bolognese 2.0.1 → 2.7.0

data/spec/fixtures/datacite.json

@@ -1,89 +0,0 @@
-{
-  "id": "https://doi.org/10.5438/4k3m-nyvg",
-  "types": {
-    "resourceTypeGeneral": "Text",
-    "resourceType": "BlogPosting",
-    "schemaOrg": "ScholarlyArticle",
-    "citeproc": "article-journal",
-    "bibtex": "article",
-    "ris": "RPRT"
-  },
-  "doi": "10.5438/4k3m-nyvg",
-  "identifiers": [
-    {
-      "identifierType": "DOI",
-      "identifier": "https://doi.org/10.5438/4k3m-nyvg"
-    },
-    {
-      "identifierType": "Local accession number",
-      "identifier": "MS-49-3632-5083"
-    }
-  ],
-  "creators": [{
-    "type": "Person",
-    "id": "http://orcid.org/0000-0003-1419-2405",
-    "name": "Fenner, Martin",
-    "givenName": "Martin",
-    "familyName": "Fenner"
-  }],
-  "titles": [{
-    "title": "Eating your own Dog Food"
-  }],
-  "publisher": "DataCite",
-  "publicationYear": "2016",
-  "subjects": [
-    {
-      "subject": "datacite"
-    },
-    {
-      "subject": "doi"
-    },
-    {
-      "subject": "metadata"
-    }
-  ],
-  "dates": [
-    {
-      "dateType": "Created",
-      "date": "2016-12-20"
-    },
-    {
-      "dateType": "Issued",
-      "date": "2016-12-20"
-    },
-    {
-      "dateType": "Updated",
-      "date": "2016-12-20"
-    }
-  ],
-  "relatedIdentifiers": [
-    {
-      "relatedIdentifier": "10.5438/0000-00ss",
-      "relatedIdentifierType": "DOI",
-      "relationType": "IsPartOf"
-    },
-    {
-      "relatedIdentifier": "10.5438/0012",
-      "relatedIdentifierType": "DOI",
-      "relationType": "References"
-    },
-    {
-      "relatedIdentifier": "10.5438/55e5-t5c0",
-      "relatedIdentifierType": "DOI",
-      "relationType": "References"
-    }
-  ],
-  "version": "1.0",
-  "descriptions": [
-    {
-      "descriptionType": "SeriesInformation",
-      "description": "Volume(1) Series(3)"
-    },
-    {
-    "descriptionType": "Abstract",
-    "description": "Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for..."
-    }
-  ],
-  "schemaVersion": "http://datacite.org/schema/kernel-4",
-  "agency": "datacite"
-}

data/spec/fixtures/datacite.xml

@@ -1,40 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
-  <identifier identifierType="DOI">10.5438/4K3M-NYVG</identifier>
-  <creators>
-    <creator>
-      <creatorName>Fenner, Martin</creatorName>
-      <givenName>Martin</givenName>
-      <familyName>Fenner</familyName>
-      <nameIdentifier schemeURI="http://orcid.org/" nameIdentifierScheme="ORCID">0000-0003-1419-2405</nameIdentifier>
-    </creator>
-  </creators>
-  <titles>
-    <title>Eating your own Dog Food</title>
-  </titles>
-  <publisher>DataCite</publisher>
-  <publicationYear>2016</publicationYear>
-  <resourceType resourceTypeGeneral="Text">BlogPosting</resourceType>
-  <alternateIdentifiers>
-    <alternateIdentifier alternateIdentifierType="Local accession number">MS-49-3632-5083</alternateIdentifier>
-  </alternateIdentifiers>
-  <subjects>
-    <subject>datacite</subject>
-    <subject>doi</subject>
-    <subject>metadata</subject>
-  </subjects>
-  <dates>
-    <date dateType="Created">2016-12-20</date>
-    <date dateType="Issued">2016-12-20</date>
-    <date dateType="Updated">2016-12-20</date>
-  </dates>
-  <relatedIdentifiers>
-    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.5438/0012</relatedIdentifier>
-    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.5438/55E5-T5C0</relatedIdentifier>
-    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsPartOf">10.5438/0000-00SS</relatedIdentifier>
-  </relatedIdentifiers>
-  <version>1.0</version>
-  <descriptions>
-    <description descriptionType="Abstract">Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for...</description>
-  </descriptions>
-</resource>

data/spec/fixtures/datacite_dataset.xml

@@ -1,58 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<resource xmlns="http://datacite.org/schema/kernel-3" xmlns:dim="http://www.dspace.org/xmlns/dspace/dim" xmlns:dryad="http://purl.org/dryad/terms/" xmlns:dspace="http://www.dspace.org/xmlns/dspace/dim" xmlns:mets="http://www.loc.gov/METS/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd">
-  <identifier identifierType="DOI">10.5061/DRYAD.8515</identifier>
-  <version>1</version>
-  <creators>
-    <creator>
-      <creatorName>Ollomo, Benjamin</creatorName>
-    </creator>
-    <creator>
-      <creatorName>Durand, Patrick</creatorName>
-    </creator>
-    <creator>
-      <creatorName>Prugnolle, Franck</creatorName>
-    </creator>
-    <creator>
-      <creatorName>Douzery, Emmanuel J. P.</creatorName>
-    </creator>
-    <creator>
-      <creatorName>Arnathau, Céline</creatorName>
-    </creator>
-    <creator>
-      <creatorName>Nkoghe, Dieudonné</creatorName>
-    </creator>
-    <creator>
-      <creatorName>Leroy, Eric</creatorName>
-    </creator>
-    <creator>
-      <creatorName>Renaud, François</creatorName>
-    </creator>
-  </creators>
-  <titles>
-    <title>Data from: A new malaria agent in African hominids.</title>
-  </titles>
-  <publisher>Dryad Digital Repository</publisher>
-  <publicationYear>2011</publicationYear>
-  <subjects>
-    <subject>Phylogeny</subject>
-    <subject>Malaria</subject>
-    <subject>Parasites</subject>
-    <subject>Taxonomy</subject>
-    <subject>Mitochondrial genome</subject>
-    <subject>Africa</subject>
-    <subject>Plasmodium</subject>
-  </subjects>
-  <resourceType resourceTypeGeneral="Dataset">DataPackage</resourceType>
-  <alternateIdentifiers>
-    <alternateIdentifier alternateIdentifierType="citation">Ollomo B, Durand P, Prugnolle F, Douzery EJP, Arnathau C, Nkoghe D, Leroy E, Renaud F (2009) A new malaria agent in African hominids. PLoS Pathogens 5(5): e1000446.</alternateIdentifier>
-  </alternateIdentifiers>
-  <relatedIdentifiers>
-    <relatedIdentifier relatedIdentifierType="DOI" relationType="HasPart">10.5061/DRYAD.8515/1</relatedIdentifier>
-    <relatedIdentifier relatedIdentifierType="DOI" relationType="HasPart">10.5061/DRYAD.8515/2</relatedIdentifier>
-    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsReferencedBy">10.1371/JOURNAL.PPAT.1000446</relatedIdentifier>
-    <relatedIdentifier relatedIdentifierType="PMID" relationType="IsReferencedBy">19478877</relatedIdentifier>
-  </relatedIdentifiers>
-  <rightsList>
-    <rights rightsURI="http://creativecommons.org/publicdomain/zero/1.0/" />
-  </rightsList>
-</resource>

data/spec/fixtures/datacite_malformed_creator.xml

@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<resource xmlns="http://datacite.org/schema/kernel-4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
-  <identifier identifierType="DOI">10.25670/oi2018-001on</identifier>
-  <titles>
-    <title xml:lang="sl">Učinkovitost kanabinoidov pri zdravljenju raka</title>
-    <title xml:lang="sl" titleType="Subtitle">mit ali resnica</title>
-    <title xml:lang="en" titleType="TranslatedTitle">Therapeutic Efficacy of Cannabinoids in Cancer Treatment</title>
-    <title xml:lang="en" titleType="Subtitle">Myth or Fact</title>
-  </titles>
-  <creators>
-    <creator>
-      <creatorName nameType="Personal">Grošelj, Blaž</creatorName>
-      <givenName>Blaž</givenName>
-      <familyName>Grošelj</familyName>
-      <affiliation>Onkološki inštitut Ljubljana</affiliation>
-      <creatorName nameType="Personal">Oražem, Miha </creatorName>
-      <givenName>Miha</givenName>
-      <familyName>Oražem</familyName>
-      <affiliation>Onkološki inštitut Ljubljana</affiliation>
-      <creatorName nameType="Personal">Kovač, Viljem</creatorName>
-      <givenName>Viljem</givenName>
-      <familyName>Kovač</familyName>
-      <affiliation>Onkološki inštitut Ljubljana</affiliation>
-    </creator>
-  </creators>
-  <publisher>Onkološki inštitut Ljubljana</publisher>
-  <publicationYear>2018</publicationYear>
-  <resourceType resourceTypeGeneral="Text">Journal Article</resourceType>
-  <subjects>
-    <subject subjectScheme="DDC">610 Medical sciences; Medicine</subject>
-    <subject xml:lang="en">cancer</subject>
-    <subject xml:lang="en">cannabinoids</subject>
-  </subjects>
-  <dates>
-    <date dateType="Issued">2018-06-20</date>
-  </dates>
-  <relatedIdentifiers>
-    <relatedIdentifier relatedIdentifierType="ISSN" relationType="IsPartOf">1581-3215</relatedIdentifier>
-  </relatedIdentifiers>
-  <descriptions>
-    <description xml:lang="en" descriptionType="Other">The use of cannabis derivatives (cannabinoids) in oncology is sometimes indicated in the symptomatic treatment of nausea and vomiting, in pain management and in some neuropsychiatric disorders. In the recent years, there has been a growing interest in determining the anticancer effects of cannabinoids. Based on our clinical experience, we know that many patients use cannabinoids, among them also those with the aim of curing their disease. But despite the extensive and convincing data on the anticancer properties of cannabinoids from in vitro studies on cell cultures and studies on animal models, these properties have not (yet) been confirmed in a clinical trial. This paper summarises the currently available data on the potential of cannabinoid use in the clinical practice of oncology.</description>
-    <description descriptionType="SeriesInformation" xml:lang="sl">Onkologija, leto XXII, št. 1, junij 2018</description>
-    <description descriptionType="SeriesInformation" xml:lang="en">Onkologija, Volume XXII, No. 1, June 2018</description>
-  </descriptions>
-  <language>sl</language>
-  <formats>
-    <format>pdf</format>
-  </formats>
-  <rightsList>
-    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International license (CC BY 4.0)</rights>
-  </rightsList>
-</resource>

data/spec/fixtures/datacite_missing_creator.xml

@@ -1,33 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
-  <identifier identifierType="DOI">10.5438/4K3M-NYVG</identifier>
-  <creators/>
-  <titles>
-    <title>Eating your own Dog Food</title>
-  </titles>
-  <publisher>DataCite</publisher>
-  <publicationYear>2016</publicationYear>
-  <resourceType resourceTypeGeneral="Text">BlogPosting</resourceType>
-  <alternateIdentifiers>
-    <alternateIdentifier alternateIdentifierType="Local accession number">MS-49-3632-5083</alternateIdentifier>
-  </alternateIdentifiers>
-  <subjects>
-    <subject>datacite</subject>
-    <subject>doi</subject>
-    <subject>metadata</subject>
-  </subjects>
-  <dates>
-    <date dateType="Created">2016-12-20</date>
-    <date dateType="Issued">2016-12-20</date>
-    <date dateType="Updated">2016-12-20</date>
-  </dates>
-  <relatedIdentifiers>
-    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.5438/0012</relatedIdentifier>
-    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.5438/55E5-T5C0</relatedIdentifier>
-    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsPartOf">10.5438/0000-00SS</relatedIdentifier>
-  </relatedIdentifiers>
-  <version>1.0</version>
-  <descriptions>
-    <description descriptionType="Abstract">Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for...</description>
-  </descriptions>
-</resource>

data/spec/fixtures/datacite_schema_3.xml

@@ -1,58 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<resource xmlns="http://datacite.org/schema/kernel-3" xmlns:dim="http://www.dspace.org/xmlns/dspace/dim" xmlns:dryad="http://purl.org/dryad/terms/" xmlns:dspace="http://www.dspace.org/xmlns/dspace/dim" xmlns:mets="http://www.loc.gov/METS/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd">
-  <identifier identifierType="DOI">10.5061/DRYAD.8515</identifier>
-  <version>1</version>
-  <creators>
-    <creator>
-      <creatorName>Ollomo, Benjamin</creatorName>
-    </creator>
-    <creator>
-      <creatorName>Durand, Patrick</creatorName>
-    </creator>
-    <creator>
-      <creatorName>Prugnolle, Franck</creatorName>
-    </creator>
-    <creator>
-      <creatorName>Douzery, Emmanuel J. P.</creatorName>
-    </creator>
-    <creator>
-      <creatorName>Arnathau, Céline</creatorName>
-    </creator>
-    <creator>
-      <creatorName>Nkoghe, Dieudonné</creatorName>
-    </creator>
-    <creator>
-      <creatorName>Leroy, Eric</creatorName>
-    </creator>
-    <creator>
-      <creatorName>Renaud, François</creatorName>
-    </creator>
-  </creators>
-  <titles>
-    <title>Data from: A new malaria agent in African hominids.</title>
-  </titles>
-  <publisher>Dryad Digital Repository</publisher>
-  <publicationYear>2011</publicationYear>
-  <subjects>
-    <subject>Phylogeny</subject>
-    <subject>Malaria</subject>
-    <subject>Parasites</subject>
-    <subject>Taxonomy</subject>
-    <subject>Mitochondrial genome</subject>
-    <subject>Africa</subject>
-    <subject>Plasmodium</subject>
-  </subjects>
-  <resourceType resourceTypeGeneral="Dataset">DataPackage</resourceType>
-  <alternateIdentifiers>
-    <alternateIdentifier alternateIdentifierType="citation">Ollomo B, Durand P, Prugnolle F, Douzery EJP, Arnathau C, Nkoghe D, Leroy E, Renaud F (2009) A new malaria agent in African hominids. PLoS Pathogens 5(5): e1000446.</alternateIdentifier>
-  </alternateIdentifiers>
-  <relatedIdentifiers>
-    <relatedIdentifier relatedIdentifierType="DOI" relationType="HasPart">10.5061/DRYAD.8515/1</relatedIdentifier>
-    <relatedIdentifier relatedIdentifierType="DOI" relationType="HasPart">10.5061/DRYAD.8515/2</relatedIdentifier>
-    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsReferencedBy">10.1371/JOURNAL.PPAT.1000446</relatedIdentifier>
-    <relatedIdentifier relatedIdentifierType="PMID" relationType="IsReferencedBy">19478877</relatedIdentifier>
-  </relatedIdentifiers>
-  <rightsList>
-    <rights rightsURI="http://creativecommons.org/publicdomain/zero/1.0/" />
-  </rightsList>
-</resource>

data/spec/fixtures/datacite_software.json

@@ -1,21 +0,0 @@
-{
-  "id": "https://doi.org/10.5063/f1m61h5x",
-  "types": {
-    "resource-type-general": "Software",
-    "resource-type": "Software"
-  },
-  "doi": "10.5063/F1M61H5X",
-  "creators": [{
-    "type": "Person",
-    "name": "Matthew B. Jones",
-    "givenName": "Matthew B.",
-    "familyName": "Jones"
-  }],
-  "titles": [{
-    "title": "dataone: R interface to the DataONE network of data repositories"
-  }],
-  "publisher": "KNB Data Repository",
-  "publication-year": "2016",
-  "schema-version": "http://datacite.org/schema/kernel-3",
-  "agency": "datacite"
-}

data/spec/fixtures/datacite_software_missing_comma.json

@@ -1,18 +0,0 @@
-{
-  "id": "https://doi.org/10.5063/f1m61h5x",
-  "doi": "10.5063/F1M61H5X"
-  "creator": {
-    "type": "Person",
-    "name": "Matthew B. Jones",
-    "givenName": "Matthew B.",
-    "familyName": "Jones"
-  },
-  "title": "dataone: R interface to the DataONE network of data repositories",
-  "publisher": "KNB Data Repository",
-  "publication-year": "2016",
-  "resource-type-general": "Software",
-  "resource-type": "Software",
-  "date-published": "2016",
-  "schema-version": "http://datacite.org/schema/kernel-3",
-  "provider": "DataCite"
-}

data/spec/fixtures/datacite_software_overlapping_keys.json

@@ -1,18 +0,0 @@
-{
-  "id": "https://doi.org/10.5063/f1m61h5x",
-  "id": "10.5063/F1M61H5X",
-  "creator": {
-    "type": "Person",
-    "name": "Matthew B. Jones",
-    "givenName": "Matthew B.",
-    "familyName": "Jones"
-  },
-  "title": "dataone: R interface to the DataONE network of data repositories",
-  "publisher": "KNB Data Repository",
-  "publication-year": "2016",
-  "resource-type-general": "Software",
-  "resource-type": "Software",
-  "date-published": "2016",
-  "schemaVersion": "http://datacite.org/schema/kernel-3",
-  "provider": "DataCite"
-}

data/spec/fixtures/datacite_software_version.json

@@ -1,74 +0,0 @@
-{
-  "id": "https://doi.org/10.5281/zenodo.2598836",
-  "doi": "10.5281/ZENODO.2598836",
-  "url": "https://zenodo.org/record/2598836",
-  "types": {
-    "ris": "COMP",
-    "bibtex": "misc",
-    "citeproc": "article",
-    "schemaOrg": "SoftwareSourceCode",
-    "resourceTypeGeneral": "Software"
-  },
-  "creators": [
-    {
-      "name": "Lab For Exosphere And Near Space Environment Studies",
-      "affiliation": []
-    }
-  ],
-  "titles": [
-    {
-      "title": "lenses-lab/LYAO_RT-2018JA026426: Original Release"
-    }
-  ],
-  "publisher": "Zenodo",
-  "container": {},
-  "contributors": [],
-  "dates": [
-    {
-      "date": "2019-03-20",
-      "dateType": "Issued"
-    }
-  ],
-  "publicationYear": 2019,
-  "identifiers": [
-    {
-      "identifier": "https://doi.org/10.5281/zenodo.2598836",
-      "identifierType": "DOI"
-    },
-    {
-      "identifier": "https://zenodo.org/record/2598836",
-      "identifierType": "URL"
-    }
-  ],
-  "version": "1.0.0",
-  "rightsList": [
-    {
-      "rights": "Open Access",
-      "rightsUri": "info:eu-repo/semantics/openAccess"
-    }
-  ],
-  "descriptions": [
-    {
-      "description": "Original executables used by Gallant et al. for JGR publication 2018JA026426.",
-      "descriptionType": "Abstract"
-    }
-  ],
-  "relatedIdentifiers": [
-    {
-      "relationType": "IsSupplementTo",
-      "relatedIdentifier": "https://github.com/lenses-lab/LYAO_RT-2018JA026426/tree/1.0.0",
-      "relatedIdentifierType": "URL"
-    },
-    {
-      "relationType": "IsVersionOf",
-      "relatedIdentifier": "10.5281/zenodo.2598835",
-      "relatedIdentifierType": "DOI"
-    }
-  ],
-  "schemaVersion": "http://datacite.org/schema/kernel-4",
-  "providerId": "cern",
-  "clientId": "cern.zenodo",
-  "agency": "datacite",
-  "state": "findable"
-}
-   

data/spec/fixtures/edam_package.json

@@ -1,12 +0,0 @@
-{
-  "name": "edam-browser",
-  "description": "The EDAM Browser is a client-side web-based visualization javascript widget. Its goals are to help describing bio-related resources and service with EDAM, and to facilitate and foster community contributions to EDAM.",
-  "author": "Bryan Brancotte",
-  "version": "1.0.0",
-  "scripts": {
-    "test": "jshint js/*js"
-  },
-  "devDependencies": {
-    "jshint": "^2.9.5"
-  }
-}

data/spec/fixtures/funding_reference.xml

@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
-  <identifier identifierType="DOI">10.7907/G31J-CH52</identifier>
-  <creators>
-    <creator>
-      <creatorName>Singhal,Vipul</creatorName>
-    </creator>
-  </creators>
-  <titles>
-    <title>Modeling, Computation, and Characterization to Accelerate the Development of Synthetic Gene Circuits in Cell-Free Extracts</title>
-  </titles>
-  <publisher>California Institute of Technology</publisher>
-  <publicationYear>2019</publicationYear>
-  <resourceType resourceTypeGeneral="Text">Dissertation</resourceType>
-  <alternateIdentifiers>
-    <alternateIdentifier alternateIdentifierType="Eprint_ID">11161</alternateIdentifier>
-  </alternateIdentifiers>
-  <subjects>
-    <subject>Synthetic Biology</subject>
-    <subject>System Identification</subject>
-    <subject>Control Theory</subject>
-    <subject>Mathematical Modeling</subject>
-    <subject>Chemical Reaction Networks</subject>
-    <subject>Transcription</subject>
-    <subject>Translation</subject>
-    <subject>Gene Regulatory Networks</subject>
-    <subject>Calibration</subject>
-    <subject>Computation and Neural Systems</subject>
-  </subjects>
-  <fundingReferences>
-    <fundingReference/>
-    <fundingReference/>
-    <fundingReference>
-      <funderName>Agency for Science, Technology and Research (Singapore)</funderName>
-    </fundingReference>
-    <fundingReference/>
-  </fundingReferences>
-  <dates>
-    <date dateType="Issued">2019</date>
-  </dates>
-  <version>Final</version>
-  <descriptions>
-    <description descriptionType="Abstract">Synthetic biology may be defined as an attempt at using engineering principles to design and build novel biological functionalities. An important class of such functionalities involves the bottom up design of genetic networks (or 'circuits') to control cellular behavior. Performing design iterations on these circuits in vivo is often a time consuming process. One approach that has been developed to address these long design times is to use E. coli cell extracts as simplified circuit prototyping environments. The analogy with similar approaches in engineering, such as prototyping using wind tunnels and breadboards, may be extended by developing accompanying computer aided design tools. In this thesis, we discuss the development of computational and mathematical tools to accelerate circuit prototyping in the TX-TL cell free prototyping platform, and demonstrate some applications of these tools.
-
-We start by discussing the problem of reducing circuit behavior variability between different batches of TX-TL cell extracts. To this end, we demonstrate a model-based methodology for calibrating extract batches, and for using the calibrations to 'correct' the behavior of genetic circuits between batches. We also look at the interaction of this methodology with the phenomenon of parameter non-identifiability, which occurs when the parameter identification inverse problem has multiple solutions. In particular, we derive conditions under which parameter non-identifiability does not hinder our modeling objectives, and subsequently demonstrate the use of such non-identifiable models in performing data variability reduction. 
-
-Next, we describe txtlsim, a MATLAB Simbiology based toolbox for automatically generating models of genetic circuits in TX-TL, and for using these models for part characterization and circuit behavior prediction. Large genetic circuits can have non-negligible resource usage needs, leading to unintended interactions between circuit nodes arising due to the loading of cellular machinery, transcription factors or other regulatory elements. The usage of consumable resources like nucleotides and amino acids can also have non-trivial effects on complex genetic circuits. These types of effects are handled by the modeling framework of txtlsim in a natural way.
-
-We also highlight mcmc-simbio, a smaller toolbox within txtlsim for performing concurrent Bayesian parameter inference on Simbiology models. Concurrent inference here means that a common set of parameters can be identified using data from an ensemble of different circuits and experiments, with each experiment informing a subset of the parameters. The combination of the concurrence feature with the fact that Markov chain Monte Carlo based Bayesian inference methods allow for the direct visualization of parameter non-identifiability enables the design of ensembles of experiments that reduce such non-identifiability.
-
-Finally, we end with a method for performing model order reduction on transcription and translation elongation models while maintaining the ability of these models to track resource consumption. We show that due to their network topology, our models cannot be brought into the two-timescale form of singular perturbation theory when written in species concentration coordinates. We identify a coordinate system in which singular perturbation theory may be applied to chemical reaction networks more naturally, and use this to achieve the desired model reduction.</description>
-  </descriptions>
-</resource>

data/spec/fixtures/gtex.xml

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-  <identifier identifierType="DOI">10.25491/9HX8-KE93</identifier>  
-  <creators> 
-    <creator> 
-      <creatorName nameType="Organizational">The GTEx Consortium</creatorName> 
-    </creator> 
-  </creators>  
-  <titles> 
-    <title>DroNc-seq data</title> 
-  </titles>  
-  <publisher>GTEx</publisher>  
-  <publicationYear>2017</publicationYear>  
-  <subjects> 
-    <subject>gtex</subject>  
-    <subject>annotation</subject>  
-    <subject>phenotype</subject>  
-    <subject>gene regulation</subject>  
-    <subject>transcriptomics</subject> 
-  </subjects>  
-  <fundingReferences> 
-    <fundingReference> 
-      <funderName>Common Fund of the Office of the Director of the NIH</funderName>  
-      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000052</funderIdentifier> 
-    </fundingReference>  
-    <fundingReference> 
-      <funderName>National Cancer Institute (NCI)</funderName>  
-      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000054</funderIdentifier> 
-    </fundingReference>  
-    <fundingReference> 
-      <funderName>National Human Genome Research Institute (NHGRI)</funderName>  
-      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000051</funderIdentifier> 
-    </fundingReference>  
-    <fundingReference> 
-      <funderName>National Heart, Lung, and Blood Institute (NHLBI)</funderName>  
-      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000050</funderIdentifier> 
-    </fundingReference>  
-    <fundingReference> 
-      <funderName>National Institute on Drug Abuse (NIDA)</funderName>  
-      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000026</funderIdentifier> 
-    </fundingReference>  
-    <fundingReference> 
-      <funderName>National Institute of Mental Health (NIMH)</funderName>  
-      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000025</funderIdentifier> 
-    </fundingReference>  
-    <fundingReference> 
-      <funderName>National Institute of Neurological Disorders and Stroke (NINDS)</funderName>  
-      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000065</funderIdentifier> 
-    </fundingReference> 
-  </fundingReferences>  
-  <resourceType resourceTypeGeneral="Dataset">DroNc-seq data</resourceType>  
-  <dates> 
-    <date dateType="Issued">2017</date> 
-  </dates>  
-  <relatedIdentifiers> 
-    <relatedIdentifier relationType="Documents" relatedIdentifierType="URL">http://identifiers.org/dbgap:phs000424.v7.p2</relatedIdentifier>  
-    <relatedIdentifier relationType="IsDocumentedBy" relatedIdentifierType="DOI">https://doi.org/10.1038/nature24277</relatedIdentifier>  
-    <relatedIdentifier relationType="IsSupplementTo" relatedIdentifierType="DOI">https://doi.org/10.1038/nmeth.4407</relatedIdentifier> 
-    <relatedIdentifier relationType="IsPartOf" relatedIdentifierType="URL">https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000663</relatedIdentifier> 
-  </relatedIdentifiers> 
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-    <format>application/tar</format> 
-  </formats> 
-  <sizes> 
-    <size>15.7M</size> 
-  </sizes>
-  <descriptions> 
-    <description descriptionType="SeriesInformation">GTEx</description> 
-  </descriptions> 
-</resource>

data/spec/fixtures/maremma/codemeta.json

@@ -1,36 +0,0 @@
-{
-	"@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
-	"@type": "SoftwareSourceCode",
-	"@id": "https://doi.org/10.5438/QEG0-3GM3",
-	"authors": {
-		"@id": "http://orcid.org/0000-0003-0077-4738",
-		"@type": "person",
-		"name": "Martin Fenner",
-		"affiliation": "DataCite",
-		"mustBeCited": true,
-		"isMaintainer": true,
-		"isRightsHolder": true
-	},
-	"identifier": "https://doi.org/10.5438/QEG0-3GM3",
-	"codeRepository": "https://github.com/datacite/maremma",
-	"controlledTem": "software",
-	"dateCreated": "2015-11-28",
-	"datePublished": "2017-02-24",
-	"dateModified": "2017-02-24",
-	"description": "Simplifies network calls, including json/xml parsing and error handling. Based on Faraday.",
-	"isAutomatedBuild": true,
-	"licenseId": "MIT",
-	"publisher": "DataCite",
-	"tags": [
-		"faraday",
-		"excon",
-		"net/http"
-	],
-	"title": "Maremma: a Ruby library for simplified network calls",
-	"programmingLanguage": {
-		"name": "Ruby",
-		"version": "≥ 2.3.3",
-		"URL": "https://www.ruby-lang.org"
-	},
-	"readme": "https://github.com/datacite/maremma/blob/master/README.md"
-}