Project Management Methodology}

We use an Agile Scrum framework. Projects go through assessment,
requirements and high-level design, then detailed requirements
gathering, iteratively defining requirements in greater detail for
product delivery within each 2-week sprint. Project and Product Managers
work closely with stakeholders to define and approve requirements,
design, and acceptance criteria for implementation and delivery.

Once the project's business requirements are validated, Epics (major
areas of functionality) and User Stories (descriptions of smaller areas
of functionality) are created. The Product Manager works with the
Technical Lead to determine dependencies within stories and across
Epics. The Team schedules these components across sprints for releases
as required and on schedule.

Two week sprints provide insight with regular incremental progress and
stakeholders can view working code continuously. Problems in the
translation of requirements into functionality are identified and fixed
quickly maximizing efficiency. Frequent progress markers highlight the
pace of the project, allowing for resource adjustments for timely
delivery.

\textbf{Experience with Methodology}

The Product Development and Agile Scrum approach has proven successful
in efficiently producing high-quality projects at COS including:

\begin{itemize}
\tightlist
\item
  OSF services
\item
  OSF.io features
\item
  API integrations
\item
  Preprints
\item
  Registries
\item
  SHARE
\end{itemize}

\textbf{Consortium Projects}

COS has \href{https://cos.io/about/our-partners/}{extensive experience
with collaborative partnerships with consortia and external
stakeholders}. All collaborative engagements include clearly defined
points-of-contact for ongoing communication. COS's
\href{http://share.osf.io/}{SHARE} project has many
consortium-management parallels with The Commons. SHARE is a partnership
with the \href{http://www.arl.org/}{Association of Research Libraries}
and stakeholder partners the \href{http://www.aau.edu/}{Association of
American Universities} and the \href{http://www.aplu.org/}{Association
of Public Land-grant Universities}. COS is the technical partner and
coordinates with the SHARE leadership team in product vision
requirements and engagement with the library community. ~Likewise
\href{https://www.fbo.gov/index?s=opportunity\&mode=form\&id=498e3d5371eb019f37554e3aaf04333e\&tab=core\&_cview=0}{NGS2
is a DARPA}-funded project for which COS is the technical and evaluation
partner. COS provides project management of the whole program
particularly with regard to performer teams' research and technical work
via OSF.

\href{https://cos.io/our-products/osf-preprints/}{Community preprint
services hosted by COS} also operate via this partnership model. Each
service maintains their independent governance body for defining the
operating principles of their service. COS coordinates communication
across service providers manages individual relationships with each
service and delivers on the
\href{https://docs.google.com/spreadsheets/d/1SocElbBjc_Nhme4-SJv2_zytBd1ys8R5aZDb3POe94c/edit\#gid=1340026270}{technical
requirements to support those services}. Others include
\href{https://copdessdirectory.osf.io/}{COPDESS} with the
\href{https://sites.agu.org/}{American Geophysical Union} the
\href{http://www.internationalsituationsproject.com/?locale=en-US}{International
Situations Project} and \href{https://lookit.mit.edu/}{Lookit}. Project
success is a function of reliable clear lines of communication and
collaborative planning and execution.

\section*{Interactions with the Governance Body and Reporting (up to 500
words)}

{\label{181776}}

\emph{The successful bidder and manager of the CS will have to engage
with a Governance Body (GB), managed by ASAPbio. The CS Provider(s) will
file a yearly public report to the GB and Funders. The GB will be making
recommendations on the performance of the CS Provider(s) to the funders
for the purpose of releasing yearly funds to the CS Provider(s). The GB
will also set standards for intake of content to the CS and will set
yearly priorities and make recommendations. Models similar to this
arrangement include Europe PMC and the Protein Data Bank. Please provide
any comments or ideas on the relationship and interactions that you (if
you obtain the contract) would like to establish with the GB.}

The GB bears responsibility for establishing the policies of The
Commons; technical partners bear responsibility for delivering
infrastructure to abide by those policies. Coordination can follow COS's
community partner model adapted to suit the needs of the GB.

We recommend:

\par\null

\begin{itemize}
\tightlist
\item
  \textbf{Yearly in-person meetings of the GB and technical partners}.
  These 1-2 day meetings will devote a portion of time for reviewing
  progress of the technical infrastructure development, marketing and
  adoption of the service, and service administration activity. But,
  because these activities will be reported frequently during the year,
  most of the in-person meeting time will be used for strategic planning
  of the next period's requirements, implementation, and marketing
  priorities. As such, these meetings will be action-oriented
  collaborative planning sessions.
\item
  \textbf{Quarterly virtual meetings of the GB and technical partners}.
  These 2-3 hour virtual meetings will be devoted to reporting on
  technical development, marketing outcomes, service administration and
  near-term priorities for the next quarter. With advance communication,
  these meeting times can be used efficiently to leverage the insight
  and feedback of the GB to shape the priorities for the next quarter of
  service development and activity.
\item
  \textbf{Monthly ``newsletter'' updates + asynchronously email list
  discussion}. An email list can facilitate asynchronous communication
  among the GB and technical partners for monthly activity reports of
  sprint outcomes and real-time tactical discussion, particularly for
  marketing efforts.
\item
  \textbf{Established points-of-contact (POCs) for real-time
  communication and coordination}. For ongoing implementation work,
  established POCs for COS, technical partners, and the GB are
  essential. This small group can meet on a regular basis to discuss
  sprint planning and project progress. There are at least 2 primary
  points-of-contact: (1) Nici Pfeiffer, Product Lead, with POCs for
  product implementation and operation, and (2) Rusty Speidel, Marketing
  Lead, with POCs for marketing and community building at ASAPbio.
\end{itemize}

Four key phases of the development process that occur at a high
levelwith the GB and at an execution level via the POCs in
quarterlypriorities and two-week sprint cycles:

\begin{tabular}{ll}
\textbf{Phase} &   \textbf{Definition} \\

Discovery and Assessment & Discovery includes assessment and definition of project goals key deliverables contract terms. Assessment includes definition of and agreement with ASAPBio on project goals deliverables high-level scope (including what is out of scope) project assumptions, dependencies, risks levels of effort project milestones \\

Requirements and High-Level Design & Phase includes definition of and agreement with ASAPBio on full scope of business requirements feature acceptance criteria  UX definition/illustration of information architecture, key site pages, any custom feature areas technical approach document which combines overall technical approach for feature, including database design and implementation instructions specification which combines all of the above items into one document upon which the development team can execute \\

Iterative Implementation and Testing (Conversion Process) & Phase includes detailed feature and functional requirements full UI completion and implementation implementation and testing of features loading, proofing, finalization of content regression and manual testing demonstrations of functionality released \\

Post Launch Support & customer support, defect resolution continual manual and automated regression testing on-going site maintenance new feature development
\end{tabular} % test







\section*{Execution and Development (up to 3000
words)}

{\label{846069}}

\emph{See}
\href{https://docs.google.com/document/d/1hUYTxY0E83GEoDgg3wDW-cYdIde00Bid4dcskECw1F0/edit\#heading=h.tqhgtwyds56h}{\emph{Requirements
for the Central Service}}\emph{. Please address your strategy to
implementing each requirement referring to the numbering described in
that section. If a consortium indicate which organizations would be
responsible for which components.}

Requirements are itemized by ``\textbf{Done}'' for those in production
or ``\textbf{ToDo}'' for those to be built and naming ``COS'' or
``partners'' leading execution.

\emph{Preprints Commons Database}

\emph{Act as a repository for life sciences preprints, which includes:}

\emph{~~~~~~~~~~~~Author's original manuscript (.doc, .tex etc.) and the
converted manuscript (XML);}

\par\null

{[}\textbf{Done: COS}{]} OSF preprints become part of the OSF repository
along with any associated data, materials, protocols, and connections
with other repositories. Metadata is aggregated by SHARE (11 preprint
sources, \textgreater{}2 million preprints).

{[}\textbf{ToDo: COS}{]} COS will ingest preprint full-text when allowed
by license, indexed for discovery, and archived for preservation and to
facilitate programmatic access for data-mining research applications.

\emph{All files associated with that manuscript, such as figures and any
supplementary data; including video and datasets, or links to data
stored in appropriate external repositories;}

\textbf{{[}Done: COS{]}} As an interface to the OSF The Commons can make
use of all its repository capabilities. Users can
\href{http://help.osf.io/m/preprints/l/685323-add-supplemental-files-to-a-preprint}{add
supplementary data materials links or other files}. When made publicly
accessible files are displayed with the preprint and available via API.
OSF can surface links to external repositories or integrate the external
repositories to appear native to the OSF via add-ons. Eight storage
add-ons are available now--figshare, dataverse, box.com, dropbox, Google
Drive, GitHub, Owncloud, and Amazon S3--and five more in Q2 2017--Dryad
Bitbucket Gitlab OneDrive and Fedora.

On registration (i.e., timestamped, project snapshotting) in the OSF,
data is copied from all connected services into a preservation
environment. In the future, that environment can be an integrated,
external repository. For example, on sharing a preprint, (1) authors may
connect private storage to facilitate later sharing, or (2) authors may
transfer data from active storage to preservation storage.

\textbf{{[}ToDo: COS{]}} We will add domain-specific repositories.
Letters of support from 15 are attached:
\href{http://datadryad.org/}{Dryad},
\href{http://www.rcsb.org/pdb/home/home.do}{Protein Data Bank},
\href{http://childes.talkbank.org/}{TalkBank},
\href{https://www.niagads.org/}{NIAGADS},
\href{http://neuromorpho.org/}{NeuroMorpho},
\href{http://www.icpsr.umich.edu/icpsrweb/content/NAHDAP/staff.html}{NAHDAP},
\href{https://www.icpsr.umich.edu/icpsrweb/}{ICPSR},
\href{http://figshare.com}{Figshare},
\href{http://flybase.org/}{flybase},
\href{http://phenome.jax.org/}{Mouse Phenome Database},
\href{https://dataverse.harvard.edu/}{Dataverse},
\href{http://protocols.io/}{Protocols},
\href{https://www.synapse.org/}{Sage Bionetworks (Synapse)},
\href{http://dip.doe-mbi.ucla.edu/dip/Main.cgi}{DIP} and
\href{https://www.vectorbase.org/}{Vector Base}. An integrated seamless
mechanism for deposit of data materials and protocols to domain-relevant
repositories will increase discovery and deposit by authors and
discovery by readers.

\emph{Appropriate metadata}

\textbf{{[}Done: COS}{]} The submission process collects metadata
including title, authors, abstract, discipline, keywords, peer-reviewed
DOI, license. Metadata is available via API and HTML meta tags for
discoverability (e.g., Google Scholar, FAIR).

SHARE harvests data across preprint services regardless of metadata
schema. The data is queryable and normalized to a schema developed for
working with diverse sources (draws heavily from schema.org and
DataCite). SHARE is relatively schema-agnostic--flexible to additions
across sources.

\textbf{{[}ToDo: COS}{]} The GB will define metadata standards for The
Commons. Fields will be added to relevant workflows (e.g., submission,
moderation).

\emph{Includes a stable, long-term preservation strategy.}

\textbf{{[}ToDo: COS{]}} We will add domain-specific repositories.
Letters of support from 15 are attached:
\href{http://datadryad.org/}{Dryad},
\href{http://www.rcsb.org/pdb/home/home.do}{Protein Data Bank},
\href{http://childes.talkbank.org/}{TalkBank},
\href{https://www.niagads.org/}{NIAGADS},
\href{http://neuromorpho.org/}{NeuroMorpho},
\href{http://www.icpsr.umich.edu/icpsrweb/content/NAHDAP/staff.html}{NAHDAP},
\href{https://www.icpsr.umich.edu/icpsrweb/}{ICPSR},
\href{http://figshare.com}{Figshare},
\href{http://flybase.org/}{flybase},
\href{http://phenome.jax.org/}{Mouse Phenome Database},
\href{https://dataverse.harvard.edu/}{Dataverse},
\href{http://protocols.io/}{Protocols},
\href{https://www.synapse.org/}{Sage Bionetworks (Synapse)},
\href{http://dip.doe-mbi.ucla.edu/dip/Main.cgi}{DIP}, and
\href{https://www.vectorbase.org/}{Vector Base}. An integrated seamless
mechanism for deposit of data materials and protocols to domain-relevant
repositories will increase discovery and deposit by authors and
discovery by readers.

{[}\textbf{ToDo: COS}{]} COS is exploring technologies and partnerships
to add preservation features including the use of torrent protocols for
distributing publicly stored data, the blockchain to create a
guaranteed-immutable provenance record, mirroring of public content that
individuals could backup or host on cheap, commodity hardware, and
partnerships like Internet Archive. The latter includes connecting
institutional systems for automatic preservation (e.g., CurateND, Notre
Dame).

\emph{At inception of the preprint service, the database should be
populated with legacy preprints and associated metadata from existing
approved servers. Conversion of these legacy files to XML could be
considered but is not a specific requirement for this application.}

{[}\textbf{Done: COS}{]} The GB will decide eligibility for aggregated
search. Metadata is already harvested by SHARE; adding preprint services
is trivial.

{[}\textbf{ToDo: COS}{]} Before launch, COS will harvest full-text
preprints from eligible services to accompany metadata harvested by
SHARE. Documents will run through a text-extraction pipeline and be
indexed for discovery purposes. Word and LaTeX should be convertible to
XML; PDF will be difficult (see section 4).

\emph{The provider(s) of these services are also required to remove or
flag any manuscripts that violate the standards set forth by the
Governance Body.}

{[}\textbf{Done: COS}{]} Moderation is manual; an administrator
moderation dashboard is prototyped and scheduled for July 2017 release.

{[}\textbf{ToDo: COS}{]} The GB will define moderation standards for The
Commons. The dashboard will enable administrators to apply those
standards to new submissions. The GB will decide whether to include
preprints from services that do not provide the necessary metadata
(e.g., license information). Ideally, The Commons will facilitate
standards for metadata across external services.

\emph{Preprints Commons Human Interface}

\emph{~~~~~~~~~~~~Provide a web interface for browsing and searching.}

\emph{~~~~~~~~~~~~~~~~~~~~~~~~Display abstracts and links to source}

\emph{~~~~~~~~~~~~~~~~~~~~~~~~Potentially provide download functionality
for content held in the CS in a variety of formats: PDF, XML, HTML, etc}

\emph{~~~~~~~~~~~~~~~~~~~~~~~~Display snippets (like Google Books) to
place full-text search results in context}

\emph{~~~~~~~~~~~~~~~~~~~~~~~~If the source is not available elsewhere,
or with consent of the ingestion source, display the full manuscript and
~~~~~~~~~~~~~~~~~~~~~~~~figures/supplementary files.}

\emph{~~~~~~~~~~~~~~~~~~~~~~~~Display a clear statement indicating that
the material is a preprint}

\emph{~~~~~~~~~~~~~~~~~~~~~~~~Link to other versions of the manuscript
elsewhere, especially journal versions, using Crossref metadata or
information from ~~~~~~~~~~~~~~~~~~~~~~~~other sources}

\emph{~~~~~~~~~~~~~~~~~~~~~~~~Schema.org tags}

\emph{~~~~~~~~~~~~~~~~~~~~~~~~Make available metrics and anonymized
usage data to humans.}

\emph{~~~~~~~~~~~~~~~~~~~~~~~~Be developed in line with good
user-experience web principles, be fully responsive}

\emph{~~~~~~~~~~~~~~~~~~~~~~~~Support login functionality - via ORCID}

\par\null

{[}\textbf{Done: COS}{]} The preprints search interface offers
aggregated search, faceting by preprint service and discipline and sort
by search relevance or upload date (Figure
{\ref{493406}}).

\par\null\selectlanguage{english}
\begin{figure}[h!]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/Fig1-COS/Fig1-COS}
\caption{{\textbf{Aggregated Search display. ~}
{\label{493406}}
Individual search results show title authors date discipline tags
abstract and source by default (left panel) and full abstract links to
sources and keyword tags after expanding the entry (right panel). Search
and submission interfaces have modern responsive intuitive designs for
use on any device.
{\label{493406}}%
}}
\end{center}
\end{figure}\selectlanguage{english}
\begin{figure}[h!]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/Fig2COS/Fig2COS}
\caption{{Individual search result panel - expanded view
{\label{426700}}%
}}
\end{center}
\end{figure}\selectlanguage{english}
\begin{figure}[h!]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/fig3cos/fig3cos}
\caption{{Individual search result - default view
{\label{435676}}%
}}
\end{center}
\end{figure}



The full-text interface presents metadata cleanly including metrics and
links (if available) to the published version. Preprint files are
rendered in the browser and many formats are supported
(\href{https://osf.io/vj54c}{Figure 3}). If the author adds datasets
figures materials or other files they also render in the browser.
Intuitive version control enables preprint updates with prior versions
linked.

Authors can login using ORCID, OSF, or institutional account if their
institution has enabled SSO. Viewers can download the preprint in its
original format, share a persistent link to the preprint via social
media buttons, copy a preformatted citation of the preprint, and follow
links to authors' profile pages to discover other work.

\par\null\selectlanguage{english}
\begin{figure}[h!]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/Fig4-Cos/Fig4-Cos}
\caption{{Hosted full-text preprint
{\label{562856}}%
}}
\end{center}
\end{figure}



\par\null

{[}\textbf{ToDo: COS}{]} All but three items in ASAPbio's requirements
are complete (items: ii, iii, and vi from Section 2 above). Integration
with Crossref metadata for easier discovery of other versions. On
inclusion of full-text, context of results will be displayed. OSF's
rendering system supports conversion pipelines, UI to download in
alternative formats will be available. For item ix, we will conduct an
accessibility review.

\emph{Provide an alerting tool that delivers emails/other notifications
to authors when content of interest (by keyword, author, citing their
article, etc) appears.}

{[}\textbf{Done: COS}{]} Users can receive notifications never, as they
occur, or as a daily digest. Notifications are enabled for behaviors
related to commenting and adding files. Users have control of
notification settings at the user and project level. Authors could elect
to receive notifications for some preprints and not others.

{[}\textbf{ToDo: COS}{]} Subscriptions to notifications by author,
keyword, discipline, service. Surfacing notifications control about
one's own preprints more efficiently.

\emph{Respondents are also invited to highlight other functionality they
would suggest the site should support, although all features and
functionality of the CS will require Governance Body approval.}

See section 9 (page 20)

\emph{Preprints Commons Machine Interface}

\begin{quote}
\emph{API for manuscripts}

\begin{quote}
\begin{quote}
\emph{Make available the full text of preprints (converted version and
author's original files) by RESTful API and bulk download}

\emph{OAI-PMH endpoint, or equivalent if standards change over time}

\emph{Capture metrics on API use}
\end{quote}
\end{quote}
\end{quote}

{[}\textbf{Done: COS}{]} A RESTful API is available for hosted
preprints; converted output will be added.

{[}\textbf{ToDo: COS}{]} For full-text harvested from other services, a
similar API will be available. Bulk downloads will be accessible as
time-based archive files, torrents, and, potentially, rsync. An OAI-PMH
is due for release in May 2017. A new metrics API aligned with community
efforts (COUNTER) is scheduled for Q3 for more robust queries.

\emph{Screening training set}

\begin{quote}
\begin{quote}
\emph{Make available all manuscripts (both those that passed screening
and those that did not) and their screening histories for bulk download,
with any sensitive information redacted. This corpus will be used to
train automated screening algorithms}.
\end{quote}
\end{quote}

\par\null

{[}\textbf{ToDo: COS}{]} We need clarification of the requirements for
this item. Creating a full dataset will be straightforward if preprint
services are willing and able to share full-text of approved and
rejected manuscripts.

We also need clarification on how the automated screening algorithms can
be trained if the sensitive information is redacted and the redacted
information is the basis for rejection. Our operating assumption is that
the training dataset will remain secure. Researchers developing
screening algorithms would gain approved access.

\emph{Manuscript Conversion Tool}

\begin{quote}
\begin{quote}
\emph{Convert the full text of manuscripts to XML or equivalent, tagged
according to JATS4R standards. As a minimum it should be possible to
convert a .docx or .tex file to XML. The feasibility of converting a
.pdf file to XML should be discussed.}
\end{quote}
\end{quote}

\par\null

{[}\textbf{Done: Partners}{]} Manuscripts completes document import and
export operations with a cross-platform component executable as a web
service that orchestrates pre-existing open source and custom document
transformation steps. Heuristics infer and correct format specific
issues in Word, LaTeX and Markdown documents. A dozen input formats are
supported (DOC, DOCX, DocBook XML, Evernote XML, EPUB, LaTeX, Markdown,
ODT, OPML, Markdown variants, ReStructured Text, Microsoft style RTF,
Textile).

The document importers support scholarly needs: footnotes, endnotes,
equations, cross-references, embedded citation metadata is processed
from EndNote, Papers, Zotero, Mendeley formatted field codes in case of
docx, tracked changes are automatically applied. Citations, equations,
figures and tables with their captions are captured from LaTeX and
converted to XML. The implementation is hardened based on a large
collection of user provided documents.

{[}\textbf{To do: Partners}{]} Prepare for open sourcing. We expect to
achieve basic PDF-to-XML extraction: indexing grade text, extracting
figures, document outline. Experience to date suggests that efforts to
infer structure in PDF documents beyond this carries high implementation
risk and diminishing returns; PDF is a format for drawing for print,
translating it into structured rich text only incrementally improves
indexing quality, and will not yield XML to produce a readable document.

\emph{Allow authors to preview, proof, and modify the converted XML
through an author-friendly interface}

{[}\textbf{Done: Partners}{]} Editing experience is fully WYSIWYG. The
format produced by the editor follows the JATS4R recommendations and
document validity is enforced continuously as user edits are persisted
to a version history. In addition to JATS4R, Manuscripts can provide
HTML5 export capabilities, normalised to the Scholarly HTML tagging
conventions drafted by the W3C Scholarly HTML Community Group.

{[}\textbf{ToDo: Partners}{]} These services will be adapted to allow
preprints authors to preview, proof, and modify the converted XML. The
editing experience will be integrated with the preprints infrastructure
for accounts, storage, and notifications.

\emph{The manuscript conversion tool must be able to interoperate with a
wide range of preprint servers and journals that operate on different
technological platforms.}

{[}\textbf{ToDo: Partners}{]} The service will be modularized such that
preprint services could integrate with their own workflows. We will
expose PressRoom document conversion service via REST API.

\emph{The conversion process could occupy several different positions in
the pipeline of manuscripts, and the preferred position will depend on
input from the GB and the ingestion sources. Describe how you would
implement the following options (and any others that you foresee will be
compatible with many ingestion sources) and indicate which you see as
the preferred option.}

\emph{All material coming into the Commons from ingest sources will be
ingested as structured XML. In this case, the conversion tool is offered
as a software or hosted as a Commons service accessible by API, and
individual ingest sources are responsible for implementing it or
generating XML by alternative means.}

\emph{Material coming from ingest sources can be provided to the Commons
as the author's original manuscript file (such as .docx or .tex). In
this case, the Commons would convert the manuscript and contact authors
(ie by email) to invite them to proof a rendition of the manuscript
after conversion to XML. The ingest source could later retrieve the
converted manuscript from the Commons.}

\emph{The conversion tool could function upstream of ingest sources. A
submission tool hosted by the CS could convert manuscripts for author
proofing and then provide options for authors to send the converted
manuscripts (or original files, or PDFs) to other ingest sources.}

{[}\textbf{ToDo: Partners}{]} A RESTful web service to document
conversion will accept any 14 supported input file formats as input, and
provide HTML5 or JATS XML as output. This includes document conversion
and a native desktop-based application for proofing.

\emph{Automated Screening Tool}

\begin{quote}
\begin{quote}
\emph{Flag manuscripts with certain characteristics similar to
manuscripts that have not passed screening. Initially, include factors
that may include single authorship, presence of keywords, lack of
scientific writing style, image style, lack of biological subject
matter, presence of human faces, etc.}
\end{quote}
\end{quote}

{[}\textbf{ToDo: COS}{]} As the corpus of preprints builds in a format
conducive to programmatic access (e.g., JATS), properties of the
preprints will be extracted and persisted. As submissions are determined
to be spam, non-scientific, etc., these properties will be associated
with the reason for disqualification. This data will be used to compare
incoming submissions as part of the submission pipeline, flagging for
human intervention distribution outliers and manuscripts similar to
those previously disqualified (compared using multiple metrics that can
be used in, e.g., random forest models and support vector machines). We
will ask peer preprint services for access to their screened-out
manuscripts, if they have license to share them for the corpus.

Early comparison data will come from metadata currently harvested by
SHARE and full-text collected for use in The Commons aggregated search
and machine-learning corpus. Heuristic and targeted identification will
flag submissions. Face recognition (e.g. OpenCV) will be run against
extracted figures to notify moderators of potential ethical violations.

Lee Giles (PSU; CiteSeerx) will consult for these tasks, especially for
advanced use-cases.

\emph{Use external services (like plagiarism detection) but ideally
develop a viable open source alternative in the long term.}

{[}\textbf{ToDo: COS}{]} Membership with Crossref supports using their
Similarity Check (powered by iThenticate) to flag suspected plagiarism.
Other screening tools will be made open-source, but, for plagiarism in
particular, the tool would require a corpus that is most likely
impractical to license from publishers compared to using a service like
Similarity Check, which has been pre-negotiated for members.

\emph{Provide service accessible by API}

{[}\textbf{ToDo: COS}{]} Pipelines created for screening will be
accessible by API.

\emph{The Commons Ingest Service}

\begin{quote}
\emph{Support the ingest of manuscripts from approved sources through an
API. Recognising that, potentially, some approved ingest sources may not
have an API to access their content, suppliers should indicate the
approach they would adopt to access and ingest this content.}
\end{quote}

\emph{}

{[}\textbf{Done: COS}{]} SHARE (\url{http://share.osf.io/}) harvests
bioRxiv and PeerJ and others via whatever means the service suggests or
legally allows; that will continue for content eligible as defined by
the GB. By the time the grant period begins, we expect that most
preprint services relevant to biomedicine will be harvested. Full-text
will be added to the harvesting process.

\par\null

\emph{Support the ingest of the authors' original manuscript file and
the converted manuscript in XML, appropriate metadata, and associated
files (figures and supplementary files) or links to these files if too
large or more appropriate for a domain-specific repository.}

{[}\textbf{ToDo: COS/Partners}{]} SHARE will incorporate ingestion of
full-text manuscripts, associated files, and links when they are
available and allowed by licensing and agreements with source providers.
This can also be applied to back-harvesting. With XML conversion tools,
we will also incorporate converted manuscripts when possible.

\emph{Support the ingest of required metadata including author
information (funding source, ORCID, etc as~specified by GB), screening
history, and manuscript transferrequest if applicable.}

{[}\textbf{Done: COS}{]} SHARE's metadata schema includes a variety of
standard fields for scholarly works, if they are available from the
source. For full documentation, see \url{http://share.osf.io/}.

{[}\textbf{ToDo: COS}{]} We will add metadata specified by the GB for
potential ingestion from approved sources.

\emph{Assign Crossref preprint DOIs to manuscript and associated
supplementary files, if not already provided by the ingestion source.}

{[}\textbf{Done: COS}{]} Users can manually request DOI's for
registrations. Automated minting of DOIs will be complete by June 2017.

{[}\textbf{ToDo: COS}{]} SHARE will incorporate assigning DOIs to
preprints and attached files upon submission if there is no existing
DOI.

\emph{The Commons Direct Submission Service}

\emph{Provide a direct Commons submission interface for human users.
Include converting author manuscripts to XML (with proofing) and collect
all applicable metadata.}

\par\null\selectlanguage{english}
\begin{figure}[h!]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/COS/COS}
\caption{{Overview of submission workflow
{\label{844961}}%
}}
\end{center}
\end{figure}



{[}\textbf{Done: COS}{]} The submission process is branded for each
service and efficiently captures key metadata. Figures 4 and 5
illustrate the submission workflow with SocArXiv branding.

\par\null\par\null\selectlanguage{english}
\begin{figure}[h!]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/figcos/figcos}
\caption{{Expansion of one component of the submission workflow.
{\label{809853}}%
}}
\end{center}
\end{figure}



{[}\textbf{ToDo: COS/Partners}{]} The GB might define additional
metadata requirements. These can be incorporated into the submission
workflow. For direct submissions, conversion to XML will occur at
submission.

\emph{Provide a human screening service for evaluating content entering
through this pathway. This must comply with Governance Body standards.}

{[}\textbf{Done: COS}{]} At present, human moderation of submissions is
completed manually. By July 2017, the administrative layer for
moderation will be in production.

{[}\textbf{ToDo: COS}{]} The GB may identify additional metadata
requirements in 7a. That metadata will be incorporated into the
administrative view for the moderation service.

\emph{Offer a Commons journal transfer system}

\emph{Initially, support FTP transfer}

\emph{Later interface with top five manuscript systems (Editorial
Manager, eJPress, ScholarOne, Highwire's BenchPress, Aptara PowerReview)
in use in life sciences journals with APIs.}

\emph{Upon request from author, transfer manuscript to journals.}

{[}\textbf{Done: Partners}{]} Manuscripts and Authorea provide export
mechanisms to other services such as Editorial Manager, eJournalPress,
Medium, WordPress, Atom Publishing Protocol.

{[}\textbf{ToDo: Partners}{]} Export mechanisms can be added, but these
depend on the availability of appropriate APIs and potential licensing
costs imposed by those providers.

\emph{Communication and Marketing}

\emph{The above services should be promoted to the community of users
(life scientists, developers, funders and institutions, etc) in order to
increase awareness and adoption.}

See Section \#8. (page 23)

\emph{Other proposed functionality for The Commons (from Preprint
Commons: Human Interface 2c.)}

{[}\textbf{Done: COS}{]} The following are some additional features
available to the The Commons that are already in production:

\begin{itemize}
\tightlist
\item
  File organizing interface
\item
  Versioning of preprints
\item
  Infrastructure scalability for high concurrency
\item
  Integration of preprint with the research lifecycle
\item
  Living projects with private and public components linked to the
  preprint for ongoing deposit and management of data, code, and other
  research activities
\item
  Enriched permissions system for authors
\item
  Notifications for authors/users
\item
  Download files as a zip from the project
\item
  View-only links for sharing private parts of the project linked to
  others -- e.g., making private data and code available for peer review
  when the preprint is submitted
\item
  Institutional login (150+ institutions by start of grant period)
\item
  Sharing preprint and files on social media
\item
  Activity logs for preprint project history
\item
  SPAM detection
\item
  Google Scholar optimization
\item
  Automated citation generation with multiple formats
\item
  API integration with data storage solutions and repositories (e.g.,
  direct surfacing of data and figures stored on figshare with the
  hosted preprint)
\end{itemize}

{[}\textbf{ToDo: COS}{]} The OSF scholarly commons is in continuous
development. The development priorities for this public goods
infrastructure is in COS's Strategic Plan. Because of the modular
design, improvements benefit all services using it.

\emph{Provide a timeline for implementation elaborating or modifying the
one proposed in}
\href{https://docs.google.com/document/d/1hUYTxY0E83GEoDgg3wDW-cYdIde00Bid4dcskECw1F0/edit\#heading=h.nl0cbzt8jlcv}{\emph{Staging}}\emph{.}

\emph{The following timeline for implementation is copied and adapted
from the RFA. We accelerate the timeline to reflect what is already
completed and in production
(}\href{http://osf.io/preprints/}{\emph{http://osf.io/preprints/}}\emph{)
to Stage 0.}

Stage 0 = {[}\textbf{Accelerated from ASAPbio's 6 month milestone to 0
month milestone}{]} Milestones to be completed on the project start date
or whatever date the ASAPbio GB is ready for launch.

\begin{itemize}
\tightlist
\item
  Launch of The Commons, populated by legacy preprints from approved
  sources in their original formats (.pdf, .doc, .html, .xml etc.).
\item
  New manuscripts can enter the database by The Commons ingest service.
\item
  Ingest service collects required metadata (what metadata is required
  can be updated following determination by the Governing Board).
\item
  The ingest service can collect all associated files (supplementary
  figures, data, movies, etc) and assigns DOIs.
\item
  The Commons offers a web interface for browsing and searching
  manuscripts.
\item
  The Commons renders ingested preprints in the browser supporting a
  wide variety of original formats.
\item
  Usage metrics shared openly.
\item
  \emph{{[}Accelerated from 18 month milestone{]}} API for machine
  access to preprint metadata is available.
\item
  Service can refer authors to appropriate external repositories if file
  size limits are exceeded.
\item
  {[}\emph{Additional feature}{]} Authors can integrate external
  repository with ingested preprint from variety of repositories (e.g.,
  figshare, dataverse)
\item
  {[}\emph{Additional feature}{]} Full co-author accounts and
  permissions integration to ingestion service. Adding unregistered
  co-authors. Unregistered author account claiming.
\item
  {[}\emph{Additional feature}{]} Updating preprints to newer version
\item
  {[}\emph{Additional feature}{]} Login via institution credentials
  (150+ institutions at start date)
\item
  {[}\emph{Additional feature}{]} Facilitate sharing of preprint via
  social media
\end{itemize}

Stage 1 = Milestones to be completed within 6 months of project start

\par\null

\begin{itemize}
\tightlist
\item
  Indexing of preprint files from other services for full-text search.
\item
  Commons search results display text that has been extracted from PDFs
  to show search terms in context. If preprints are displayed, they can
  be displayed as PDFs. All pages are tagged with schema.org meta tags
  to ensure that content is discoverable.
\item
  Ingestion sources are requested to provide all manuscripts regardless
  of whether they passed screening. While rejected manuscripts will not
  be displayed to users, they will be later used to train screening
  systems (possibly anonymized).
\item
  All preprints are accessible by bulk download.
\item
  Researchers are able to sign up for alert services to be notified by
  email (or RSS or Atom feed or other notification system) of new
  preprints relating to search terms of interest.
\item
  {[}\emph{Additional feature}{]} Initial release of conversion and
  editing system.
\end{itemize}

\par\null

Stage 2 = Milestones to be completed 18 months after project start

\begin{itemize}
\tightlist
\item
  Preprint conversion tool is operating. All newly received preprints
  are converted to XML. Older preprints for which a compatible authors'
  file is available will be converted as well.
\item
  API for machine access to full-text preprints is available.
\end{itemize}

\par\null

Stage 3 = Milestones to be completed 3 years after project start

\begin{itemize}
\tightlist
\item
  Automated manuscript screening system. Trained by the corpus of both
  accepted and rejected manuscripts submitted to the Preprints Commons,
  this tool will flag manuscripts that are likely to require careful
  human screening. Easy for ingestion sources to use, either locally or
  by API calls.
\end{itemize}

\emph{Describe how you would manage the submission and hosting (or
referrals to other databases) of large datasets (including a potential
ceiling).}

The Commons is an independent, branded interface using the OSF--a
scholarly commons for connecting, managing, and preserving the research
lifecycle. OSF provides data archiving and facilitates connections to
other storage providers. OSF presently offers no limits on total storage
and 5GB upload limits per file. Continued availability of unlimited free
storage depends on growth in demand. We do not expect challenges with
storage demands of preprints. Whether there are storage limits or not,
users can easily connect to integrated storage solutions. We will work
with domain repositories to integrate with The Commons. Letters of
support are included from 15 services.

\section*{Sustainability plan (up to 500
words)}

{\label{507082}}

\emph{ASAPbio will request funding for 5 years. Full or partial funding
may be available on the longer term, but bidders should describe
sustainable business models that would be compatible with their
organization(s) and with the principles of the Central Service. These
might include submission fees or fee-for-service arrangements. In our
view, unfavorable business models include those where the provider of
the service may have a conflict of interest in providing support for
preprints as a public good. The Sustainability Plan is provisional and
does not commit the bidder(s), ASAPbio, or the Governance Body to
execute the plan provided in this RFA.}

The Commons, as designed and executed by COS, will be a free,
open-source service. The initial creation and scaling of the service
will require the most capital investment. We expect that this period of
support will be funded by grants and philanthropic contributions. There
is opportunity for significant savings from economies of scale with
COS's advanced, layered, and composable infrastructure. Nevertheless,
public goods infrastructure must confront the reality of sustainability.

COS is developing a community-based funding and governance model that
will foster a sustainable public goods infrastructure. This model
applies to The Commons and all of the other use cases of the shared
infrastructure:

\begin{enumerate}
\tightlist
\item
  Transparent accounting of the costs to build and maintain all public
  goods services
\item
  A distributed financial responsibility model in which each community's
  responsibility is identified as the proportion of its use of the
  services using layered accounting of costs
\item
  When not violating donor privacy, transparent accounting of
  contributions to financial and operational sustainability by
  communities and stakeholders
\item
  Simple pricing and transparent accounting of funding shortfalls can
  facilitate stakeholder-wide problem-solving for the value of
  maintaining the public goods infrastructure. Like other public goods,
  ongoing investment reflects the community's valuation of the services.
\item
  Community-based governance to define strategic direction, maintain the
  services, and ensure sustainability of those services providing value
  meeting or exceeding their costs.
\end{enumerate}

A successful financial responsibility model must address the free rider
problem and organizational constraints on willingness and ability to
contribute. Developing, testing, and refining this concept will be an
iterative activity, and will follow from lessons learned by similar
efforts (e.g., arXiv). The RFA suggests that a sustainability plan
should be in effect after the five-year funding period. We expect to
initiate the transition to a distributed funding model immediately with
understanding that full testing and adoption is a multi-year effort.
Progress on the model and actual evidence for sustainability will be a
primary activity for COS and the technical partners, the Governing
Board, and for the funding community supporting The Commons.

\par\null

COS operates by key principles for advancing public goods. These
principles are part of the COS's \href{https://osf.io/x2w9h}{strategic
plan} and are relevant for sustainability. Public goods infrastructure
cannot be entrusted to a single organization. COS's sustainability
framework embraces community governance:

\begin{enumerate}
\tightlist
\item
  COS prioritizes reuse or connection to existing open tools and
  resources.
\item
  All COS-maintained tools and services are open-source and publicly
  available.
\item
  COS maintains terms of service, privacy, and security standards that
  are user-centered.
\item
  COS ensures that data accumulated through its services will remain
  accessible and avoid user lock-in.
\item
  COS operates as a community-based organization with inclusive
  representation.
\item
  COS tools and services should be maintained by an inclusive community
  of stakeholders.
\item
  COS members are dedicated to serving the mission over serving the
  interests of the organization.
\end{enumerate}

Lastly, as a provider of public goods, COS does not need to survive as
an organization for the services to survive for the community. All
products have open, liberal licenses. If COS disappears, other groups
can operate services that are still providing value for the community.

\section*{Communications, marketing, and maintenance (up to 1000
words)}

{\label{330101}}

\emph{Describe any relevant past experience in marketing. With reference
to other projects you have managed, describe how you promoted the
service to the main stakeholders. Also, highlight what marketing
strategies worked well, and what approaches were less successful.}

COS is a technology and culture change organization. COS's mission is to
increase openness integrity and reproducibility of research. It has
succeeded in a global communications campaign to shift interest toward
openness and reproducibility with media-intensive coverage of evidence
for the challenges of openness and reproducibility and promotion of
solutions such as \href{http://osf.io}{OSF}
\href{http://osf.io/preprints}{OSF Preprints} and
\href{http://osf.io/registries}{OSF Registries} for researchers and
\href{http://cos.io/top}{TOP Guidelines}
\href{https://osf.io/tvyxz/wiki}{badges for open practices} and
\href{http://cos.io/rr}{Registered Reports} products for journals
funders and institutions.

Example: In 2015 we published the results of our
\href{http://science.sciencemag.org/content/349/6251/aac4716}{Reproducibility
Project: Psychology} that highlighted challenges of reproducing a
substantial portion of 100 published findings in that field. Careful
planning helped manage a story prone to misunderstanding that was
covered globally in almost every major media outlet and market.
Ultimately this was named one of the biggest science stories of the
year. Our consistent messaging coupled the challenges of reproducibility
and the opportunity that openness provides for addressing those
challenges.

We have similar experience with our ongoing
\href{https://elife.elifesciences.org/collections/reproducibility-project-cancer-biology}{Reproducibility
Project: Cancer Biology} and with other initiatives highlighting the
challenges of openness and reproducibility and the solutions that OSF
preprints TOP Guidelines and other initiatives provide. The combination
of our mission research products and communications strategy has helped
COS become a prominent credible voice for open science. This leadership
position and communications strategy will easily integrate efforts to
advance The Commons via well-known marketing mechanisms.

\textbf{Earned Media:} Our community team press contacts and influencer
channels provide means of spreading thought leadership case studies and
referral campaigns. COS's status as a mission-driven non-profit driving
research culture-change and technology initiatives provides
\href{https://cos.io/about/news/}{unusually strong access} to
high-viewership science (e.g. Nature Science) and general media outlets
(e.g. NY Times WaPo Atlantic 538).

\textbf{Shared Media} : Inexpensive, transactional,
conversational--shared media has been a primary driver of growth in COS
traffic, user base, customer service responsiveness, and consumption of
COS content. With shared media, we react quickly to customer needs and
changing conditions. We also use social platforms to drive referrals via
our Ambassador program, an international group of researchers that
amplify our marketing efforts in their communities.

\textbf{Owned Media:} Training content marketing events and email are
some of our more successful growth strategies. We provide
\href{https://cos.io/our-services/training-services/}{OSF training
webinars and onsite workshops} throughout the community several times
per month. These have immediate transactional impact are easy to measure
and adjust and are relatively inexpensive. Thought leadership in the
form of papers infographics and case studies can be married with
specific calls to action. Our \href{https://cos.io/blog}{blog} features
case studies tips for using our products to increase research efficiency
and open science news. Finally because COS is partly an academic
research organization it has unusual access to leading or participating
in scholarly meetings and giving academic lectures and symposia (STM NAS
AAMC AAAS NIH NSF DARPA disciplinary meetings).

\textbf{Paid Media} : Paid media supports transactional product
marketing and lead generation tactics such as e-commerce. On its own, we
have found that it takes multiple touches using paid media to get
results. Searches tend to be more about short-term needs and specific
product or service requirements. In the context of The Commons, we
expect that paid media will be effective as a complement to a
community-based effort promoting awareness and support for preprints.

\emph{Describe your marketing strategy for The Commons.}

The norms in research are determined within the community itself.
Research communities resist external, commercial influence. We operate
as a community-based culture change agent. Our strategy includes:

\textbf{Science news media.} COS will leverage its leadership position
in open science to identify and promote preprints as a solution that
accelerates and improves openness of research. For example, this
solution will be present explicitly or implicitly in coverage of its
metascience efforts, and culture change engagements.

\begin{enumerate}
\tightlist
\item
  \href{http://cos.io/news/}{Science news media}. COS will leverage its
  leadership position in open science to identify and promote preprints
  as a solution that accelerates and improves openness of research. For
  example this solution will be present explicitly or implicitly in
  coverage of its metascience efforts and culture change engagements.
\item
  \textbf{Community Network.} We will grow and empower the active
  community supporting preprints in the life sciences and provide them
  with content, resources, and opportunities to engage their colleagues.
  For example, we will support and participate in symposia at small and
  large substance area conferences, write and support blog and society
  newsletter stories, grow the ambassador program and support
  researchers' outreach to local and discipline colleagues. With our
  rapidly expanding social network of leaders and influencers in
  biomedicine, we will activate relevant societies, institutions,
  funders and individuals that have credibility in the community and
  whose vocal support is critical for broad adoption.
\item
  \textbf{Social Media.} Preprint adoption can be promoted
  ``naturalistically'' via sharing of preprints on social media and
  thought leadership from community members.
\item
  \textbf{Paid Media}. Paid media will be used alongside the high
  credibility, community marketing to guide researchers toward The
  Commons for discovery and deposit of their research.
\end{enumerate}

\emph{Describe any relevant past experience in enforcing content
standards in a database. Describe how records violating agreed-upon
standards were removed and after what decision processes.}

\emph{OSF has legal and ethical responsibilities for its role as a data
repository for private or public storage. COS and users'
responsibilities are articulated in OSF's}
\href{https://github.com/CenterForOpenScience/cos.io/blob/master/TERMS_OF_USE.md}{\emph{Terms
of Service}} \emph{and}
\href{https://github.com/CenterForOpenScience/cos.io/blob/master/PRIVACY_POLICY.md}{\emph{Privacy
Policy}}\selectlanguage{ngerman}\emph{. For addressing copyright violations OSF operates in
accordance with the Digital Millennium Copyright Act (17 USC § 512).
Notifications of claimed copyright infringement are sent to COS's
Designated Agent and claims are evaluated and documented promptly in
accordance with those legal requirements including rapid triage
temporarily blocking access removing content and occasionally engaging
legal counsel for review. Following the full investigation the
Designated Agent documents the process and resolution and informs
relevant parties. The terms of use also clarify conditions under which
COS may remove unlawful or offensive items.}

\emph{Describe your strategy for removing or flagging content in the
Central Service that violates guidelines set forth by the Governance
Body. These are yet to be determined, but will likely include dual use
research, plagiarised work, or papers with ethically questionable
content.}

Our service administration team will review submissions according to the
guidelines defined by the GB. This will complement automated services
such as Crossref's plagiarism detection service. Key issues will be
moderated prior to preprint posting, and post-moderation will be
possible based on reporting by users or other identification of
questionable content. OSF already offers a withdrawal mechanism for
inappropriate content. The service administration team will scale as
demand for The Commons increases to assure reliable, timely service.

\section*{}

{\label{452594}}

\section*{Budget (spreadsheet and up to 1000 word
justification)}

{\label{452594}}

\emph{Provide a detailed annual project budget for 5 years of operation
in a spreadsheet assuming the schedule of growth listed in}
\href{https://docs.google.com/document/d/1hUYTxY0E83GEoDgg3wDW-cYdIde00Bid4dcskECw1F0/edit\#heading=h.26hvdlo96pqp}{\emph{Expected
manuscript volumes}}\emph{. Provide a written justification of this
budget in less than 1000 words.}

\emph{}

Cost estimates presume continuing feature development of The Commons for
the five-year grant period. If the GB reduces feature development
requests and transitions service toward maintenance of the existing
feature set, then the budget for development staff would be renegotiated
yearly to reflect actual development needs. Likewise, budget estimates
for storage and use are based on the growth estimates provided in the
ASAPbio RFA. As a non-profit, mission-driven organization, COS is
committed to providing and maintaining The Commons at cost and will
employ transparent accounting for reporting and negotiating yearly
support. The same approach will guide transition to a distributed
sustaining finance model.

\textbf{COS}

\textbf{Product development and maintenance} : COS's primary roles are
the technical development of the preprints repository, aggregation
service (SHARE), submission workflow, user and administrator interfaces,
integrations with data repositories and other services, and service
administration. This will be accomplished with a substantial investment
of personnel across the infrastructure team. Management/team leads will
devote 2 person months each. Infrastructure staffing includes Product
with team lead and 1 FTE product manager; Labs with CTO and 1 FTE
developer for exploration, prototyping, and architecture; Engineering
with Technical Lead and Senior Project Manager and 6 FTE developers for
SHARE (2), service and repository integrations (1), Preprint services
(2), add-ons/service integrations (1) and 1 FTE designer and a 0.33 FTE
technical evangelist for service and repository integrations; QA with QA
Lead with 1 FTE QA Associate for automated, manual, and regression
testing.

\par\null

Technical partner resourcing will be administered through COS. A 0.67
FTE developer and 0.5 FTE senior test engineer will provide key
deliverables of conversion tool set. Professional and consulting fees
are also reserved for specialized support or mini-awards to external
groups and individual freelance developers that offer relevant expertise
and open-source services, and for nominal awards to biomedical data
repositories to facilitate API integrations. We include a yearly expert
group meeting for planning and co-development of conversion and
screening tools.

\par\null

\textbf{Marketing and community engagement} : COS will lead marketing
initiatives for The Commons and collaborate with other stakeholders on
community development. This includes participation and promotion at
society meetings and conferences; partnership development with service
providers, societies, funders, institutions, and journals; webinars and
education campaigns; and execution on the marketing strategy.
Management/team leads will devote 2 person months each. Community
staffing includes the community manager with support from 1 FTE
community relations specialist, and the marketing manager with support
from 1 FTE marketing specialist. Travel resources for 24 trips per year
will support marketing and community engagement at society and relevant
service meetings, and bringing key partners together for collaboration.
Substantial resources are identified to support specific marketing
activities for earned, shared, owned, and paid media. This budget can be
adjusted if responsibilities for marketing will be shared with ASAPbio.
Details of budget estimates for each activity appear as a budget
appendix.

\par\null

\textbf{Sustainability} : COS will lead development and implementation
of a sustainability model. Work on establishing the sustainability model
and transitioning to a fully distributed stakeholder funding model will
begin immediately so The Commons can transition smoothly to the new
model after the grant period. Sustainability staffing includes the
Funder and Donor Relations lead with support from a grants specialist
and 1 FTE sustainability account manager. This team will work with the
GB and other stakeholders on the definition and strategic plan for the
sustainability model, and the execution of that model with
supporters/institutions.

\par\null

\textbf{Organizational leadership, operations, and events} : COS
operational staff will ensure the efficient execution of the grant,
organizational policies, finances, HR, and hosting of events. Two person
months of support per year are identified for the Director of Operations
and accounting, grants administration, bookkeeper, and events support
staff. Also, COS's Executive Director will devote 2 person months to
supporting internal product vision, strategy, and execution and external
community engagement and collaboration.

\par\null

\textbf{Hosting} : Hosting costs are expected to grow during the five
year project period. There is potential for substantial variability in
hosting costs depending on the extent to which authors attach data to
preprints. We generated two total cost estimates: (1) 5mb (0.0049gB)
average per preprint - assumes occasional storage beyond the preprint,
and (2) 0.19gB average per preprint - current average OSF project size.
Our proposed budget uses the smaller estimate applied to ASAPbio's
provided projections and can be revisited after year 1.

\par\null

\textbf{Screening} : Estimates based on ASAPbio's provided usage
projections for Similarity Check through Crossref.

\par\null

\textbf{Service administration, support, helpdesk:} Service
administration will be supervised by a combination of the community and
product team leads. The service administrators will be responsible for
rapid review and support of The Commons user community. The budget
anticipates yearly growth in the staffing necessary for maintaining
timely and efficient service administration beginning with 2 FTEs.
Future needs will depend on rate of growth and effectiveness of
automated screening tools.

\par\null

\textbf{Other direct expenses} : Other direct expenses include computer
purchases (8 per year assuming replacement once every 3 years), software
licenses and internal data back-ups, 10 Salesforce licenses for the
community, marketing, and funding teams, and 3 Desk.com licenses for the
helpdesk.

\par\null

\textbf{Facilities and administrative expenses} : Feedback from ASAPbio
organizers suggested that there should be no F\&A/indirect costs, and
instead all costs itemized in the budget. The budget includes a portion
of COS's costs for organizational items including rent, parking,
facilities maintenance, furniture, supplies, internet, operational
services, legal consulting, depreciation, and accounting/payroll fees.

\emph{Please list costs associated with Component 8, the CS direct
submission service, in a separate section, as its implementation (and
timing thereof) will be decided by the Governance Body in consideration
of the productive development of the preprint ecosystem.}

The direct submission service is already in production, so has no costs
or necessary time lag for initial implementation. The GB will decide
whether and when to offer direct submission. If the GB requires
additional features for the submission service prior to service launch,
then there will be some direct costs and time associated with
development. Based on the requirements described in the RFA, it is
unlikely that costs directly associated with ASAPbio's minimal viable
product requirements for submission only would exceed \$150,000.

\emph{Estimate the cost per gigabyte for hosting figures, videos, large
datasets, etc.}

Storage: \$0.03/GB; Bandwidth (Egress): \$0.12/GB

\section*{References (up to 5 names)}

{\label{186828}}

\emph{Provide the names, titles, and email addresses of up to 5
unassociated individuals (who have not been employed by your
organization(s) in the past 3 years) who could be contacted with regard
to the ability of your organization(s) to execute the work described in
this proposal.}

\textbf{References}

Philip Bourne Director, Data Science Institute, University of
Virginia,~\href{mailto:peb6a@virginia.edu}{\nolinkurl{peb6a@virginia.edu}}~

Stuart Buck VP of Research
Integrity,~\href{mailto:sbuck@arnoldfoundation.org}{\nolinkurl{sbuck@arnoldfoundation.org}}~Laura
and John Arnold Foundation

Philip Cohen Professor, University of
Maryland,~\href{mailto:pnc@umd.edu}{\nolinkurl{pnc@umd.edu}}~Director,
SocArXiv

Marcia McNutt President, National Academy of
Sciences,~\href{mailto:MMcNutt@nas.edu}{\nolinkurl{MMcNutt@nas.edu}}~

Bodo Stern Chief Development and Strategy Officer
\href{mailto:sternb@hhmi.org}{\nolinkurl{sternb@hhmi.org}}~ Howard
Hughes Medical Institute

\textbf{Letters of support}

Attached are 32 letters of support for this proposal from a variety of
preprint services (12) data repositories in biomedicine or allied fields
(15) and other stakeholder organizations (5). Note that NIH staff cannot
write letters of support. Nevertheless we expect to work with
NIH-administered repositories (e.g. NDAR RGR PubChem GenBank dbGaP).
Supporting services and organizations include:

Data Repositories

\href{http://www.rcsb.org/pdb/home/home.do}{Protein Data Bank}

\href{http://www.rcsb.org/pdb/home/home.do}{}\href{http://childes.talkbank.org/}{TalkBank}

\href{http://childes.talkbank.org/}{}\href{https://www.niagads.org/}{NIAGADS}

\href{http://neuromorpho.org/}{NeuroMorpho}

\href{http://www.icpsr.umich.edu/icpsrweb/content/NAHDAP/staff.html}{NAHDAP}

\href{http://www.icpsr.umich.edu/icpsrweb/content/NAHDAP/staff.html}{}\href{https://www.icpsr.umich.edu/icpsrweb/}{ICPSR}

\href{http://figshare.com}{Figshare}

\href{http://flybase.org/}{Flybase}

\href{http://phenome.jax.org/}{Mouse}\href{http://phenome.jax.org/}{Phenome
Database}

\href{http://datadryad.org/}{Dryad}

\href{https://dataverse.harvard.edu/}{Dataverse}

\href{https://dataverse.harvard.edu/}{}\href{http://protocols.io/}{Protocols}

\href{https://www.synapse.org/}{Sage Bionetworks (Synapse)}

\href{https://www.vectorbase.org/}{VectorBase}

\href{https://www.vectorbase.org/}{}\href{http://dip.doe-mbi.ucla.edu/dip/Main.cgi}{DIP}

Preprint Services

\href{https://twitter.com/paleorxiv?lang=en}{PaleorXiv}

\href{https://twitter.com/paleorxiv?lang=en}{}\href{https://www.maregroup.org/}{MarXiv}

\href{https://www.maregroup.org/}{}\href{https://osf.io/preprints/bitss}{BITSS}

\href{http://socarxiv.org/}{SocArXiv}

\href{https://www.mindandlife.org/}{MindrXiv}

\href{http://scielo.org/}{SciELO}

\href{http://psyarxiv.org/}{PsyArXiv}

\href{http://agrixiv.org/}{AgriXiv}

\href{http://arxiv.org/}{arXiv}

\href{http://engrxiv.org/}{engrXiv}

\href{http://biorxiv.org/}{bioRxiv}

\href{https://www.fusfoundation.org/}{Focused Ultrasound}

Other Stakeholders

\href{http://arl.org/}{Association of Research Libraries}

\href{http://arl.org/}{}\href{http://www.hhmi.org/}{Howard Hughes
Medical Institute}

\href{http://www.electrochem.org/}{Electrochemical Society}

\href{https://www.healthra.org/}{Health Research Alliance}

\href{https://www.gbsi.org/}{Global Biological Standards Institute}

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