Using lazy evaluation to simulate realistic-size repertoires in models of the immune system View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

1998-07

AUTHORS

Derek J. Smith, Stephanie Forrest, David H. Ackley, Alan S. Perelson

ABSTRACT

We describe a method of implementing efficient computer simulations of immune systems that have a large number of unique B-and/or T-cell clones. The method uses an implementation technique called lazy evaluation to create the illusion that all clones are being simulated, while only actually simulating a much smaller number of clones that can respond to the antigens in the simulation. The method is effective because only 0.001–0.01% of clones can typically be stimulated by an antigen, and because many simulations involve only a small number of distinct antigens. A lazy simulation of a realistic number of clones and 10 distinct antigens is 1000 times faster and 10 000 times smaller than a conventional simulation—making simulations of immune systems with realistic-size repertoires computationally tractable. More... »

PAGES

647-658

References to SciGraph publications

  • 1994-09. Capacity of a model immune network in BULLETIN OF MATHEMATICAL BIOLOGY
  • 1991. Genetic algorithms and the immune system in PARALLEL PROBLEM SOLVING FROM NATURE
  • 1992. Growth and Recruitment in the Immune Network in THEORETICAL AND EXPERIMENTAL INSIGHTS INTO IMMUNOLOGY
  • 1999. Immunological Memory is Associative* in ARTIFICIAL IMMUNE SYSTEMS AND THEIR APPLICATIONS
  • 1985. Miranda: A non-strict functional language with polymorphic types in FUNCTIONAL PROGRAMMING LANGUAGES AND COMPUTER ARCHITECTURE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1006/bulm.1997.0035

    DOI

    http://dx.doi.org/10.1006/bulm.1997.0035

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1002737222

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/9659009


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/01", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Mathematical Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Algorithms", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Antigens", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "B-Lymphocytes", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Clone Cells", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Computer Simulation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Immune System", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Immunization", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Models, Immunological", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Receptors, Antigen, B-Cell", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Software Validation", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Department of Computer Science, University of New Mexico, 87131, Albuquerque, NM, USA", 
              "id": "http://www.grid.ac/institutes/grid.266832.b", 
              "name": [
                "Department of Computer Science, University of New Mexico, 87131, Albuquerque, NM, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Smith", 
            "givenName": "Derek J.", 
            "id": "sg:person.01164420614.61", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01164420614.61"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Computer Science, University of New Mexico, 87131, Albuquerque, NM, USA", 
              "id": "http://www.grid.ac/institutes/grid.266832.b", 
              "name": [
                "Department of Computer Science, University of New Mexico, 87131, Albuquerque, NM, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Forrest", 
            "givenName": "Stephanie", 
            "id": "sg:person.0712103012.64", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0712103012.64"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Computer Science, University of New Mexico, 87131, Albuquerque, NM, USA", 
              "id": "http://www.grid.ac/institutes/grid.266832.b", 
              "name": [
                "Department of Computer Science, University of New Mexico, 87131, Albuquerque, NM, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ackley", 
            "givenName": "David H.", 
            "id": "sg:person.01004556010.49", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01004556010.49"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Theoretical Division, Los Alamos National Laboratory, 87545, Los Alamos, NM, USA", 
              "id": "http://www.grid.ac/institutes/grid.148313.c", 
              "name": [
                "Theoretical Division, Los Alamos National Laboratory, 87545, Los Alamos, NM, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Perelson", 
            "givenName": "Alan S.", 
            "id": "sg:person.01335541022.50", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01335541022.50"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1007/978-3-642-59901-9_6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014799722", 
              "https://doi.org/10.1007/978-3-642-59901-9_6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/978-3-642-76977-1_14", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015772065", 
              "https://doi.org/10.1007/978-3-642-76977-1_14"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1016/s0092-8240(05)80296-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1054613801", 
              "https://doi.org/10.1016/s0092-8240(05)80296-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/3-540-15975-4_26", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016631723", 
              "https://doi.org/10.1007/3-540-15975-4_26"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bfb0029771", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043228475", 
              "https://doi.org/10.1007/bfb0029771"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "1998-07", 
        "datePublishedReg": "1998-07-01", 
        "description": "We describe a method of implementing efficient computer simulations of immune systems that have a large number of unique B-and/or T-cell clones. The method uses an implementation technique called lazy evaluation to create the illusion that all clones are being simulated, while only actually simulating a much smaller number of clones that can respond to the antigens in the simulation. The method is effective because only 0.001\u20130.01% of clones can typically be stimulated by an antigen, and because many simulations involve only a small number of distinct antigens. A lazy simulation of a realistic number of clones and 10 distinct antigens is 1000 times faster and 10 000 times smaller than a conventional simulation\u2014making simulations of immune systems with realistic-size repertoires computationally tractable.", 
        "genre": "article", 
        "id": "sg:pub.10.1006/bulm.1997.0035", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2564417", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1018370", 
            "issn": [
              "0092-8240", 
              "1522-9602"
            ], 
            "name": "Bulletin of Mathematical Biology", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "4", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "60"
          }
        ], 
        "keywords": [
          "immune system", 
          "distinct antigens", 
          "cell clones", 
          "antigen", 
          "small number", 
          "clones", 
          "evaluation", 
          "repertoire", 
          "number", 
          "time", 
          "large number", 
          "method", 
          "system", 
          "technique", 
          "model", 
          "illusion", 
          "realistic number", 
          "lazy evaluation", 
          "computer simulation", 
          "simulations", 
          "efficient computer simulations", 
          "implementation techniques", 
          "lazy simulation", 
          "conventional simulation\u2014making simulations", 
          "simulation\u2014making simulations", 
          "realistic-size repertoires"
        ], 
        "name": "Using lazy evaluation to simulate realistic-size repertoires in models of the immune system", 
        "pagination": "647-658", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1002737222"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1006/bulm.1997.0035"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "9659009"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1006/bulm.1997.0035", 
          "https://app.dimensions.ai/details/publication/pub.1002737222"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2021-12-01T19:10", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20211201/entities/gbq_results/article/article_295.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1006/bulm.1997.0035"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1006/bulm.1997.0035'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1006/bulm.1997.0035'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1006/bulm.1997.0035'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1006/bulm.1997.0035'


     

    This table displays all metadata directly associated to this object as RDF triples.

    174 TRIPLES      22 PREDICATES      68 URIs      55 LITERALS      17 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1006/bulm.1997.0035 schema:about N01989bd27eb142e4bd6dc9b07ffb782f
    2 N03e98abce2b149cfaccfa397c96ef1e2
    3 N0acc45a2eb3c4589b0f0439f9e4ca0d2
    4 N17b44d4734f34166b90cc7b1addc3c2d
    5 N542623497b4a43cda4d652f7049bca1b
    6 N7575a4a6714a4f418ff96146dc467b95
    7 N9663a4a60e5640108cb446be3fa9a8b8
    8 Nafeec09fae90439fb351556d401291e3
    9 Nc224babc1237493687bc1cb866f28d6c
    10 Ne44d35433a794c62b64af2b1c6ad4f9d
    11 anzsrc-for:01
    12 anzsrc-for:06
    13 schema:author N88936b7d2d184f99ab8c465893ec9481
    14 schema:citation sg:pub.10.1007/3-540-15975-4_26
    15 sg:pub.10.1007/978-3-642-59901-9_6
    16 sg:pub.10.1007/978-3-642-76977-1_14
    17 sg:pub.10.1007/bfb0029771
    18 sg:pub.10.1016/s0092-8240(05)80296-4
    19 schema:datePublished 1998-07
    20 schema:datePublishedReg 1998-07-01
    21 schema:description We describe a method of implementing efficient computer simulations of immune systems that have a large number of unique B-and/or T-cell clones. The method uses an implementation technique called lazy evaluation to create the illusion that all clones are being simulated, while only actually simulating a much smaller number of clones that can respond to the antigens in the simulation. The method is effective because only 0.001–0.01% of clones can typically be stimulated by an antigen, and because many simulations involve only a small number of distinct antigens. A lazy simulation of a realistic number of clones and 10 distinct antigens is 1000 times faster and 10 000 times smaller than a conventional simulation—making simulations of immune systems with realistic-size repertoires computationally tractable.
    22 schema:genre article
    23 schema:inLanguage en
    24 schema:isAccessibleForFree true
    25 schema:isPartOf N737a303c2503469988942ea56ef9a8d6
    26 Na7853c1124be4e70aeaa5f4d1897e7a5
    27 sg:journal.1018370
    28 schema:keywords antigen
    29 cell clones
    30 clones
    31 computer simulation
    32 conventional simulation—making simulations
    33 distinct antigens
    34 efficient computer simulations
    35 evaluation
    36 illusion
    37 immune system
    38 implementation techniques
    39 large number
    40 lazy evaluation
    41 lazy simulation
    42 method
    43 model
    44 number
    45 realistic number
    46 realistic-size repertoires
    47 repertoire
    48 simulations
    49 simulation—making simulations
    50 small number
    51 system
    52 technique
    53 time
    54 schema:name Using lazy evaluation to simulate realistic-size repertoires in models of the immune system
    55 schema:pagination 647-658
    56 schema:productId N1252a7b185bd43f8a0e35835d9de2cab
    57 Na7a5b70d5c26499f97670b6918e7231c
    58 Nfba8df730cea4155b874dd9457bcd4f0
    59 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002737222
    60 https://doi.org/10.1006/bulm.1997.0035
    61 schema:sdDatePublished 2021-12-01T19:10
    62 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    63 schema:sdPublisher N5e087be054854bcab2c69ccbcfea66ba
    64 schema:url https://doi.org/10.1006/bulm.1997.0035
    65 sgo:license sg:explorer/license/
    66 sgo:sdDataset articles
    67 rdf:type schema:ScholarlyArticle
    68 N01989bd27eb142e4bd6dc9b07ffb782f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    69 schema:name Models, Immunological
    70 rdf:type schema:DefinedTerm
    71 N03e98abce2b149cfaccfa397c96ef1e2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    72 schema:name Clone Cells
    73 rdf:type schema:DefinedTerm
    74 N0acc45a2eb3c4589b0f0439f9e4ca0d2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    75 schema:name Immune System
    76 rdf:type schema:DefinedTerm
    77 N1252a7b185bd43f8a0e35835d9de2cab schema:name doi
    78 schema:value 10.1006/bulm.1997.0035
    79 rdf:type schema:PropertyValue
    80 N17b44d4734f34166b90cc7b1addc3c2d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    81 schema:name Immunization
    82 rdf:type schema:DefinedTerm
    83 N542623497b4a43cda4d652f7049bca1b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    84 schema:name Software Validation
    85 rdf:type schema:DefinedTerm
    86 N5e087be054854bcab2c69ccbcfea66ba schema:name Springer Nature - SN SciGraph project
    87 rdf:type schema:Organization
    88 N737a303c2503469988942ea56ef9a8d6 schema:issueNumber 4
    89 rdf:type schema:PublicationIssue
    90 N73facbac2270440988ff1fef4826e303 rdf:first sg:person.0712103012.64
    91 rdf:rest Ncbdcd7ce34924d22a1c10c9e02f2bd3f
    92 N7575a4a6714a4f418ff96146dc467b95 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    93 schema:name Antigens
    94 rdf:type schema:DefinedTerm
    95 N88936b7d2d184f99ab8c465893ec9481 rdf:first sg:person.01164420614.61
    96 rdf:rest N73facbac2270440988ff1fef4826e303
    97 N9663a4a60e5640108cb446be3fa9a8b8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    98 schema:name Computer Simulation
    99 rdf:type schema:DefinedTerm
    100 Na7853c1124be4e70aeaa5f4d1897e7a5 schema:volumeNumber 60
    101 rdf:type schema:PublicationVolume
    102 Na7a5b70d5c26499f97670b6918e7231c schema:name dimensions_id
    103 schema:value pub.1002737222
    104 rdf:type schema:PropertyValue
    105 Nafeec09fae90439fb351556d401291e3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    106 schema:name Algorithms
    107 rdf:type schema:DefinedTerm
    108 Nc224babc1237493687bc1cb866f28d6c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    109 schema:name Receptors, Antigen, B-Cell
    110 rdf:type schema:DefinedTerm
    111 Ncbdcd7ce34924d22a1c10c9e02f2bd3f rdf:first sg:person.01004556010.49
    112 rdf:rest Ned13173afefb4b4c8ee425d4bc62b165
    113 Ne44d35433a794c62b64af2b1c6ad4f9d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    114 schema:name B-Lymphocytes
    115 rdf:type schema:DefinedTerm
    116 Ned13173afefb4b4c8ee425d4bc62b165 rdf:first sg:person.01335541022.50
    117 rdf:rest rdf:nil
    118 Nfba8df730cea4155b874dd9457bcd4f0 schema:name pubmed_id
    119 schema:value 9659009
    120 rdf:type schema:PropertyValue
    121 anzsrc-for:01 schema:inDefinedTermSet anzsrc-for:
    122 schema:name Mathematical Sciences
    123 rdf:type schema:DefinedTerm
    124 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    125 schema:name Biological Sciences
    126 rdf:type schema:DefinedTerm
    127 sg:grant.2564417 http://pending.schema.org/fundedItem sg:pub.10.1006/bulm.1997.0035
    128 rdf:type schema:MonetaryGrant
    129 sg:journal.1018370 schema:issn 0092-8240
    130 1522-9602
    131 schema:name Bulletin of Mathematical Biology
    132 schema:publisher Springer Nature
    133 rdf:type schema:Periodical
    134 sg:person.01004556010.49 schema:affiliation grid-institutes:grid.266832.b
    135 schema:familyName Ackley
    136 schema:givenName David H.
    137 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01004556010.49
    138 rdf:type schema:Person
    139 sg:person.01164420614.61 schema:affiliation grid-institutes:grid.266832.b
    140 schema:familyName Smith
    141 schema:givenName Derek J.
    142 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01164420614.61
    143 rdf:type schema:Person
    144 sg:person.01335541022.50 schema:affiliation grid-institutes:grid.148313.c
    145 schema:familyName Perelson
    146 schema:givenName Alan S.
    147 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01335541022.50
    148 rdf:type schema:Person
    149 sg:person.0712103012.64 schema:affiliation grid-institutes:grid.266832.b
    150 schema:familyName Forrest
    151 schema:givenName Stephanie
    152 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0712103012.64
    153 rdf:type schema:Person
    154 sg:pub.10.1007/3-540-15975-4_26 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016631723
    155 https://doi.org/10.1007/3-540-15975-4_26
    156 rdf:type schema:CreativeWork
    157 sg:pub.10.1007/978-3-642-59901-9_6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014799722
    158 https://doi.org/10.1007/978-3-642-59901-9_6
    159 rdf:type schema:CreativeWork
    160 sg:pub.10.1007/978-3-642-76977-1_14 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015772065
    161 https://doi.org/10.1007/978-3-642-76977-1_14
    162 rdf:type schema:CreativeWork
    163 sg:pub.10.1007/bfb0029771 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043228475
    164 https://doi.org/10.1007/bfb0029771
    165 rdf:type schema:CreativeWork
    166 sg:pub.10.1016/s0092-8240(05)80296-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1054613801
    167 https://doi.org/10.1016/s0092-8240(05)80296-4
    168 rdf:type schema:CreativeWork
    169 grid-institutes:grid.148313.c schema:alternateName Theoretical Division, Los Alamos National Laboratory, 87545, Los Alamos, NM, USA
    170 schema:name Theoretical Division, Los Alamos National Laboratory, 87545, Los Alamos, NM, USA
    171 rdf:type schema:Organization
    172 grid-institutes:grid.266832.b schema:alternateName Department of Computer Science, University of New Mexico, 87131, Albuquerque, NM, USA
    173 schema:name Department of Computer Science, University of New Mexico, 87131, Albuquerque, NM, USA
    174 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...