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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Onto-Tools: new additions and improvements in 2006.
PMID 17584796 · PMC1933142 · Nucleic acids research · 2007 · 8 claims · 3 setups
OE2GO enables functional profiling for organisms lacking public-domain annotations by allowing users to supply custom GO-format annotation files and OBO-format ontology files
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Recent additions and improvements to the Onto-Tools.
PMID 15980579 · PMC1160233 · Nucleic acids research · 2005 · 7 claims · 3 setups
The Onto-Tools back-end database was redesigned around the Entrez Gene data model after NCBI phased out LocusLink in February 2005.
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Peptide bioinformatics: peptide classification using peptide machines.
PMID 19065810 · PMC7122642 · Methods in molecular biology (Clifton, N.J.) · 2008 · 8 claims · 4 setups
The bio-basis function, which converts peptides into numerical vectors using nongapped pairwise homology alignment scores against indicator peptides, can statistically quantify peptide similarity for classification.
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Has reproduction · 71
Sustainable data analysis with Snakemake.
PMID 34035898 · PMC8114187 · F1000Research · 2021 · 8 claims · 4 setups
Reproducibility alone is insufficient for sustainable data analysis; transparency and adaptability are equally important additional properties.
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YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.
PMID 15929789 · PMC1175843 · BMC bioinformatics · 2005 · 7 claims · 3 setups
YANA integrates METATOOL to provide a graphical, platform-independent front-end for editing, calculating, visualizing, and comparing elementary flux modes, with SBML support.