MFsim—an open Java all-in-one rich-client simulation environment for mesoscopic simulation View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2020-05-01

AUTHORS

Karina van den Broek, Mirco Daniel, Matthias Epple, Jan-Mathis Hein, Hubert Kuhn, Stefan Neumann, Andreas Truszkowski, Achim Zielesny

ABSTRACT

MFsim is an open Java all-in-one rich-client computing environment for mesoscopic simulation with Jdpd as its default simulation kernel for Molecular Fragment (Dissipative Particle) Dynamics. The new environment comprises the complete preparation-simulation–evaluation triad of a mesoscopic simulation task and especially enables biomolecular simulation tasks with peptides and proteins. Productive highlights are a SPICES molecular structure editor, a PDB-to-SPICES parser for particle-based peptide/protein representations, a support of polymer definitions, a compartment editor for complex simulation box start configurations, interactive and flexible simulation box views including analytics, simulation movie generation or animated diagrams. As an open project, MFsim allows for customized extensions for different fields of research. More... »

PAGES

29

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13321-020-00432-9

DOI

http://dx.doi.org/10.1186/s13321-020-00432-9

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1127311418

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/33430951


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/2008/03", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Chemical Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0303", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Macromolecular and Materials Chemistry", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany", 
          "id": "http://www.grid.ac/institutes/None", 
          "name": [
            "Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany", 
            "Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "van den Broek", 
        "givenName": "Karina", 
        "id": "sg:person.011777342042.92", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011777342042.92"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany", 
          "id": "http://www.grid.ac/institutes/None", 
          "name": [
            "Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Daniel", 
        "givenName": "Mirco", 
        "id": "sg:person.016332325241.06", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016332325241.06"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany", 
          "id": "http://www.grid.ac/institutes/grid.5718.b", 
          "name": [
            "Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Epple", 
        "givenName": "Matthias", 
        "id": "sg:person.011342402346.80", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011342402346.80"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany", 
          "id": "http://www.grid.ac/institutes/None", 
          "name": [
            "Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hein", 
        "givenName": "Jan-Mathis", 
        "id": "sg:person.012010516471.36", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012010516471.36"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "CAM-D Technologies GmbH, Solingen, Germany", 
          "id": "http://www.grid.ac/institutes/None", 
          "name": [
            "CAM-D Technologies GmbH, Solingen, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kuhn", 
        "givenName": "Hubert", 
        "id": "sg:person.012147605703.08", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012147605703.08"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "GNWI \u2013 Gesellschaft f\u00fcr naturwissenschaftliche Informatik mbH, Dortmund, Germany", 
          "id": "http://www.grid.ac/institutes/None", 
          "name": [
            "GNWI \u2013 Gesellschaft f\u00fcr naturwissenschaftliche Informatik mbH, Dortmund, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Neumann", 
        "givenName": "Stefan", 
        "id": "sg:person.01272673554.14", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01272673554.14"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Yara Deutschland, D\u00fclmen, Germany", 
          "id": "http://www.grid.ac/institutes/None", 
          "name": [
            "Yara Deutschland, D\u00fclmen, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Truszkowski", 
        "givenName": "Andreas", 
        "id": "sg:person.01156445154.10", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01156445154.10"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany", 
          "id": "http://www.grid.ac/institutes/None", 
          "name": [
            "Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Zielesny", 
        "givenName": "Achim", 
        "id": "sg:person.0615402654.46", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0615402654.46"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1186/s13321-018-0294-7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1106083226", 
          "https://doi.org/10.1186/s13321-018-0294-7"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00396-004-1137-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030164848", 
          "https://doi.org/10.1007/s00396-004-1137-9"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13321-018-0278-7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1104132414", 
          "https://doi.org/10.1186/s13321-018-0278-7"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13321-014-0045-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050326719", 
          "https://doi.org/10.1186/s13321-014-0045-3"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2020-05-01", 
    "datePublishedReg": "2020-05-01", 
    "description": "MFsim is an open Java all-in-one rich-client computing environment for mesoscopic simulation with Jdpd as its default simulation kernel for Molecular Fragment (Dissipative Particle) Dynamics. The new environment comprises the complete preparation-simulation\u2013evaluation triad of a mesoscopic simulation task and especially enables biomolecular simulation tasks with peptides and proteins. Productive highlights are a SPICES molecular structure editor, a PDB-to-SPICES parser for particle-based peptide/protein representations, a support of polymer definitions, a compartment editor for complex simulation box start configurations, interactive and flexible simulation box views including analytics, simulation movie generation or animated diagrams. As an open project, MFsim allows for customized extensions for different fields of research.", 
    "genre": "article", 
    "id": "sg:pub.10.1186/s13321-020-00432-9", 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1042252", 
        "issn": [
          "1758-2946"
        ], 
        "name": "Journal of Cheminformatics", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "12"
      }
    ], 
    "keywords": [
      "simulation tasks", 
      "mesoscopic simulations", 
      "computing environment", 
      "simulation kernel", 
      "movie generation", 
      "simulation environment", 
      "structure editor", 
      "open project", 
      "start configuration", 
      "Java", 
      "task", 
      "different fields", 
      "protein representation", 
      "new environment", 
      "analytics", 
      "environment", 
      "fragment dynamics", 
      "parser", 
      "editors", 
      "kernel", 
      "simulations", 
      "representation", 
      "peptides", 
      "project", 
      "extension", 
      "PDB", 
      "definition", 
      "support", 
      "view", 
      "generation", 
      "research", 
      "configuration", 
      "triad", 
      "diagram", 
      "field", 
      "protein", 
      "highlights", 
      "dynamics"
    ], 
    "name": "MFsim\u2014an open Java all-in-one rich-client simulation environment for mesoscopic simulation", 
    "pagination": "29", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1127311418"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/s13321-020-00432-9"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "33430951"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/s13321-020-00432-9", 
      "https://app.dimensions.ai/details/publication/pub.1127311418"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-12-01T06:41", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20221201/entities/gbq_results/article/article_834.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1186/s13321-020-00432-9"
  }
]
 

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.10.1186/s13321-020-00432-9'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s13321-020-00432-9'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13321-020-00432-9'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13321-020-00432-9'


 

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

173 TRIPLES      21 PREDICATES      67 URIs      55 LITERALS      7 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/s13321-020-00432-9 schema:about anzsrc-for:03
2 anzsrc-for:0303
3 schema:author N23ac27edffa6434885625dc27951e4e8
4 schema:citation sg:pub.10.1007/s00396-004-1137-9
5 sg:pub.10.1186/s13321-014-0045-3
6 sg:pub.10.1186/s13321-018-0278-7
7 sg:pub.10.1186/s13321-018-0294-7
8 schema:datePublished 2020-05-01
9 schema:datePublishedReg 2020-05-01
10 schema:description MFsim is an open Java all-in-one rich-client computing environment for mesoscopic simulation with Jdpd as its default simulation kernel for Molecular Fragment (Dissipative Particle) Dynamics. The new environment comprises the complete preparation-simulation–evaluation triad of a mesoscopic simulation task and especially enables biomolecular simulation tasks with peptides and proteins. Productive highlights are a SPICES molecular structure editor, a PDB-to-SPICES parser for particle-based peptide/protein representations, a support of polymer definitions, a compartment editor for complex simulation box start configurations, interactive and flexible simulation box views including analytics, simulation movie generation or animated diagrams. As an open project, MFsim allows for customized extensions for different fields of research.
11 schema:genre article
12 schema:isAccessibleForFree true
13 schema:isPartOf N143709e05f4d46c4b9851dbad4a53034
14 N29cad0e5f6a942af8db3edf8d4eb2c44
15 sg:journal.1042252
16 schema:keywords Java
17 PDB
18 analytics
19 computing environment
20 configuration
21 definition
22 diagram
23 different fields
24 dynamics
25 editors
26 environment
27 extension
28 field
29 fragment dynamics
30 generation
31 highlights
32 kernel
33 mesoscopic simulations
34 movie generation
35 new environment
36 open project
37 parser
38 peptides
39 project
40 protein
41 protein representation
42 representation
43 research
44 simulation environment
45 simulation kernel
46 simulation tasks
47 simulations
48 start configuration
49 structure editor
50 support
51 task
52 triad
53 view
54 schema:name MFsim—an open Java all-in-one rich-client simulation environment for mesoscopic simulation
55 schema:pagination 29
56 schema:productId N10b0dca442d24f849e69d67cc0f23b7f
57 N1e2924356b97409aafc6b939896fab6c
58 Ne5e4c0a0ea80443fbeb66896ea504169
59 schema:sameAs https://app.dimensions.ai/details/publication/pub.1127311418
60 https://doi.org/10.1186/s13321-020-00432-9
61 schema:sdDatePublished 2022-12-01T06:41
62 schema:sdLicense https://scigraph.springernature.com/explorer/license/
63 schema:sdPublisher N918a4d3ba9524486b34ed12edc7f1d4f
64 schema:url https://doi.org/10.1186/s13321-020-00432-9
65 sgo:license sg:explorer/license/
66 sgo:sdDataset articles
67 rdf:type schema:ScholarlyArticle
68 N10b0dca442d24f849e69d67cc0f23b7f schema:name doi
69 schema:value 10.1186/s13321-020-00432-9
70 rdf:type schema:PropertyValue
71 N143709e05f4d46c4b9851dbad4a53034 schema:issueNumber 1
72 rdf:type schema:PublicationIssue
73 N1e2924356b97409aafc6b939896fab6c schema:name pubmed_id
74 schema:value 33430951
75 rdf:type schema:PropertyValue
76 N23ac27edffa6434885625dc27951e4e8 rdf:first sg:person.011777342042.92
77 rdf:rest N7b3fa0c7ef064c7e95bd43dedfac3248
78 N29cad0e5f6a942af8db3edf8d4eb2c44 schema:volumeNumber 12
79 rdf:type schema:PublicationVolume
80 N3f88e40db38f44fb93d8e2d69e3b1288 rdf:first sg:person.01272673554.14
81 rdf:rest N940e13e7043e4c0f811aeae275a5ad59
82 N5a8f29b91f954d72b0d521da64753bde rdf:first sg:person.011342402346.80
83 rdf:rest Nf100f55676f64dce9d10bf790abaab85
84 N629b9a74ee4c4d748dff2c15a114044f rdf:first sg:person.012147605703.08
85 rdf:rest N3f88e40db38f44fb93d8e2d69e3b1288
86 N7b3fa0c7ef064c7e95bd43dedfac3248 rdf:first sg:person.016332325241.06
87 rdf:rest N5a8f29b91f954d72b0d521da64753bde
88 N918a4d3ba9524486b34ed12edc7f1d4f schema:name Springer Nature - SN SciGraph project
89 rdf:type schema:Organization
90 N940e13e7043e4c0f811aeae275a5ad59 rdf:first sg:person.01156445154.10
91 rdf:rest Nc1c4130aea424a99a48b69ad931a7f8a
92 Nc1c4130aea424a99a48b69ad931a7f8a rdf:first sg:person.0615402654.46
93 rdf:rest rdf:nil
94 Ne5e4c0a0ea80443fbeb66896ea504169 schema:name dimensions_id
95 schema:value pub.1127311418
96 rdf:type schema:PropertyValue
97 Nf100f55676f64dce9d10bf790abaab85 rdf:first sg:person.012010516471.36
98 rdf:rest N629b9a74ee4c4d748dff2c15a114044f
99 anzsrc-for:03 schema:inDefinedTermSet anzsrc-for:
100 schema:name Chemical Sciences
101 rdf:type schema:DefinedTerm
102 anzsrc-for:0303 schema:inDefinedTermSet anzsrc-for:
103 schema:name Macromolecular and Materials Chemistry
104 rdf:type schema:DefinedTerm
105 sg:journal.1042252 schema:issn 1758-2946
106 schema:name Journal of Cheminformatics
107 schema:publisher Springer Nature
108 rdf:type schema:Periodical
109 sg:person.011342402346.80 schema:affiliation grid-institutes:grid.5718.b
110 schema:familyName Epple
111 schema:givenName Matthias
112 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011342402346.80
113 rdf:type schema:Person
114 sg:person.01156445154.10 schema:affiliation grid-institutes:None
115 schema:familyName Truszkowski
116 schema:givenName Andreas
117 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01156445154.10
118 rdf:type schema:Person
119 sg:person.011777342042.92 schema:affiliation grid-institutes:None
120 schema:familyName van den Broek
121 schema:givenName Karina
122 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011777342042.92
123 rdf:type schema:Person
124 sg:person.012010516471.36 schema:affiliation grid-institutes:None
125 schema:familyName Hein
126 schema:givenName Jan-Mathis
127 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012010516471.36
128 rdf:type schema:Person
129 sg:person.012147605703.08 schema:affiliation grid-institutes:None
130 schema:familyName Kuhn
131 schema:givenName Hubert
132 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012147605703.08
133 rdf:type schema:Person
134 sg:person.01272673554.14 schema:affiliation grid-institutes:None
135 schema:familyName Neumann
136 schema:givenName Stefan
137 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01272673554.14
138 rdf:type schema:Person
139 sg:person.016332325241.06 schema:affiliation grid-institutes:None
140 schema:familyName Daniel
141 schema:givenName Mirco
142 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016332325241.06
143 rdf:type schema:Person
144 sg:person.0615402654.46 schema:affiliation grid-institutes:None
145 schema:familyName Zielesny
146 schema:givenName Achim
147 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0615402654.46
148 rdf:type schema:Person
149 sg:pub.10.1007/s00396-004-1137-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030164848
150 https://doi.org/10.1007/s00396-004-1137-9
151 rdf:type schema:CreativeWork
152 sg:pub.10.1186/s13321-014-0045-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050326719
153 https://doi.org/10.1186/s13321-014-0045-3
154 rdf:type schema:CreativeWork
155 sg:pub.10.1186/s13321-018-0278-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1104132414
156 https://doi.org/10.1186/s13321-018-0278-7
157 rdf:type schema:CreativeWork
158 sg:pub.10.1186/s13321-018-0294-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1106083226
159 https://doi.org/10.1186/s13321-018-0294-7
160 rdf:type schema:CreativeWork
161 grid-institutes:None schema:alternateName CAM-D Technologies GmbH, Solingen, Germany
162 GNWI – Gesellschaft für naturwissenschaftliche Informatik mbH, Dortmund, Germany
163 Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany
164 Yara Deutschland, Dülmen, Germany
165 schema:name CAM-D Technologies GmbH, Solingen, Germany
166 GNWI – Gesellschaft für naturwissenschaftliche Informatik mbH, Dortmund, Germany
167 Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany
168 Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany
169 Yara Deutschland, Dülmen, Germany
170 rdf:type schema:Organization
171 grid-institutes:grid.5718.b schema:alternateName Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany
172 schema:name Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany
173 rdf:type schema:Organization
 




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


...