Deliverables
This in accompaniment to the standard format developed in WP2, Task 2.4.
Release of a version of CellMissy that can import data from the public repositoryRelease of a version of CellMissy that can import data from the public repository.
Project progress report for Year 2Yearly progress report of the project.
Report on the structures and approaches set up for maintenance and updates to the standardsReport on the structures and approaches set up for maintenance and updates to the standards.
Release of standards compliant CellMissy versionThis version of CellMissy will comply to the standards version submitted for community review, and will have prototype submission functionality to the central repository.
Project progress report for Year 1Yearly progress report of the project.
Project progress report for Year 3Yearly progress report of the project.
Report on the two CMSO workshops and proceedings manuscripts in year 1Report on the two CMSO workshops and proceedings manuscripts in year 1.
Report on experimental procedures and multi-parameter analysis from tumor and immune cell models for computational multiscale analysisStandardized procedures and data sets from patient-derived tumor and immune cell models
Report on the development of meta-scale analysis algorithms
Report on the development of meta-scale analysis algorithms.
Report on the two CMSO workshops and proceedings manuscripts in year 3Report on the two CMSO workshops and proceedings manuscripts in year 3.
Support for the CMSO standards in IB’s relevant commercial softwareImplementation of the CMSO standards in IB’s relevant software tool(s).
Report on the maintenance and updates carried out on the standard, and the plans for further support beyond project endReport on the maintenance and updates carried out on the standard, and the plans for further support beyond project end.
Report on the two CMSO workshops and proceedings manuscripts in year 2Report on the two CMSO workshops and proceedings manuscripts in year 2.
Standardized, refined procedures and data sets from tumor and immune cell models for computational multi-scale analysisFirst release of the functional repository
The functionality included will be: a data storage and submission back-end with links to the UK image storage system, a user-oriented front-end that allows querying of the data, and retrieval of submitted data sets.
Creation of project websiteCreation of project website.
Release of a medical-oriented knowledgebaseRelease of a medical-oriented knowledgebase, built on the data in the public repository.
Release of an open semantic validation framework for MIACME compliance verificationRelease of an open semantic validation framework for MIACME compliance verification.
Implementation of automated MIACME compliance validationImplementation of automated MIACME compliance validation.
Report on the development of quality control algorithmsReport on the development of quality control algorithms.
Creation of the Cell Migration Standardization Organization (CMSO)This includes a description of the Steering Committee, working groups with Chair and Secretary, web site and mailing list, and approved community review process and Editor.
Requirements analysis for the cell migration repositoryRequirements analysis for the cell migration repository.
Report on the development of dedicated cell migration feature extraction algorithmsReport on the development of dedicated cell migration feature extraction algorithms.
Implementation of a discussion forum moduleImplementation of a discussion forum module.
Release of the standard format for cell migration dataThis will take place via registration in BioSharing, and submission of the data standard package (including formal standard format, example files, specification documentation, a CV term-mapping schema, and compatible software libraries) to the CMSO community review process.
Report on the creation of a CVThis includes the analysis and re-use of existing CVs, a community approved procedure for extension and maintenance of CV terms within CMSO, along with appointment of a CV Editor, and the creation of the first new, field-specific terms, either as additions to an existing CV, or in a newly created one.
Implementation of REST and BioMart servicesImplementation of REST and BioMart data access interfaces.
Release of the MIACME minimal reporting requirementsThis release will take place via registration in BioSharing, and submission of the finalized MIACME document to the CMSO community review process, including a checklist version to aid compliance verification.
Submission of the second position paperThis paper will describe the fully operational public data repository and its role in establishing an open data exchange ecosystem.
Submission of the first position paperThis paper will be related to the submission of all standards to the CMSO community review process.
Report on the development of multiscale analysis algorithms for complex multivariate dataReport on the development of multiscale analysis algorithms for complex multivariate data.
Publications
Author(s):
Gwendolien Sergeant, Lennart Martens, Marleen Van Troys, Paola Masuzzo
Published in:
Bioinformatics, 2018, ISSN 1367-4803
Publisher:
Oxford University Press
DOI:
10.1093/bioinformatics/bty634
Author(s):
Peter Friedl, Roberto Mayor
Published in:
Cold Spring Harbor Perspectives in Biology, Issue 9/4, 2017, Page(s) a029199, ISSN 1943-0264
Publisher:
Cold Spring Harbor Laboratory Press
DOI:
10.1101/cshperspect.a029199
Author(s):
Eleanor Williams, Josh Moore, Simon W Li, Gabriella Rustici, Aleksandra Tarkowska, Anatole Chessel, Simone Leo, Bálint Antal, Richard K Ferguson, Ugis Sarkans, Alvis Brazma, Rafael E Carazo Salas, Jason R Swedlow
Published in:
Nature Methods, Issue 14/8, 2017, Page(s) 775-781, ISSN 1548-7091
Publisher:
Nature Publishing Group
DOI:
10.1038/nmeth.4326
Author(s):
Xiaowei Gong, Yuliia Didan, John G Lock, Staffan Strömblad
Published in:
The EMBO Journal, Issue 37/17, 2018, Page(s) e98994, ISSN 0261-4189
Publisher:
Nature Publishing Group
DOI:
10.15252/embj.201898994
Author(s):
Whetzel, Patricia L; Overton, James A.; Phillip Lord; Yu Lin; Jennifer Fostel; Monnie McGee; Anita Bandrowski; Ryan Brinkman; Stoeckert, Christian J.; Chibucos, Marcus C.; Bjoern Peters; Helen Parkinson; Soldatova, Larisa N; James Malone; Taylor, Chris F; Mathias Brochhausen; Lister, Allyson L; Kevin Clancy; Philippe Rocca-Serra; Mark Jensen; Susanna-Assunta Sansone; Carlo Torniai; Michel Dumontie
Published in:
PLoS ONE, Issue 11, 2016, Page(s) p e0154556, ISSN 1932-6203
Publisher:
Public Library of Science
DOI:
10.1371/journal.pone.0154556
Author(s):
Jonathan P. Tennant, François Waldner, Damien C. Jacques, Paola Masuzzo, Lauren B. Collister, Chris. H. J. Hartgerink
Published in:
F1000Research, Issue 5, 2016, Page(s) 632, ISSN 2046-1402
Publisher:
F1000 Research Ltd.
DOI:
10.12688/f1000research.8460.1
Author(s):
Paola Masuzzo, Lynn Huyck, Aleksandra Simiczyjew, Christophe Ampe, Lennart Martens, Marleen Van Troys
Published in:
Scientific Reports, Issue 7, 2017, Page(s) 42383, ISSN 2045-2322
Publisher:
Nature Publishing Group
DOI:
10.1038/srep42383
Author(s):
Anika Klingberg, Anja Hasenberg, Isis Ludwig-Portugall, Anna Medyukhina, Linda Männ, Alexandra Brenzel, Daniel R. Engel, Marc Thilo Figge, Christian Kurts, Matthias Gunzer
Published in:
Journal of the American Society of Nephrology, Issue 28/2, 2017, Page(s) 452-459, ISSN 1046-6673
Publisher:
Lippincott Williams & Wilkins Ltd.
DOI:
10.1681/ASN.2016020232
Author(s):
Mark D. Wilkinson, Susanna-Assunta Sansone, Erik Schultes, Peter Doorn, Luiz Olavo Bonino da Silva Santos, Michel Dumontier
Published in:
Scientific Data, Issue 5/1, 2018, Page(s) 180118, ISSN 2052-4463
Publisher:
Springer Nature
DOI:
10.1038/sdata.2018.118
Author(s):
Alejandra N Gonzalez-Beltran, Paola Masuzzo, Christophe Ampe, Gert-Jan Bakker, Sébastien Besson, Robert H Eibl, Peter Friedl, Matthias Gunzer, Mark Kittisopikul, Sylvia E Le Dévédec, Simone Leo, Josh Moore, Yael Paran, Jaime Prilusky, Philippe Rocca-Serra, Philippe Roudot, Marc Schuster, Gwendolien Sergeant, Staffan Strömblad, Jason R Swedlow, Merijn van Erp, Marleen Van Troys, Assaf Zaritsk
Published in:
GigaScience, Issue 9/5, 2020, ISSN 2047-217X
Publisher:
Oxford University Press
DOI:
10.1093/gigascience/giaa041
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