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).

• SNP-RFLPing: restriction enzyme mining for SNPs in genomes.

  PMID 16503968 · PMC1386656 · BMC genomics · 2006 · 8 claims · 2 setups

  Full-text index only

  SNP-RFLPing accepts three flexible input types (dbSNP rs#/ss# IDs, HUGO gene name/Entrez gene ID, or free-form SNP-in-sequence including IUPAC or [dNTP1/dNTP2] formats) for human, rat, and mouse genomes

  software existing string-matching feature

• Chemist: A Domain-Specific Language by Chemists for Chemists.

  PMID 40815845 · PMC12400401 · The journal of physical chemistry. A · 2025 · 8 claims · 2 setups

  Has reproduction · 89

  Interpackage modules are rare for the most computationally expensive QC algorithms (integral transformations, Fock builds, sigma vector formation) because their APIs are difficult to define using general-purpose programming language (GPPL) types alone.

  nwchemex self-consistent software proof-of-concept

• Software JimenaE allows efficient dynamic simulations of Boolean networks, centrality and system state analysis.

  PMID 36725967 · PMC9892028 · Scientific reports · 2023 · 8 claims · 4 setups

  Has reproduction · 74

  JimenaE simulates Boolean networks dynamically and systematically calculates all system states rather than heuristically as SQUAD does.

  mesenchymal arabidopsis dendritic network boolean dynamic immune

• Software for tag single nucleotide polymorphism selection.

  PMID 16004730 · PMC3525260 · Human genomics · 2005 · 8 claims · 3 setups

  Full-text index only

  Pairwise R2 methods tend to pick more tagging SNPs than strictly needed because they miss redundancy where two or more tag SNPs jointly predict an untagged SNP with no single direct surrogate.

  tgfbr1 encode candidate tag haplotype

• A comprehensive literature review of haplotyping software and methods for use with unrelated individuals.

  PMID 15814067 · PMC3525117 · Human genomics · 2005 · 7 claims · 2 setups

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  Forty-six haplotyping programs were identified and reviewed, split into 43 designed for individual genotype data and three designed for pooled DNA samples.

  pubmed identified literature software