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COMBINE Archive Specification Version 1

Frank T. Bergmann, Nicolas Rodriguez, Nicolas Le Novère
2015 Journal of Integrative Bioinformatics  
), OMEX is the basis of the COMBINE Archive.  ...  The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type.  ...  Since the COMBINE archive is in general less specified, future convergences will be easy to implement 35 once agreed upon. 20list in 2009, and briefly described in SED-ML Level 1 Version 1(Waltemath et  ... 
doi:10.1515/jib-2015-261 fatcat:735lll2xlfa5zbvm7eoruv2n6y

COMBINE Archive Specification Version 1

Frank T Bergmann, Nicolas Rodriguez, Nicolas Le Novère
2015 Journal of Integrative Bioinformatics  
Together with the other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive.  ...  The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type.  ...  Since the COMBINE archive is in general less specified, future convergences will be easy to implement 35 once agreed upon. 20list in 2009, and briefly described in SED-ML Level 1 Version 1(Waltemath et  ... 
doi:10.2390/biecoll-jib-2015-261 pmid:26528559 fatcat:hpqz5ix5enenljdh2mywiym2wu

Specifications of standards in systems and synthetic biology: status and developments in 2021

Falk Schreiber, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath
2021 Journal of Integrative Bioinformatics  
Language Level 1 Version 4, and OMEX Metadata specification Version 1.2.  ...  This document can also be consulted to identify the latest specifications of all COMBINE standards.  ...  Acknowledgements: We thank all members of the COMBINE initiative for their help. DPN is supported by the National Institutes of Health [P41EB023912].  ... 
doi:10.1515/jib-2021-0026 pmid:34674411 pmcid:PMC8573232 fatcat:abs7qckeyfdeddd4x5z6g54ape

One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project [article]

Frank T. Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro (+4 others)
2014 arXiv   pre-print
The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type.  ...  Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software.  ...  Available at http://lenoverelab.org/sites/default/files/documents/recon2-1-x.omex Figure 1 : 1 Schematic representation of the structure of a COMBINE Archive, a (possibly encrypted) zipped version of an  ... 
arXiv:1407.4992v2 fatcat:x2pn25x6rvdznfzgc7hlhip7aq

A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos

Martin Scharm, Dagmar Waltemath
2016 F1000Research  
How to cite this article: A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles 2016, :2421 (doi: in embryos [version 1; referees: 1 approved, 2 approved with reservations]  ...  Bergmann FT, Adams R, Moodie S, et al.: COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics. 2014; 15(1): 369.  ...  Acknowledgements We would like to thank Vasundra Touré for her help with creating the SBGN-compliant visualisations of the model and Matthias König for running and testing the archive in Tellurium.  ... 
doi:10.12688/f1000research.9379.1 pmid:27830063 pmcid:PMC5082596 fatcat:mrrmaxj7w5fqtp3hwneheihynq

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

Frank T Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K Miller, David P Nickerson, Brett G Olivier, Nicolas Rodriguez (+6 others)
2014 BMC Bioinformatics  
The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type.  ...  Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software.  ...  requirements: none License: non-applicable Any restrictions to use by non-academics: none Figure 1 1 Schematic representation of the structure of a COMBINE Archive, a (possibly encrypted) zipped version  ... 
doi:10.1186/s12859-014-0369-z pmid:25494900 pmcid:PMC4272562 fatcat:3dqofrgqz5f2dlivtikejgyonu

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017

Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath
2018 Journal of Integrative Bioinformatics  
This paper provides an overview of existing COMBINE standards and presents developments of the last year.  ...  The regular special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards by providing unified, easily citable access.  ...  , Version 2 [12] • SBML Level 3 Package: Hierarchical Model Composition, Version 1 [13] • SBML Level 3 Package: Qualitative Models, Version 1 [14] • SBML Level 3 Package: Layout, Version 1 [15]  ... 
doi:10.1515/jib-2018-0013 pmid:29596055 fatcat:prdywukrwzfitieltnzlu7rzj4

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016

Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath
2016 Journal of Integrative Bioinformatics  
This special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access  ...  , Version 2 [12] • SBML Level 3 Package: Hierarchical Model Composition, Version 1 [13] • SBML Level 3 Package: Qualitative Models, Version 1 [14] • SBML Level 3 Package: Layout, Version 1 [15]  ...  The current specification is SED-ML Level 1 Version 2 [18] . CellML, to store and exchange reusable, modular computer-based mathematical models [19] .  ... 
doi:10.1515/jib-2016-289 fatcat:6dtmkxiz3jejvf3lrzjdjscxtu

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019

Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath
2019 Journal of Integrative Bioinformatics  
The articles in this issue contain updated specifications of SBGN Process Description Level 1 Version 2, SBML Level 3 Core Version 2 Release 2, SBOL Version 2.3.0, and SBOL Visual Version 2.1.  ...  This special issue of the Journal of Integrative Bioinformatics presents an overview of COMBINE standards and their latest specifications.  ...  These are: -COMBINE Archive [34] , specification is COMBINE Archive 1.0 [35] ; -Identifiers.org URIs [36] , community resources to provide persistent identification (no specification); -Systems Biology  ... 
doi:10.1515/jib-2019-0035 pmid:31301675 pmcid:PMC6798822 fatcat:rzfr2orbfjgwpfz4ei72tpi53i

Versioning for Linked Data: Archiving Systems and Benchmarks

Vassilis Papakonstantinou, Giorgos Flouris, Irini Fundulaki, Kostas Stefanidis, Giannis Roussakis
2016 International Semantic Web Conference  
The aim of this paper is to describe the way that such RDF archiving systems could be evaluated by presenting the different benchmarks in the literature, as long as the stateof-the-art archiving systems  ...  Our suggestion, which is a combination of them, is shown in Figure 1 . Firstly, queries are distinguished based on their focus, into version and delta queries.  ...  More specifically, each original resource (identified in memento terminology with URI-R) may have one or more mementoes (identified with URI-M i , i = 1, .., n) which are the archived representations of  ... 
dblp:conf/semweb/Papakonstantinou16 fatcat:ocqosfapdrgb3c6sliqblwibjy

On Designing Archiving Policies for Evolving RDF Datasets on the Web [chapter]

Kostas Stefanidis, Ioannis Chrysakis, Giorgos Flouris
2014 Lecture Notes in Computer Science  
This paper studies the trade-offs involved in these approaches, in the context of archiving dynamic RDF datasets over the Web.  ...  This is especially true for datasets stored in the Web, where the interlinking aspect, combined with the lack of central control, do not allow synchronized evolution of interlinked datasets.  ...  To do this, properties such as applicability, expressing whether a part of a version can be used for evaluating a specific query, and combining ability, expressing whether two parts of a version can be  ... 
doi:10.1007/978-3-319-12206-9_4 fatcat:65sqnfpr4bfs3amgoxkcgsjqgu

FAIR Digital Objects with Structured Trait Data in the GFBio Portal

Anton Link, Stefan Seifert, Tanja Weibulat, Wolfgang Reichert, Markus Weiss, Dagmar Triebel
2021 Zenodo  
A combination of EML metadata and research data in the XML-based TDWG approved standard SDD (Structured Descriptive Data) is appropriate to create well structured trait data (EML-SDD).  ...  Poster GFBio-04 from the GFBio General Assembly 2021 of "Work Package 2 - Data Submission, Ingest, Archiving & Publication" of the GFBio Project summarizing the projects and subtasks work and outcome between  ...  Xper3PI, TOWARDS SNSB LANDING PAGES Figure 1 : 1 Figure 1: Access to EML-SDD zip archives (use cases) via the GFBio Data Portal Figure 4 4 Figure 4 Loginto the GWDG Figure 4 : 4 Figure 4: DataCite  ... 
doi:10.5281/zenodo.5793759 fatcat:rtpskc4cbjhdzobjuieqitn234

BioSimulators: a central registry of simulation engines and services for recommending specific tools [article]

Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks (+59 others)
2022 arXiv   pre-print
The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML, and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards  ...  We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations.  ...  Briefly, BioSimulators-utils executes each simulation task in each SED-ML file in a COMBINE archive by (1) resolving the model for the task, (2) modifying the model according to the changes specified in  ... 
arXiv:2203.06732v1 fatcat:z3hje6q3lrapph7kigfwtqk3ai

OMEX metadata specification (version 1.2)

John H. Gennari, Matthias König, Goksel Misirli, Maxwell L. Neal, David P. Nickerson, Dagmar Waltemath
2021 Journal of Integrative Bioinformatics  
Distributing modeling projects within an OMEX archive is a best practice established by COMBINE, and the OMEX metadata specification presented here provides a harmonized, community-driven approach for  ...  This document details version 1.2 of the specification, which builds on version 1.0 published last year in this journal.  ...  Acknowledgements This specification has been developed with the valuable input of Daniel Cook, Jonathan Cooper, Andreas Dräger, Alan Garny, Nick Juty, Jonathan Karr, Chris Myers, and Herbert Sauro.  ... 
doi:10.1515/jib-2021-0020 pmid:34668356 pmcid:PMC8560343 fatcat:2rzioyl35vhb7aswcj4yarcr2q

Access Interfaces for Open Archival Information Systems based on the OAI-PMH and the OpenURL Framework for Context-Sensitive Services [article]

Jeroen Bekaert, Herbert Van de Sompel
2005 arXiv   pre-print
The proposed interfaces are based on the two formal specifications that have recently emerged from the Digital Library community: The Open Archive Initiative Protocol for Metadata Harvesting (OAI-PMH)  ...  In recent years, a variety of digital repository and archival systems have been developed and adopted.  ...  a single archive, several versions of specific Content Information may exist.  ... 
arXiv:cs/0509090v1 fatcat:yxe7glm535d4ndxuyttv7wngku
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