Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution
Abstract Researchers in ecology and evolutionary biology are increasingly dependent on computational code to conduct research. Hence, the use of efficient methods to share, reproduce, and collaborate on code as well as document research is fundamental. GitHub is an online, cloud‐based service that c...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2023-06-01
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| Series: | Methods in Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1111/2041-210X.14108 |
| _version_ | 1827888333129252864 |
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| author | Pedro Henrique Pereira Braga Katherine Hébert Emma J. Hudgins Eric R. Scott Brandon P. M. Edwards Luna L. Sánchez Reyes Matthew J. Grainger Vivienne Foroughirad Friederike Hillemann Allison D. Binley Cole B. Brookson Kaitlyn M. Gaynor Saeed Shafiei Sabet Ali Güncan Helen Weierbach Dylan G. E. Gomes Robert Crystal‐Ornelas |
| author_facet | Pedro Henrique Pereira Braga Katherine Hébert Emma J. Hudgins Eric R. Scott Brandon P. M. Edwards Luna L. Sánchez Reyes Matthew J. Grainger Vivienne Foroughirad Friederike Hillemann Allison D. Binley Cole B. Brookson Kaitlyn M. Gaynor Saeed Shafiei Sabet Ali Güncan Helen Weierbach Dylan G. E. Gomes Robert Crystal‐Ornelas |
| author_sort | Pedro Henrique Pereira Braga |
| collection | DOAJ |
| description | Abstract Researchers in ecology and evolutionary biology are increasingly dependent on computational code to conduct research. Hence, the use of efficient methods to share, reproduce, and collaborate on code as well as document research is fundamental. GitHub is an online, cloud‐based service that can help researchers track, organize, discuss, share, and collaborate on software and other materials related to research production, including data, code for analyses, and protocols. Despite these benefits, the use of GitHub in ecology and evolution is not widespread. To help researchers in ecology and evolution adopt useful features from GitHub to improve their research workflows, we review 12 practical ways to use the platform. We outline features ranging from low to high technical difficulty, including storing code, managing projects, coding collaboratively, conducting peer review, writing a manuscript, and using automated and continuous integration to streamline analyses. Given that members of a research team may have different technical skills and responsibilities, we describe how the optimal use of GitHub features may vary among members of a research collaboration. As more ecologists and evolutionary biologists establish their workflows using GitHub, the field can continue to push the boundaries of collaborative, transparent, and open research. |
| first_indexed | 2024-03-12T20:33:11Z |
| format | Article |
| id | doaj.art-55ed7ece79cc48b9a720a89a9dd43597 |
| institution | Directory Open Access Journal |
| issn | 2041-210X |
| language | English |
| last_indexed | 2024-03-12T20:33:11Z |
| publishDate | 2023-06-01 |
| publisher | Wiley |
| record_format | Article |
| series | Methods in Ecology and Evolution |
| spelling | doaj.art-55ed7ece79cc48b9a720a89a9dd435972023-08-01T18:55:43ZengWileyMethods in Ecology and Evolution2041-210X2023-06-011461364138010.1111/2041-210X.14108Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolutionPedro Henrique Pereira Braga0Katherine Hébert1Emma J. Hudgins2Eric R. Scott3Brandon P. M. Edwards4Luna L. Sánchez Reyes5Matthew J. Grainger6Vivienne Foroughirad7Friederike Hillemann8Allison D. Binley9Cole B. Brookson10Kaitlyn M. Gaynor11Saeed Shafiei Sabet12Ali Güncan13Helen Weierbach14Dylan G. E. Gomes15Robert Crystal‐Ornelas16Department of Biology Concordia University Montréal Québec CanadaDépartement de Biologie Université de Sherbrooke Sherbrooke Québec CanadaDepartment of Biology Carleton University Ottawa Ontario CanadaCommunications & Cyber Technologies University of Arizona Arizona Tucson USADepartment of Biology Carleton University Ottawa Ontario CanadaSchool of Natural Sciences University of California Merced California USATerrestrial Biodiversity Norwegian Institute for Nature Research – NINA Trondheim NorwayDepartment of Biology Georgetown University Washington District of Columbia USADepartment of Human Behavior, Ecology and Culture Max Planck Institute for Evolutionary Anthropology Leipzig GermanyDepartment of Biology Carleton University Ottawa Ontario CanadaDepartment of Biological Sciences University of Alberta Edmonton Alberta CanadaDepartments of Zoology and Botany University of British Columbia Vancouver British Columbia CanadaFisheries Department, Faculty of Natural Resources University of Guilan Sowmeh Sara IranDepartment of Plant Protection, Faculty of Agriculture Ordu University Ordu TurkeyEarth and Environmental Sciences Area, Lawrence Berkeley National Laboratory Berkeley California USACooperative Institute for Marine Resources Studies, Hatfield Marine Science Center Oregon State University Newport Oregon USAEarth and Environmental Sciences Area, Lawrence Berkeley National Laboratory Berkeley California USAAbstract Researchers in ecology and evolutionary biology are increasingly dependent on computational code to conduct research. Hence, the use of efficient methods to share, reproduce, and collaborate on code as well as document research is fundamental. GitHub is an online, cloud‐based service that can help researchers track, organize, discuss, share, and collaborate on software and other materials related to research production, including data, code for analyses, and protocols. Despite these benefits, the use of GitHub in ecology and evolution is not widespread. To help researchers in ecology and evolution adopt useful features from GitHub to improve their research workflows, we review 12 practical ways to use the platform. We outline features ranging from low to high technical difficulty, including storing code, managing projects, coding collaboratively, conducting peer review, writing a manuscript, and using automated and continuous integration to streamline analyses. Given that members of a research team may have different technical skills and responsibilities, we describe how the optimal use of GitHub features may vary among members of a research collaboration. As more ecologists and evolutionary biologists establish their workflows using GitHub, the field can continue to push the boundaries of collaborative, transparent, and open research.https://doi.org/10.1111/2041-210X.14108collaborationdata managementecoinformaticsGitHubopen scienceproject management |
| spellingShingle | Pedro Henrique Pereira Braga Katherine Hébert Emma J. Hudgins Eric R. Scott Brandon P. M. Edwards Luna L. Sánchez Reyes Matthew J. Grainger Vivienne Foroughirad Friederike Hillemann Allison D. Binley Cole B. Brookson Kaitlyn M. Gaynor Saeed Shafiei Sabet Ali Güncan Helen Weierbach Dylan G. E. Gomes Robert Crystal‐Ornelas Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution Methods in Ecology and Evolution collaboration data management ecoinformatics GitHub open science project management |
| title | Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution |
| title_full | Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution |
| title_fullStr | Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution |
| title_full_unstemmed | Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution |
| title_short | Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution |
| title_sort | not just for programmers how github can accelerate collaborative and reproducible research in ecology and evolution |
| topic | collaboration data management ecoinformatics GitHub open science project management |
| url | https://doi.org/10.1111/2041-210X.14108 |
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