{"entity": "researcher", "timestamp": "2026-08-22T07:48:03.944Z", "family": "Bouarroudj", "given": "Lisa", "initials": "L", "orcid": "0009-0001-1177-7873", "affiliations": ["Universit\u00e9 Paris Cit\u00e9, CNRS, Institut Jacques Monod"], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/456c7e6a80d741fd8ab75b3758bf3004.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/456c7e6a80d741fd8ab75b3758bf3004"}}, "publications": [{"entity": "publication", "iuid": "56dee80846884efcbe03c9d07b714ad0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/56dee80846884efcbe03c9d07b714ad0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/56dee80846884efcbe03c9d07b714ad0"}}, "title": "MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations", "authors": [{"family": "Tiemann", "given": "Johanna K S", "initials": "JKS", "orcid": "0000-0001-7551-6245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2f12eb57ed14a91b3df667fe4b022c2.json"}}, {"family": "Szczuka", "given": "Magdalena", "initials": "M", "orcid": "0009-0001-8044-540X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5740340dc2b346bba6d437834f642fab.json"}}, {"family": "Bouarroudj", "given": "Lisa", "initials": "L", "orcid": "0009-0001-1177-7873", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/456c7e6a80d741fd8ab75b3758bf3004.json"}}, {"family": "Oussaren", "given": "Mohamed", "initials": "M", "orcid": "0009-0003-8309-2157", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22d02bd66230462ca0dbe78d2400469c.json"}}, {"family": "Garcia", "given": "Steven", "initials": "S", "orcid": "0009-0000-1155-930X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74ca241e099d4434b1ceb1dd0bed3233.json"}}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ", "orcid": "0000-0003-2049-3378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce04593b5b24aaa8978fda1447dd0bf.json"}}, {"family": "Delemotte", "given": "Lucie", "initials": "L", "orcid": "0000-0002-0828-3899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87eaf619d7bd487ebdbe68c46b827e66.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}, {"family": "Baaden", "given": "Marc", "initials": "M", "orcid": "0000-0001-6472-0486", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc9b18f15c5a47abb66bd9fb90effe9c.json"}}, {"family": "Lindorff-Larsen", "given": "Kresten", "initials": "K", "orcid": "0000-0002-4750-6039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cd1f0559c6d4d58a1459dd38f851c93.json"}}, {"family": "Chavent", "given": "Matthieu", "initials": "M", "orcid": "0000-0003-4524-4773", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e5e4d37f7184fd8969c4af58a8565ef.json"}}, {"family": "Poulain", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4177-3619", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e45351bd8b9412dac4ec451fa16c201.json"}}], "type": "posted-content", "published": "2024-07-01", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.90061.2", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:55:44.502Z", "modified": "2026-08-20T13:55:44.611Z"}, {"entity": "publication", "iuid": "f4877a69c72044ba8c47ba778924e318", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f4877a69c72044ba8c47ba778924e318.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f4877a69c72044ba8c47ba778924e318"}}, "title": "Author response: MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations", "authors": [{"family": "Tiemann", "given": "Johanna K S", "initials": "JKS", "orcid": "0000-0001-7551-6245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2f12eb57ed14a91b3df667fe4b022c2.json"}}, {"family": "Szczuka", "given": "Magdalena", "initials": "M", "orcid": "0009-0001-8044-540X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5740340dc2b346bba6d437834f642fab.json"}}, {"family": "Bouarroudj", "given": "Lisa", "initials": "L", "orcid": "0009-0001-1177-7873", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/456c7e6a80d741fd8ab75b3758bf3004.json"}}, {"family": "Oussaren", "given": "Mohamed", "initials": "M", "orcid": "0009-0003-8309-2157", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22d02bd66230462ca0dbe78d2400469c.json"}}, {"family": "Garcia", "given": "Steven", "initials": "S", "orcid": "0009-0000-1155-930X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74ca241e099d4434b1ceb1dd0bed3233.json"}}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ", "orcid": "0000-0003-2049-3378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce04593b5b24aaa8978fda1447dd0bf.json"}}, {"family": "Delemotte", "given": "Lucie", "initials": "L", "orcid": "0000-0002-0828-3899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87eaf619d7bd487ebdbe68c46b827e66.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}, {"family": "Baaden", "given": "Marc", "initials": "M", "orcid": "0000-0001-6472-0486", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc9b18f15c5a47abb66bd9fb90effe9c.json"}}, {"family": "Lindorff-Larsen", "given": "Kresten", "initials": "K", "orcid": "0000-0002-4750-6039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cd1f0559c6d4d58a1459dd38f851c93.json"}}, {"family": "Chavent", "given": "Matthieu", "initials": "M", "orcid": "0000-0003-4524-4773", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e5e4d37f7184fd8969c4af58a8565ef.json"}}, {"family": "Poulain", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4177-3619", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e45351bd8b9412dac4ec451fa16c201.json"}}], "type": "peer-review", "published": "2024-07-01", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.90061.2.sa4", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:55:46.445Z", "modified": "2026-08-20T13:55:46.525Z"}, {"entity": "publication", "iuid": "96d4789a51954c96a8389faa7efa0fb6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/96d4789a51954c96a8389faa7efa0fb6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/96d4789a51954c96a8389faa7efa0fb6"}}, "title": "MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations.", "authors": [{"family": "Tiemann", "given": "Johanna K S", "initials": "JKS", "orcid": "0000-0001-7551-6245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2f12eb57ed14a91b3df667fe4b022c2.json"}}, {"family": "Szczuka", "given": "Magdalena", "initials": "M", "orcid": "0009-0001-8044-540X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5740340dc2b346bba6d437834f642fab.json"}}, {"family": "Bouarroudj", "given": "Lisa", "initials": "L", "orcid": "0009-0001-1177-7873", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/456c7e6a80d741fd8ab75b3758bf3004.json"}}, {"family": "Oussaren", "given": "Mohamed", "initials": "M", "orcid": "0009-0003-8309-2157", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22d02bd66230462ca0dbe78d2400469c.json"}}, {"family": "Garcia", "given": "Steven", "initials": "S", "orcid": "0009-0000-1155-930X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74ca241e099d4434b1ceb1dd0bed3233.json"}}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ", "orcid": "0000-0003-2049-3378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce04593b5b24aaa8978fda1447dd0bf.json"}}, {"family": "Delemotte", "given": "Lucie", "initials": "L", "orcid": "0000-0002-0828-3899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87eaf619d7bd487ebdbe68c46b827e66.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}, {"family": "Baaden", "given": "Marc", "initials": "M", "orcid": "0000-0001-6472-0486", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc9b18f15c5a47abb66bd9fb90effe9c.json"}}, {"family": "Lindorff-Larsen", "given": "Kresten", "initials": "K", "orcid": "0000-0002-4750-6039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cd1f0559c6d4d58a1459dd38f851c93.json"}}, {"family": "Chavent", "given": "Matthieu", "initials": "M", "orcid": "0000-0003-4524-4773", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e5e4d37f7184fd8969c4af58a8565ef.json"}}, {"family": "Poulain", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4177-3619", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e45351bd8b9412dac4ec451fa16c201.json"}}], "type": "preprint", "published": "2024-05-03", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "The rise of open science and the absence of a global dedicated data repository for molecular dynamics (MD) simulations has led to the accumulation of MD \ufb01les in generalist data repositories, constituting the dark matter of MD - data that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found and indexed about 250,000 \ufb01les and 2,000 datasets from Zenodo, Figshare and Open Science Framework. With a focus on \ufb01les produced by the Gromacs MD software, we illustrate the potential offered by the mining of publicly available MD data. We identi\ufb01ed systems with speci\ufb01c molecular composition and were able to characterize essential parameters of MD simulation such as temperature and simulation length, and could identify model resolution, such as all-atom and coarse-grain. Based on this analysis, we inferred metadata to propose a search engine prototype to explore the MD data. To continue in this direction, we call on the community to pursue the effort of sharing MD data, and to report and standardize metadata to reuse this valuable matter.", "doi": "10.1101/2023.05.02.538537", "pmid": "37205542", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10187166"}, {"db": "pii", "key": "2023.05.02.538537"}], "notes": [], "created": "2026-08-21T09:29:08.109Z", "modified": "2026-08-21T09:29:08.202Z"}, {"entity": "publication", "iuid": "68fe85342766477891596af2b588e5c6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/68fe85342766477891596af2b588e5c6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/68fe85342766477891596af2b588e5c6"}}, "title": "MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations", "authors": [{"family": "Tiemann", "given": "Johanna K S", "initials": "JKS", "orcid": "0000-0001-7551-6245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2f12eb57ed14a91b3df667fe4b022c2.json"}}, {"family": "Szczuka", "given": "Magdalena", "initials": "M", "orcid": "0009-0001-8044-540X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5740340dc2b346bba6d437834f642fab.json"}}, {"family": "Bouarroudj", "given": "Lisa", "initials": "L", "orcid": "0009-0001-1177-7873", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/456c7e6a80d741fd8ab75b3758bf3004.json"}}, {"family": "Oussaren", "given": "Mohamed", "initials": "M", "orcid": "0009-0003-8309-2157", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22d02bd66230462ca0dbe78d2400469c.json"}}, {"family": "Garcia", "given": "Steven", "initials": "S", "orcid": "0009-0000-1155-930X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74ca241e099d4434b1ceb1dd0bed3233.json"}}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ", "orcid": "0000-0003-2049-3378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce04593b5b24aaa8978fda1447dd0bf.json"}}, {"family": "Delemotte", "given": "Lucie", "initials": "L", "orcid": "0000-0002-0828-3899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87eaf619d7bd487ebdbe68c46b827e66.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}, {"family": "Baaden", "given": "Marc", "initials": "M", "orcid": "0000-0001-6472-0486", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc9b18f15c5a47abb66bd9fb90effe9c.json"}}, {"family": "Lindorff-Larsen", "given": "Kresten", "initials": "K", "orcid": "0000-0002-4750-6039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cd1f0559c6d4d58a1459dd38f851c93.json"}}, {"family": "Chavent", "given": "Matthieu", "initials": "M", "orcid": "0000-0003-4524-4773", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e5e4d37f7184fd8969c4af58a8565ef.json"}}, {"family": "Poulain", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4177-3619", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e45351bd8b9412dac4ec451fa16c201.json"}}], "type": "posted-content", "published": "2023-09-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.90061.1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:55:42.485Z", "modified": "2026-08-20T13:55:42.757Z"}]}