Capture, dissemination and analysis of multiscale cell migration data for biological and clinical applications (MULTIMOT)

Resultado final

Release of software libraries for the standard format

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 repository

Release of a version of CellMissy that can import data from the public repository.

Project progress report for Year 2

Yearly progress report of the project.

Report on the structures and approaches set up for maintenance and updates to the standards

Report on the structures and approaches set up for maintenance and updates to the standards.

Release of standards compliant CellMissy version

This 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 1

Yearly progress report of the project.

Project progress report for Year 3

Yearly progress report of the project.

Report on the two CMSO workshops and proceedings manuscripts in year 1

Report 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 analysis
Standardized 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 3

Report on the two CMSO workshops and proceedings manuscripts in year 3.

Support for the CMSO standards in IB’s relevant commercial software

Implementation 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 end

Report 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 2

Report 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 analysis
First 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 website

Creation of project website.

Release of a medical-oriented knowledgebase

Release of a medical-oriented knowledgebase, built on the data in the public repository.

Release of an open semantic validation framework for MIACME compliance verification

Release of an open semantic validation framework for MIACME compliance verification.

Implementation of automated MIACME compliance validation

Implementation of automated MIACME compliance validation.

Report on the development of quality control algorithms

Report 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 repository

Requirements analysis for the cell migration repository.

Report on the development of dedicated cell migration feature extraction algorithms

Report on the development of dedicated cell migration feature extraction algorithms.

Implementation of a discussion forum module

Implementation of a discussion forum module.

Release of the standard format for cell migration data

This 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 CV

This 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 services

Implementation of REST and BioMart data access interfaces.

Release of the MIACME minimal reporting requirements

This 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 paper

This paper will describe the fully operational public data repository and its role in establishing an open data exchange ecosystem.

Submission of the first position paper

This 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 data

Report on the development of multiscale analysis algorithms for complex multivariate data.

Publicaciones

DoRes within CellMissy: dose-response analysis on cell migration and related data

Autores: Gwendolien Sergeant, Lennart Martens, Marleen Van Troys, Paola Masuzzo
Publicado en: Bioinformatics, 2018, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/bty634

Tuning Collective Cell Migration by Cell–Cell Junction Regulation

Autores: Peter Friedl, Roberto Mayor
Publicado en: Cold Spring Harbor Perspectives in Biology, Edición 9/4, 2017, Página(s) a029199, ISSN 1943-0264
Editor: Cold Spring Harbor Laboratory Press
DOI: 10.1101/cshperspect.a029199

Image Data Resource: a bioimage data integration and publication platform

Autores: 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
Publicado en: Nature Methods, Edición 14/8, 2017, Página(s) 775-781, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.1038/nmeth.4326

KIF13A‐regulated RhoB plasma membrane localization governs membrane blebbing and blebby amoeboid cell migration

Autores: Xiaowei Gong, Yuliia Didan, John G Lock, Staffan Strömblad
Publicado en: The EMBO Journal, Edición 37/17, 2018, Página(s) e98994, ISSN 0261-4189
Editor: Nature Publishing Group
DOI: 10.15252/embj.201898994

The ontology for biomedical investigations

Autores: 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
Publicado en: PLoS ONE, Edición 11, 2016, Página(s) p e0154556, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0154556

The academic, economic and societal impacts of Open Access: an evidence-based review

Autores: Jonathan P. Tennant, François Waldner, Damien C. Jacques, Paola Masuzzo, Lauren B. Collister, Chris. H. J. Hartgerink
Publicado en: F1000Research, Edición 5, 2016, Página(s) 632, ISSN 2046-1402
Editor: F1000 Research Ltd.
DOI: 10.12688/f1000research.8460.1

An end-to-end software solution for the analysis of high-throughput single-cell migration data

Autores: Paola Masuzzo, Lynn Huyck, Aleksandra Simiczyjew, Christophe Ampe, Lennart Martens, Marleen Van Troys
Publicado en: Scientific Reports, Edición 7, 2017, Página(s) 42383, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/srep42383

Fully Automated Evaluation of Total Glomerular Number and Capillary Tuft Size in Nephritic Kidneys Using Lightsheet Microscopy

Autores: Anika Klingberg, Anja Hasenberg, Isis Ludwig-Portugall, Anna Medyukhina, Linda Männ, Alexandra Brenzel, Daniel R. Engel, Marc Thilo Figge, Christian Kurts, Matthias Gunzer
Publicado en: Journal of the American Society of Nephrology, Edición 28/2, 2017, Página(s) 452-459, ISSN 1046-6673
Editor: Lippincott Williams & Wilkins Ltd.
DOI: 10.1681/ASN.2016020232

A design framework and exemplar metrics for FAIRness

Autores: Mark D. Wilkinson, Susanna-Assunta Sansone, Erik Schultes, Peter Doorn, Luiz Olavo Bonino da Silva Santos, Michel Dumontier
Publicado en: Scientific Data, Edición 5/1, 2018, Página(s) 180118, ISSN 2052-4463
Editor: Springer Nature
DOI: 10.1038/sdata.2018.118

Community standards for open cell migration data

Autores: 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
Publicado en: GigaScience, Edición 9/5, 2020, ISSN 2047-217X
Editor: Oxford University Press
DOI: 10.1093/gigascience/giaa041

Resultado final

Publicaciones

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