{ "access": { "embargo": { "active": false, "reason": null }, "files": "public", "record": "public", "status": "open" }, "created": "2017-10-06T20:41:45.851829+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "files": { "count": 2, "enabled": true, "entries": { "Report.pdf": { "checksum": "md5:07b990dbc7ea6a21c549966fb24d870d", "ext": "pdf", "id": "9830e141-6ddd-4ca4-b5db-688db2e716e0", "key": "Report.pdf", "metadata": null, "mimetype": "application/pdf", "size": 131564 }, "Supplementary tables.xlsx": { "checksum": "md5:c91e02d9517f77224f949913cb0f6224", "ext": "xlsx", "id": "0125dbfd-745f-44a6-b1f4-a6eade1a9bee", "key": "Supplementary tables.xlsx", "metadata": null, "mimetype": "application/octet-stream", "size": 17610 } }, "order": [], "total_bytes": 149174 }, "id": "1004135", "is_draft": false, "is_published": true, "links": { "access": "https://zenodo.org/api/records/1004135/access", "access_links": "https://zenodo.org/api/records/1004135/access/links", "access_request": "https://zenodo.org/api/records/1004135/access/request", "access_users": "https://zenodo.org/api/records/1004135/access/users", "archive": "https://zenodo.org/api/records/1004135/files-archive", "archive_media": "https://zenodo.org/api/records/1004135/media-files-archive", "communities": "https://zenodo.org/api/records/1004135/communities", "communities-suggestions": "https://zenodo.org/api/records/1004135/communities-suggestions", "doi": "https://doi.org/10.5281/zenodo.1004135", "draft": "https://zenodo.org/api/records/1004135/draft", "files": "https://zenodo.org/api/records/1004135/files", "latest": "https://zenodo.org/api/records/1004135/versions/latest", "latest_html": "https://zenodo.org/records/1004135/latest", "media_files": "https://zenodo.org/api/records/1004135/media-files", "parent": "https://zenodo.org/api/records/1004134", "parent_doi": "https://zenodo.org/doi/10.5281/zenodo.1004134", "parent_html": "https://zenodo.org/records/1004134", "requests": "https://zenodo.org/api/records/1004135/requests", "reserve_doi": "https://zenodo.org/api/records/1004135/draft/pids/doi", "self": "https://zenodo.org/api/records/1004135", "self_doi": "https://zenodo.org/doi/10.5281/zenodo.1004135", "self_html": "https://zenodo.org/records/1004135", "self_iiif_manifest": "https://zenodo.org/api/iiif/record:1004135/manifest", "self_iiif_sequence": "https://zenodo.org/api/iiif/record:1004135/sequence/default", "versions": "https://zenodo.org/api/records/1004135/versions" }, "media_files": { "count": 0, "enabled": false, "entries": {}, "order": [], "total_bytes": 0 }, "metadata": { "additional_descriptions": [ { "description": "The school was partly supported by ERASynBio award to JRK, LS, and MLS; Horizon 2020 award 634942 to LS; and National Science Foundation award 1649014 to JRK.", "type": { "id": "notes", "title": { "de": "Anmerkungen", "en": "Notes" } } } ], "creators": [ { "affiliations": [ { "name": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" } ], "person_or_org": { "family_name": "Karr", "given_name": "Jonathan R", "identifiers": [ { "identifier": "0000-0002-2605-5080", "scheme": "orcid" } ], "name": "Karr, Jonathan R", "type": "personal" } }, { "affiliations": [ { "name": "Centre for Genomic Regulation, Barcelona, Spain" } ], "person_or_org": { "family_name": "Lluch-Senar", "given_name": "Maria", "identifiers": [ { "identifier": "0000-0001-7568-4353", "scheme": "orcid" } ], "name": "Lluch-Senar, Maria", "type": "personal" } }, { "affiliations": [ { "name": "Centre for Genomic Regulation, Barcelona, Spain" } ], "person_or_org": { "family_name": "Serrano", "given_name": "Luis", "identifiers": [ { "identifier": "0000-0002-5276-1392", "scheme": "orcid" } ], "name": "Serrano, Luis", "type": "personal" } }, { "affiliations": [ { "name": "Centre for Genomic Regulation, Barcelona, Spain" } ], "person_or_org": { "family_name": "Kastelic", "given_name": "Damjana", "name": "Kastelic, Damjana", "type": "personal" } } ], "description": "
Whole-cell models that predict phenotype from genotype are needed to advance biology, bioengineering, and medicine. Achieving whole-cell models will require extensive collaboration among modelers, experimentalists, mathematicians, computer scientists, and software engineers. In September 2017, we organized the second Whole-Cell Modeling Summer School to continue to build a whole-cell community by training new researchers. The school created new whole-cell training materials; trained 18 students, postdoctoral scholars, and faculty; and generated ideas about how to better teach whole-cell modeling. To build a whole-cell modeling community, we plan to continue to organize schools, continue to improve these schools based on the lessons that we learned this year, and initiate an annual workshop and/or online seminar series to facilitate sustained discussion about whole-cell modeling.
", "funding": [ { "award": { "acronym": "MycoSynVac", "id": "00k4n6c32::634942", "identifiers": [ { "identifier": "https://cordis.europa.eu/projects/634942", "scheme": "url" } ], "number": "634942", "program": "H2020", "title": { "en": "Engineering of Mycoplasma pneumoniae as a broad-spectrum animal vaccine" } }, "funder": { "id": "00k4n6c32", "name": "European Commission" } }, { "award": { "id": "021nxhr62::1548123", "number": "1548123", "title": { "en": "ERASynBio: MiniCell - A Model-driven Approach to Minimal Cell Engineering" } }, "funder": { "id": "021nxhr62", "name": "National Science Foundation" } } ], "languages": [ { "id": "eng", "title": { "en": "English" } } ], "publication_date": "2017-10-05", "publisher": "Zenodo", "references": [ { "reference": "Tomita, M. Whole-cell simulation: a grand challenge of the 21st century. Trends Biotechnol 19, 205\u2013210 (2001)." }, { "reference": "Karr, J. R., Takahashi, K. & Funahashi, A. The principles of whole-cell modeling. Curr Opin Microbiol 27, 18\u201324 (2015)." }, { "reference": "Carrera, J. & Covert, M. W. Why build whole-cell models? Trends Cell Biol 25, 719\u2013722 (2015)." }, { "reference": "Karr, J. R. et al. A whole-cell computational model predicts phenotype from genotype. Cell 150, 389\u2013401 (2012)." }, { "reference": "Macklin, D. N., Ruggero, N. A. & Covert, M. W. The future of whole-cell modeling. Curr Opin Biotechnol 28, 111\u2013115 (2014)." }, { "reference": "Goldberg, A. P. et al. Emerging whole-cell modeling principles and methods. Curr Opin Biotechnol (In submission)." }, { "reference": "Szigeti, B et al. A blueprint for human whole-cell modeling. Curr Opin Syst Biol (In submis- sion)." }, { "reference": "Karr, J. R., Lluch-Senar, M, Serrano, L & Carrera, J. The 2016 Whole-Cell Modeling Summer School http://www.karrlab.org/static/doc/papers/Karr2016.pdf (2016)." }, { "reference": "Waltemath, D. et al. Toward community standards and software for whole-cell modeling. IEEE Trans Biomed Eng 63, 2007\u20132014 (2016)." }, { "reference": "Karr, J. R., Lluch-Senar, M, Serrano, L & Kastelic, D. 2017 Whole-Cell Modeling Summer School http://www.wholecell.org/school-2017 (2017)." }, { "reference": "Karr, J. R. & Goldberg, A. P. An introduction to whole-cell modeling http://intro-to-wc- modeling.readthedocs.io (2017)." }, { "reference": "European Molecular Biology Organization. Practical course funding http://www.embo.org/ funding-awards/courses-workshops/practical-courses (2017)." } ], "resource_type": { "id": "publication-report", "title": { "de": "Bericht", "en": "Report" } }, "rights": [ { "description": { "en": "The Creative Commons Attribution license allows re-distribution and re-use of a licensed work on the condition that the creator is appropriately credited." }, "icon": "cc-by-icon", "id": "cc-by-4.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/licenses/by/4.0/legalcode" }, "title": { "en": "Creative Commons Attribution 4.0 International" } } ], "subjects": [ { "subject": "systems biology" }, { "subject": "computational biology" }, { "subject": "dynamical modeling" }, { "subject": "cell biology" } ], "title": "The 2017 Whole-Cell Modeling Summer School" }, "parent": { "access": { "owned_by": { "user": 10581 } }, "communities": { "default": "0b38b9de-2850-4276-9828-7532c6348702", "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2016-02-19T01:07:35+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "0b38b9de-2850-4276-9828-7532c6348702", "links": {}, "metadata": { "curation_policy": "Any study using the IMP software can be deposited here.", "description": "Integrative modeling of proteins and their assemblies using disparate sources of experimental, theoretical, and statistical information, using the Integrative Modeling Platform (IMP) software.", "page": "", "title": "Integrative Modeling" }, "revision_id": 0, "slug": "integrativemodeling", "updated": "2016-08-25T07:52:53+00:00" } ], "ids": [ "0b38b9de-2850-4276-9828-7532c6348702" ] }, "id": "1004134", "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.1004134", "provider": "datacite" } } }, "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.1004135", "provider": "datacite" }, "oai": { "identifier": "oai:zenodo.org:1004135", "provider": "oai" } }, "revision_id": 6, "stats": { "all_versions": { "data_volume": 18711058.0, "downloads": 176, "unique_downloads": 170, "unique_views": 94, "views": 97 }, "this_version": { "data_volume": 18711058.0, "downloads": 176, "unique_downloads": 170, "unique_views": 94, "views": 97 } }, "status": "published", "updated": "2020-01-20T14:56:09.169385+00:00", "versions": { "index": 1, "is_latest": true } }