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Application form NWO – Open Science Fund – 2023
Section 1a – Details of the applicant
Name
Prof. dr. M.E. (Marcel) Visser
Affiliation – institution
Netherlands Institute of Ecology (NIOO - KNAW)
Affiliation – department
Department of Animal Ecology
Position
Head of Department
End date of contract
Permanent position
E-mail address
m.visser@nioo.knaw.nl
ORCID ID
https://orcid.org/0000-0002-1456-1939
Section 1b – Details of the team members
Name team member 1
Dr. A. (Antica) Culina
Affiliation
NIOO-KNAW and Ruder Boskovic Institute (Croatia)
E-mail address
a.culina@nioo.knaw.nl
ORCID ID
http://orcid.org/0000-0003-2910-8085
Name team member 2
Dr. S.J.G. (Stefan) Vriend
Affiliation
NIOO-KNAW
E-mail address
s.vriend@nioo.knaw.nl
ORCID ID
https://orcid.org/0000-0002-9006-5988
Name team member 3
Dr. J.B. (Joseph) Burant
Affiliation
NIOO-KNAW
E-mail address
j.burant@nioo.knaw.nl
ORCID ID
https://orcid.org/0000-0002-0713-3100
Section 2 - Public summary
English public summary
Increasing transparency and reproducibility are key objectives of Open Science. To support an open and
transparent research landscape, CoreBirds will link datasets, analytical codes, and publications resulting from
long-term studies of wild bird populations. We will build upon an already existing database and network of
researchers (SPI-Birds), and will create a library of peer-reviewed codes. This will greatly stimulate reuse of code,
enhance the transparency of scientific outputs and thereby broaden the potential user base of SPI-Birds. Once
implemented, this working model will encourage other research communities in the long tail of life sciences to
close their research life cycle.
Word count (max 100): 100
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Application form NWO – Open Science Fund – 2023
Dutch public summary
Open Science heeft als kerndoelen het verhogen van transparantie en reproduceerbaarheid van onderzoek. We
gaan hieraan met CoreBirds bijdragen door datasets, analytische codes en publicaties te integreren, waarbij we
langetermijnstudies van vogelpopulaties als onderzoeksveld gebruiken. Daarbij bouwen we voort op een al
bestaande database en netwerk van onderzoekers (SPI-Birds). Door het opzetten van een bibliotheek van
gepeerreviewde codes geven we een belangrijke impuls aan de herbruikbaarheid van code en de transparantie van
wetenschap, en verbreden we de SPI-Birds’ gebruikersgroep. We stimuleren hiermee ook andere
onderzoeksgemeenschappen in de ‘long tail’ van levenswetenschappen om hun onderzoekscyclus te sluiten.
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Section 3 – Project proposal
3.1 The details of proposal
Proposed project title
and acronym
CoreBirds: Connecting Open Research outputs in the Ecology of Birds
Project duration (in
months)
12 months
The project will
primarily address
Open platforms or tools
The project will
secondarily address
FAIR workflows and interoperability standards
Relevance for a specific
discipline
22.40.00 Ecology
22.60.00 Zoology
3.2 The vision for your project (Criterion: Alignment with the aim of the Call for proposals)
Vision
Closing the research life cycle by connecting different types of outputs (raw data, processed data, codes for data
processing and analysis, publications) is a central goal of Open Science, yet is rarely accomplished [1-2]. This is
especially the case in fields like ecology [3-4], in which long-term observational data have been collected and
analysed, often opportunistically and without coordination between researchers.
Our vision is to develop a FAIR and transparent research landscape of datasets, codes and publications that are
connected by digital identifiers and rich metadata. These aims will contribute to the reproducibility of scientific
findings, and allow accessible reuse of data and code by other researchers. While we base our work on a specific
community (see below), we will highlight the potential broader application of our standards and protocols by other
communities.
Our project will build upon the existing effort of SPI-Birds Network and Database (www.spibirds.org). SPI-Birds is a
global and growing network of long-term observational data on individually-marked breeding birds, and currently
includes data from 114 study sites across 25 countries, representing more than 200 populations of 33 different
species (Figure 1). The breadth of geographic areas and habitats offers enormous opportunities for examining how
birds exposed to diverse conditions respond to environmental stressors. However, the lack of (meta)data standards
and low code reproducibility slow scientific progress towards answering important research questions, such as
how species respond to climate change or disease outbreaks [5].
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Application form NWO – Open Science Fund – 2023
Figure 1. The current geographic range of SPI-Birds and examples of species coverage
Aims and alignment with the call
To achieve our vision of closing the research life cycle, we have two aims:
(1) Create a library of data processing and analytical codes, and implement a peer review process. These codes
will be fitted to existing SPI-Birds standardised data, ensuring that the codes themselves are also
standardised and applicable to any other SPI-Birds dataset.
(2) Broaden the range of active and potential SPI-Birds contributors and users by increasing metadata
interoperability and organising workshops on the use of SPI-Birds’ data and code libraries.
Such an open ecosystem of data and associated code meets the aim of the call by addressing the topics of
reproducibility and reusability of research, and integrating workflows for FAIR research outputs. It further
stimulates wider adoption of Open Science practices among researchers.
Open Science impact
Reusability of research software and code is gaining traction. CoreBirds will be at the forefront of initiatives to aid
these goals in ecology. Once implemented, CoreBirds will provide an example of how different research outputs
can be managed and integrated to contribute to more transparent and reproducible science, which may be
replicated by adjacent research communities.
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3.3 Project plan (Criterion: Feasibility of the project plan)
Activities and methods
The groundwork for CoreBirds is the SPI-Birds Network & Database, developed since 2019 and hosted by
NIOO-KNAW. SPI-Birds has already developed a common FAIR data standard for long-term bird studies collecting
individual-level data [6], recently updated to align with Darwin Core [7]. As a grassroots initiative with an existing
platform and established research community, SPI-Birds is well-positioned for this proposal, making it plausible
that we are able to move beyond the state of the art in Open Science.
To meet our first aim, we will conduct two tasks:
Task 1.1 Establish the code library
We will develop a library of data processing and analytical codes implemented in GitHub. The codes will be
documented, searchable and linked to datasets (hosted at SPI-Birds) and resulting publications. These codes will be
applied to standardised SPI-Birds data so workflows developed for one dataset can be used on others. The codes
will also be archived on Zenodo, ensuring referenceability through versioned DOIs. All codes will be annotated,
allowing clear understanding of all data processing and analytical steps. Initially, we will populate the library with
codes to answer several key questions in evolutionary ecology that are within the expertise of the team members.
After the library is set up, the user community can search, use, and extend existing codes, or submit new codes.
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Application form NWO – Open Science Fund – 2023
Task 1.2 Implement a code peer-review process
Codes submitted to the library will be peer-reviewed within the community. Initially, we will test and review codes
within the project team and a small number of users. Later, peer review will involve a larger community (as
showcased in the workshop).
Our second aim will be achieved in two tasks:
Task 2.1 Extend the metadata fields to incorporate information and links to a range of other ecological and
biological databases. Specifically, we will refine and expand metadata on environmental attributes, using both
user-provided data (e.g., vegetation) and automated import from external data sources (e.g., climate,
https://www.worldclim.org, or high-resolution land cover, https://land.copernicus.eu).
Task 2.2 Expand the user base by organising workshops on data and library use
The workshops will also highlight the potential application of our reproducible workflows in other research
communities. One suitable venue for a workshop is the semi-regular Hole-Nesting Birds meeting, which includes
many active and potential SPI-Birds contributors.
Figure 2. Overview of aims and tasks of CoreBirds
Dissemination
The code library will be openly available on GitHub. Project outcomes will be disseminated to the research
community through a methodological publication in a scientific journal, through presentation at a conference, and
via two workshops (task 2.2). The first workshop will be aimed at those working on similar data, within-community
reproducibility and code review. The second workshop will facilitate the use of the data and library by a larger
community. Project updates will be disseminated via social media and the existing SPI-Birds Newsletter (published
bi-annually).
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Application form NWO – Open Science Fund – 2023
Project timeline
Figure 3. Timeline of tasks and technical support employment
Word count (max 500): 496 words
3.4 Project roles and expertise (Criterion: Feasibility of the project plan)
We will address these tasks with an interdisciplinary team of ecologists, Open Science experts, and experts in data
science and computer science. The applicants include the co-founders of the SPI-Birds Network & Database (MEV,
AC, SJGV) and current SPI-Birds developer (SJGV). Team members are expert in various areas of ecology, including
population ecology (MEV, SJGV, JBB, [8]), evolutionary ecology (MEV, AC, [9]), seasonality (MEV, JBB, [10]), spatial
ecology (MEV, SJGV, [11]), as well as meta-science (AC, [12]), data management (AC, SJGV, JBB, [13]), and Open
Science practices (all). The experiences of the applicants in developing SPI-Birds standards, as well as their large
network of interdisciplinary collaborators, will be key to the success of this project.
We seek funding for a short-term contract position (see section 3.5) for someone with expertise in data
management and Open Science, including version control (Git/GitHub), reproducible reports (markdown/Quarto),
data integration, data standards, and metadata schema/ontologies. Together with the project team, this person
will build on the existing SPI-Birds data and metadata standards, as well as implement analytical codes that have
already been created for SPI-Birds data.
Before the position is filled, the team will acquire codes already developed for use on SPI-Birds data, so that the
technical support person has a set of codes to test and populate the library with. In addition, SJGV and JBB will
make an inventory of metadata attributes, so that the technical support person can directly implement them in
SPI-Birds’ metadata standard from the outset.
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3.5 Budget table
Type of costs
Short description
Costs in euros
Personnel
9-month technical support personnel (1.0 FTE)
€45.560
Dissemination
Organisation of two workshops for potential users
€3.500
Travel
Presenting at conferences in the Netherlands
€900
Total request from NWO
€49.960
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Application form NWO – Open Science Fund – 2023
3.6 Budget justification (Criterion: Feasibility of the project plan)
Personnel: We have allocated part of our budget to hire a technical support person on a 9-month contract position
on salary scale 10.1 (3.098 euro per month + employer costs), which is consistent with the anticipated educational
background (MSc or equivalent) and experience level. The calculation is based on the NWO’s formula for
calculating staff costs, and includes base monthly salary for the targeted pay scale (as of July 2022), holiday and
end-of-year bonuses, and mark-ups. Given the expertise and the hands-on involvement of the project team we
estimate that a 9-month position within the 12-month project duration will be sufficient for the technical support
person.
Dissemination: Estimate of costs associated with organising and hosting two workshops (one at NIOO-KNAW and
the second potentially in conjunction with a larger conference), including costs of audio/video equipment,
refreshments, and other materials. This budget item will also cover other knowledge mobilisation costs.
Travel: Estimates for travel and registration costs associated with presentation of the knowledge outputs at local
and/or national conferences. We anticipate that this budget will cover the costs of two national conferences.
Word count (max 200): 184 words
Section 4 – Open Science track record of the applicant
I am driving FAIR and Open Science practices in ecology in a number of ways. I have several publications on new
Open Science related methods and community standards (three papers in Nature Ecology & Evolution: [12,14,15]).
In my publications I have always strived to provide open access to data (I have deposited >40 datasets related to
my publications in data repositories). I am one of the founders of SPI-Birds (https://www.spibirds.org, [6]) for
which Antica Culina and I were awarded the “Dutch Data Incentive Prize for the Medical and Life Sciences” 2020 by
Research Data Netherlands. SPI-Birds makes data on long-term populations of individually-marked birds FAIR by
providing metadata on these studies and by building population-specific pipelines transforming datasets as stored
by data contributors into a standard format, greatly facilitating meta-analysis on a large set of studies [11,16].
Furthermore, I am the lead PI of LTER-LIFE (www.lter-life.nl), a FAIR and Open Research infrastructure that aims to
enable ecologists to create Digital Twins of entire ecosystems. Overall, I am well embedded in the Open Science
community and made contributions to the development of resources and tools, enabling ecologists to carry out
Open Science practices.
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Section 5 – Data management (Criterion: Feasibility of the project plan)
5.1 Will this project involve re-using existing research data?
Yes: Are there any constraints on its re-use?
The project will use the datasets already hosted at SPI-Birds. SPI-Birds is principally a metadata hub and currently
does not serve as a primary data repository for most of the relevant data. As a result, data reuse depends on the
data contributor who hosts the original data. However, an increasing number of data contributors has been making
their data open thanks to continuous efforts and education provided by the applicants of this proposal. In its
development stage, the CoreBirds will use the subset of the datasets that are either open or for which permission
for use has been obtained from the data contributors (among those seven datasets managed by the applicant’s
institution NIOO-KNAW). Data contributors retain custody of the data and, following the SPI-Birds Data Access
Policy, “data user[s] agree not to redistribute original data and documentation without permission from the
[originator]”. As the founders and maintainers of SPI-Birds, we do not anticipate any difficulties in accessing data
for this project. Data contributors will be invited as full collaborators on any outputs that include their data.
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Application form NWO – Open Science Fund – 2023
5.2 Will data be collected or generated that are suitable for reuse?
No: Please elaborate
This proposal is focused on the reuse of existing long-term data that have been collected and made suitable for
reuse under FAIR principles, and does not generate new data per se. Any derivative datasets (e.g., summary
information, analytical outputs), as well as any data used in the analyses underlying scientific outputs will, when
possible, be shared in their entirety. Data will be archived in open access data repositories (e.g., Zenodo) and
referenced in the corresponding output. Data sharing will always comply with the SPI-Birds Data Access Policy. To
ensure reproducibility, any code or other scripts produced for extracting, processing, and analysing the data will
always be shared in an openly accessible format and linked with the archived datasets.
5.3 After the project has been completed, how will the data be stored for the long-term and made available for the
use by third parties? Are there possible restrictions to data sharing or embargo reasons? Please state these here.
Datasets have already been collected and made FAIR via SPI-Birds Network and Database. Data are hosted at
NIOO-KNAW and backed up daily. Datasets are either stored under open licence, or they can be requested by
potential users. In the latter case, the request is sent to the data contributor who can set conditions to data use. So
far, all the requests for data use have been approved. All metadata are open, and thus all populations can be
found, and their access options are clearly stated.
5.4 Will any costs (financial and time) related to data management and sharing/preservation be incurred?
No: All the necessary resources (financial and time) to store and prepare data for sharing/preservation are or will
be available at no extra cost.
Section 6 – Software sustainability (Criterion: Feasibility of the project plan)
6.1 Will software be generated during the project?
Yes: Please answer questions 6.2, 6.3, 6.4 and 6.5
6.2 How will the software be licensed and be made available for re-use?
Data processing and analytical codes will be available in our library on GitHub and archived on Zenodo under the
Creative Commons Attribution 4.0 International licence (CC BY 4.0;
https://creativecommons.org/licenses/by/4.0/).
6.3 What measures are needed to make the software appropriate for long-term (re-)use by third parties?
The library requires a moderator who i) handles the submission of new codes and new versions of codes, ii)
searches for experts to peer review submissions and updates, and iii) checks whether codes require an update
when dependencies (e.g., software packages) have been modified. Within CoreBirds these tasks will be under the
responsibility of the technical support person (to be hired). In the long term, the SPI-Birds team of coordinators
and developers that currently manage SPI-Birds Network and Database will take over this role.
6.4 How large do you expect the community that will potentially use the software to be, and do you expect outside
contributors to the software?
The data hosted at SPI-Birds has a long history in facilitating large collaborations and comparative analyses in
ecology and evolution. Now embodied as the SPI-Birds Network, we envision that this group of researchers will
capitalise on the development of a library of standardised data processing and analytical codes, which lowers the
threshold to take up extensive collaborative scientific projects even more. This community also has a strong
foothold in developing new theories and mathematical models, tested using the rich data they collect, which we
anticipate being submitted to the code library. Further, the large number of records of individual birds make
SPI-Birds Database a rich source of intraspecific biodiversity, a currently underdeveloped and generally
underappreciated dimension of biodiversity. As SPI-Birds continues to grow, especially geographically and
taxonomically, we expect biodiversity and conservation scientists also among the wide range of users of the code
library.
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Application form NWO – Open Science Fund – 2023
6.5 What expertise do you expect to be needed to make the software appropriate for long-term re-use by third
parties? Is this expertise available?
We expect that the bulk of codes submitted to the library will be developed in R, which is the leading coding
language used by researchers in ecology. As the codes will be submitted and peer reviewed by members of the
user community themselves, we envision that the accessibility and adaptability of the codes is safeguarded. In
addition, we will encourage users to provide feedback, communicate bugs in codes and/or submit code revisions
through GitHub’s issue feature and other resources [3]. At the same time, the SPI-Birds team will moderate the
library and call for code updates, e.g., when dependencies are updated.
Section 7 – Literature references
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Akker, A. van't Veer, and R. Zurita-Milla, (2021) Towards wide-scale adoption of open science practices: the role of
open science communities, Science and Public Policy 48, 605-611, DOI: 10.1093/scipol/scab039
[2] D.G.E. Gomes, P. Pottier, R. Crystal-Ornelas, E. J. Hudgins, V. Foroughirad, L.L. Sánchez-Reyes, R. Turba, P.A.
Martinez, D. Moreau, M.G. Bertram, C.A. Smout, and K.M. Gaynor, (2022) Why don't we share data and code?
Perceived barriers and benefits to public archiving practices, Proceedings of the Royal Society B 289, 20221113,
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Foroughirad, F. Hillemann, A.D. Binley, C.B. Brookson, K.M. Gaynor, S.S. Sabet, A. Güncan, H. Weierbach, D.G.E.
Gomes, and R. Crystal-Ornelas, (2023) Not just for programmers: How GitHub can accelerate collaborative and
reproducible research in ecology and evolution, Methods in Ecology and Evolution, DOI: 10.1111/2041-210X.14108
[4] T. Poisot, A. Bruneau, A. Gonzalez, D. Gravel, and P Peres-Neto, (2019) Ecological data should not be so hard to
find and reuse, Trends in Ecology & Evolution 34, 494-496, DOI: 10.1016/j.tree.2019.04.005
[5] V. Radchuk, T. Reed, C. Teplitsky, M. van de Pol, A. Charmantier, C. Hassall, P. Adamík, F. Adriaensen, M.P. Ahola,
P. Arcese, J.M. Avilés, J. Balbontin, K.S. Berg, A. Borras, S. Burthe, J. Clobert, N. Dehnhard, F. de Lope, A.A. Dhondt,
N.J. Dingemanse, H. Doi, T. Eeva, J. Fickel, I. Filella, F. Fossøy, A.E. Goodenough, S.J.G. Hall, B. Hansson, M. Harris, D.
Hasselquist, T. Hickler, J. Joshi, H. Kharouba, J.G. Martínez, J.-B. Mihoub, J.A. Mills, M. Molina-Morales, A. Moksnes,
A. Ozgul, D. Parejo, P. Pilard, M. Poisbleau, F. Rousset, M.-O. Rödel, D. Scott, J.C. Senar, C. Stefanescu, B.G. Stokke, T.
Kusano, M. Tarka, C.E. Tarwater, K. Thonicke, J. Thorley, A. Wilting, P. Tryjanowski, J. Merilä, B.C. Sheldon, A.P.
Møller, E. Matthysen, F. Janzen, F.S. Dobson, M.E. Visser, S.R. Beissinger, A. Courtiol, and S. Kramer-Schadt, (2019)
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studies: the SPI-Birds data hub, Journal of Animal Ecology 90, 2147-2160, DOI: 10.1111/1365-2656.13388
[7] J. Wieczorek, D. Bloom, R. Guralnick, S. Blum, M. Döring, R. Giovanni, T. Robertson, and D. Vieglais, (2012),
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[8] M. Gamelon, S.J.G. Vriend, S. Engen, F. Adriaensen, A.A. Dhondt, S.R. Evans, E. Matthysen, B.C. Sheldon, and
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dependence improves predictions of fluctuations in population size, Ecology Letters 22, 797-806, DOI:
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[11] S.J.G. Vriend, V. Grøtan, M. Gamelon, F. Adriaensen, M.P. Ahola, E. Álvarez, L.D. Bailey, E. Barba, J.-C. Bouvier,
M.D. Burgess, A. Bushuev, C. Camacho, D. Canal, A. Charmantier, E.F. Cole, C.Cusimano, B.F. Doligez, S.M. Drobniak,
A. Dubiec, M. Eens, T.Eeva, K.E. Erikstad, P.N. Ferns, A.E. Goodenough, I.R. Hartley, S.A. Hinsley, E. Ivankina, R.
Juškaitis, B. Kempenaers, A.B. Kerimov, J.A. Kålås, C. Lavigne, A. Leivits, M.C. Mainwaring, J. Martínez-Padilla, E.
Matthysen, K. van Oers, M. Orell, R. Pinxten, T.K. Reiertsen, S. Rytkönen, J.C. Senar, B.C. Sheldon, A. Sorace, J.
Török, E. Vatka, M.E. Visser, and B.-E. Sæther, (2022) Temperature synchronizes temporal variation in laying dates
across European hole-nesting passerines, Ecology 104, e3908, DOI: 10.1002/ecy.3908
[12] A. Culina, T. Crowther, J.J.C. Ramakers, P. Gienapp, and M.E. Visser, (2018) Use of the open data in
evolutionary ecology: how to do meta-analysis of open datasets, Nature Ecology & Evolution 2, 1053-1056, DOI:
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Application form NWO – Open Science Fund – 2023
10.1038/S41559-018-0579-2
[13] E.K. Bledsoe, J.B. Burant, G.T. Higino, D.G. Roche, S.A. Binning, K. Finlay, J. Pither, L.S. Pollock, J.M. Sunday, and
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[16] L.D. Bailey, M. van de Pol, F. Adriaensen, A. Arct, E. Barba, P.E. Bellamy, S. Bonamour, J.-C. Bouvier, M.D.
Burgess, A. Charmantier, C. Cusimano, B. Doligez, S.M. Drobniak, A. Dubiec, M. Eens, T. Eeva, P.N. Ferns, A.E.
Goodenough, I.R. Hartley, S.A. Hinsley, E. Ivankina, R. Juškaitis, B. Kempenaers, A.B. Kerimov, C. Lavigne, A. Leivits,
M.C. Mainwaring, E. Matthysen, J.-Å. Nilsson, M. Orell, S. Rytkönen, J.C. Senar, B.C. Sheldon, A. Sorace, M.J.
Stenning, J. Török, K. van Oers, E. Vatka, S.J.G. Vriend, and M.E. Visser, (2022) Bird populations most exposed to
climate change are less sensitive to climatic variation, Nature Communications 13, 2112, DOI:
10.1038/s41467-022-29635-4
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Application form NWO – Open Science Fund – 2023
By submitting this form, I declare that:
I and all the individuals involved in this proposals satisfy the nationally and internationally accepted standards for
scientific conduct as stated in the Netherlands Code of Conduct for Research Integrity (The Universities of the
Netherlands): Yes
The research organisation has been informed of this grant application and the research organisation accepts the grant
conditions of this programme: Yes
The team members named in this form have read and agreed with the submission of this proposal and have agreed
with their role and intended contribution to the project, should this be awarded: Yes
I have completed this application form truthfully: Yes
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