{"version":"desci-nodes-0.2.0","components":[{"id":"root","name":"root","type":"data-bucket","payload":{"cid":"bafybeiejjvssyzobhcc67sz5c2yrqlhm23iedrtfaeo7k7jrhilzvhj3p4","path":"root"}},{"id":"7f690ffc-f3dd-44ee-b1e8-52054db9d444","name":"Read the Paper","type":"pdf","payload":{"url":"bafybeiervzok2sd5dw4f2dhljqsadelv5jf5wfgzwjbuzffp5tb7mckvm4","path":"root/experimenting with reproducibility.pdf","keywords":["Reproducibility","Reusability","Scientific data","Bioinformatics","High-preformance computing"],"description":"This research report delves into the challenges of reproducing a published bioinformatics method, despite the availability of code and data. The authors detail their attempts to re-run the analysis, reimplement the method in Python to bypass MATLAB dependency, and assess the reusability of their reimplementation. The report also discusses solutions to improve reproducibility and research efficiency, and provides documentation and tutorials for the Python package StratiPy. Readers are encouraged to explore the reproducibility case study using the provided Jupyter/IPython notebook or Docker container.","annotations":[{"id":"c087cc6f-73c3-4d0c-97d4-ca168cc2e073","startX":0.08786127167630058,"startY":0.335387323943662,"endX":0.9167630057803469,"endY":0.6443661971830986,"pageIndex":3,"text":"Reproduce Figure 2 [Fig 2](#/code/8fa3dcf6-0ed1-4ede-b41d-7f291bd51eda?path=reproducibility/reproducibility.ipynb&line=11)\n"}]},"starred":true},{"id":"8fa3dcf6-0ed1-4ede-b41d-7f291bd51eda","name":"Explore StratiPy Code","type":"code","payload":{"url":"bafybeidwlgqdigdeazgya3sheka6xdpf5uhavjjsg2pbtvgact2g7dcbve","path":"root/StratiPy","externalUrl":"https://github.com/GHFC/StratiPy"},"starred":true},{"id":"a4ac25e7-f6f9-4d61-a9ef-afc285de8283","name":"Go to Journal Site","type":"link","subtype":"other","payload":{"url":"https://doi.org/10.1093/gigascience/giy077","path":"root/External Links/Go to Journal Site"},"starred":true}],"authors":[{"name":"Yang-Min Kim","role":"Author","googleScholar":"https://scholar.google.com/citations?user=_8qNwoAAAAAJ&hl=en&oi=ao","orcid":"0000-0002-1583-3297"},{"name":"Jean-Baptiste Poline","role":"Author","googleScholar":"","orcid":"0000-0002-9794-749X"},{"name":"Guillaume Dumas","role":"Author","googleScholar":"https://scholar.google.com/citations?hl=en&user=TakXk9MAAAAJ","orcid":"0000-0002-2253-1844"}],"title":"Reproducibility in Bioinformatics","defaultLicense":"CC BY","researchFields":["Bioinformatics","Metascience"],"dpid":{"prefix":"beta","id":"49"}}