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| Lukas Buecherl | University of Colorado Boulder | In person <br/> COMBINE Archive, SBML, SBOL and SBOL Visual, SED-ML <br/>Genetic Design Automation |
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| Kevin Chen | University of Washington | In person <br/> BioPAX, CellML, COMBINE Archive, NeuroML, OMEX Metadata, SBML, SED-ML |
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| Rafael Costa | FCT-NOVA, NOVA School of Science and Technology | Remotely (virtually) <br/> COMBINE Archive, SBML |
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| Carissa Bleker | National Institute of Biology, Slovenia | COMBINE Archive, Multicellular modeling, SBGN, SBML, SED-ML, FROG, ELIXIR Systems Biology community |
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| Chris Evelo | Maastricht University, The Netherlands | BioPAX, SBGN, SBML, WikiPathways, ELIXIR's task on PBPK modelling and SBML conversions for that |
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| Francis Chemorion | University of Pompeu Fabra, InSilicoTrials Technologies | BioPAX, CellML, COMBINE Archive, Multicellular modeling, NeuroML, OMEX Metadata, SBGN, SBML, SBOL and SBOL Visual, SED-ML, PE-TAB, FROG, I am a phd student researching the management of clinical, biological and simulated data for uniform simulation workflows in the Disc4All project https://disc4all.upf.edu|
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| Gaoxiang(Gavin) Zhou | University of Pittsburgh, 4200 Fifth Ave, Pittsburgh PA 15260 | BioPAX, CellML, COMBINE Archive, SBML, SBOL and SBOL Visual, PE-TAB, Dish2.0 https://github.com/pitt-miskov-zivanov-lab/DiSH BioRECIPE https://github.com/pitt-miskov-zivanov-lab/BioRECIPE Model analysis in sensitivity etc |
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| Gaoxiang(Gavin) Zhou | University of Pittsburgh, 4200 Fifth Ave, Pittsburgh PA 15260 | BioPAX, CellML, COMBINE Archive, SBML, SBOL and SBOL Visual, PE-TAB, Dish2.0 https://github.com/pitt-miskov-zivanov-lab/ BioRECIPE https://github.com/pitt-miskov-zivanov-lab/BioRECIPE Model analysis in sensitivity etc |
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| Haomiao Luo | University of Pittsburgh | BioRECIPE, CAR T cell, DiSH, BioRECIPE, http://www.nmzlab.pitt.edu|
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| Herbert Sauro | University of Washington, Seattle, USA | COMBINE Archive, Multicellular modeling, OMEX Metadata, SBML, SED-ML |
| Luna Li | University of Washington | COMBINE Archive, Multicellular modeling, OMEX Metadata, SBML, SED-ML, FROG; Working at the Center for Reproducible Biomedical Modeling on standardizing and annotating models |
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| Adel Heydarabadipour | University of Washington | SBGN, SBML; Model Visualization |
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| Lucian Smith | University of Washington | COMBINE Archive, Multicellular modeling, OMEX Metadata, SBML, SED-ML, FROG; I work with the Center for Reproducible Biomomedical Modeling (https://reproduciblebiomodels.org/), particularly working on Tellurium, Roadrunner, and Antimony |
| Goksel Misirli | Keele University | Multicellular modeling, OMEX Metadata, SBML, SBOL and SBOL Visual |
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| Metehan Unal | Keele University | SBOL and SBOL Visual; I am a postdoctoral research associate at the School of Computer Science and Mathematics of Keele University. I am working on a BBSRC-funded project to create, visualise and validate biological designs. |
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| Felipe Xavier Buson | University of Bristol | SBOL and SBOL Visual |
description: Registration for the meeting is open and is free. Please register at the link below as soon as possible. This will help us plan the schedule and match your interests to the timing of the breakouts, etc. Note, only registered attendees will be sent information related to video conferencing links, etc.
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The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology, synthetic biology and related fields. HARMONY is a codefest-type meeting, with a focus on development of the standards, interoperability and infrastructure. There are generally not many general discussions or oral presentations during HARMONY; instead, the time is devoted to allowing hands-on hacking and interaction between people focused on practical development of software and standards.
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HARMONY 2021 will be an online only meeting similar to COMBINE 2020 (http://co.mbine.org/events/COMBINE_2020). Most of the day will be scheduled by the communities as breakouts. In addition, we will have some time each day for community discussion and wrap-ups of breakouts and advertisements for following breakouts.
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HARMONY 2021 will be an online only meeting similar to COMBINE 2020. Most of the day will be scheduled by the communities as breakouts. In addition, we will have some time each day for community discussion and wrap-ups of breakouts and advertisements for following breakouts.
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@@ -51,14 +51,14 @@ MIRIAM guidelines are composed of three parts: #Reference correspondence, #Attri
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* The referenced information should be described using a triplet {collection, identifier, qualifier}:
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* The annotation should be written as a Uniform Resource Identifier (URI).
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* The identifier should be considered within the context of the framework of the collection.
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* Collection namespace and identifier are be combined into a single URI, such as: https://identifiers.org/collection/identifier. For example: https://identifiers.org/uniprot/P62158.
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* Collection namespace and identifier are be combined into a single URI, such as: https://identifiers.org/collection/identifier. For example: https://identifiers.org/uniprot/P62158.
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* Qualifiers (optional) should refine the link between the model constituent and the piece of knowledge: “has a”, “is version of”, “is homolog to”, etc.
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* The standard set of valid URIs is agreed upon by the community. A database and the associated API (Web Services) have been developed at the EBI to provide the generation and interpretation of URIs.
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## MIRIAM URIs
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An important part of the MIRIAM guidelines consists of the controlled annotation of model components, based on Uniform Resource Identifiers (URIs). In order to support this task, a set of controlled URIs were created: MIRIAM URIs. These allowed the unique and unambiguous identification of a model component, in a stable and perennial manner. The #MIRIAM Registry and Identifiers.org system are a set of services and resources that provide support for generating, interpreting and resolving MIRIAM URIs.
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MIRIAM URIs are composed of two main parts: the first defines a namespace that particular 'entities of the same type' may occupy. This is called a collection. The second component precisely identifies a given entity within this collection, called a record. For example, 'https://identifiers.org/pubmed/16333295' is the MIRIAM URI that identifies the publication of the MIRIAM Standard within the PubMed data collection. Here, 'https://identifiers.org/pubmed' defines the collection (PubMed), and '16333295' precisely identifies the record within it.
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MIRIAM URIs are composed of two main parts: the first defines a namespace that particular 'entities of the same type' may occupy. This is called a collection. The second component precisely identifies a given entity within this collection, called a record. For example, https://identifiers.org/pubmed/16333295 is the MIRIAM URI that identifies the publication of the MIRIAM Standard within the PubMed data collection. Here, https://identifiers.org/pubmed defines the collection (PubMed), and '16333295' precisely identifies the record within it.
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## MIRIAM Registry and Identifiers.org
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In order to enable the interoperability of this annotation scheme, the community has to agree upon a set of recognised collections. The MIRIAM Registry is an online service created to catalogue these collections, their URIs and the corresponding physical URLs or resources, whether they are controlled vocabularies or databases.
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Le Novère N, Courtot M, Laibe C (2007)
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Adding semantics in kinetics models of biochemical pathways.
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Proceedings of the 2nd International Symposium on experimental standard conditions of enzyme characterizations, available at http://www.beilstein-institut.de/index.php?id=196
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Proceedings of the 2nd International Symposium on experimental standard conditions of enzyme characterizations
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Le Novère N., Finney A., Hucka M., Bhalla U., Campagne F., Collado-Vides J., Crampin E., Halstead M., Klipp E., Mendes P., Nielsen P., Sauro H., Shapiro B., Snoep J.L., Spence H.D., Wanner B.L. (2005)
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Minimum Information Requested In the Annotation of biochemical Models (MIRIAM)
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