Scikick: A sidekick for workflow clarity and reproducibility during extensive data analysis
Reproducibility is crucial for scientific progress, yet a clear research data analysis workflow is challenging to implement and maintain. As a result, a record of computational steps performed on the data to arrive at the key research findings is often missing. We developed Scikick, a tool that ease...
Saved in:
| Published in | PloS one Vol. 18; no. 7; p. e0289171 |
|---|---|
| Main Authors | , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Public Library of Science
27.07.2023
|
| Subjects | |
| Online Access | Get full text |
Cover
Loading…
| Abstract | Reproducibility is crucial for scientific progress, yet a clear research data analysis workflow is challenging to implement and maintain. As a result, a record of computational steps performed on the data to arrive at the key research findings is often missing. We developed Scikick, a tool that eases the configuration, execution, and presentation of scientific computational analyses. Scikick allows for workflow configurations with notebooks as the units of execution, defines a standard structure for the project, automatically tracks the defined interdependencies between the data analysis steps, and implements methods to compile all research results into a cohesive final report. Utilities provided by Scikick help turn the complicated management of transparent data analysis workflows into a standardized and feasible practice. Scikick version 0.2.1 code and documentation is available as supplementary material. The Scikick software is available on GitHub (
https://github.com/matthewcarlucci/scikick
) and is distributed with PyPi (
https://pypi.org/project/scikick/
) under a GPL-3 license. |
|---|---|
| AbstractList | Reproducibility is crucial for scientific progress, yet a clear research data analysis workflow is challenging to implement and maintain. As a result, a record of computational steps performed on the data to arrive at the key research findings is often missing. We developed Scikick, a tool that eases the configuration, execution, and presentation of scientific computational analyses. Scikick allows for workflow configurations with notebooks as the units of execution, defines a standard structure for the project, automatically tracks the defined interdependencies between the data analysis steps, and implements methods to compile all research results into a cohesive final report. Utilities provided by Scikick help turn the complicated management of transparent data analysis workflows into a standardized and feasible practice. Scikick version 0.2.1 code and documentation is available as supplementary material. The Scikick software is available on GitHub (https://github.com/matthewcarlucci/scikick) and is distributed with PyPi (https://pypi.org/project/scikick/) under a GPL-3 license. Reproducibility is crucial for scientific progress, yet a clear research data analysis workflow is challenging to implement and maintain. As a result, a record of computational steps performed on the data to arrive at the key research findings is often missing. We developed Scikick, a tool that eases the configuration, execution, and presentation of scientific computational analyses. Scikick allows for workflow configurations with notebooks as the units of execution, defines a standard structure for the project, automatically tracks the defined interdependencies between the data analysis steps, and implements methods to compile all research results into a cohesive final report. Utilities provided by Scikick help turn the complicated management of transparent data analysis workflows into a standardized and feasible practice. Scikick version 0.2.1 code and documentation is available as supplementary material. The Scikick software is available on GitHub ( Reproducibility is crucial for scientific progress, yet a clear research data analysis workflow is challenging to implement and maintain. As a result, a record of computational steps performed on the data to arrive at the key research findings is often missing. We developed Scikick, a tool that eases the configuration, execution, and presentation of scientific computational analyses. Scikick allows for workflow configurations with notebooks as the units of execution, defines a standard structure for the project, automatically tracks the defined interdependencies between the data analysis steps, and implements methods to compile all research results into a cohesive final report. Utilities provided by Scikick help turn the complicated management of transparent data analysis workflows into a standardized and feasible practice. Scikick version 0.2.1 code and documentation is available as supplementary material. The Scikick software is available on GitHub ( https://github.com/matthewcarlucci/scikick ) and is distributed with PyPi ( https://pypi.org/project/scikick/ ) under a GPL-3 license. Reproducibility is crucial for scientific progress, yet a clear research data analysis workflow is challenging to implement and maintain. As a result, a record of computational steps performed on the data to arrive at the key research findings is often missing. We developed Scikick, a tool that eases the configuration, execution, and presentation of scientific computational analyses. Scikick allows for workflow configurations with notebooks as the units of execution, defines a standard structure for the project, automatically tracks the defined interdependencies between the data analysis steps, and implements methods to compile all research results into a cohesive final report. Utilities provided by Scikick help turn the complicated management of transparent data analysis workflows into a standardized and feasible practice. Scikick version 0.2.1 code and documentation is available as supplementary material. The Scikick software is available on GitHub (https://github.com/matthewcarlucci/scikick) and is distributed with PyPi (https://pypi.org/project/scikick/) under a GPL-3 license.Reproducibility is crucial for scientific progress, yet a clear research data analysis workflow is challenging to implement and maintain. As a result, a record of computational steps performed on the data to arrive at the key research findings is often missing. We developed Scikick, a tool that eases the configuration, execution, and presentation of scientific computational analyses. Scikick allows for workflow configurations with notebooks as the units of execution, defines a standard structure for the project, automatically tracks the defined interdependencies between the data analysis steps, and implements methods to compile all research results into a cohesive final report. Utilities provided by Scikick help turn the complicated management of transparent data analysis workflows into a standardized and feasible practice. Scikick version 0.2.1 code and documentation is available as supplementary material. The Scikick software is available on GitHub (https://github.com/matthewcarlucci/scikick) and is distributed with PyPi (https://pypi.org/project/scikick/) under a GPL-3 license. |
| Audience | Academic |
| Author | Petronis, Art Oh, Gabriel Kriščiūnas, Algimantas Koncevičius, Karolis Gibas, Povilas Carlucci, Matthew Bareikis, Tadas |
| AuthorAffiliation | 1 The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada 2 Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania 3 Stanford University School of Medicine, Stanford, California, United States of America Politecnico di Milano, ITALY |
| AuthorAffiliation_xml | – name: 1 The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada – name: Politecnico di Milano, ITALY – name: 2 Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania – name: 3 Stanford University School of Medicine, Stanford, California, United States of America |
| Author_xml | – sequence: 1 givenname: Matthew surname: Carlucci fullname: Carlucci, Matthew – sequence: 2 givenname: Tadas surname: Bareikis fullname: Bareikis, Tadas – sequence: 3 givenname: Karolis surname: Koncevičius fullname: Koncevičius, Karolis – sequence: 4 givenname: Povilas surname: Gibas fullname: Gibas, Povilas – sequence: 5 givenname: Algimantas surname: Kriščiūnas fullname: Kriščiūnas, Algimantas – sequence: 6 givenname: Art surname: Petronis fullname: Petronis, Art – sequence: 7 givenname: Gabriel orcidid: 0000-0002-7651-1312 surname: Oh fullname: Oh, Gabriel |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/37498822$$D View this record in MEDLINE/PubMed |
| BookMark | eNqNkltrFDEYhgep2IP-A9EBQfRi10kyk0NvZCkeCoWCVW-8CNkcdtPNJmsy07r_3oydlZ1SRHKR8OV53yRvvuPiwAevi-I5qKYAEfDuOnTRCzfd5PK0gpQBAh4VR4AhOMGwQgd768PiOKXrqmoQxfhJcYhIzSiF8Kj4cSXtysrVaTkrk1W6X5cmxPI2xJVx4baUTkTbbkvhVRn1JgbVSTu3rq-pLlq_KPWvVvtkb3SpRCsyKdw22fS0eGyES_rZMJ8U3z5--Hr2eXJx-en8bHYxkRiSdsIIJqaqBZorg7WuK60gmdcUqco0gBmR30abOTKGaAw0xaJRAmBCpYCAAYxOipd3vhsXEh9ySRzSGjLUQMYy8X4guvlaK6l9G4Xjm2jXIm55EJaPd7xd8kW44aDKUQFIs8ObwSGGn51OLV_bJLVzwuvQ_TmsrhgBDczoq3vow1caqIVwmltvQj5Y9qZ8RhqKEa4RytT0ASoPpddW5p83NtdHgrcjQWba_D0L0aXEz6--_D97-X3Mvt5jl1q4dpmC61obfBqDL_aj_pvxruUycHoHyBhSitpwaVvR--SnWZcj531_70LjfX_zob-zuL4n3vn_U_YbiSH_gg |
| CitedBy_id | crossref_primary_10_1038_s41467_023_42588_6 |
| Cites_doi | 10.1038/nbt.3820 10.1002/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N 10.1093/gigascience/giaa140 10.3389/fninf.2017.00076 10.1038/s41592-019-0654-x 10.1371/journal.pcbi.1007007 10.3390/info11020108 10.1038/nbt.3780 10.1126/science.aah6168 10.1201/9781315204963 10.12688/f1000research.29032.2 10.1371/journal.pone.0177459 10.1126/scitranslmed.aaf5027 10.1190/1.1822162 10.1126/science.359.6377.725 10.1201/9781138359444 10.1038/s41562-016-0021 |
| ContentType | Journal Article |
| Copyright | Copyright: © 2023 Carlucci et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. COPYRIGHT 2023 Public Library of Science 2023 Carlucci et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2023 Carlucci et al 2023 Carlucci et al 2023 Carlucci et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
| Copyright_xml | – notice: Copyright: © 2023 Carlucci et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. – notice: COPYRIGHT 2023 Public Library of Science – notice: 2023 Carlucci et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. – notice: 2023 Carlucci et al 2023 Carlucci et al – notice: 2023 Carlucci et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
| DBID | AAYXX CITATION NPM IOV ISR 3V. 7QG 7QL 7QO 7RV 7SN 7SS 7T5 7TG 7TM 7U9 7X2 7X7 7XB 88E 8AO 8C1 8FD 8FE 8FG 8FH 8FI 8FJ 8FK ABJCF ABUWG AEUYN AFKRA ARAPS ATCPS AZQEC BBNVY BENPR BGLVJ BHPHI C1K CCPQU D1I DWQXO FR3 FYUFA GHDGH GNUQQ H94 HCIFZ K9. KB. KB0 KL. L6V LK8 M0K M0S M1P M7N M7P M7S NAPCQ P5Z P62 P64 PATMY PDBOC PHGZM PHGZT PIMPY PJZUB PKEHL PPXIY PQEST PQGLB PQQKQ PQUKI PTHSS PYCSY RC3 7X8 5PM |
| DOI | 10.1371/journal.pone.0289171 |
| DatabaseName | CrossRef PubMed Gale In Context: Opposing Viewpoints Gale in Context: Science ProQuest Central (Corporate) Animal Behavior Abstracts Bacteriology Abstracts (Microbiology B) Biotechnology Research Abstracts Nursing & Allied Health Database Ecology Abstracts Entomology Abstracts (Full archive) Immunology Abstracts Meteorological & Geoastrophysical Abstracts Nucleic Acids Abstracts Virology and AIDS Abstracts Agricultural Science Collection Health & Medical Collection ProQuest Central (purchase pre-March 2016) Medical Database (Alumni Edition) ProQuest Pharma Collection Public Health Database Technology Research Database ProQuest SciTech Collection ProQuest Technology Collection ProQuest Natural Science Collection Hospital Premium Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) Materials Science & Engineering Collection ProQuest Central (Alumni) ProQuest One Sustainability ProQuest Central UK/Ireland Advanced Technologies & Aerospace Collection Agricultural & Environmental Science Collection ProQuest Central Essentials Biological Science Collection ProQuest Central ProQuest Technology Collection Natural Science Collection Environmental Sciences and Pollution Management ProQuest One Community College ProQuest Materials Science Collection ProQuest Central Engineering Research Database Proquest Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student AIDS and Cancer Research Abstracts SciTech Premium Collection ProQuest Health & Medical Complete (Alumni) Materials Science Database Nursing & Allied Health Database (Alumni Edition) Meteorological & Geoastrophysical Abstracts - Academic ProQuest Engineering Collection ProQuest Biological Science Collection Agricultural Science Database Health & Medical Collection (Alumni) Medical Database Algology Mycology and Protozoology Abstracts (Microbiology C) Biological Science Database Engineering Database Nursing & Allied Health Premium Advanced Technologies & Aerospace Database ProQuest Advanced Technologies & Aerospace Collection Biotechnology and BioEngineering Abstracts Environmental Science Database Materials Science Collection ProQuest Central Premium ProQuest One Academic (New) Publicly Available Content Database ProQuest Health & Medical Research Collection ProQuest One Academic Middle East (New) ProQuest One Health & Nursing ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Applied & Life Sciences ProQuest One Academic ProQuest One Academic UKI Edition Engineering Collection Environmental Science Collection Genetics Abstracts MEDLINE - Academic PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef PubMed Agricultural Science Database Publicly Available Content Database ProQuest Central Student ProQuest Advanced Technologies & Aerospace Collection ProQuest Central Essentials Nucleic Acids Abstracts SciTech Premium Collection Environmental Sciences and Pollution Management ProQuest One Applied & Life Sciences ProQuest One Sustainability Health Research Premium Collection Meteorological & Geoastrophysical Abstracts Natural Science Collection Health & Medical Research Collection Biological Science Collection ProQuest Central (New) ProQuest Medical Library (Alumni) Engineering Collection Advanced Technologies & Aerospace Collection Engineering Database Virology and AIDS Abstracts ProQuest Biological Science Collection ProQuest One Academic Eastern Edition Agricultural Science Collection ProQuest Hospital Collection ProQuest Technology Collection Health Research Premium Collection (Alumni) Biological Science Database Ecology Abstracts ProQuest Hospital Collection (Alumni) Biotechnology and BioEngineering Abstracts Environmental Science Collection Entomology Abstracts Nursing & Allied Health Premium ProQuest Health & Medical Complete ProQuest One Academic UKI Edition Environmental Science Database ProQuest Nursing & Allied Health Source (Alumni) Engineering Research Database ProQuest One Academic Meteorological & Geoastrophysical Abstracts - Academic ProQuest One Academic (New) Technology Collection Technology Research Database ProQuest One Academic Middle East (New) Materials Science Collection ProQuest Health & Medical Complete (Alumni) ProQuest Central (Alumni Edition) ProQuest One Community College ProQuest One Health & Nursing ProQuest Natural Science Collection ProQuest Pharma Collection ProQuest Central ProQuest Health & Medical Research Collection Genetics Abstracts ProQuest Engineering Collection Biotechnology Research Abstracts Health and Medicine Complete (Alumni Edition) ProQuest Central Korea Bacteriology Abstracts (Microbiology B) Algology Mycology and Protozoology Abstracts (Microbiology C) Agricultural & Environmental Science Collection AIDS and Cancer Research Abstracts Materials Science Database ProQuest Materials Science Collection ProQuest Public Health ProQuest Nursing & Allied Health Source ProQuest SciTech Collection Advanced Technologies & Aerospace Database ProQuest Medical Library Animal Behavior Abstracts Materials Science & Engineering Collection Immunology Abstracts ProQuest Central (Alumni) MEDLINE - Academic |
| DatabaseTitleList | Agricultural Science Database PubMed CrossRef MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: 8FG name: ProQuest Technology Collection url: https://search.proquest.com/technologycollection1 sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Sciences (General) |
| DocumentTitleAlternate | Workflow clarity and reproducibility with Scikick |
| EISSN | 1932-6203 |
| ExternalDocumentID | 2842935299 PMC10374128 A758636433 37498822 10_1371_journal_pone_0289171 |
| Genre | Journal Article |
| GeographicLocations | United States |
| GeographicLocations_xml | – name: United States |
| GrantInformation_xml | – fundername: ; grantid: No 09.3.3-LMT-K-712-17-0008 |
| GroupedDBID | --- 123 29O 2WC 53G 5VS 7RV 7X2 7X7 7XC 88E 8AO 8C1 8CJ 8FE 8FG 8FH 8FI 8FJ A8Z AAFWJ AAUCC AAWOE AAYXX ABDBF ABIVO ABJCF ABUWG ACGFO ACIHN ACIWK ACPRK ACUHS ADBBV AEAQA AENEX AEUYN AFKRA AFPKN AFRAH AHMBA ALIPV ALMA_UNASSIGNED_HOLDINGS AOIJS APEBS ARAPS ATCPS BAWUL BBNVY BCNDV BENPR BGLVJ BHPHI BKEYQ BPHCQ BVXVI BWKFM CCPQU CITATION CS3 D1I D1J D1K DIK DU5 E3Z EAP EAS EBD EMOBN ESX EX3 F5P FPL FYUFA GROUPED_DOAJ GX1 HCIFZ HH5 HMCUK HYE IAO IEA IGS IHR IHW INH INR IOV IPY ISE ISR ITC K6- KB. KQ8 L6V LK5 LK8 M0K M1P M48 M7P M7R M7S M~E NAPCQ O5R O5S OK1 OVT P2P P62 PATMY PDBOC PHGZM PHGZT PIMPY PQQKQ PROAC PSQYO PTHSS PV9 PYCSY RNS RPM RZL SV3 TR2 UKHRP WOQ WOW ~02 ~KM ADRAZ BBORY IPNFZ NPM RIG PMFND 3V. 7QG 7QL 7QO 7SN 7SS 7T5 7TG 7TM 7U9 7XB 8FD 8FK AZQEC C1K DWQXO FR3 GNUQQ H94 K9. KL. M7N P64 PJZUB PKEHL PPXIY PQEST PQGLB PQUKI RC3 7X8 5PM ESTFP |
| ID | FETCH-LOGICAL-c627t-9767f04a3bdf6ee40ed27b483d0f519fa28985b3ff7e61e86a5da1678ca219163 |
| IEDL.DBID | M48 |
| ISSN | 1932-6203 |
| IngestDate | Thu Nov 28 02:59:12 EST 2024 Thu Aug 21 18:36:42 EDT 2025 Fri Jul 11 11:13:09 EDT 2025 Fri Jul 25 11:19:57 EDT 2025 Tue Jun 17 21:22:55 EDT 2025 Tue Jun 10 21:27:35 EDT 2025 Fri Jun 27 06:08:37 EDT 2025 Fri Jun 27 05:49:13 EDT 2025 Thu May 22 21:21:53 EDT 2025 Thu Apr 03 06:58:27 EDT 2025 Thu Apr 24 23:06:47 EDT 2025 Tue Jul 01 03:52:57 EDT 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 7 |
| Language | English |
| License | Copyright: © 2023 Carlucci et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Creative Commons Attribution License |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c627t-9767f04a3bdf6ee40ed27b483d0f519fa28985b3ff7e61e86a5da1678ca219163 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Competing Interests: The authors have declared that no competing interests exist. |
| ORCID | 0000-0002-7651-1312 |
| OpenAccessLink | http://journals.scholarsportal.info/openUrl.xqy?doi=10.1371/journal.pone.0289171 |
| PMID | 37498822 |
| PQID | 2842935299 |
| PQPubID | 1436336 |
| PageCount | e0289171 |
| ParticipantIDs | plos_journals_2842935299 pubmedcentral_primary_oai_pubmedcentral_nih_gov_10374128 proquest_miscellaneous_2844097152 proquest_journals_2842935299 gale_infotracmisc_A758636433 gale_infotracacademiconefile_A758636433 gale_incontextgauss_ISR_A758636433 gale_incontextgauss_IOV_A758636433 gale_healthsolutions_A758636433 pubmed_primary_37498822 crossref_citationtrail_10_1371_journal_pone_0289171 crossref_primary_10_1371_journal_pone_0289171 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2023-07-27 |
| PublicationDateYYYYMMDD | 2023-07-27 |
| PublicationDate_xml | – month: 07 year: 2023 text: 2023-07-27 day: 27 |
| PublicationDecade | 2020 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States – name: San Francisco – name: San Francisco, CA USA |
| PublicationTitle | PloS one |
| PublicationTitleAlternate | PLoS One |
| PublicationYear | 2023 |
| Publisher | Public Library of Science |
| Publisher_xml | – name: Public Library of Science |
| References | Y. Xie (pone.0289171.ref011) 2016 F Mölder (pone.0289171.ref015) 2021; 10 Y Xie (pone.0289171.ref008) 2018 S Lau (pone.0289171.ref010) 2020 V Stodden (pone.0289171.ref005) 2016; 354 J Howard (pone.0289171.ref013) 2020; 11 JF Claerbout (pone.0289171.ref004) 1992 pone.0289171.ref012 pone.0289171.ref023 A Rule (pone.0289171.ref009) 2019; 15 P Di Tommaso (pone.0289171.ref016) 2017; 35 GM Kurtzer (pone.0289171.ref022) 2017; 12 B. Gough (pone.0289171.ref014) 2009 BK Beaulieu-Jones (pone.0289171.ref020) 2017; 35 ER Gansner (pone.0289171.ref018) 2000; 30 D. Merkel (pone.0289171.ref021) 2014; 2014 MR Munafò (pone.0289171.ref002) 2017; 1 M. Hutson (pone.0289171.ref006) 2018; 359 T Reiter (pone.0289171.ref017) 2021; 10 HE Plesser (pone.0289171.ref003) 2018; 11 T Kluyver (pone.0289171.ref007) 2016 SN Goodman (pone.0289171.ref001) 2016; 8 RA Amezquita (pone.0289171.ref019) 2019; 17 |
| References_xml | – volume: 35 start-page: 316 issue: 4 year: 2017 ident: pone.0289171.ref016 article-title: Nextflow enables reproducible computational workflows publication-title: Nat Biotechnol doi: 10.1038/nbt.3820 – ident: pone.0289171.ref023 – volume: 30 start-page: 1203 issue: 11 year: 2000 ident: pone.0289171.ref018 article-title: An open graph visualization system and its applications to software engineering publication-title: Softw Pract Exp doi: 10.1002/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N – volume: 10 issue: 1 year: 2021 ident: pone.0289171.ref017 article-title: Streamlining data-intensive biology with workflow systems publication-title: Gigascience doi: 10.1093/gigascience/giaa140 – volume-title: GNU Scientific Library Reference Manual—Third Edition year: 2009 ident: pone.0289171.ref014 – volume: 11 year: 2018 ident: pone.0289171.ref003 article-title: Reproducibility vs. Replicability: A Brief History of a Confused Terminology publication-title: Front Neuroinform doi: 10.3389/fninf.2017.00076 – volume: 17 start-page: 137 issue: 2 year: 2019 ident: pone.0289171.ref019 article-title: Orchestrating single-cell analysis with Bioconductor publication-title: Nat Methods doi: 10.1038/s41592-019-0654-x – volume: 15 issue: 7 year: 2019 ident: pone.0289171.ref009 article-title: Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1007007 – volume: 11 start-page: 108 issue: 2 year: 2020 ident: pone.0289171.ref013 article-title: Fastai: A Layered API for Deep Learning publication-title: Information doi: 10.3390/info11020108 – volume: 2014 start-page: 2 issue: 239 year: 2014 ident: pone.0289171.ref021 article-title: Docker: lightweight linux containers for consistent development and deployment publication-title: Linux J – ident: pone.0289171.ref012 – volume: 35 start-page: 342 issue: 4 year: 2017 ident: pone.0289171.ref020 article-title: Reproducibility of computational workflows is automated using continuous analysis publication-title: Nat Biotechnol doi: 10.1038/nbt.3780 – volume: 354 start-page: 1240 issue: 6317 year: 2016 ident: pone.0289171.ref005 article-title: Enhancing reproducibility for computational methods publication-title: Science doi: 10.1126/science.aah6168 – volume-title: bookdown: Authoring Books and Technical Documents with R Markdown year: 2016 ident: pone.0289171.ref011 doi: 10.1201/9781315204963 – volume: 10 start-page: 33 issue: 33 year: 2021 ident: pone.0289171.ref015 article-title: Sustainable data analysis with Snakemake publication-title: F1000Res doi: 10.12688/f1000research.29032.2 – start-page: 87 volume-title: Positioning and Power in Academic Publishing: Players, Agents and Agendas year: 2016 ident: pone.0289171.ref007 – volume: 12 start-page: e0177459 issue: 5 year: 2017 ident: pone.0289171.ref022 article-title: Singularity: Scientific containers for mobility of compute publication-title: PLoS One doi: 10.1371/journal.pone.0177459 – volume: 8 start-page: 341ps12 issue: 341 year: 2016 ident: pone.0289171.ref001 article-title: What does research reproducibility mean? publication-title: Sci Transl Med doi: 10.1126/scitranslmed.aaf5027 – start-page: 601 volume-title: SEG Technical Program Expanded Abstracts 1992 year: 1992 ident: pone.0289171.ref004 doi: 10.1190/1.1822162 – start-page: 1 volume-title: 2020 IEEE Symposium on Visual Languages and Human-Centric Computing (VL/HCC) year: 2020 ident: pone.0289171.ref010 – volume: 359 start-page: 725 issue: 6377 year: 2018 ident: pone.0289171.ref006 article-title: Artificial intelligence faces reproducibility crisis publication-title: Science doi: 10.1126/science.359.6377.725 – start-page: 303 volume-title: R Markdown: The Definitive Guide year: 2018 ident: pone.0289171.ref008 doi: 10.1201/9781138359444 – volume: 1 start-page: 1 issue: 1 year: 2017 ident: pone.0289171.ref002 article-title: A manifesto for reproducible science publication-title: Nature Human Behaviour doi: 10.1038/s41562-016-0021 |
| SSID | ssj0053866 |
| Score | 2.43006 |
| Snippet | Reproducibility is crucial for scientific progress, yet a clear research data analysis workflow is challenging to implement and maintain. As a result, a record... |
| SourceID | plos pubmedcentral proquest gale pubmed crossref |
| SourceType | Open Website Open Access Repository Aggregation Database Index Database Enrichment Source |
| StartPage | e0289171 |
| SubjectTerms | Analysis Archives & records Automation Biology and life sciences Computer and Information Sciences Computer applications Configurations Data analysis Data mining Datasets Engineering and Technology Evaluation Information management Reproducibility Research and Analysis Methods Software Workflow |
| SummonAdditionalLinks | – databaseName: ProQuest Technology Collection dbid: 8FG link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1Lb9QwELZguXBB9AFdKK1BSMAhbRI7draXalV1KZUACSiqxCHyE6qukoXsCvXfM5M4oUEVcIviSZR4Hv7GHn8m5HlqHOCMiY7iSWohQXFxpLlWkbRMc-GYEhYTxbfvxMkZPz3PzsOEWx3KKruY2ARqWxmcI9-HMAojUwbR83DxPcJTo3B1NRyhcZvcSWCkwZKufPa6i8Tgy0KE7XJMJvtBO3uLqnR7uMKWyGQwHIWgPFrMq_omxPln4eS1kWh2n9wLEJJOW52vkVuuXCdrwUlr-jIwSb_aIF_g5uWFuTygU4rHcuI1BZRKsRrLz6uf1EBiCzicqtJS5LdE-te2XvaKtjsYaTNNjkXuFKtJQbJlMdkkZ7PjT0cnUThNITIilcsIcIf0MVdMWy-cA7XYVGqeMxt7gHFeQYfkmWbeSycSlwuVWZXAWGYURDWAbQ_IqISe2yLUi9hrK1MLcIG7VOUGEmzJlFZxBsk5HxPWdWphAtU4nngxL5r1MwkpR9tVBaqiCKoYk6h_atFSbfxDfhf1VbQbRntPLaaQAgkGSIuNybNGAnkuSiyk-apWdV28ef_5P4Q-fhgIvQhCvoI_MSpsXoDPQf6sgeT2QBK81Qyat9C6uh-qi992DU92Fndz89O-GV-KxXGlq1aNDLKWARIbk4etgfYdyCSfQBIFLfnAdHsBpBcftpQX3xqacdxBygG-PPr7dz0md1MAfjjfncptMlr-WLknANSWeqfxxl_CIj_q priority: 102 providerName: ProQuest |
| Title | Scikick: A sidekick for workflow clarity and reproducibility during extensive data analysis |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/37498822 https://www.proquest.com/docview/2842935299 https://www.proquest.com/docview/2844097152 https://pubmed.ncbi.nlm.nih.gov/PMC10374128 http://dx.doi.org/10.1371/journal.pone.0289171 |
| Volume | 18 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV3fb9MwELZG98ILYvxa2SgGIQEPqZI4sVMkhMrUMpA20KCo0h4iO7ZhWpV0SyvYC387d4kTEVTEXqKqPkfJ2Rd_Z999R8izMDOAM0bK80ehBgfF-J6KlPSEZirihkmu0VE8OuaHs-jDPJ5vkaZmq1NgudG1w3pSs8vF8OfF1Rsw-NdV1QYRNJ2GyyI3Qzw5CzCpfBvWJoE1DY6i9lwBrLs6vUTU4vHQZy6Z7l936SxW7pPdWy6KchMe_Tus8o91anqb3HIAk47rGbFDtkx-h-w4Ey7pC8cz_fIuOYU_z8-y81d0TLFoJ_6mgGEpxmrZRfGDZqAbQOlU5poi-yWSw9bRtFe0zm-k1SY6hsBTjDUFyZrj5B6ZTSdfDg49V2vBy3goVh6gEmH9SDKlLTcGBk2HQkUJ074FkGclKCSJFbNWGB6YhMtYywBWukzCNw9A3X3Sy0Fzu4Ra7lulRagBTEQmlEkG7rdgUkk_Btc96hPWKDXNHBE51sNYpNXpmgCHpFZVikORuqHoE6_ttayJOP4j_xjHK63TSVs7TsfgIHEGOIz1ydNKAlkwcgyz-SbXZZm-__j1GkKfTzpCz52QLeBNMulSG-BxkF2rI7nfkQRbzjrNuzi7mhcqUwAPgMdiwAzQs5lxm5uftM14Uwydy02xrmSQ0wxwWp88qCdoq0AmohG4WNCSdKZuK4Dk492W_Ox7RUKO-aURgJuH19HiHrkZAjjEPfFQ7JPe6nJtHgGYW6kBuSHmAq7JQYDX6bsB2X47Of50Mqi2RwaV_eL11-Q3kSRP6Q |
| linkProvider | Scholars Portal |
| linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV3db9MwELdGeYAXxPhaYTCDQMBDtiRO7BQJoQooLftAgg1N4iH4E6ZVSSGtpv1T_I3cJU4haAJe9lbVl8ixz7_7nX13JuRhrC3wjIEKwkFswEGxYaASJQNhmEq4ZZIbdBR39_j4IHl7mB6ukB9tLgyGVbaYWAO1KTXukW8BjIJlSgE9X8y-BXhrFJ6utldoNGqxbU9PwGWrnk9ewfw-iuPR6_2X48DfKhBoHot5APZXuDCRTBnHrYXumVioJGMmdEBnnAQXJEsVc05YHtmMy9TICDBdS1jdQF_gvRfIxYSBJcfM9NGbFvkBOzj36XlMRFteGzZnZWE38UQvElHH_Hkj0JtNy-oshvtnoOZvlm90lVzxlJUOGx1bJSu2uEZWPShU9ImvXP30OvkEfx4f6eNndEjxGlD8TYEVU4z-ctPyhGpwpIH3U1kYivU0sdxsE597SpuMSVpvy2NQPcXoVZBsqqbcIAfnMs43Sa-AkVsj1PHQKSNiA_QksbHMNDj0gkklw9QqlvQJawc11760Od6wMc3r8zoBLk4zVDlORe6nok-C5VOzprTHP-Q3cL7yJkF1iQz5EFwuzoDZsT55UEtgXY0CA3e-yEVV5ZN3H_9D6MP7jtBjL-RK-BItfbIEdAfrdXUk1zuSgA6607yG2tV-UJX_WkfwZKtxZzffXzbjSzEYr7DlopbBKmnA_PrkVqOgywFkIhmA0wYtWUd1lwJYzrzbUhx9rcuaY8ZqAnTp9t_7tUEujfd3d_Kdyd72HXI5BtKJe-2xWCe9-feFvQskca7u1SuTks_nDQU_AVmpfMw |
| linkToPdf | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV3fb9MwELZGkRAviPFrhcEMAgEPWRM7tVMkhKqNamUwEGxoEg_Bjm2YViWFtJr2r_HXcZc4gaAJeNlbVV8i53z-_J19dybkIcss8IyRDsIRM-Cg2DDQsVaBNFzHwnIlDDqKb_bEzkH86nB4uEJ-NLkwGFbZYGIF1KbIcI98ADAKK9MQ0HPgfFjEu-3Ji_m3AG-QwpPW5jqN2kR27ekJuG_l8-k2jPUjxiYv97d2An_DQJAJJhcBrMXShbHi2jhhLXTVMKnjhJvQAbVxCtyRZKi5c9KKyCZCDY2KAN8zBTMdqAy89wK5KLlMcI4lW214CeCIED5Vj8to4C1jc17kdhNP9yIZdZZCvyD05rOiPIvt_hm0-dsqOLlKrnj6Sse1va2SFZtfI6seIEr6xFexfnqdfII_j4-y42d0TPFKUPxNgSFTjARzs-KEZuBUgw9AVW4o1tbE0rN1rO4prbMnabVFjwH2FCNZQbKuoHKDHJyLnm-SXg6aWyPUidBpI5kBqhJbppIMnHvJlVbh0Goe9wlvlJpmvsw53rYxS6uzOwnuTq2qFIci9UPRJ0H71Lwu8_EP-Q0cr7ROVm1RIh2D-yU4sDzeJw8qCayxkaO1flHLskynbz_-h9CH9x2hx17IFfAlmfKJE9AdrN3VkVzvSAJSZJ3mNbSu5oPK9Necgicbizu7-X7bjC_FwLzcFstKBiumAQvsk1u1gbYK5DIegQMHLUnHdFsBLG3ebcmPvlYlzjF7NQbqdPvv_doglwAE0tfTvd075DID_onb7kyuk97i-9LeBb640PeqiUnJ5_NGgp-O4oDN |
| 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=Scikick%3A+A+sidekick+for+workflow+clarity+and+reproducibility+during+extensive+data+analysis&rft.jtitle=PloS+one&rft.au=Carlucci%2C+Matthew&rft.au=Bareikis%2C+Tadas&rft.au=Koncevicius%2C+Karolis&rft.au=Gibas%2C+Povilas&rft.date=2023-07-27&rft.pub=Public+Library+of+Science&rft.issn=1932-6203&rft.eissn=1932-6203&rft.volume=18&rft.issue=7&rft.spage=e0289171&rft_id=info:doi/10.1371%2Fjournal.pone.0289171&rft.externalDBID=IOV&rft.externalDocID=A758636433 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1932-6203&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1932-6203&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1932-6203&client=summon |