[ { "key": "KXPN9V2U", "version": 217, "library": { "type": "group", "id": 613123, "name": "Digital Skills and Scholarship for Researchers", "links": { "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/613123/items/KXPN9V2U", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers/items/KXPN9V2U", "type": "text/html" } }, "meta": { "createdByUser": { "id": 205483, "username": "kubke", "name": "Fabiana Kubke", "links": { "alternate": { "href": "https://www.zotero.org/kubke", "type": "text/html" } } }, "lastModifiedByUser": { "id": 3367611, "username": "neil.birrell", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/neil.birrell", "type": "text/html" } } }, "creatorSummary": "Gallagher et al.", "parsedDate": "2024-12-09", "numChildren": 0 }, "data": { "key": "KXPN9V2U", "version": 217, "itemType": "journalArticle", "title": "Ten simple rules for training scientists to make better software", "creators": [ { "creatorType": "author", "firstName": "Kit", "lastName": "Gallagher" }, { "creatorType": "author", "firstName": "Richard", "lastName": "Creswell" }, { "creatorType": "author", "firstName": "Ben", "lastName": "Lambert" }, { "creatorType": "author", "firstName": "Martin", "lastName": "Robinson" }, { "creatorType": "author", "firstName": "Chon Lok", "lastName": "Lei" }, { "creatorType": "author", "firstName": "Gary R.", "lastName": "Mirams" }, { "creatorType": "author", "firstName": "David J.", "lastName": "Gavaghan" } ], "abstractNote": "", "publicationTitle": "PLOS Computational Biology", "publisher": "Public Library of Science", "place": "", "date": "12/09/2024", "volume": "20", "issue": "9", "section": "", "partNumber": "", "partTitle": "", "pages": "e1012410", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLOS Computational Biology", "DOI": "10.1371/journal.pcbi.1012410", "citationKey": "", "url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012410", "accessDate": "2024-09-13T12:34:35Z", "PMID": "", "PMCID": "", "ISSN": "1553-7358", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "PLoS Journals", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Computer software", "type": 1 }, { "tag": "Human learning", "type": 1 }, { "tag": "Industrial research", "type": 1 }, { "tag": "Open source software", "type": 1 }, { "tag": "Programming languages", "type": 1 }, { "tag": "Software development", "type": 1 }, { "tag": "Software engineering", "type": 1 }, { "tag": "Software tools", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2024-09-13T12:34:35Z", "dateModified": "2024-09-13T12:34:35Z" } }, { "key": "CDTQBFF5", "version": 217, "library": { "type": "group", "id": 613123, "name": "Digital Skills and Scholarship for Researchers", "links": { "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/613123/items/CDTQBFF5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers/items/CDTQBFF5", "type": "text/html" } }, "meta": { "createdByUser": { "id": 205483, "username": "kubke", "name": "Fabiana Kubke", "links": { "alternate": { "href": "https://www.zotero.org/kubke", "type": "text/html" } } }, "lastModifiedByUser": { "id": 3367611, "username": "neil.birrell", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/neil.birrell", "type": "text/html" } } }, "creatorSummary": "Plaisier et al.", "parsedDate": "2024-12-09", "numChildren": 0 }, "data": { "key": "CDTQBFF5", "version": 217, "itemType": "journalArticle", "title": "Design and implementation of an asynchronous online course-based undergraduate research experience (CURE) in computational genomics", "creators": [ { "creatorType": "author", "firstName": "Seema B.", "lastName": "Plaisier" }, { "creatorType": "author", "firstName": "Danielle O.", "lastName": "Alarid" }, { "creatorType": "author", "firstName": "Joelle A.", "lastName": "Denning" }, { "creatorType": "author", "firstName": "Sara E.", "lastName": "Brownell" }, { "creatorType": "author", "firstName": "Kenneth H.", "lastName": "Buetow" }, { "creatorType": "author", "firstName": "Katelyn M.", "lastName": "Cooper" }, { "creatorType": "author", "firstName": "Melissa A.", "lastName": "Wilson" } ], "abstractNote": "As genomics technologies advance, there is a growing demand for computational biologists trained for genomics analysis but instructors face significant hurdles in providing formal training in computer programming, statistics, and genomics to biology students. Fully online learners represent a significant and growing community that can contribute to meet this need, but they are frequently excluded from valuable research opportunities which mostly do not offer the flexibility they need. To address these opportunity gaps, we developed an asynchronous course-based undergraduate research experience (CURE) for computational genomics specifically for fully online biology students. We generated custom learning materials and leveraged remotely accessible computational tools to address 2 novel research questions over 2 iterations of the genomics CURE, one testing bioinformatics approaches and one mining cancer genomics data. Here, we present how the instructional team distributed analysis needed to address these questions between students over a 7.5-week CURE and provided concurrent training in biology and statistics, computer programming, and professional development. Scores from identical learning assessments administered before and after completion of each CURE showed significant learning gains across biology and coding course objectives. Open-response progress reports were submitted weekly and identified self-reported adaptive coping strategies for challenges encountered throughout the course. Progress reports identified problems that could be resolved through collaboration with instructors and peers via messaging platforms and virtual meetings. We implemented asynchronous communication using the Slack messaging platform and an asynchronous journal club where students discussed relevant publications using the Perusall social annotation platform. The online genomics CURE resulted in unanticipated positive outcomes, including students voluntarily discussing plans to continue research after the course. These outcomes underscore the effectiveness of this genomics CURE for scientific training, recruitment and student-mentor relationships, and student successes. Asynchronous genomics CUREs can contribute to a more skilled, diverse, and inclusive workforce for the advancement of biomedical science.", "publicationTitle": "PLOS Computational Biology", "publisher": "Public Library of Science", "place": "", "date": "12/09/2024", "volume": "20", "issue": "9", "section": "", "partNumber": "", "partTitle": "", "pages": "e1012384", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLOS Computational Biology", "DOI": "10.1371/journal.pcbi.1012384", "citationKey": "", "url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012384", "accessDate": "2024-09-13T12:34:28Z", "PMID": "", "PMCID": "", "ISSN": "1553-7358", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "PLoS Journals", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Computational biology", "type": 1 }, { "tag": "Genome analysis", "type": 1 }, { "tag": "Genomics", "type": 1 }, { "tag": "Human learning", "type": 1 }, { "tag": "Instructors", "type": 1 }, { "tag": "Peer review", "type": 1 }, { "tag": "Software engineering", "type": 1 }, { "tag": "Undergraduates", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2024-09-13T12:34:28Z", "dateModified": "2024-09-13T12:34:28Z" } }, { "key": "6PDS4UWY", "version": 217, "library": { "type": "group", "id": 613123, "name": "Digital Skills and Scholarship for Researchers", "links": { "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/613123/items/6PDS4UWY", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers/items/6PDS4UWY", "type": "text/html" } }, "meta": { "createdByUser": { "id": 205483, "username": "kubke", "name": "Fabiana Kubke", "links": { "alternate": { "href": "https://www.zotero.org/kubke", "type": "text/html" } } }, "lastModifiedByUser": { "id": 3367611, "username": "neil.birrell", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/neil.birrell", "type": "text/html" } } }, "creatorSummary": "Abdill et al.", "parsedDate": "2024-10-09", "numChildren": 0 }, "data": { "key": "6PDS4UWY", "version": 217, "itemType": "journalArticle", "title": "A how-to guide for code sharing in biology", "creators": [ { "creatorType": "author", "firstName": "Richard J.", "lastName": "Abdill" }, { "creatorType": "author", "firstName": "Emma", "lastName": "Talarico" }, { "creatorType": "author", "firstName": "Laura", "lastName": "Grieneisen" } ], "abstractNote": "In 2024, all biology is computational biology. Computer-aided analysis continues to spread into new fields, becoming more accessible to researchers trained in the wet lab who are eager to take advantage of growing datasets, falling costs, and novel assays that present new opportunities for discovery. It is currently much easier to find guidance for implementing these techniques than for reporting their use, leaving biologists to guess which details and files are relevant. In this essay, we review existing literature on the topic, summarize common tips, and link to additional resources for training. Following this overview, we then provide a set of recommendations for sharing code, with an eye toward guiding those who are comparatively new to applying open science principles to their computational work. Taken together, we provide a guide for biologists who seek to follow code sharing best practices but are unsure where to start.", "publicationTitle": "PLOS Biology", "publisher": "Public Library of Science", "place": "", "date": "10/09/2024", "volume": "22", "issue": "9", "section": "", "partNumber": "", "partTitle": "", "pages": "e3002815", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLOS Biology", "DOI": "10.1371/journal.pbio.3002815", "citationKey": "", "url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002815", "accessDate": "2024-09-13T12:34:18Z", "PMID": "", "PMCID": "", "ISSN": "1545-7885", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "PLoS Journals", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Automation", "type": 1 }, { "tag": "Computational biology", "type": 1 }, { "tag": "Computer software", "type": 1 }, { "tag": "Data visualization", "type": 1 }, { "tag": "Open science", "type": 1 }, { "tag": "Open source software", "type": 1 }, { "tag": "Operating systems", "type": 1 }, { "tag": "Software tools", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2024-09-13T12:34:18Z", "dateModified": "2024-09-13T12:34:18Z" } }, { "key": "8387E9N4", "version": 216, "library": { "type": "group", "id": 613123, "name": "Digital Skills and Scholarship for Researchers", "links": { "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/613123/items/8387E9N4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers/items/8387E9N4", "type": "text/html" } }, "meta": { "createdByUser": { "id": 205483, "username": "kubke", "name": "Fabiana Kubke", "links": { "alternate": { "href": "https://www.zotero.org/kubke", "type": "text/html" } } }, "lastModifiedByUser": { "id": 3367611, "username": "neil.birrell", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/neil.birrell", "type": "text/html" } } }, "creatorSummary": "Landry", "parsedDate": "2024-08-21", "numChildren": 0 }, "data": { "key": "8387E9N4", "version": 216, "itemType": "journalArticle", "title": "What I learnt from running a coding bootcamp", "creators": [ { "creatorType": "author", "firstName": "Christian", "lastName": "Landry" } ], "abstractNote": "By creating a bespoke learning environment for 25 students, I found a way to raise the coding level of my entire laboratory.", "publicationTitle": "Nature", "publisher": "Nature Publishing Group", "place": "", "date": "2024-08-21", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1038/d41586-024-02745-3", "citationKey": "", "url": "https://www.nature.com/articles/d41586-024-02745-3", "accessDate": "2024-08-22T06:01:16Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www.nature.com", "callNumber": "", "rights": "2024 Springer Nature Limited", "extra": "Bandiera_abtest: a\nCg_type: Career Column\nSubject_term: Careers, Lab life, Education", "tags": [ { "tag": "Careers", "type": 1 }, { "tag": "Education", "type": 1 }, { "tag": "Lab life", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2024-08-22T06:01:16Z", "dateModified": "2024-08-22T06:01:16Z" } }, { "key": "QDNXU8T2", "version": 216, "library": { "type": "group", "id": 613123, "name": "Digital Skills and Scholarship for Researchers", "links": { "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/613123/items/QDNXU8T2", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers/items/QDNXU8T2", "type": "text/html" } }, "meta": { "createdByUser": { "id": 205483, "username": "kubke", "name": "Fabiana Kubke", "links": { "alternate": { "href": "https://www.zotero.org/kubke", "type": "text/html" } } }, "lastModifiedByUser": { "id": 3367611, "username": "neil.birrell", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/neil.birrell", "type": "text/html" } } }, "creatorSummary": "Bayarri et al.", "parsedDate": "2024-06-20", "numChildren": 0 }, "data": { "key": "QDNXU8T2", "version": 216, "itemType": "journalArticle", "title": "Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows", "creators": [ { "creatorType": "author", "firstName": "Genís", "lastName": "Bayarri" }, { "creatorType": "author", "firstName": "Pau", "lastName": "Andrio" }, { "creatorType": "author", "firstName": "Josep Lluís", "lastName": "Gelpí" }, { "creatorType": "author", "firstName": "Adam", "lastName": "Hospital" }, { "creatorType": "author", "firstName": "Modesto", "lastName": "Orozco" } ], "abstractNote": "Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work presents a collection of FAIR notebooks covering various areas of the biomolecular simulation field, such as molecular dynamics (MD), protein–ligand docking, molecular checking/modeling, molecular interactions, and free energy perturbations. Workflows can be launched with myBinder or easily installed in a local system. The collection of notebooks aims to provide a compilation of demonstration workflows, and it is continuously updated and expanded with examples using new methodologies and tools.", "publicationTitle": "PLOS Computational Biology", "publisher": "Public Library of Science", "place": "", "date": "Jun 20, 2024", "volume": "20", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "e1012173", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLOS Computational Biology", "DOI": "10.1371/journal.pcbi.1012173", "citationKey": "", "url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012173", "accessDate": "2024-06-22T01:11:02Z", "PMID": "", "PMCID": "", "ISSN": "1553-7358", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "PLoS Journals", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Biochemical simulations", "type": 1 }, { "tag": "Computer software", "type": 1 }, { "tag": "Molecular structure", "type": 1 }, { "tag": "Protein extraction", "type": 1 }, { "tag": "Protein interactions", "type": 1 }, { "tag": "Protein structure", "type": 1 }, { "tag": "Protein structure databases", "type": 1 }, { "tag": "Protein structure prediction", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2024-06-22T01:11:02Z", "dateModified": "2024-06-22T01:11:02Z" } }, { "key": "USAIYACP", "version": 216, "library": { "type": "group", "id": 613123, "name": "Digital Skills and Scholarship for Researchers", "links": { "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/613123/items/USAIYACP", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers/items/USAIYACP", "type": "text/html" } }, "meta": { "createdByUser": { "id": 205483, "username": "kubke", "name": "Fabiana Kubke", "links": { "alternate": { "href": "https://www.zotero.org/kubke", "type": "text/html" } } }, "lastModifiedByUser": { "id": 3367611, "username": "neil.birrell", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/neil.birrell", "type": "text/html" } } }, "creatorSummary": "Conte et al.", "parsedDate": "2024-06-20", "numChildren": 0 }, "data": { "key": "USAIYACP", "version": 216, "itemType": "journalArticle", "title": "Ten simple rules to make computable knowledge shareable and reusable", "creators": [ { "creatorType": "author", "firstName": "Marisa L.", "lastName": "Conte" }, { "creatorType": "author", "firstName": "Peter", "lastName": "Boisvert" }, { "creatorType": "author", "firstName": "Philip", "lastName": "Barrison" }, { "creatorType": "author", "firstName": "Farid", "lastName": "Seifi" }, { "creatorType": "author", "firstName": "Zach", "lastName": "Landis-Lewis" }, { "creatorType": "author", "firstName": "Allen", "lastName": "Flynn" }, { "creatorType": "author", "firstName": "Charles P.", "lastName": "Friedman" } ], "abstractNote": "Computable biomedical knowledge (CBK) is: “the result of an analytic and/or deliberative process about human health, or affecting human health, that is explicit, and therefore can be represented and reasned upon using logic, formal standards, and mathematical approaches.” Representing biomedical knowledge in a machine-interpretable, computable form increases its ability to be discovered, accessed, understood, and deployed. Computable knowledge artifacts can greatly advance the potential for implementation, reproducibility, or extension of the knowledge by users, who may include practitioners, researchers, and learners. Enriching computable knowledge artifacts may help facilitate reuse and translation into practice. Following the examples of 10 Simple Rules papers for scientific code, software, and applications, we present 10 Simple Rules intended to make shared computable knowledge artifacts more useful and reusable. These rules are mainly for researchers and their teams who have decided that sharing their computable knowledge is important, who wish to go beyond simply describing results, algorithms, or models via traditional publication pathways, and who want to both make their research findings more accessible, and to help others use their computable knowledge. These rules are roughly organized into 3 categories: planning, engineering, and documentation. Finally, while many of the following examples are of computable knowledge in biomedical domains, these rules are generalizable to computable knowledge in any research domain.", "publicationTitle": "PLOS Computational Biology", "publisher": "Public Library of Science", "place": "", "date": "Jun 20, 2024", "volume": "20", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "e1012179", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLOS Computational Biology", "DOI": "10.1371/journal.pcbi.1012179", "citationKey": "", "url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012179", "accessDate": "2024-06-22T01:10:55Z", "PMID": "", "PMCID": "", "ISSN": "1553-7358", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "PLoS Journals", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Citation analysis", "type": 1 }, { "tag": "Computer software", "type": 1 }, { "tag": "Machine learning", "type": 1 }, { "tag": "Metadata", "type": 1 }, { "tag": "Ontologies", "type": 1 }, { "tag": "Open source software", "type": 1 }, { "tag": "Peer review", "type": 1 }, { "tag": "Reproducibility", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2024-06-22T01:10:55Z", "dateModified": "2024-06-22T01:10:55Z" } }, { "key": "GIMI6LRN", "version": 216, "library": { "type": "group", "id": 613123, "name": "Digital Skills and Scholarship for Researchers", "links": { "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/613123/items/GIMI6LRN", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers/items/GIMI6LRN", "type": "text/html" } }, "meta": { "createdByUser": { "id": 205483, "username": "kubke", "name": "Fabiana Kubke", "links": { "alternate": { "href": "https://www.zotero.org/kubke", "type": "text/html" } } }, "lastModifiedByUser": { "id": 3367611, "username": "neil.birrell", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/neil.birrell", "type": "text/html" } } }, "creatorSummary": "Robinson et al.", "parsedDate": "2024-06-20", "numChildren": 0 }, "data": { "key": "GIMI6LRN", "version": 216, "itemType": "journalArticle", "title": "Ten simple rules for computational biologists collaborating with wet lab researchers", "creators": [ { "creatorType": "author", "firstName": "Mark D.", "lastName": "Robinson" }, { "creatorType": "author", "firstName": "Peiying", "lastName": "Cai" }, { "creatorType": "author", "firstName": "Martin", "lastName": "Emons" }, { "creatorType": "author", "firstName": "Reto", "lastName": "Gerber" }, { "creatorType": "author", "firstName": "Pierre-Luc", "lastName": "Germain" }, { "creatorType": "author", "firstName": "Samuel", "lastName": "Gunz" }, { "creatorType": "author", "firstName": "Siyuan", "lastName": "Luo" }, { "creatorType": "author", "firstName": "Giulia", "lastName": "Moro" }, { "creatorType": "author", "firstName": "Emanuel", "lastName": "Sonder" }, { "creatorType": "author", "firstName": "Anthony", "lastName": "Sonrel" }, { "creatorType": "author", "firstName": "Jiayi", "lastName": "Wang" }, { "creatorType": "author", "firstName": "David", "lastName": "Wissel" }, { "creatorType": "author", "firstName": "Izaskun", "lastName": "Mallona" } ], "abstractNote": "Computational biologists are frequently engaged in collaborative data analysis with wet lab researchers. These interdisciplinary projects, as necessary as they are to the scientific endeavor, can be surprisingly challenging due to cultural differences in operations and values. In this Ten Simple Rules guide, we aim to help dry lab researchers identify sources of friction and provide actionable tools to facilitate respectful, open, transparent, and rewarding collaborations.", "publicationTitle": "PLOS Computational Biology", "publisher": "Public Library of Science", "place": "", "date": "Jun 20, 2024", "volume": "20", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "e1012174", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLOS Computational Biology", "DOI": "10.1371/journal.pcbi.1012174", "citationKey": "", "url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012174", "accessDate": "2024-06-22T01:10:46Z", "PMID": "", "PMCID": "", "ISSN": "1553-7358", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "PLoS Journals", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Analysts", "type": 1 }, { "tag": "Biologists", "type": 1 }, 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In this new edition of Reinventing Paulo Freire, Antonia Darder re-examines his legacy through reflections on Freirean pedagogy and the narratives of teachers who reinvent his work. The fully revised first part provides important historical, political, and economic connections between major societal concerns and educational questions raised by Freire and their link to the contemporary moment, including questions tied to neoliberalism, coloniality, and educational inequalities. At the heart of the book is a critical understanding of how Freire’s pedagogy of love can inform, in theory and practice, a humanizing approach to teaching and learning. \nPowerful teacher narratives offer examples of a living praxis, committed to democratic classroom life and the emancipation of subaltern communities. The narratives clearly illustrate how Freire’s ideas can be put concretely into practice in schools and communities. These reflections on Freirean praxis are sure to spark conversation and inspiration in teacher education courses. Through a close theoretical engagement of Freire’s ideas and key insights garnered from lived experiences, the book speaks to the ways Freire can still inspire contemporary educators to adopt the spirit of　liberatory pedagogy, By so doing, Reinventing Paulo Freire is certain to advance his theories in new ways, both to those familiar with his work and to those studying Freire for the first time.", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "2", "date": "2017-06-05", "publisher": "Routledge", "place": "New York", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "numPages": "236", "ISBN": "978-1-315-56077-9", "DOI": "10.4324/9781315560779", "citationKey": "", "url": "", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Reinventing Paulo Freire", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "228JPJPL" ], "relations": {}, "dateAdded": "2021-11-19T01:31:42Z", "dateModified": "2021-11-19T01:31:42Z" } }, { "key": "RRVNLX49", "version": 215, "library": { "type": "group", "id": 613123, "name": "Digital Skills and Scholarship for Researchers", "links": { "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/613123/items/RRVNLX49", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers/items/RRVNLX49", "type": "text/html" } }, "meta": { "createdByUser": { "id": 205483, "username": "kubke", "name": "Fabiana Kubke", "links": { "alternate": { "href": "https://www.zotero.org/kubke", "type": "text/html" } } }, "lastModifiedByUser": { "id": 3367611, "username": "neil.birrell", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/neil.birrell", "type": "text/html" } } }, "creatorSummary": "Gay", "parsedDate": "1994", "numChildren": 0 }, "data": { "key": "RRVNLX49", "version": 215, "itemType": "journalArticle", "title": "Coming of Age Ethnically: Teaching Young Adolescents of Color", "creators": [ { "creatorType": "author", "firstName": "Geneva", "lastName": "Gay" } ], "abstractNote": "", "publicationTitle": "Theory Into Practice", "publisher": "Taylor & Francis, Ltd.", "place": "", "date": "1994", "volume": "33", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "149-155", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "https://www.jstor.org/stable/1476501", "accessDate": "2021-11-15T03:37:18Z", "PMID": "", "PMCID": "", "ISSN": "0040-5841", "archive": "", "archiveLocation": "", "shortTitle": "Coming of Age Ethnically", "language": "", "libraryCatalog": "JSTOR", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "228JPJPL" ], "relations": {}, "dateAdded": "2021-11-19T01:31:42Z", "dateModified": "2021-11-19T01:31:42Z" } }, { "key": "HB97ZXPL", "version": 215, "library": { "type": "group", "id": 613123, "name": "Digital Skills and Scholarship for Researchers", "links": { "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/613123/items/HB97ZXPL", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers/items/HB97ZXPL", "type": "text/html" } }, "meta": { "createdByUser": { "id": 205483, "username": "kubke", "name": "Fabiana Kubke", "links": { "alternate": { "href": "https://www.zotero.org/kubke", "type": "text/html" } } }, "lastModifiedByUser": { "id": 3367611, "username": "neil.birrell", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/neil.birrell", "type": "text/html" } } }, "creatorSummary": "Reilly", "parsedDate": "2010-09-01", "numChildren": 0 }, "data": { "key": "HB97ZXPL", "version": 215, "itemType": "journalArticle", "title": "Tuakana–Teina Relationship and Leadership in Ancient Mangaia and Aotearoa", "creators": [ { "creatorType": "author", "firstName": "Michael P.J.", "lastName": "Reilly" } ], "abstractNote": "The relationship between tuakana and teina (the older and younger sibling or cousin of same sex) is the tumu (foundation, origin, cause) of rank in eastern Polynesia. By examining historical documents from selected island societies, namely, Mangaia and Aotearoa, we can understand the dynamics of this relationship as part of their world-view. Normally tuakana and teina had close, cooperative, mutually respectful and loyal relationships; the teina supporting their elder. Sometimes, however, the moral balance between them was affected either by one of them acting inappropriately towards the other, or by hostile acts from others. To remedy these threats to social cohesion, various strategies were adopted, including peace-making, flight or spatial separation, or fighting. 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It begins with explaining my views of culturally responsive teaching and how I incorporate cultural responsiveness in my writing to teach readers what it means. These general conceptual frameworks are followed by a discussion of some specific actions essential to its implementation. They are restructuring teacher attitudes and beliefs about cultural, ethnic, and racial diversity; resisting resistance to cultural diversity in teacher education and classroom instruction; centering culture and difference in the teaching process; and establishing pedagogical connections between culturally responsive teaching and subjects and skills routinely taught in schools. Excerpts from samples of my own and others' scholarship are woven throughout to exemplify general patterns, themes, and principles of culturally responsive teaching.", "publicationTitle": "Curriculum Inquiry", "publisher": "Wiley", "place": "", "date": "2013", "volume": "43", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "48-70", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "https://www.jstor.org/stable/23524357", "accessDate": "2021-11-15T03:34:09Z", "PMID": "", "PMCID": "", "ISSN": "0362-6784", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "JSTOR", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "228JPJPL" ], "relations": {}, "dateAdded": "2021-11-19T01:31:42Z", "dateModified": "2021-11-19T01:31:42Z" } }, { "key": "QMKWIWLF", "version": 215, "library": { "type": "group", "id": 613123, "name": "Digital Skills and Scholarship for Researchers", "links": { "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/613123/items/QMKWIWLF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers/items/QMKWIWLF", "type": "text/html" } }, "meta": { "createdByUser": { "id": 205483, "username": "kubke", "name": "Fabiana Kubke", "links": { "alternate": { "href": "https://www.zotero.org/kubke", "type": "text/html" } } }, "lastModifiedByUser": { "id": 3367611, "username": "neil.birrell", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/neil.birrell", "type": "text/html" } } }, "creatorSummary": "Fox and Gay", "parsedDate": "1995", "numChildren": 0 }, "data": { "key": "QMKWIWLF", "version": 215, "itemType": "journalArticle", "title": "Integrating Multicultural and Curriculum Principles in Teacher Education", "creators": [ { "creatorType": "author", "firstName": "Wanda", "lastName": "Fox" }, { "creatorType": "author", "firstName": "Geneva", "lastName": "Gay" } ], "abstractNote": "", "publicationTitle": "Peabody Journal of Education", "publisher": "Taylor & Francis, Ltd.", "place": "", "date": "1995", "volume": "70", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "64-82", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "https://www.jstor.org/stable/1492897", "accessDate": "2021-11-15T03:34:55Z", "PMID": "", "PMCID": "", "ISSN": "0161-956X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "JSTOR", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "228JPJPL" ], "relations": {}, "dateAdded": "2021-11-19T01:31:42Z", "dateModified": "2021-11-19T01:31:42Z" } }, { "key": "G7MVI53H", "version": 215, "library": { "type": "group", "id": 613123, "name": "Digital Skills and Scholarship for Researchers", "links": { "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/613123/items/G7MVI53H", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/digital_skills_and_scholarship_for_researchers/items/G7MVI53H", "type": "text/html" } }, "meta": { "createdByUser": { "id": 205483, "username": "kubke", "name": "Fabiana Kubke", "links": { "alternate": { "href": "https://www.zotero.org/kubke", "type": "text/html" } } }, "lastModifiedByUser": { "id": 3367611, "username": "neil.birrell", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/neil.birrell", "type": "text/html" } } }, "creatorSummary": "Gay", "parsedDate": "1990", "numChildren": 0 }, "data": { "key": "G7MVI53H", "version": 215, "itemType": "journalArticle", "title": "Achieving Educational Equality through Curriculum Desegregation", "creators": [ { "creatorType": "author", "firstName": "Geneva", "lastName": "Gay" } ], "abstractNote": "", "publicationTitle": "The Phi Delta Kappan", "publisher": "Phi Delta Kappa International", "place": "", "date": "1990", "volume": "72", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "56-62", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "https://www.jstor.org/stable/20404310", "accessDate": "2021-11-15T03:35:38Z", "PMID": "", "PMCID": "", "ISSN": "0031-7217", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "JSTOR", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "228JPJPL" ], "relations": {}, "dateAdded": "2021-11-19T01:31:42Z", "dateModified": "2021-11-19T01:31:42Z" } } ]