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Category Archives: data archiving
GEOME is putting genetic data in its place
Infrastructure to make genetic data widely available for research beyond its initial publication has been a theme of the genomics revolution, from GenBank to the Sequence Read Archive. For molecular ecologists, though, genetic data is only half of our field … Continue reading
Posted in bioinformatics, community, data archiving
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Simple rules for organizing data in a spreadsheet
Most scientists collect and organize at least some data in spreadsheets, usually Excel or Google Sheets, despite the potential pitfalls of using such products (there are even archives of spreadsheet horror stories). The most commonly bemoaned problem in Biology, that … Continue reading
Posted in data archiving, howto, methods
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Where credit is due
I am trying to keep this short. You might remember my recent blog post on data sharing. I basically wanted to point out that data acquisition can be an art on its own. It can take months of planning, applying … Continue reading
Posted in bioinformatics, career, community, data archiving, genomics, science publishing
Tagged authorship, co-author, public database
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Towards unrestricted use of public genomic data
Last week, a friend sent me this policy forum article published in Science. Fifty co-authors, mostly tenured and from prestigious universities, some of them among my dearest idols, have written this piece to call for publicly available genome data. What … Continue reading
Posted in career, community, data archiving, genomics, science publishing
Tagged career, genomics, open science
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Best practices in sample naming
Wherein I try to save me from myself Let’s imagine a young scientist, bursting to the seems with enthusiasm and schemes to uncover the secrets of the biological world. Everything is new and she learns as she goes! Let’s call … Continue reading
How to make the most out of your phylogenetic study
Phylogenetic studies are crucial for ecology and evolution. However, their usefulness for comparative biology or meta-analyses can vary considerably. Especially the inclusion of unidentified species (“Balanus sp.”) obstructs their use in comparative studies. How can I attach life history or morphological data … Continue reading
Posted in data archiving, evolution, howto, phylogenetics, Uncategorized
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Journals must boost data sharing
Here’s the text from Tim’s recent (3rd April) Correspondence piece in Nature The journal ecosystem is a powerful filter of scientific literature, promoting the best work into the best journals. Why not use a similar mechanism to encourage more comprehensive … Continue reading
Posted in data archiving, science publishing
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By popular request …
The original data set of Joshua tree presence locations, which I used as an example in my post about estimating species distribution models in R, is now available for download from Dryad. Thanks to my coauthors for agreeing to share … Continue reading
Posted in data archiving, howto, methods
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How to Backup and Store your Next-Generation Sequencing (NGS) data
Congratulations! You have recently received a file path to retrieve your hard-earned next-generation sequencing data. You quickly transfer the files to the computing cluster you work on or perhaps, if you only have a few lanes of data, to your … Continue reading
Posted in bioinformatics, data archiving, genomics, howto
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