Experiments
Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).
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CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.
PMID 34210356 · PMC8247108 · Genome biology · 2021 · 7 claims · 2 setups
A centralised hub model built on the CLIMB compute infrastructure (CLIMB-COVID) can integrate SARS-CoV-2 genomic sequencing data and sample metadata from a decentralised, autonomous network of sequencing sites into a single canonical dataset.
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Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.
PMID 16246909 · PMC1266070 · Nucleic acids research · 2005 · 8 claims · 6 setups
The BioCyc collection has been expanded to 160 pathway/genome databases (PGDBs) organized into three curation tiers.
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Has reproduction · 43
TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.
PMID 36469333 · PMC9825751 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups
TransFlow is a Snakemake- and Conda-based workflow that combines state-of-the-art tools into a single, fast, scalable pipeline for MTBC WGS-based transmission analysis.
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TreeFam: a curated database of phylogenetic trees of animal gene families.
PMID 16381935 · PMC1347480 · Nucleic acids research · 2006 · 7 claims · 6 setups
Tree-based inference of orthologs and paralogs is more robust than BLAST-based methods because evolutionary rates (and thus pairwise BLAST scores) vary across gene family members