The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook anal...
Uloženo v:
| Vydáno v: | Frontiers in physiology Ročník 9; s. 680 - 13 |
|---|---|
| Hlavní autoři: | , , , , , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
Switzerland
Frontiers
19.06.2018
Frontiers Media S.A |
| Témata: | |
| ISSN: | 1664-042X, 1664-042X |
| On-line přístup: | Získat plný text |
| Tagy: |
Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
|
| Abstract | Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve. The CoLoMoTo Interactive Notebook provides a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks. This framework combines the power of different technologies to ensure repeatability and to reduce users' learning curve of these technologies. The framework is distributed as a Docker image with the tools ready to be run without any installation step besides Docker, and is available on Linux, macOS, and Microsoft Windows. The embedded computational workflows are edited with a Jupyter web interface, enabling the inclusion of textual annotations, along with the explicit code to execute, as well as the visualization of the results. The resulting notebook files can then be shared and re-executed in the same environment. To date, the CoLoMoTo Interactive Notebook provides access to the software tools GINsim, BioLQM, Pint, MaBoSS, and Cell Collective, for the modeling and analysis of Boolean and multi-valued networks. More tools will be included in the future. We developed a Python interface for each of these tools to offer a seamless integration in the Jupyter web interface and ease the chaining of complementary analyses. |
|---|---|
| AbstractList | Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve. The CoLoMoTo Interactive Notebook provides a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks. This framework combines the power of different technologies to ensure repeatability and to reduce users' learning curve of these technologies. The framework is distributed as a Docker image with the tools ready to be run without any installation step besides Docker, and is available on Linux, macOS, and Microsoft Windows. The embedded computational workflows are edited with a Jupyter web interface, enabling the inclusion of textual annotations, along with the explicit code to execute, as well as the visualization of the results. The resulting notebook files can then be shared and re-executed in the same environment. To date, the CoLoMoTo Interactive Notebook provides access to the software tools GINsim, BioLQM, Pint, MaBoSS, and Cell Collective, for the modeling and analysis of Boolean and multi-valued networks. More tools will be included in the future. We developed a Python interface for each of these tools to offer a seamless integration in the Jupyter web interface and ease the chaining of complementary analyses. Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve. The CoLoMoTo Interactive Notebook provides a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks. This framework combines the power of different technologies to ensure repeatability and to reduce users' learning curve of these technologies. The framework is distributed as a Docker image with the tools ready to be run without any installation step besides Docker, and is available on Linux, macOS, and Microsoft Windows. The embedded computational workflows are edited with a Jupyter web interface, enabling the inclusion of textual annotations, along with the explicit code to execute, as well as the visualization of the results. The resulting notebook files can then be shared and re-executed in the same environment. To date, the CoLoMoTo Interactive Notebook provides access to the software tools GINsim, BioLQM, Pint, MaBoSS, and Cell Collective, for the modeling and analysis of Boolean and multi-valued networks. More tools will be included in the future. We developed a Python interface for each of these tools to offer a seamless integration in the Jupyter web interface and ease the chaining of complementary analyses.Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve. The CoLoMoTo Interactive Notebook provides a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks. This framework combines the power of different technologies to ensure repeatability and to reduce users' learning curve of these technologies. The framework is distributed as a Docker image with the tools ready to be run without any installation step besides Docker, and is available on Linux, macOS, and Microsoft Windows. The embedded computational workflows are edited with a Jupyter web interface, enabling the inclusion of textual annotations, along with the explicit code to execute, as well as the visualization of the results. The resulting notebook files can then be shared and re-executed in the same environment. To date, the CoLoMoTo Interactive Notebook provides access to the software tools GINsim, BioLQM, Pint, MaBoSS, and Cell Collective, for the modeling and analysis of Boolean and multi-valued networks. More tools will be included in the future. We developed a Python interface for each of these tools to offer a seamless integration in the Jupyter web interface and ease the chaining of complementary analyses. Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve. The CoLoMoTo Interactive Notebook provides a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks.This framework combines the power of different technologies to ensure repeatability and to reduce users' learning curve of these technologies. The framework is distributed as a Docker image with the tools ready to be run without any installation step besides Docker, and is available on Linux, macOS, and Microsoft Windows. The embedded computational workflows are edited with a Jupyter web interface, enabling the inclusion of textual annotations, along with the explicit code to execute, as well as the visualisation of the results. The resulting notebook files can then be shared and re-executed in the same environment. To date, the CoLoMoTo Interactive Notebook provides access to software tools including GINsim, BioLQM, Pint, MaBoSS, and Cell Collective for the modelling and analysis of Boolean and multi-valued networks. More tools will be included in the future. We developed a Python interface for each of these tools to offer a seamless integration in the Jupyter web interface and ease the chaining of complementary analyses. |
| Author | Hernandez, Céline Zinovyev, Andrei Helikar, Tomáš Calzone, Laurence Levy, Nicolas Monteiro, Pedro T. Chaouiya, Claudine Cohen-Boulakia, Sarah Thieffry, Denis Naldi, Aurélien Stoll, Gautier Paulevé, Loïc |
| AuthorAffiliation | 8 Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer , Villejuif , France 14 MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology , Paris , France 7 Université Pierre et Marie Curie , Paris , France 11 Department of Biochemistry, University of Nebraska-Lincoln , Lincoln, NE , United States 3 École Normale Supérieure de Lyon , Lyon , France 12 Institut Curie, PSL Research University , Paris , France 9 INESC-ID/Instituto Superior Técnico, University of Lisbon , Lisbon , Portugal 6 Institut National de la Santé et de la Recherche Médicale, U1138 , Paris , France 15 Lobachevsky University , Nizhni Novgorod , Russia 4 Université Paris Descartes/Paris V, Sorbonne Paris Cité , Paris , France 2 Laboratoire de Recherche en Informatique UMR8623, Université Paris-Sud, Centre National de la Recherche Scientifique, Université Paris-Saclay , Orsay , France 5 Équipe 11 Labellisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers , Paris , France 10 Instit |
| AuthorAffiliation_xml | – name: 12 Institut Curie, PSL Research University , Paris , France – name: 13 Institut National de la Santé et de la Recherche Médicale, U900 , Paris , France – name: 8 Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer , Villejuif , France – name: 5 Équipe 11 Labellisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers , Paris , France – name: 11 Department of Biochemistry, University of Nebraska-Lincoln , Lincoln, NE , United States – name: 14 MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology , Paris , France – name: 7 Université Pierre et Marie Curie , Paris , France – name: 2 Laboratoire de Recherche en Informatique UMR8623, Université Paris-Sud, Centre National de la Recherche Scientifique, Université Paris-Saclay , Orsay , France – name: 1 Computational Systems Biology Team, Institut de Biologie de I'Ecole Normale Supérieure, Centre National de la Recherche Scientifique UMR8197, Institut National de la Santé et de la Recherche Médicale U1024, École Normale Supérieure, PSL Université , Paris , France – name: 3 École Normale Supérieure de Lyon , Lyon , France – name: 15 Lobachevsky University , Nizhni Novgorod , Russia – name: 4 Université Paris Descartes/Paris V, Sorbonne Paris Cité , Paris , France – name: 9 INESC-ID/Instituto Superior Técnico, University of Lisbon , Lisbon , Portugal – name: 6 Institut National de la Santé et de la Recherche Médicale, U1138 , Paris , France – name: 10 Instituto Gulbenkian de Ciência , Oeiras , Portugal |
| Author_xml | – sequence: 1 givenname: Aurélien surname: Naldi fullname: Naldi, Aurélien – sequence: 2 givenname: Céline surname: Hernandez fullname: Hernandez, Céline – sequence: 3 givenname: Nicolas surname: Levy fullname: Levy, Nicolas – sequence: 4 givenname: Gautier surname: Stoll fullname: Stoll, Gautier – sequence: 5 givenname: Pedro T. surname: Monteiro fullname: Monteiro, Pedro T. – sequence: 6 givenname: Claudine surname: Chaouiya fullname: Chaouiya, Claudine – sequence: 7 givenname: Tomáš surname: Helikar fullname: Helikar, Tomáš – sequence: 8 givenname: Andrei surname: Zinovyev fullname: Zinovyev, Andrei – sequence: 9 givenname: Laurence surname: Calzone fullname: Calzone, Laurence – sequence: 10 givenname: Sarah surname: Cohen-Boulakia fullname: Cohen-Boulakia, Sarah – sequence: 11 givenname: Denis surname: Thieffry fullname: Thieffry, Denis – sequence: 12 givenname: Loïc surname: Paulevé fullname: Paulevé, Loïc |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29971009$$D View this record in MEDLINE/PubMed https://hal.science/hal-01794294$$DView record in HAL |
| BookMark | eNp1kk1vEzEQhleoiJbSOye0RzgkjD-yu-aAFCKgkUIRKEjcLK8_ErebndTeDcq_x5uUqq2ED7Y1876PPZp5mZ202Nose01gzFgl3rvteh_HFEg1BigqeJadkaLgI-D098mD-2l2EeM1pMWBApAX2SkVoiQA4izbL9c2n-ECv-ES83nb2aB053c2v8LO1og3H_Kp1jZGXzc2V63Jf9ptQNPrQ2CGm23fqc5jq5p8mrZ9tDF3GPIfvWr8kEqwTx4bXHmdNFe2-4PhJr7KnjvVRHtxd55nv758Xs4uR4vvX-ez6WKkOSEwqkrHy6LU2mjtKAfGHKHKUkaM4FQA46BKBqyuuTKk1KLmBuraaUUrM3E1O8_mR65BdS23wW9U2EtUXh4CGFZShc7rxkqhqOFG6QoE49oqoWumWeEMYaSojUusj0fWtq831mjbdkE1j6CPM61fyxXuZJG6xMkkAd4dAesntsvpQg4xIOVQFt_RpH1791jA297GTm581LZpVGuxj5JCwSkTMBmwbx7-6578r89JAEeBDhhjsO5eQkAO0yQP0ySHaZKHaUqW4olF-2OjU2W--b_xL45R0mM |
| CitedBy_id | crossref_primary_10_1186_s12859_025_06212_2 crossref_primary_10_1186_s12859_023_05326_9 crossref_primary_10_3389_fphys_2018_01605 crossref_primary_10_1093_bib_bbaa046 crossref_primary_10_1093_bioinformatics_btaf123 crossref_primary_10_1109_ACCESS_2021_3097550 crossref_primary_10_1016_j_tcs_2024_114505 crossref_primary_10_3389_fmolb_2020_502573 crossref_primary_10_1016_j_csbj_2022_10_003 crossref_primary_10_1098_rsfs_2025_0002 crossref_primary_10_1016_j_coisb_2021_100386 crossref_primary_10_3389_fmicb_2024_1368377 crossref_primary_10_1016_j_jtbi_2023_111682 crossref_primary_10_1177_11769351221087028 crossref_primary_10_1093_bioadv_vbaf082 crossref_primary_10_1371_journal_pcbi_1011620 crossref_primary_10_1016_j_jtbi_2022_111025 crossref_primary_10_3390_biomedicines9111655 crossref_primary_10_1016_j_immuno_2025_100060 crossref_primary_10_1038_s41592_022_01479_2 crossref_primary_10_1371_journal_pone_0226388 crossref_primary_10_1038_s41467_020_18112_5 crossref_primary_10_15252_msb_202110387 crossref_primary_10_24072_pcjournal_255 crossref_primary_10_1093_bib_bbaf002 crossref_primary_10_3389_fmolb_2021_754444 crossref_primary_10_1093_bib_bbac212 crossref_primary_10_3389_fphys_2018_00787 crossref_primary_10_3389_fphys_2020_558606 crossref_primary_10_1186_s12859_021_04158_9 crossref_primary_10_3390_ijms22094897 crossref_primary_10_1016_j_csbj_2021_08_028 crossref_primary_10_1371_journal_pcbi_1011254 crossref_primary_10_1038_s41540_023_00294_5 crossref_primary_10_1242_dev_189944 crossref_primary_10_1038_s41540_025_00532_y crossref_primary_10_1371_journal_pcbi_1010408 crossref_primary_10_1103_PhysRevResearch_5_033009 |
| Cites_doi | 10.1371/journal.pcbi.1001122 10.1103/PhysRevE.97.042308 10.1158/1078-0432.CCR-13-0043 10.1093/bioinformatics/btw682 10.1186/s12918-016-0288-x 10.1109/TCBB.2017.2749225. 10.1186/1752-0509-5-198 10.1093/bioinformatics/btg015 10.1186/1752-0509-7-135 10.1186/1752-0509-6-133 10.1186/1751-0473-3-16 10.1371/journal.pcbi.1004591 10.1186/1752-0509-6-96 10.3389/fphys.2018.00787 10.1016/j.jbiotec.2017.06.007 10.1093/biostatistics/kxp014 10.1007/11880646_10 10.1016/0022-5193(73)90247-6 10.1093/bioinformatics/btl210 10.1038/483531a 10.1016/j.future.2017.01.012 10.1126/scisignal.aaa5764 10.1093/bioinformatics/btv013 10.1038/nbt1156 10.1093/bioinformatics/bti1048 10.1007/s11786-008-0064-4 10.1201/b16868 10.3389/fgene.2016.00094 10.1093/bioinformatics/btq124 10.1093/bioinformatics/bts480 10.7554/eLife.04333 10.1093/bioinformatics/btx123 10.1186/1471-2105-15-221 10.1371/journal.pone.0045780 10.1093/bioinformatics/btn336 10.1186/1752-0509-6-116 10.1093/bioinformatics/btw457 10.1126/scitranslmed.aaf5027 10.1038/nmeth0310-167 10.1016/j.tcs.2010.10.021 10.1093/nar/gkq429 10.1161/CIRCRESAHA.114.303819 10.3389/fphys.2018.00646 10.1016/0022-5193(69)9001 10.1515/jib-2015-270 10.3389/fbioe.2014.00086 10.1038/533452a 10.1145/2213836.2213908 10.1016/j.biosystems.2016.07.009 10.1038/535355b 10.1371/journal.pone.0067111 |
| ContentType | Journal Article |
| Copyright | licence_http://creativecommons.org/publicdomain/zero Copyright © 2018 Naldi, Hernandez, Levy, Stoll, Monteiro, Chaouiya, Helikar, Zinovyev, Calzone, Cohen-Boulakia, Thieffry and Paulevé. 2018 Naldi, Hernandez, Levy, Stoll, Monteiro, Chaouiya, Helikar, Zinovyev, Calzone, Cohen-Boulakia, Thieffry and Paulevé |
| Copyright_xml | – notice: licence_http://creativecommons.org/publicdomain/zero – notice: Copyright © 2018 Naldi, Hernandez, Levy, Stoll, Monteiro, Chaouiya, Helikar, Zinovyev, Calzone, Cohen-Boulakia, Thieffry and Paulevé. 2018 Naldi, Hernandez, Levy, Stoll, Monteiro, Chaouiya, Helikar, Zinovyev, Calzone, Cohen-Boulakia, Thieffry and Paulevé |
| DBID | AAYXX CITATION NPM 7X8 1XC VOOES 5PM DOA |
| DOI | 10.3389/fphys.2018.00680 |
| DatabaseName | CrossRef PubMed MEDLINE - Academic Hyper Article en Ligne (HAL) Hyper Article en Ligne (HAL) (Open Access) PubMed Central (Full Participant titles) DOAJ Directory of Open Access Journals |
| DatabaseTitle | CrossRef PubMed MEDLINE - Academic |
| DatabaseTitleList | MEDLINE - Academic PubMed |
| Database_xml | – sequence: 1 dbid: DOA name: DOAJ Directory of Open Access Journals url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 3 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Anatomy & Physiology Computer Science |
| EISSN | 1664-042X |
| EndPage | 13 |
| ExternalDocumentID | oai_doaj_org_article_9a2d4dac80934cea9cb3c36fd1316bdf PMC6018415 oai:HAL:hal-01794294v2 29971009 10_3389_fphys_2018_00680 |
| Genre | Journal Article |
| GrantInformation_xml | – fundername: NIGMS NIH HHS grantid: R35 GM119770 – fundername: Agence Nationale de la Recherche grantid: ANR-15-CE15-0006-01; ANR-16-CE12-0034; ANR-11-LABEX-0045-DIGICOSME; ANR-11-IDEX-0003-02 – fundername: National Institutes of Health grantid: 5R35GM119770-02 – fundername: Fundação para a Ciência e a Tecnologia grantid: PTDC/BEX-BCB/0772/2014; PTDC/EEI-CTP/2914/2014 |
| GroupedDBID | 53G 5VS 9T4 AAFWJ AAKDD AAYXX ACGFO ACGFS ADBBV ADRAZ AENEX AFPKN ALMA_UNASSIGNED_HOLDINGS AOIJS BCNDV CITATION DIK EMOBN F5P GROUPED_DOAJ GX1 HYE KQ8 M48 M~E O5R O5S OK1 PGMZT RNS RPM ACXDI IPNFZ NPM RIG 7X8 1XC VOOES 5PM |
| ID | FETCH-LOGICAL-c4110-87f4767ccdccf24033f12ae231d94290340a7303bb4ad17c9b4d0bbfca28d5fb3 |
| IEDL.DBID | DOA |
| ISSN | 1664-042X |
| IngestDate | Fri Oct 03 12:46:27 EDT 2025 Thu Aug 21 14:15:49 EDT 2025 Wed Nov 26 06:49:07 EST 2025 Fri Sep 05 07:31:40 EDT 2025 Thu Apr 03 07:11:59 EDT 2025 Tue Nov 18 22:29:42 EST 2025 Sat Nov 29 06:27:01 EST 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Keywords | computational systems biology model analysis Python programming language reproducibility Boolean networks |
| Language | English |
| License | licence_http://creativecommons.org/publicdomain/zero/: http://creativecommons.org/publicdomain/zero This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c4110-87f4767ccdccf24033f12ae231d94290340a7303bb4ad17c9b4d0bbfca28d5fb3 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Reviewed by: Oksana Sorokina, University of Edinburgh, United Kingdom; Kyle B. Gustafson, Naval Surface Warfare Center Carderock Division (NSWCCD), United States This article was submitted to Systems Biology, a section of the journal Frontiers in Physiology Edited by: Pierre De Meyts, de Duve Institute, Belgium |
| ORCID | 0000-0002-7835-1148 0000-0003-2350-0756 0000-0002-9517-7284 0000-0002-7439-1441 0000-0002-6495-2655 0000-0002-0862-4139 0000-0001-8664-1340 0000-0002-7219-2027 |
| OpenAccessLink | https://doaj.org/article/9a2d4dac80934cea9cb3c36fd1316bdf |
| PMID | 29971009 |
| PQID | 2064239055 |
| PQPubID | 23479 |
| ParticipantIDs | doaj_primary_oai_doaj_org_article_9a2d4dac80934cea9cb3c36fd1316bdf pubmedcentral_primary_oai_pubmedcentral_nih_gov_6018415 hal_primary_oai_HAL_hal_01794294v2 proquest_miscellaneous_2064239055 pubmed_primary_29971009 crossref_primary_10_3389_fphys_2018_00680 crossref_citationtrail_10_3389_fphys_2018_00680 |
| PublicationCentury | 2000 |
| PublicationDate | 2018-06-19 |
| PublicationDateYYYYMMDD | 2018-06-19 |
| PublicationDate_xml | – month: 06 year: 2018 text: 2018-06-19 day: 19 |
| PublicationDecade | 2010 |
| PublicationPlace | Switzerland |
| PublicationPlace_xml | – name: Switzerland |
| PublicationTitle | Frontiers in physiology |
| PublicationTitleAlternate | Front Physiol |
| PublicationYear | 2018 |
| Publisher | Frontiers Frontiers Media S.A |
| Publisher_xml | – name: Frontiers – name: Frontiers Media S.A |
| References | Cohen-Boulakia (B12) 2017; 75 Naldi (B31) 2018; 9 Veliz-Cuba (B52) 2014; 15 Richter (B39) 2010; 7 Begley (B7) 2012; 483 Baker (B4) 2016; 533 Batt (B6) 2005; 21 Müssel (B30) 2010; 26 Paulevé (B36) Kauffman (B24) 1969; 22 Le Novère (B27) 2005; 23 Fauré (B15) 2006; 22 Abou-Jaoudé (B1) 2015; 2 Waltemath (B53); 7 Gan (B18) 2018; 97 Siebert (B41) 2009; 2 Chaouiya (B9) 2013; 7 Naldi (B32) 2015; 31 Peng (B37) 2009; 10 Traynard (B51) 2016; 32 Santori (B40) 2016; 535 Stoll (B45) 2017; 33 Helikar (B22) 2012; 6 Waltemath (B54); 5 Goble (B20) 2010; 38 Smith (B42) 2013; 19 Klarner (B25) 2017; 33 Yaffe (B56) 2015; 8 Freire (B17) 2016 Garg (B19) 2008; 24 Chaouiya (B10) 2015; 12 Cimatti (B11) 2002 Errington (B14) 2014; 3 Goodman (B21) 2016; 8 Stodden (B43) 2013; 8 Begley (B8) 2015; 116 Thomas (B49) 1973; 42 Todd (B50) 2012; 7 Lewis (B29) 2016; 10 Terfve (B48) 2012; 6 Ragan-Kelley (B38) 2014 Abou-Jaoudé (B2) 2016; 7 Albert (B3) 2008; 3 Drummond (B13) 2009 Köster (B26) 2012; 28 Paulevé (B35) 2017 Ostrowski (B34) 2016; 149 Talcott (B47) 2006 Hucka (B23) 2003; 19 Stodden (B44) 2014 Naldi (B33) 2011; 412 Bartocci (B5) 2016; 12 Levy (B28) 2018; 9 Wittig (B55) 2017; 261 Freire (B16) 2012 Stoll (B46) 2012; 6 22460880 - Nature. 2012 Mar 28;483(7391):531-3 25674559 - Front Bioeng Biotechnol. 2015 Jan 28;2:86 21552546 - PLoS Comput Biol. 2011 Apr;7(4):e1001122 26528568 - J Integr Bioinform. 2015 Sep 04;12(2):270 20195246 - Nat Methods. 2010 Mar;7(3):167-8 27587700 - Bioinformatics. 2016 Sep 1;32(17):i772-i780 25552691 - Circ Res. 2015 Jan 2;116(1):116-26 18614585 - Bioinformatics. 2008 Sep 1;24(17):1917-25 16333295 - Nat Biotechnol. 2005 Dec;23(12):1509-15 27484338 - Biosystems. 2016 Nov;149:139-153 16873462 - Bioinformatics. 2006 Jul 15;22(14):e124-31 24321545 - BMC Syst Biol. 2013 Dec 10;7:135 20378558 - Bioinformatics. 2010 May 15;26(10):1378-80 26795950 - PLoS Comput Biol. 2016 Jan 21;12(1):e1004591 27422148 - BMC Syst Biol. 2016 Jul 15;10(1):52 22871178 - BMC Syst Biol. 2012 Aug 07;6:96 27797783 - Bioinformatics. 2017 Mar 1;33(5):770-772 27303434 - Front Genet. 2016 May 31;7:94 22908215 - Bioinformatics. 2012 Oct 1;28(19):2520-2 23049686 - PLoS One. 2012;7(10):e45780 25619997 - Bioinformatics. 2015 Apr 1;31(7):1154-9 22932419 - BMC Syst Biol. 2012 Aug 29;6:116 27443731 - Nature. 2016 Jul 20;535(7612):355 24965213 - BMC Bioinformatics. 2014 Jun 26;15:221 29758614 - Phys Rev E. 2018 Apr;97(4-1):042308 22172142 - BMC Syst Biol. 2011 Dec 15;5:198 27225100 - Nature. 2016 May 25;533(7604):452-4 23580781 - Clin Cancer Res. 2013 Jun 1;19(11):2828-33 23079107 - BMC Syst Biol. 2012 Oct 18;6:133 5803332 - J Theor Biol. 1969 Mar;22(3):437-67 12611808 - Bioinformatics. 2003 Mar 1;19(4):524-31 4588055 - J Theor Biol. 1973 Dec;42(3):563-85 27252173 - Sci Transl Med. 2016 Jun 1;8(341):341ps12 19014577 - Source Code Biol Med. 2008 Nov 14;3:16 28881959 - Bioinformatics. 2017 Jul 15;33(14):2226-2228 15961457 - Bioinformatics. 2005 Jun;21 Suppl 1:i19-28 25490932 - Elife. 2014 Dec 10;3:null 28885158 - IEEE/ACM Trans Comput Biol Bioinform. 2017 Sep 06;:null 20501605 - Nucleic Acids Res. 2010 Jul;38(Web Server issue):W677-82 19535325 - Biostatistics. 2009 Jul;10(3):405-8 23805293 - PLoS One. 2013 Jun 21;8(6):e67111 25852185 - Sci Signal. 2015 Apr 07;8(371):eg5 28606610 - J Biotechnol. 2017 Nov 10;261:229-237 |
| References_xml | – volume-title: Proceedings of International Conference on Computer-Aided Verification (CAV 2002), Vol. 2404 of LNCS year: 2002 ident: B11 article-title: NuSMV Version 2: an OpenSource Tool for Symbolic Model Checking – volume: 7 start-page: e1001122 ident: B53 article-title: Minimum Information About a Simulation Experiment (MIASE) publication-title: PLoS Comput. Biol. doi: 10.1371/journal.pcbi.1001122 – volume: 97 start-page: 042308 year: 2018 ident: B18 article-title: General method to find the attractors of discrete dynamic models of biological systems publication-title: Phys. Rev. E doi: 10.1103/PhysRevE.97.042308 – volume: 19 start-page: 2828 year: 2013 ident: B42 article-title: A proposal regarding reporting of in vitro testing results publication-title: Clin. Cancer Res. doi: 10.1158/1078-0432.CCR-13-0043 – volume: 33 start-page: 770 year: 2017 ident: B25 article-title: PyBoolNet: a python package for the generation, analysis and visualization of Boolean networks publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw682 – volume: 10 start-page: 52 year: 2016 ident: B29 article-title: Where next for the reproducibility agenda in computational biology? publication-title: BMC Syst. Biol. doi: 10.1186/s12918-016-0288-x – ident: B36 article-title: Reduction of qualitative models of biological networks for transient dynamics analysis publication-title: IEEE/ACM Trans. Comput. Biol. Bioinform doi: 10.1109/TCBB.2017.2749225. – volume: 5 start-page: 198 ident: B54 article-title: Reproducible computational biology experiments with SED-ML – the Simulation Experiment Description Markup Language publication-title: BMC Syst. Biol. doi: 10.1186/1752-0509-5-198 – volume-title: Proceedings of the Evaluation Methods for Machine Learning Workshop at the 26th ICML year: 2009 ident: B13 article-title: Replicability is not reproducibility: nor is it good science – volume: 19 start-page: 524 year: 2003 ident: B23 article-title: The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models publication-title: Bioinformatics doi: 10.1093/bioinformatics/btg015 – volume: 7 start-page: 135 year: 2013 ident: B9 article-title: SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools publication-title: BMC Syst. Biol. doi: 10.1186/1752-0509-7-135 – volume: 6 start-page: 133 year: 2012 ident: B48 article-title: CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms publication-title: BMC Syst. Biol. doi: 10.1186/1752-0509-6-133 – volume: 3 start-page: 16 year: 2008 ident: B3 article-title: Boolean network simulations for life scientists publication-title: Source Code Biol. Med. doi: 10.1186/1751-0473-3-16 – volume: 12 start-page: e1004591 year: 2016 ident: B5 article-title: Computational modeling, formal analysis, and tools for systems biology publication-title: PLOS Comput. Biol. doi: 10.1371/journal.pcbi.1004591 – volume: 6 start-page: 96 year: 2012 ident: B22 article-title: The Cell Collective: toward an open and collaborative approach to systems biology publication-title: BMC Syst. Biol. doi: 10.1186/1752-0509-6-96 – volume: 9 start-page: 787 year: 2018 ident: B28 article-title: Prediction of mutations to control pathways enabling tumour cell invasion with the CoLoMoTo interactive notebook (tutorial) publication-title: Front. Physiol doi: 10.3389/fphys.2018.00787 – volume: 261 start-page: 229 year: 2017 ident: B55 article-title: Data management and data enrichment for systems biology projects publication-title: J. Biotechnol. doi: 10.1016/j.jbiotec.2017.06.007 – volume: 10 start-page: 405 year: 2009 ident: B37 article-title: Reproducible research and biostatistics publication-title: Biostatistics doi: 10.1093/biostatistics/kxp014 – start-page: 221 volume-title: Transactions on Computational Systems Biology VI year: 2006 ident: B47 article-title: Multiple representations of biological processes doi: 10.1007/11880646_10 – volume: 42 start-page: 563 year: 1973 ident: B49 article-title: Boolean formalization of genetic control circuits publication-title: J. Theor. Biol. doi: 10.1016/0022-5193(73)90247-6 – volume: 22 start-page: 124 year: 2006 ident: B15 article-title: Dynamical analysis of a generic boolean model for the control of the mammalian cell cycle publication-title: Bioinformatics doi: 10.1093/bioinformatics/btl210 – volume-title: AGU Fall Meeting Abstracts year: 2014 ident: B38 article-title: The Jupyter/IPython architecture: a unified view of computational research, from interactive exploration to communication and publication – volume: 483 start-page: 531 year: 2012 ident: B7 article-title: Drug development: raise standards for preclinical cancer research publication-title: Nature doi: 10.1038/483531a – volume: 75 start-page: 284 year: 2017 ident: B12 article-title: Scientific workflows for computational reproducibility in the life sciences: status, challenges and opportunities publication-title: Fut. Gen. Comput. Syst. doi: 10.1016/j.future.2017.01.012 – volume: 8 start-page: eg5 year: 2015 ident: B56 article-title: Reproducibility in science publication-title: Sci. Signal. doi: 10.1126/scisignal.aaa5764 – volume: 31 start-page: 1154 year: 2015 ident: B32 article-title: Cooperative development of logical modelling standards and tools with CoLoMoTo publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv013 – volume: 23 start-page: 1509 year: 2005 ident: B27 article-title: Minimum information requested in the annotation of biochemical models (MIRIAM) publication-title: Nat. Biotechnol. doi: 10.1038/nbt1156 – volume: 21 start-page: i19 year: 2005 ident: B6 article-title: Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response publication-title: Escherichia coli. Bioinformatics doi: 10.1093/bioinformatics/bti1048 – start-page: 370 volume-title: CMSB 2017 - 15th Conference on Computational Methods for Systems Biology Volume 10545 of Lecture Notes in Computer Science year: 2017 ident: B35 article-title: Pint: a static analyzer for transient dynamics of qualitative networks with IPython interface – volume: 2 start-page: 421 year: 2009 ident: B41 article-title: Deriving behavior of boolean bioregulatory networks from subnetwork dynamics publication-title: Math. Comput. Sci. doi: 10.1007/s11786-008-0064-4 – volume-title: Implementing Reproducible Research year: 2014 ident: B44 doi: 10.1201/b16868 – volume: 7 start-page: 94 year: 2016 ident: B2 article-title: Logical modeling and dynamical analysis of cellular networks publication-title: Front. Genet. doi: 10.3389/fgene.2016.00094 – volume: 26 start-page: 1378 year: 2010 ident: B30 article-title: BoolNet–an R package for generation, reconstruction and analysis of Boolean networks publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq124 – volume: 28 start-page: 2520 year: 2012 ident: B26 article-title: Snakemake - a scalable bioinformatics workflow engine publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts480 – volume: 3 start-page: e04333 year: 2014 ident: B14 article-title: An open investigation of the reproducibility of cancer biology research publication-title: Elife doi: 10.7554/eLife.04333 – volume: 33 start-page: 2226 year: 2017 ident: B45 article-title: MaBoSS 2.0: an environment for stochastic Boolean modeling publication-title: Bioinformatics doi: 10.1093/bioinformatics/btx123 – volume: 15 start-page: 221 year: 2014 ident: B52 article-title: Steady state analysis of boolean molecular network models via model reduction and computational algebra publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-15-221 – start-page: 108 volume-title: Dagstuhl Seminar 16041 year: 2016 ident: B17 article-title: Reproducibility of data-oriented experiments in e-science – volume: 7 start-page: e45780 year: 2012 ident: B50 article-title: Ergodic sets as cell phenotype of budding yeast cell cycle publication-title: PLoS ONE doi: 10.1371/journal.pone.0045780 – volume: 24 start-page: 1917 year: 2008 ident: B19 article-title: Synchronous versus asynchronous modeling of gene regulatory networks publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn336 – volume: 6 start-page: 116 year: 2012 ident: B46 article-title: Continuous time boolean modeling for biological signaling: application of gillespie algorithm publication-title: BMC Systems Biology doi: 10.1186/1752-0509-6-116 – volume: 32 start-page: i772 year: 2016 ident: B51 article-title: Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw457 – volume: 8 start-page: 341p year: 2016 ident: B21 article-title: What does research reproducibility mean? publication-title: Sci. Transl. Med. doi: 10.1126/scitranslmed.aaf5027 – volume: 7 start-page: 167 year: 2010 ident: B39 article-title: Systematic variation improves reproducibility of animal experiments publication-title: Nat. Methods doi: 10.1038/nmeth0310-167 – volume: 412 start-page: 2207 year: 2011 ident: B33 article-title: Dynamically consistent reduction of logical regulatory graphs publication-title: Theor. Comput. Sci. doi: 10.1016/j.tcs.2010.10.021 – volume: 38 start-page: W677 year: 2010 ident: B20 article-title: myExperiment: a repository and social network for the sharing of bioinformatics workflows publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkq429 – volume: 116 start-page: 116 year: 2015 ident: B8 article-title: Reproducibility in science improving the standard for basic and preclinical research publication-title: Circ. Res. doi: 10.1161/CIRCRESAHA.114.303819 – volume: 9 start-page: 646 year: 2018 ident: B31 article-title: Logical modelling and analysis of cellular regulatory networks with GINsim 3.0 publication-title: Front. Physiol. doi: 10.3389/fphys.2018.00646 – volume: 22 start-page: 437 year: 1969 ident: B24 article-title: Metabolic stability and epigenesis in randomly constructed genetic nets publication-title: J. Theor. Biol. doi: 10.1016/0022-5193(69)9001 – volume: 12 start-page: 270 year: 2015 ident: B10 article-title: The Systems Biology Markup Language (SBML) level 3 package: qualitative models, version 1, release 1 publication-title: J. Integr. Bioinform. doi: 10.1515/jib-2015-270 – volume: 2 start-page: 86 year: 2015 ident: B1 article-title: Model checking to assess t-helper cell plasticity publication-title: Front. Bioeng. Biotechnol. doi: 10.3389/fbioe.2014.00086 – volume: 533 start-page: 452 year: 2016 ident: B4 article-title: 1,500 scientists lift the lid on reproducibility publication-title: Nat. News doi: 10.1038/533452a – start-page: 593 volume-title: Proceedings of the 2012 ACM SIGMOD International Conference on Management of Data year: 2012 ident: B16 article-title: Computational reproducibility: state-of-the-art, challenges, and database research opportunities doi: 10.1145/2213836.2213908 – volume: 149 start-page: 139 year: 2016 ident: B34 article-title: Boolean network identification from perturbation time series data combining dynamics abstraction and logic programming publication-title: Biosystems doi: 10.1016/j.biosystems.2016.07.009 – volume: 535 start-page: 355 year: 2016 ident: B40 article-title: Journals should drive data reproducibility publication-title: Nature doi: 10.1038/535355b – volume: 8 start-page: e67111 year: 2013 ident: B43 article-title: Toward reproducible computational research: an empirical analysis of data and code policy adoption by journals publication-title: PLoS ONE doi: 10.1371/journal.pone.0067111 – reference: 20501605 - Nucleic Acids Res. 2010 Jul;38(Web Server issue):W677-82 – reference: 22172142 - BMC Syst Biol. 2011 Dec 15;5:198 – reference: 24965213 - BMC Bioinformatics. 2014 Jun 26;15:221 – reference: 20378558 - Bioinformatics. 2010 May 15;26(10):1378-80 – reference: 25552691 - Circ Res. 2015 Jan 2;116(1):116-26 – reference: 28885158 - IEEE/ACM Trans Comput Biol Bioinform. 2017 Sep 06;:null – reference: 24321545 - BMC Syst Biol. 2013 Dec 10;7:135 – reference: 27484338 - Biosystems. 2016 Nov;149:139-153 – reference: 25674559 - Front Bioeng Biotechnol. 2015 Jan 28;2:86 – reference: 22908215 - Bioinformatics. 2012 Oct 1;28(19):2520-2 – reference: 29758614 - Phys Rev E. 2018 Apr;97(4-1):042308 – reference: 19535325 - Biostatistics. 2009 Jul;10(3):405-8 – reference: 27225100 - Nature. 2016 May 25;533(7604):452-4 – reference: 26528568 - J Integr Bioinform. 2015 Sep 04;12(2):270 – reference: 16873462 - Bioinformatics. 2006 Jul 15;22(14):e124-31 – reference: 23805293 - PLoS One. 2013 Jun 21;8(6):e67111 – reference: 26795950 - PLoS Comput Biol. 2016 Jan 21;12(1):e1004591 – reference: 12611808 - Bioinformatics. 2003 Mar 1;19(4):524-31 – reference: 5803332 - J Theor Biol. 1969 Mar;22(3):437-67 – reference: 28881959 - Bioinformatics. 2017 Jul 15;33(14):2226-2228 – reference: 28606610 - J Biotechnol. 2017 Nov 10;261:229-237 – reference: 20195246 - Nat Methods. 2010 Mar;7(3):167-8 – reference: 25490932 - Elife. 2014 Dec 10;3:null – reference: 27443731 - Nature. 2016 Jul 20;535(7612):355 – reference: 27422148 - BMC Syst Biol. 2016 Jul 15;10(1):52 – reference: 25852185 - Sci Signal. 2015 Apr 07;8(371):eg5 – reference: 19014577 - Source Code Biol Med. 2008 Nov 14;3:16 – reference: 23580781 - Clin Cancer Res. 2013 Jun 1;19(11):2828-33 – reference: 21552546 - PLoS Comput Biol. 2011 Apr;7(4):e1001122 – reference: 22460880 - Nature. 2012 Mar 28;483(7391):531-3 – reference: 22932419 - BMC Syst Biol. 2012 Aug 29;6:116 – reference: 25619997 - Bioinformatics. 2015 Apr 1;31(7):1154-9 – reference: 23049686 - PLoS One. 2012;7(10):e45780 – reference: 22871178 - BMC Syst Biol. 2012 Aug 07;6:96 – reference: 27303434 - Front Genet. 2016 May 31;7:94 – reference: 15961457 - Bioinformatics. 2005 Jun;21 Suppl 1:i19-28 – reference: 23079107 - BMC Syst Biol. 2012 Oct 18;6:133 – reference: 18614585 - Bioinformatics. 2008 Sep 1;24(17):1917-25 – reference: 27797783 - Bioinformatics. 2017 Mar 1;33(5):770-772 – reference: 16333295 - Nat Biotechnol. 2005 Dec;23(12):1509-15 – reference: 27587700 - Bioinformatics. 2016 Sep 1;32(17):i772-i780 – reference: 4588055 - J Theor Biol. 1973 Dec;42(3):563-85 – reference: 27252173 - Sci Transl Med. 2016 Jun 1;8(341):341ps12 |
| SSID | ssj0000402001 |
| Score | 2.458965 |
| Snippet | Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many... |
| SourceID | doaj pubmedcentral hal proquest pubmed crossref |
| SourceType | Open Website Open Access Repository Aggregation Database Index Database Enrichment Source |
| StartPage | 680 |
| SubjectTerms | Bioinformatics Boolean networks computational systems biology Computer Science model analysis Physiology Python programming language reproducibility |
| Title | The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/29971009 https://www.proquest.com/docview/2064239055 https://hal.science/hal-01794294 https://pubmed.ncbi.nlm.nih.gov/PMC6018415 https://doaj.org/article/9a2d4dac80934cea9cb3c36fd1316bdf |
| Volume | 9 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVAON databaseName: DOAJ Directory of Open Access Journals customDbUrl: eissn: 1664-042X dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0000402001 issn: 1664-042X databaseCode: DOA dateStart: 20100101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVHPJ databaseName: ROAD: Directory of Open Access Scholarly Resources customDbUrl: eissn: 1664-042X dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0000402001 issn: 1664-042X databaseCode: M~E dateStart: 20100101 isFulltext: true titleUrlDefault: https://road.issn.org providerName: ISSN International Centre |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1Lb9QwELag4sAFAeURHpVBCIlDtHHs2DG3pWrVw3bFoUh7i_xUV2oT1N1W4tLf3hk7Xe2CBBcuOTiOY3vG8_LoG0I-cSujZMaXQvqmFMrxshVelcFZFluHsf5E6Zmaz9vFQn_fKvWFOWEZHjhv3ESb2gtvXAuut3DBaGe54zJ6xpm0PqL0rZTecqaSDEa3qGL5XhK8MD2JGCnAVC7MnZSIArmlhxJcP2iXc0yG_NPS_D1hcksDHT8lT0bTkU7zlJ-RB6F_TvanPbjNl7_oZ5qSOVOUfJ9gPTp6OMyG0-FsoCnsZ5Jko_NhnS5Iv9JpqpW4tBeBmt5TMMUT-mtqyMUexkAhzcglYUXBwqUZdSPhhdNcyRLpTOc5n3z1gvw4Pjo7PCnHKgulE6D7QRxGoaRyzjsXEZ2PR1abAHaf16CsKi4qA2KAWyuMZ8ppK3xlbXSmbn0TLX9J9vqhD68JrW1jg_QVM6EV2lujgmuMqHy0FtySpiCT-z3v3AhBjpUwLjpwRZBKXaJSh1TqEpUK8mXzxc8Mv_GXvt-QjJt-CJydGoCdupGdun-xU0E-AhPsjHEynXXYlmRXrcVNXZAP9zzSwWnEKxbTh-EaZyMRUbHCtb7KPLMZCxQ_Qinpgqgdbtr52e6bfnmeEL_Ba27B0nrzP1b4ljzGPcN0N6bfkb311XV4Tx65m_VydXVAHqpFe5AOEzxPb4_uANiVKf0 |
| linkProvider | Directory of Open Access Journals |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=The+CoLoMoTo+Interactive+Notebook%3A+Accessible+and+Reproducible+Computational+Analyses+for+Qualitative+Biological+Networks&rft.jtitle=Frontiers+in+physiology&rft.au=Naldi%2C+Aur%C3%A9lien&rft.au=Hernandez%2C+C%C3%A9line&rft.au=Levy%2C+Nicolas&rft.au=Stoll%2C+Gautier&rft.date=2018-06-19&rft.issn=1664-042X&rft.eissn=1664-042X&rft.volume=9&rft_id=info:doi/10.3389%2Ffphys.2018.00680&rft.externalDBID=n%2Fa&rft.externalDocID=10_3389_fphys_2018_00680 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1664-042X&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1664-042X&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1664-042X&client=summon |